ORCID Profile
0000-0002-7111-3024
Current Organisation
Macquarie University
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Biologically Active Molecules | Analytical Biochemistry | Epigenetics (incl. Genome Methylation and Epigenomics) | Analytical Chemistry | Medicinal and Biomolecular Chemistry | Nanotechnology | Organic Chemical Synthesis | Analytical Spectrometry | Bioprocessing, Bioproduction and Bioproducts | Nanobiotechnology |
ANZSRC Socio-Economic Objective (SEO)
Expanding Knowledge in the Biological Sciences | Service Industries Standards and Calibrations | Expanding Knowledge in the Chemical Sciences | Expanding Knowledge in the Physical Sciences | Nutraceuticals and Functional foods | Expanding Knowledge in Technology
Related Links
Publications
How to Study DNA and Proteins by Linear Dichroism Spectroscopy
Publisher: SAGE Publications
Date: 12-2008
Abstract: The technique of linear dichroism (LD) is a simple absorbance technique that uses two polarised light beams. Since only oriented molecules show different absorbances for different polarisations, LD detects only oriented molecules. In aqueous solutions, flow orientation is an attractive orientation methodology as it selects long molecules or molecular assemblies. LD thus is selective for molecules that are particularly challenging to study by more standard biophysical techniques. In this article, a brief review of the application of LD to DNA, DNA–drug systems, DNA–protein enzymatic complexes, fibrous proteins and membrane peptides and proteins is given.
Structural determinants in a library of low molecular weight gelators
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C4SM02532F
Abstract: The structures of hydrogels formed by naphthalene dipeptide library were explored using a combined approach of electron microscopy, X-ray fibre diffraction and circular dichroism.
Optically pure, water-stable metallo-helical ‘flexicate’ assemblies with antibiotic activity
Publisher: Springer Science and Business Media LLC
Date: 27-11-2011
DOI: 10.1038/NCHEM.1206
Abstract: The helicates--chiral assemblies of two or more metal atoms linked by short or relatively rigid multidentate organic ligands--may be regarded as non-peptide mimetics of α-helices because they are of comparable size and have shown some relevant biological activity. Unfortunately, these beautiful helical compounds have remained difficult to use in the medicinal arena because they contain mixtures of isomers, cannot be optimized for specific purposes, are insoluble, or are too difficult to synthesize. Instead, we have now prepared thermodynamically stable single enantiomers of monometallic units connected by organic linkers. Our highly adaptable self-assembly approach enables the rapid preparation of ranges of water-stable, helicate-like compounds with high stereochemical purity. One such iron(II) 'flexicate' system exhibits specific interactions with DNA, promising antimicrobial activity against a Gram-positive bacterium (methicillin-resistant Staphylococcus aureus, MRSA252), but also, unusually, a Gram-negative bacterium (Escherichia coli, MC4100), as well as low toxicity towards a non-mammalian model organism (Caenorhabditis elegans).
Protein Secondary Structure Prediction from Circular Dichroism Spectra Using a Self‐Organizing Map with Concentration Correction
Publisher: Wiley
Date: 02-06-2014
DOI: 10.1002/CHIR.22338
Abstract: Collecting circular dichroism (CD) spectra for protein solutions is a simple experiment, yet reliable extraction of secondary structure content is dependent on knowledge of the concentration of the protein--which is not always available with accuracy. We previously developed a self-organizing map (SOM), called Secondary Structure Neural Network (SSNN), to cluster a database of CD spectra and use that map to assign the secondary structure content of new proteins from CD spectra. The performance of SSNN is at least as good as other available protein CD structure-fitting algorithms. In this work we apply SSNN to a collection of spectra of experimental s les where there was suspicion that the nominal protein concentration was incorrect. We show that by plotting the normalized root mean square deviation of the SSNN predicted spectrum from the experimental one versus a concentration scaling-factor it is possible to improve the estimate of the protein concentration while providing an estimate of the secondary structure. For our implementation (51 data points 240-190 nm in nm increments) good fits and structure estimates were obtained if the NRMSD (normalized root mean square displacement, RMSE/data range) is <0.03 reasonable for NRMSD <0.05 and variable above this. We also augmented the reference database with 100% helical spectra and truly random coil spectra.
The Synergistic Action of Melittin and Phospholipase A2 with Lipid Membranes: Development of Linear Dichroism for Membrane-Insertion Kinetics
Publisher: Bentham Science Publishers Ltd.
Date: 11-2010
DOI: 10.2174/0929866511009011351
Abstract: Here we present data on the kinetics of insertion of melittin, a peptide from bee venom, into lipid membranes of different composition. Another component of bee venom is the enzyme phospholipase A2 (PLA₂). We have examined the interaction of melittin and PLA₂ with liposomes both separately and combined and demonstrate that they work synergistically to disrupt the membranes. A dramatic difference in the action of melittin and PLA₂ is observed when the composition of the membrane is altered. Temperature also has a large effect on the kinetics of insertion and membrane disruption. We use a combination of techniques to measure liposome size (dynamic light scattering), peptide secondary structure (circular dichroism spectroscopy), peptide orientation relative to the membrane (linear dichroism spectroscopy) and enzymatic digestion of the lipids (mass spectrometry).
The Binding of Single‐Stranded DNA and PNA to Single‐Walled Carbon Nanotubes Probed by Flow Linear Dichroism
Publisher: Wiley
Date: 25-07-2005
Abstract: The binding of single-stranded DNAs and a neutral DNA analogue (peptide nucleic acid, PNA) to single-walled carbon nanotubes in solution phase has been probed by absorbance spectroscopy and linear dichroism. The nanotubes are solubilised by aqueous sodium dodecyl sulfate, in which the nucleic acids also dissolve. The linear dichroism (LD) of the nanotubes, when subtracted from that due to the nanotubes/nucleic acid s les, gives the LD of the bound nucleic acid. The binding of the single-stranded DNA to the single-walled nanotubes is quite different from that previously observed for double-stranded DNA. It is likely that the nucleic acid bases lie flat on the nanotube surface with the backbone wrapping round the nanotube at an oblique angle in the region of 45 degrees . The net effect is like beads on a string. The base orientation with the single-stranded PNA is inverted with respect to that of the single-stranded DNA, as shown by their oppositely signed LD signals.
Structural Characterisation of the Insecticidal Toxin XptA1, Reveals a 1.15 MDa Tetramer with a Cage-like Structure
Publisher: Elsevier BV
Date: 03-2007
DOI: 10.1016/J.JMB.2006.12.057
Abstract: A recently identified class of proteins conferring insecticidal activity to several bacteria within the Enterobacteriaceae family have potential for control of commercially important insect pests. Here, we report the first purification, biophysical characterisation and 3-D structural analysis of one of the toxin components, XptA1, from Xenorhabdus nematophila PMFI296 to a resolution of 23 A. Membrane binding studies indicate that the three-component toxin system has a different mode of action from that of proteins from Bacillus thuringiensis (Bt). Biophysical characterisation of XptA1 suggests a mechanism of action of XptA1 whereby it first binds to the cell membrane forming a structure with a central cavity and forms a complex with its partners XptB1 and XptC1 producing the full insecticidal toxin. The structure of XptA1 is shown by a combination of electron microscopy, ultracentrifugation and circular dichroism spectroscopy to be a 1.15 MDa tetramer with a cage-like structure. Each of the four symmetry-related subunits has three well-defined domains and a longitudinal twist with one end narrower than the other. One third of the residues of XptA1 are alpha-helical and it is suggested the subunits associate partly via an alpha-helical coiled-coil interaction. XptA1 itself shows the same secondary structure at neutral pH and in an alkaline environment up to pH10.5. This pH tolerance indicates that the folded XptA1 can pass through the midgut of Lepidopteran insects susceptible to the insecticidal toxin complex. This implies therefore that its folded structure is important for its biological activity.
Is photocleavage of DNA by YOYO-1 using a synchrotron radiation light source sequence dependent?
Publisher: Springer Science and Business Media LLC
Date: 20-09-2011
DOI: 10.1007/S00249-011-0739-7
Abstract: The photocleavage of double-stranded and single-stranded DNA by the fluorescent dye YOYO-1 was investigated in real time by using the synchrotron radiation light source ASTRID (ISA, Denmark) both to initiate the reaction and to monitor its progress using Couette flow linear dichroism (LD) throughout the irradiation period. The dependence of LD signals on DNA sequences and on time in the intense light beam was explored and quantified for single-stranded poly(dA), poly[(dA-dT)(2)], calf thymus DNA (ctDNA) and Micrococcus luteus DNA (mlDNA). The DNA and ligand regions of the spectrum showed different LD kinetic behaviors, and there was significant sequence dependence of the kinetics. However, in contrast to expectations from the literature, we found that poly(dA), mlDNA, low salt ctDNA and low salt poly[(dA-dT)(2)] all had significant populations of groove-bound YOYO. It seems that this mode was predominantly responsible for the catalysis of DNA cleavage. In homopolymeric DNAs, intercalated YOYO was unable to cleave DNA. In mixed-sequence DNAs the data suggest that YOYO in some but not all intercalated binding sites can cause cleavage. It is also likely that cleavage occurs at transient single-stranded regions. The reaction rates for a 100 mA beam current of 0.5-μW power varied from 0.6 h(-1) for single-stranded poly(dA) to essentially zero for low salt poly[(dG-dC)(2)] and high salt poly[(dA-dT)(2)]. At the conclusion of the experiments with each kind of DNA, uncleaved DNA with intercalated YOYO remained.
Transformation of aqueous protein attenuated total reflectance infra-red absorbance spectroscopy to transmission
Publisher: Cambridge University Press (CUP)
Date: 2020
DOI: 10.1017/QRD.2020.11
Abstract: Infrared (IR) spectroscopy is increasingly being used to probe the secondary structure of proteins, especially for high-concentration s les and biopharmaceuticals in complex formulation vehicles. However, the small path lengths required for aqueous protein transmission experiments, due to high water absorbance in the amide I region of the spectrum, means that the path length is not accurately known, so only the shape of the band is ever considered. This throws away a dimension of information. Attenuated total reflectance (ATR) IR spectroscopy is much easier to implement than transmission IR spectroscopy and, for a given instrument and s le, gives reproducible spectra. However, the ATR-absorbance spectrum varies with s le concentration and instrument configuration, and its wavenumber dependence differs significantly from that observed in transmission spectroscopy. In this paper, we determine, for the first time, how to transform water and aqueous protein ATR spectra into the corresponding transmission spectra with appropriate spectral shapes and intensities. The approach is illustrated by application to water, concanavalin A, haemoglobin and lysozyme. The transformation is only as good as the available water refractive index data. A hybrid of literature data provides the best results. The transformation also allows the angle of incidence of an ATR crystal to be determined. This opens the way to using both spectral shape and spectra intensity for protein structure fitting.
Design and Non‐Covalent DNA Binding of Platinum(II) Metallacalix[4]arenes
Publisher: Wiley
Date: 06-2007
Abstract: A set of cyclic tetranuclear complexes of the metallacalix[4]arene type with formula [{Pt(en)(L)}(4)](4+) (en=ethylenediamine 2: LH=5-chloro-2-hydroxypyrimidine (5-Cl-Hpymo) 3: LH=5-bromo-2-hydroxypyrimidine (5-Br-Hpymo) 4: LH=5-iodo-2-hydroxypyrimidine (5-I-Hpymo)) have been obtained from the reaction between cis-protected square-planar [Pt(en)(H(2)O)(2)](2+) metal entities and LH in aqueous media. Additionally, the binding properties of 2, 3, 4 and their congener [{Pt(en)(L)}(4)](4+) (1: LH=2-hydroxypyrimidine (Hpymo)) with calf thymus-DNA (ct-DNA) have been studied by using different techniques including circular and linear dichroism (CD and LD, respectively) and UV-visible absorbance spectroscopies, gel electrophoresis, fluorescence competitive-binding studies and atomic force microscopy (AFM). The results are consistent with significant non-covalent interactions taking place between the polynuclear cyclic species and ct-DNA. Moreover, gel electrophoresis, linear dichroism titrations and AFM images of ct-DNA with metallacalixarenes show ct-DNA coiling at low metallacalixarene concentrations and upon subsequent increments in metallacalixarene concentration ct-DNA can be seen to uncoil with concomitant formation of long and inflexible ct-DNA structures.
Structural characterisation, stability and antibody recognition of chimeric NHBA-GNA1030: An investigational vaccine component against Neisseria meningitidis
Publisher: Elsevier BV
Date: 02-2012
DOI: 10.1016/J.VACCINE.2011.12.066
Abstract: A new generation multi-component vaccine, principally directed against serogroup B Neisseria meningitidis (4CMenB), has recently been developed. One of its components, identified through reverse vaccinology, is the neisserial heparin-binding antigen (NHBA) which is included in the formulation as a novel NHBA-GNA1030 fusion protein (NHBA-FP). We describe here the biophysical characteristics of this vaccine antigen to understand better its structural properties in solution and concurrent immunogenicity prior to formulation. By deliberately stressing the protein to lose its immune responses, we were able to study the protein's structural changes at the molecular level. The unmodified NHBA-FP was found to be mainly monomeric with mass of 67kDa and secondary structure dominated by β-sheets and turns (57% average). The antigen was very stable in storage buffer. It could be forced to unfold in a low-salt buffer resulting in the exposure of one of its two tryptophan residues at 50°C. Long-term stress studies (10-15 days at 37°C) showed modification in the chromatographic and electrophoretic profiles with progressive degradation and aggregation. Since there was little change in secondary structure (as monitored by circular dichroism and tryptophan fluorescence spectroscopy), the loss of functional immunogenicity of the thermal stressed protein could be mainly attributed to the observed fragmentation and aggregation. We therefore conclude that the maintenance of the intact, non-fragmented state of the NHBA-FP is important to preserve its functional immunogenicity. This may thus be utilised as an assay for the control testing of the protein.
The pH Dependence of Polymerization and Bundling by the Essential Bacterial Cytoskeltal Protein FtsZ
Publisher: Public Library of Science (PLoS)
Date: 28-06-2011
The Mechanics of FtsZ Fibers
Publisher: Elsevier BV
Date: 02-2012
Protein Fiber Linear Dichroism for Structure Determination and Kinetics in a Low-Volume, Low-Wavelength Couette Flow Cell
Publisher: Elsevier BV
Date: 2004
Reduction of Background Fluorescence from Impurities in Protein Samples for Raman Spectroscopy
Publisher: Hindawi Limited
Date: 24-11-2022
DOI: 10.1155/2022/1928091
Abstract: Background fluorescence remains the biggest challenge in Raman spectroscopy because of the consequent curvature of the baseline and the degradation of the signal-to-noise ratio of the Raman signal. While the concentrations of the fluorophore impurities are usually too low to be detected by other analytical methods, they are often sufficient to prevent Raman data collection. Among the different existing methods to remove the fluorescence signal, photobleaching remains the most popular due to its simplicity. However, using the spectrometer laser to photobleach is far from optimal. Most commercially available instruments have little or no choice of wavelength, and their output powers are in many cases not suitable for highly fluorescent s les such as those from biological systems (e.g., proteins). In this article, we assess practical aspects of photobleaching such as the apparent reversibility of the process and the effect of convection currents due to what we speculate to be temperature gradients across the bulk of the solution. We also introduce an affordable custom made external photobleaching unit with a choice of excitation wavelength and demonstrate its viability with a highly fluorescent bovine serum albumin protein solution, which had proved most challenging for Raman spectroscopy as it contained ∼10% w/w impurities.
Linear Dichroism Spectroscopy: Theory
Publisher: Springer Berlin Heidelberg
Date: 2018
Restriction Enzyme Kinetics Monitored by UV Linear Dichroism
Publisher: American Chemical Society (ACS)
Date: 27-06-2006
DOI: 10.1021/BI0601712
Abstract: The use of linear dichroism (LD) spectroscopy for biological applications has been brought to the forefront recently by our development of thermostated microvolume Couette cells. We present a method for following the digestion of DNA by restriction endonucleases in real time without the use of any extrinsic dyes or labels. This is accomplished using linear dichroism spectroscopy (the differential absorbance of light polarized parallel and perpendicular to the s le orientation axis). The differential absorbance signal depends on the degree of alignment of the molecules. In this case the DNA is aligned by Couette flow (flowing the solution in the annular gap between two concentric cylinders), and we monitor the increase in alignment upon linearization of a circular DNA molecule. In addition, we observe a decrease in alignment upon further digestion and subsequent shortening of the DNA. Ten enzymes were investigated: seven enzymes with a single cut site (EcoRI, KpnI, NdeI, NotI, NruI, SmaI, XbaI), two enzymes with two cut sites (BstZ17I, EagI), and one enzyme with no cut site (ClaI). LD, as implemented in this new assay, is broadly applicable across a wide range of DNA-modifying enzymes and compounds and, as such, is a useful addition to the toolbox of biological characterization.
Which is more likely: the Ray-Dutt twist or the Bailar twist?
Publisher: American Chemical Society (ACS)
Date: 09-1988
DOI: 10.1021/IC00291A001
Couette flow fluorescence detected linear dichroism for analytes in lipid bilayers
Publisher: Wiley
Date: 09-03-2023
DOI: 10.1002/CHIR.23554
Abstract: Membranes are important sites of intermolecular interactions in biological systems. However, they present significant analytical challenges as they contain multiple analytes and are dynamic in nature. In this work, we show how a Jasco J‐1500 circular dichroism spectropolarimeter can be used with a microvolume Couette flow cell and appropriate cut‐off filters to measure excitation fluorescence detected linear dichroism (FDLD) of fluorophores embedded in liposomal membranes. The result is a spectrum that selectively probes the fluorophore(s) and eliminates the scattering that is apparent in the corresponding flow linear dichroism (LD) spectrum. The FDLD spectrum is opposite in sign from the LD spectrum with relative magnitudes modified by the quantum yields of the transitions. FDLD thus enables analyte orientations to be identified in a membrane. Data for a membrane peptide, gramicidin, and two aromatic analytes, anthracene and pyrene, are presented. Issues with the “leakage” of photons by the long pass filters used is also discussed.
An extension of the quadrant rule in oxiranes to non-alkyl substituents: the CD of R (—)- and S (+)-epichlorohydrin
Publisher: Elsevier BV
Date: 05-1991
A ligand-ligand interaction model for the structures of transition metal clusters
Publisher: Elsevier BV
Date: 08-1990
Energetics of metal complex isomerization reactions
Publisher: American Chemical Society (ACS)
Date: 03-1989
DOI: 10.1021/IC00305A005
Site‐Specific Identification of an Aβ Fibril–Heparin Interaction Site by Using Solid‐State NMR Spectroscopy
Publisher: Wiley
Date: 14-11-2012
The Effect of Oligomerization on A Solid-Binding Peptide Binding to Silica-Based Materials
Publisher: MDPI AG
Date: 30-05-2020
DOI: 10.3390/NANO10061070
Abstract: The bifunctional linker-protein G (LPG) fusion protein comprises a peptide (linker) sequence and a truncated form of Streptococcus strain G148 protein G (protein G). The linker represents a multimeric solid-binding peptide (SBP) comprising 4 × 21-amino acid sequence repeats that display high binding affinity towards silica-based materials. In this study, several truncated derivatives were investigated to determine the effect of the SBP oligomerization on the silica binding function of LPG (for the sake of clarity, LPG will be referred from here on as 4 × LPG). Various biophysical characterization techniques were used to quantify and compare the truncated derivatives against 4 × LPG and protein G without linker (PG). The derivative containing two sequence repeats (2 × LPG) showed minimal binding to silica, while the truncated derivative with only a single sequence (1 × LPG) displayed no binding. The derivative containing three sequence repeats (3 × LPG) was able to bind to silica with a binding affinity of KD = 53.23 ± 4.5 nM, which is 1.5 times lower than that obtained for 4 × LPG under similar experimental conditions. Circular dichroism (CD) spectroscopy and fluorescence spectroscopy studies indicated that the SBP degree of oligomerization has only a small effect on the secondary structure (the linker unravels the beginning of the protein G sequence) and chemical stability of the parent protein G. However, based on quartz crystal microbalance with dissipation monitoring (QCM-D), oligomerization is an important parameter for a strong and stable binding to silica. The replacement of three sequence repeats by a (GGGGS)12 glycine-rich spacer indicated that the overall length rather than the SBP oligomerization mediated the effective binding to silica.
Amine induced Z-DNA in poly(dG-dC)·poly(dG-dC): Circular dichroism and gel electrophoresis study
Publisher: Royal Society of Chemistry (RSC)
Date: 2000
DOI: 10.1039/B005801G
Protein Concentration Determination Using Dyes and Beer-Lambert Law
Publisher: Springer Berlin Heidelberg
Date: 2018
Chemical Composition and Antibacterial Activity of the Essential Oil and the Gum ofPistacia lentiscusVar. chia
Publisher: American Chemical Society (ACS)
Date: 02-09-2005
DOI: 10.1021/JF050639S
Abstract: The essential oil and gum of Pistacia lentiscus var. chia, commonly known as the mastic tree, are natural antimicrobial agents that have found extensive uses in medicine in recent years. In this work, the chemical composition of mastic oil and gum was studied by GC-MS, and the majority of their components was identified. alpha-Pinene, beta-myrcene, beta-pinene, limonene, and beta-caryophyllene were found to be the major components. The antibacterial activity of 12 components of mastic oil and the oil itself was evaluated using the disk diffusion method. Furthermore, attempts were made to separate the essential oil into different fractions in order to have a better picture of the components responsible for its antibacterial activity. Several trace components that appear to contribute significantly to the antibacterial activity of mastic oil have been identified: verbenone, alpha-terpineol, and linalool. The sensitivity to these compounds was different for different bacteria tested (Escherichia coli, Staphylococcus aureus, and Bacillus subtilis), which suggests that the antibacterial efficacy of mastic oil is due to a number of its components working synergistically. The establishment of a correlation between the antibacterial activity of mastic oil and its components was the main purpose of this research. Mastic gum was also examined, but it proved to be more difficult to handle compared to the essential oil.
Structure and reactivity of transition metal complexes: A stereochemical approach
Publisher: Elsevier BV
Date: 1989
Circular Dichroism Spectroscopy of Biomacromolecules
Publisher: Springer Berlin Heidelberg
Date: 2018
Spectroscopy of model-membrane liposome-protein systems: complementarity of linear dichroism, circular dichroism, fluorescence and SERS
Publisher: Portland Press Ltd.
Date: 04-05-2021
DOI: 10.1042/ETLS20200354
Abstract: A range of membrane models have been developed to study components of cellular systems. Lipid vesicles or liposomes are one such artificial membrane model which mimics many properties of the biological system: they are lipid bilayers composed of one or more lipids to which other molecules can associate. Liposomes are thus ideal to study the roles of cellular lipids and their interactions with other membrane components to understand a wide range of cellular processes including membrane disruption, membrane transport and catalytic activity. Although liposomes are much simpler than cellular membranes, they are still challenging to study and a variety of complementary techniques are needed. In this review article, we consider several currently used analytical methods for spectroscopic measurements of unilamellar liposomes and their interaction with proteins and peptides. Among the variety of spectroscopic techniques seeing increasing application, we have chosen to discuss: fluorescence based techniques such as FRET (fluorescence resonance energy transfer) and FRAP (fluorescence recovery after photobleaching), that are used to identify localisation and dynamics of molecules in the membrane circular dichroism (CD) and linear dichroism (LD) for conformational and orientation changes of proteins on membrane binding and SERS (Surface Enhanced Raman Spectroscopy) as a rapidly developing ultrasensitive technique for site-selective molecular characterisation. The review contains brief theoretical basics of the listed techniques and recent ex les of their successful applications for membrane studies.
DNA binding of a spermine derivative: Spectroscopic study of anthracene‐9‐carbonyl‐n1‐spermine with poly[d(G‐C)·(d(G‐C))] and poly[d(A‐T) · d(A‐T)]
Publisher: Wiley
Date: 12-1994
Abstract: The binding of polyamines, including spermidine (1) and spermine (2), to poly[d(G-C).d(G-C)] was probed using spectroscopic studies of anthracene-9-carbonyl-N1-spermine (3) data from normal absorption, linear dichroism (LD), and circular dichroism (CD) are reported. Ligand LD and CD for transitions located in the DNA region of the spectrum were used. The data show that 3 binds to DNA in a manner characteristic of both its amine and polycyclic aromatic parts. With poly[(dG-dC).(dG-dC)], binding modes are occupied sequentially and different modes correspond to different structural perturbations of the DNA. The most stable binding mode for 3 with poly[d(G-C).d(G-C)] has a site size of 6 +/- 1 bases, and an equilibrium binding constant of (2.2 +/- 1.1) x 10(7) M-1 with the anthracene moiety intercalated. It dominates the spectra from mixing ratios of approximately 133:1 until 6:1 DNA phosphate: 3 is reached. The analogous data for poly[d(A-T).d(A-T)] between mixing ratios 36:1 and 7:1 indicates a site size of 8.3 +/- 1.1 bases and an equilibrium binding constant of (6.6 +/- 3.3) x 10(5) M-1. Thus, 3 binds preferentially to poly[d(G-C).d(G-C)] at these concentrations.
Intramolecular DNA coiling mediated by metallo-supramolecular cylinders: Differential binding of P and M helical enantiomers
Publisher: Proceedings of the National Academy of Sciences
Date: 16-04-2002
Abstract: We have designed a synthetic tetracationic metallo-supramolecular cylinder that targets the major groove of DNA with a binding constant in excess of 10 7 M −1 and induces DNA bending and intramolecular coiling. The two enantiomers of the helical molecule bind differently to DNA and have different structural effects. We report the characterization of the interactions by a range of biophysical techniques. The M helical cylinder binds to the major groove and induces dramatic intramolecular coiling. The DNA bending is less dramatic for the P enantiomer.
Potential injectable contraceptive steroids: testosterone buciclate
Publisher: International Union of Crystallography (IUCr)
Date: 14-02-2004
Conjugation of testosterone modifies the interaction of mono-functional cationic platinum(ii) complexes with DNA, causing significant alterations to the DNA helix
Publisher: Royal Society of Chemistry (RSC)
Date: 2010
DOI: 10.1039/C0DT00839G
Abstract: Previously a range of androgen conjugates with non-conventional platinum(II) complexes have been synthesised with the aim of enhancing cellular delivery, and which have shown increased cytotoxic activity compared with non-steroidal compounds (M. J. Hannon et al., Dalton Trans., 2010, DOI: 10.1039/c0dt00838a). To further study this, the complexes have been assessed for their ability to bind to and alter the structure of DNA. All platinum(II) complexes studied herein bind to model nucleo-bases and DNA, but to our surprise, testosterone-based complexes caused the DNA helix to undergo significant unwinding and bending, whereas non-steroidal control complexes caused minimal structural alterations. These effects are similar to those cisplatin induces on DNA structure despite the fact that these compounds produce a monofunctional lesion. This ability attributed to interactions between the DNA helix and bulky steroidal skeleton of testosterone, coupled with the enhanced cellular delivery induced by the steroid make the steroid approach an exciting way to explore non-conventional platinum drug delivery.
The synthesis and unexpected solution chemistry of thermochromic carborane-containing osmium half-sandwich complexes
Publisher: Royal Society of Chemistry (RSC)
Date: 2016
DOI: 10.1039/C5DT04398K
Abstract: The functionalisation of the 16-electron complex [Os(η 6 - p -cymene)(1,2-dicarba- closo -dodecarborane-1,2-dithiolato)] ( 1 ) with a series of Lewis bases to give the corresponding 18-electron complexes is reported.
Breaking the 200 nm Limit for Routine Flow Linear Dichroism Measurements Using UV Synchrotron Radiation
Publisher: Elsevier BV
Date: 12-2008
Nanofiber-Based Delivery of Therapeutic Peptides to the Brain
Publisher: American Chemical Society (ACS)
Date: 10-01-2013
DOI: 10.1021/NN305193D
Abstract: The delivery of therapeutic peptides and proteins to the central nervous system is the biggest challenge when developing effective neuropharmaceuticals. The central issue is that the blood-brain barrier is impermeable to most molecules. Here we demonstrate the concept of employing an hiphilic derivative of a peptide to deliver the peptide into the brain. The key to success is that the hiphilic peptide should by design self-assemble into nanofibers wherein the active peptide epitope is tightly wrapped around the nanofiber core. The nanofiber form appears to protect the hiphilic peptide from degradation while in the plasma, and the hiphilic nature of the peptide promotes its transport across the blood-brain barrier. Therapeutic brain levels of the hiphilic peptide are achieved with this strategy, compared with the absence of detectable peptide in the brain and the consequent lack of a therapeutic response when the underivatized peptide is administered.
Continuous-channel flow linear dichroism
Publisher: Royal Society of Chemistry (RSC)
Date: 2012
DOI: 10.1039/C2AY25513H
A Practical Protocol for the Reduction of Disulfide Bonds in Proteins Prior to Analysis by Mass Spectrometry
Publisher: SAGE Publications
Date: 02-2001
DOI: 10.1255/EJMS.385
Abstract: Aquick, simple applicable protocol for the reduction of protein disulfide bonds for the purposes of mass spectrometry has been established. The method utilises the chemical reducing agent dithiothreitol. Proteins with various numbers of disulfide bonds per molecule were chosen for the study to demonstrate the general applicability of the method. The results obtained under controlled conditions (concentration of reagents, pH, temperature) showed that a five-minute treatment at 70°C with 10 mM dithiothreitol in 5 mM ammonium acetate buffer pH 5.5 was sufficient for complete reduction of disulfide bonds in all investigated proteins (α-lactalbumin, lysozyme, ribonuclease, oxytocin and wheat germ agglutinin). The progress of disulfide bond reduction was observed by electrospray ionisation and Fourier transform ion cyclotron resonance mass spectrometry. Circular dichroism was used to monitor conformational changes of reduced proteins and of their unreduced counterparts undergoing the same heat treatment.
Optical properties of xanthene based fluorescent dyes studied by stretched-film linear dichroism
Publisher: Royal Society of Chemistry (RSC)
Date: 2014
DOI: 10.1039/C4RA06126H
Abstract: Xanthene dyes are commonly used to label proteins in order to probe their location and activity using fluorescence spectroscopy and microscopy.
Contributions of Hydroxyethyl Groups to the DNA Binding Affinities of Anthracene Probes
Publisher: American Chemical Society (ACS)
Date: 22-09-2006
DOI: 10.1021/JP063997M
Abstract: Contributions of hydroxyethyl functions to the DNA binding affinities of substituted anthracenes are evaluated by calorimetry and spectroscopy. Isothermal titration calorimetry indicated that binding of the ligands to calf thymus DNA (5 mM Tris buffer, 50 mM NaCl, pH 7.2, 25 degrees C) is exothermic. The binding constants increased from 1.5 x 10(4) to 1.7 x 10(6) M(-1) as a function of increase in the number of hydroxyethyl functions (0-4). DNA binding was accompanied by red-shifted absorption (approximately 630 cm(-1)), strong hypochromism (>65%), positive induced-circular dichroism bands, and negative linear dichroism signals. DNA binding, in general, increased the helix stabilities to a significant extent (DeltaT(m) approximately 7 degrees C, DeltaDeltaH approximately 3 kcal/mol, DeltaDeltaS approximately 6-20 cal/K.mol). The binding constants showed a strong correlation with the number of hydroxyethyl groups present on the anthracene ring system. Analysis of the binding data using the hydrophobicity parameter (Log P) showed a poor correlation between the binding affinity and hydrophobicity. This observation was also supported by a comparison of the affinities of probes carrying N-ethyl (Kb = 0.8 x 10(5) M(-1)) versus N-hydroxyethyl side chains (Kb = 5.5 x 10(5) M(-1)). These are the very first ex les of a strong quantitative correlation between the DNA binding affinity of a probe and the number of hydroxyethyl groups present on the probe. These quantitative findings are useful in the rational design of new ligands for high-affinity binding to DNA.
Enantiopreferential DNA binding of [ruthenium(II)(1,10-phenanthroline)3]2+ studied with linear and circular dichroism
Publisher: American Chemical Society (ACS)
Date: 02-1990
DOI: 10.1021/JA00161A050
Direct detection and measurement of wall shear stress using a filamentous bio-nanoparticle
Publisher: Springer Science and Business Media LLC
Date: 25-08-2015
DOI: 10.1007/S12274-015-0831-X
Abstract: The wall shear stress (WSS) that a moving fluid exerts on a surface affects many processes including those relating to vascular function. WSS plays an important role in normal physiology (e.g. angiogenesis) and affects the microvasculature’s primary function of molecular transport. Points of fluctuating WSS show abnormalities in a number of diseases however, there is no established technique for measuring WSS directly in physiological systems. All current methods rely on estimates obtained from measured velocity gradients in bulk flow data. In this work, we report a nanosensor that can directly measure WSS in microfluidic chambers with sub-micron spatial resolution by using a specific type of virus, the bacteriophage M13, which has been fluorescently labeled and anchored to a surface. It is demonstrated that the nanosensor can be calibrated and adapted for biological tissue, revealing WSS in micro-domains of cells that cannot be calculated accurately from bulk flow measurements. This method lends itself to a platform applicable to many applications in biology and microfluidics.
DMA-binding studies of XSPTSPSZ, derivatives of the intercalating heptad repeat of RNA polymerase II
Publisher: Wiley
Date: 05-10-1997
DOI: 10.1002/(SICI)1097-0282(19971005)42:4<387::AID-BIP2>3.0.CO;2-M
Circular dichroism of the carbonyl n-.pi.* transition: an independent systems/perturbation approach
Publisher: American Chemical Society (ACS)
Date: 04-1988
DOI: 10.1021/JA00216A003
Considerations of Noise and Measurement Reproducibility of Circular Dichroism Measurements Using Na[CoIII(EDDS)]
Publisher: Wiley
Date: 02-05-2012
DOI: 10.1002/CHIR.22005
Abstract: Although circular dichroism (CD) spectroscopy has become ubiquitous in biological, chemical, and pharmacological laboratories, several issues with instrument calibration and standardization, measurements quality, and reproducibility still remain. In the context of validating and developing a wide-wavelength-range stable standard for CD that is available in both enantiomeric forms, (R,R)- and (S,S)-Na[Co(III)(EDDS)] (where EDDS is ethylenediaminedisuccinato), we have become aware of sources of error in CD spectroscopy in addition to instrument calibration and user issues. This article summarizes those errors and suggests procedures for minimizing them by averaging over sufficient independent data accumulations with appropriate parameters.
Linear Dichroism Spectra: Measurement
Publisher: Springer Berlin Heidelberg
Date: 2018
Shape dependent protein-induced stabilization of gold nanoparticles: From a protein corona perspective Special Collection: Distinguished Australian Researchers
Publisher: Wiley
Date: 22-02-2023
DOI: 10.1002/AGT2.323
Abstract: Abstract Gold nanoparticles (AuNPs) are promising materials for many bioapplications. However, upon contacting with biological media, AuNPs undergo changes. The interaction with proteins results in the so‐called protein corona (PC) around AuNPs, leading to the new bioidentity and optical properties. Understanding the mechanisms of PC formation and its functions can help us to utilise its benefits and avoid its drawbacks. To date, most of the previous works aimed to understand the mechanisms governing PC formation and focused on the spherical nanoparticles, although non‐spherical nanoparticles are designed for a wide range of applications in biosensing. In this work, we investigated the differences in PC formation on spherical and anisotropic AuNPs (nanostars in particular) from the joint experimental (extinction spectroscopy, zeta potential and surface‐enhanced Raman scattering [SERS]) and computational methods (the finite element method and molecular dynamics [MD] simulations). We discovered that protein does not fully cover the surface of anisotropic nanoparticles, leaving SERS hot‐spots at the tips and high curvature edges ‘available’ for analyte binding (no SERS signal after pre‐incubation with protein) while providing protein‐induced stabilization (indicated by extinction spectroscopy) of the AuNPs by providing a protein layer around the particle's core. The findings are confirmed from our MD simulations, the adsorption energy significantly decreases with the increased radius of curvature, so that tips (adsorption energy: 2762.334 kJ/mol) would be the least preferential binding site compared to core (adsorption energy: 11819.263 kJ/mol). These observations will help the development of new nanostructures with improved sensing and targeting ability.
Biological Insights from a Simulation Model of the Critical FtsZ Accumulation Required for Prokaryotic Cell Division
Publisher: American Chemical Society (ACS)
Date: 10-06-2015
DOI: 10.1021/ACS.BIOCHEM.5B00261
Abstract: A simulation model of prokaryotic Z-ring assembly, based on the observed behavior of FtsZ in vitro as well as on in vivo parameters, is used to integrate critical processes in cell ision. According to the model, the cell's ability to ide depends on a "contraction parameter" (χ) that links the force of contraction to the dynamics of FtsZ. This parameter accurately predicts the outcome of ision. Evaluating the GTP binding strength, the FtsZ polymerization rate, and the intrinsic GTP hydrolysis/dissociation activity, we find that inhibition of GTP-FtsZ binding is an inefficient antibacterial target. Furthermore, simulations indicate that the temperature sensitivity of the ftsZ84 mutation arises from the conversion of FtsZ to a dual-specificity NTPase. Finally, the sensitivity to temperature of the rate of ATP hydrolysis, over the critical temperature range, leads us to conclude that the ftsZ84 mutation affects the turnover rate of the Z-ring much less strongly than previously reported.
Circular dichroism of molecules requiring two substituents for chirality
Publisher: Informa UK Limited
Date: 03-1991
Redox-active and DNA-binding coordination complexes of clotrimazole
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C4DT02883J
Abstract: The coordination compounds bind to DNA by two different binding modes depending on the concentration, sequence of the DNA, and the structure of the complex.
Multiple DNA binding modes of anthracene-9-carbonyl-N1-spermine
Publisher: Elsevier BV
Date: 06-1995
DOI: 10.1016/0968-0896(95)00086-V
Abstract: The poly(dAdT)2 complex of anthracene-9-carbonyl-N1-spermine, a spermine derivative terminally substituted with an anthracene moiety, has been studied using fluorescence, linear dichroism, circular dichroism, normal absorption spectroscopy (as a function of temperature) and computer modelling. For comparison, some data are also provided for the same ligand with poly(dGdC)2 and calf thymus DNA. Following detailed fluorescence and CD spectroscopic studies, we propose that anthracene-9-carbonyl-N1-spermine intercalates in at least two different binding orientations with poly(dAdT)2. Based on computer simulation data, we deduce that the ligand can intercalate from both the minor groove and the major groove. In contrast, intercalation with poly(dGdC)2 probably occurs only from the major groove. At high ligand concentrations, the CD spectra suggest anthracene-anthracene interactions, whilst the LD data point towards a groove-bound anthracene. Again from computer simulations, we propose binding modes consistent with these observations. Other data from the LD spectra suggest a sequential nature to the binding of the ligand to calf thymus DNA, with GC-rich sites being occupied first. At low ligand concentrations, anthracene-9-carbonyl-N1-spermine is able to stabilize poly(dAdT)2 against thermal decomposition, but not as effectively as spermine. The reverse is found to be true with calf thymus DNA. Both the anthracene-9-carbonyl-N1-spermine and spermine complexes of poly(dAdT)2 show pre-melt transitions in their melting curves. The anthracene-9-carbonyl-N1-spermine complex with poly(dAdT)2 also shows a post-melt transition.
Multiple binding modes with DNA of anthracene-9-carbonyl-N1-spermine probed by LD, CD, normal absorption, and molecular modelling compared with those of spermidine and spermine
Publisher: Elsevier BV
Date: 10-1994
Versatile Click Cyanine Amino Acid Conjugates Showing One‐Atom‐Influenced Recognition of DNA/RNA Secondary Structure and Mitochondrial Localisation in Living Cells
Publisher: Wiley
Date: 16-04-2018
Alignment of a Model Amyloid Peptide Fragment in Bulk and at a Solid Surface
Publisher: American Chemical Society (ACS)
Date: 28-05-2010
DOI: 10.1021/JP101374E
Abstract: The alignment of model amyloid peptide YYKLVFFC is investigated in bulk and at a solid surface using a range of spectroscopic methods employing polarized radiation. The peptide is based on a core sequence of the amyloid beta (Abeta) peptide, KLVFF. The attached tyrosine and cysteine units are exploited to yield information on alignment and possible formation of disulfide or dityrosine links. Polarized Raman spectroscopy on aligned stalks provides information on tyrosine orientation, which complements data from linear dichroism (LD) on aqueous solutions subjected to shear in a Couette cell. LD provides a detailed picture of alignment of peptide strands and aromatic residues and was also used to probe the kinetics of self-assembly. This suggests initial association of phenylalanine residues, followed by subsequent registry of strands and orientation of tyrosine residues. X-ray diffraction (XRD) data from aligned stalks is used to extract orientational order parameters from the 0.48 nm reflection in the cross-beta pattern, from which an orientational distribution function is obtained. X-ray diffraction on solutions subject to capillary flow confirmed orientation in situ at the level of the cross-beta pattern. The information on fibril and tyrosine orientation from polarized Raman spectroscopy is compared with results from NEXAFS experiments on s les prepared as films on silicon. This indicates fibrils are aligned parallel to the surface, with phenyl ring normals perpendicular to the surface. Possible disulfide bridging leading to peptide dimer formation was excluded by Raman spectroscopy, whereas dityrosine formation was probed by fluorescence experiments and was found not to occur except under alkaline conditions. Congo red binding was found not to influence the cross-beta XRD pattern.
Theoretical Aspects of the Enantiomeric Resolution of Dimetallo Helicates with Different Surface Topologies on Cellulose Columns
Publisher: Informa UK Limited
Date: 11-2005
Chiral Solvent Structure Around Chiral Molecules: Experimental and Theoretical Study
Publisher: American Chemical Society (ACS)
Date: 08-1994
DOI: 10.1021/JA00095A033
Circular and Linear Dichroism of Drug-DNA Systems
Publisher: Humana Press
Date: 06-11-2009
DOI: 10.1007/978-1-60327-418-0_3
Abstract: When a drug binds to DNA, its electronic structure is perturbed, and it perturbs the DNA's electronic structure. The resulting change to the electronic spectroscopy can be used to probe the drug-DNA interaction. This chapter outlines how circular and linear dichroism spectroscopy can be used to provide information about drug-DNA systems. Circular dichroism spectroscopy involves measuring the difference in absorption of left and right circularly polarized light. It is uniquely sensitive to the helicity of the molecules being studied. Linear dichroism, as the name implies, involves measuring the difference in absorption of light linearly polarized parallel and perpendicular to an orientation axis. Linear dichroism provides information about the relative orientations of subunits of an interacting system. The material presented in this chapter is by no means comprehensive the aim is to enable the user to collect reasonable quality data and to interpret it.
Rapid Injection Linear Dichroism for Studying the Kinetics of Biological Processes
Publisher: American Chemical Society (ACS)
Date: 18-07-2012
DOI: 10.1021/AC300842H
Abstract: Linear dichroism is defined as the differential absorbance of linearly polarized light oriented in two orthogonal directions by an aligned s le. The measurement of a linear dichroism (LD) spectrum of a s le provides two key pieces of structural information. First, that the s le and the chromophores within the s le are able to align. Second, given knowledge of the transition polarization directions of the chromophores, the orientation of the chromophores within the aligned s le can be resolved. It has been shown that LD can provide unique information on the structure of some of the more challenging biomolecular complexes. This has included macromolecular protein and peptide fibers such as actin, tubulin, and amyloids as well as protein-membrane complexes and DNA-protein complexes. Much of this work has been enabled by the development of a low volume Couette flow cell that efficiently aligns long molecules in solution. However, the current Couette system is inherently complex to assemble for each experiment and hence not suited to measurement of rapid reactions. In this paper we detail the development of the first rapid injection LD cell. The system utilizes a conventional stopped-flow injection system coupled to a modified low volume Couette cell, where a narrow bore capillary replaces the normal solid central rod. The system is shown to have similar optical characteristics to the conventional LD Couette flow cell but with the added benefit of a much shorter dead time (0.60 s compared to ~60). The rapid injection Couette cell has been used to measure the degradation of DNA by DNA exonuclease I, providing data that would not be available using a conventional system.
Concentration Determination Using Beer-Lambert Law
Publisher: Springer Berlin Heidelberg
Date: 2018
Oriented Circular Dichroism Spectroscopy
Publisher: Springer Berlin Heidelberg
Date: 2018
Nano-encapsulated Escherichia coli Divisome Anchor ZipA, and in Complex with FtsZ
Publisher: Springer Science and Business Media LLC
Date: 10-12-2019
DOI: 10.1038/S41598-019-54999-X
Abstract: The E . coli membrane protein ZipA, binds to the tubulin homologue FtsZ, in the early stage of cell ision. We isolated ZipA in a Styrene Maleic Acid lipid particle (SMALP) preserving its position and integrity with native E . coli membrane lipids. Direct binding of ZipA to FtsZ is demonstrated, including FtsZ fibre bundles decorated with ZipA. Using Cryo-Electron Microscopy, small-angle X-ray and neutron scattering, we determine the encapsulated-ZipA structure in isolation, and in complex with FtsZ to a resolution of 1.6 nm. Three regions can be identified from the structure which correspond to, SMALP encapsulated membrane and ZipA transmembrane helix, a separate short compact tether, and ZipA globular head which binds FtsZ. The complex extends 12 nm from the membrane in a compact structure, supported by mesoscale modelling techniques, measuring the movement and stiffness of the regions within ZipA provides molecular scale analysis and visualisation of the early isome.
Light scattering corrections to linear dichroism spectroscopy for liposomes in shear flow using calcein fluorescence and modified Rayleigh-Gans-Debye-Mie scattering
Publisher: Springer Science and Business Media LLC
Date: 25-09-2018
A Binding Mode of A-[tris(1,10-phenanthroline)ruthenium(II)]2+Exhibiting Preference for Purine-3′,5′-Pyrimidine Sites of DNA
Publisher: Informa UK Limited
Date: 12-1991
DOI: 10.1080/07391102.1991.10507936
Abstract: Molecular mechanics calculations and molecular dynamics simulations have been used to study the binding of the partially inserted major groove complex of Lambda-[Ru(1,10-phenanthroline)3]2+ with DNA. Energy refinements of this complex showed a clear preference for binding at purine-3',5'-pyrimidine sites over pyrimidine-3',5'-purine sites. The basis for this difference is shown to be a slight change in the binding orientation induced by interchanging the purine and pyrimidine bases. This in turn provides for a better secondary interaction with the helix backbone at a point beyond the immediate binding site. It is this secondary interaction that provides the additional energetic stabilisation for complexes formed at purine-3',5'-pyrimidine sites. Molecular dynamics simulations including explicit representation of solvent support these conclusions and provide an insight into the positional stability of the ligand at a particular site. Repuckering of specific deoxyribose rings to the C3'-endo conformation seems to be an important feature of the DNA/ligand complex.
The significance of ligand-ligand interactions for transition metal complex geometries
Publisher: Elsevier BV
Date: 1992
Symmetry selection rules for reaction mechanisms: application to metal-ligand isomerizations
Publisher: American Chemical Society (ACS)
Date: 02-1988
DOI: 10.1021/IC00276A006
Os2–Os4 Switch Controls DNA Knotting and Anticancer Activity
Publisher: Wiley
Date: 30-05-2016
Predicting chiral discrimination in HPLC from computer simulations
Publisher: Elsevier BV
Date: 11-2002
Comparative studies of the kinetics of macrocycle dissociation from nickel(II) in the presence of excess copper ion and 1,10-phenanthroline
Publisher: American Chemical Society (ACS)
Date: 04-1983
DOI: 10.1021/IC00151A032
Gold Nanostars with Reduced Fouling Facilitate Small Molecule Detection in the Presence of Protein
Publisher: MDPI AG
Date: 29-09-2021
DOI: 10.3390/NANO11102565
Abstract: Gold nanoparticles have the potential to be used in biomedical applications from diagnostics to drug delivery. However, interactions of gold nanoparticles with different biomolecules in the cellular environment result in the formation of a “protein corona”—a layer of protein formed around a nanoparticle, which induces changes in the properties of nanoparticles. In this work we developed methods to reproducibly synthesize spheroidal and star-shaped gold nanoparticles, and carried out a physico-chemical characterization of synthesized anionic gold nanospheroids and gold nanostars through transmission electron microscopy (TEM), dynamic light scattering (DLS), zeta potential (ZP), nanoparticles tracking analysis (NTA), ultraviolet-visible (UV–Vis) spectroscopy and estimates of surface-enhanced Raman spectroscopy (SERS) signal enhancement ability. We analyzed how they interact with proteins after pre-incubation with bovine serum albumin (BSA) via UV–Vis, DLS, ZP, NTA, SERS, cryogenic TEM (cryo-TEM) and circular dichroism (CD) spectroscopy. The tests demonstrated that the protein adsorption on the particles’ surfaces was different for spheroidal and star shaped particles. In our experiments, star shaped particles limited the protein corona formation at SERS “hot spots”. This benefits the small-molecule sensing of nanostars in biological media. This work adds more understanding about protein corona formation on gold nanoparticles of different shapes in biological media, and therefore guides design of particles for studies in vitro and in vivo.
DNA binding and bending by dinuclear complexes comprising ruthenium polypyridyl centres linked by a bis(pyridylimine) ligand
Publisher: Elsevier BV
Date: 12-2008
DOI: 10.1016/J.JINORGBIO.2008.06.006
Abstract: The interaction of enantiomerically pure dinuclear complexes of the form [Ru2(L-L)4L1]4+ (where L-L = 2,2'-bipyridine (bpy) or 1,10-phenanthroline (phen) and L1 = bis(pyridylimine) ligand ((C5H4N)CN(C6H4))2CH2)) with ct-DNA have been investigated by absorbance, circular dichroism, fluorescence displacement assays, thermal analysis, linear dichroism and gel electrophoresis. The complexes all bind more strongly to DNA than ethidium bromide, stabilise DNA and have a significant bending effect on DNA. The data for Delta,Delta-[Ru2(bpy)4L1]4+ are consistent with it binding to DNA outside the grooves wrapping the DNA about it. By way of contrast the other complexes are groove-binders. The phen complexes provide a chemically and enantiomerically stable alternative to the DNA-coiling di-iron triple-helical cylinder previously studied. In contrast to the di-iron helicates, the phen complexes show DNA sequence effects with Delta,Delta-[Ru2(phen)4L1]4+ binding preferentially to GC and Lambda,Lambda-[Ru2(phen)4L1]4+ to AT.
Acyl transfer from phosphocholinelipids to melittin
Publisher: Royal Society of Chemistry (RSC)
Date: 2011
DOI: 10.1039/C0CC04677A
Abstract: Transfer of fatty acyl groups from membrane phospholipids to melittin, a commonly studied membrane-active peptide, has been observed to occur over extended time periods. Transfer can be detected after 1-2 days and selectively targets amino groups at the N-terminal end of the peptide.
Nucleic Acid Circular Dichroism
Publisher: Springer Berlin Heidelberg
Date: 2018
Urea-Modified Self-Assembling Peptide Amphiphiles That Form Well-Defined Nanostructures and Hydrogels for Biomedical Applications.
Publisher: American Chemical Society (ACS)
Date: 02-06-2022
Abstract: Hydrogen bonding plays a critical role in the self-assembly of peptide hiphiles (PAs). Herein, we studied the effect of replacing the amide linkage between the peptide and lipid portions of the PA with a urea group, which possesses an additional hydrogen bond donor. We prepared three PAs with the peptide sequence Phe-Phe-Glu-Glu (FFEE): two are amide-linked with hydrophobic tails of different lengths and the other possesses an alkylated urea group. The differences in the self-assembled structures formed by these PAs were assessed using erse microscopies, nuclear magnetic resonance (NMR), and dichroism techniques. We found that the urea group influences the morphology and internal arrangement of the assemblies. Molecular dynamics simulations suggest that there are about 50% more hydrogen bonds in nanostructures assembled from the urea-PA than those assembled from the other PAs. Furthermore,
Investigating Binding Interactions Using Linear Dichroism and Circular Dichroism
Publisher: Springer Vienna
Date: 2011
Comments on the use of a dichromophoric circular dichroism assay for the identification of β‐turns in peptides
Publisher: Wiley
Date: 02-1994
DOI: 10.1111/J.1399-3011.1994.TB00520.X
Abstract: Use of the dichromophoric CD assay for beta-turn formation in peptide sequences has been investigated. The assay involves the observation of Cotton effects in CD spectra, originating from the approach of N- and C-terminal aromatic chromophores in tetrapeptides. The approach of the chromophores was believed to be brought about by a beta-turn in the peptide structure. Our investigations were paralleled by NMR studies which revealed the presence of a previously unreported hydrogen bond in the beta-turn conformers, which appears to play a role in the generation of the observed Cotton effects. This suggests caution in the use of the CD technique alone as an assay for beta-turn conformers in peptides.
Improved curve fitting procedures to determine equilibrium binding constants
Publisher: Royal Society of Chemistry (RSC)
Date: 2006
DOI: 10.1039/B604686J
Abstract: For ligand-biomacromolecule titration experiments it has been traditional practice to extract parameters such as the equilibrium binding constant K and the number of bases per ligand binding site n with relatively labour intensive methods, usually based on single wavelength data, such as the difference method by Rodger and Nordén coupled together with a Scatchard plot. Presented in this paper are both the theory and a least squares fitting method to derive parameters such as K and n more directly from all spectral non-linear experimental data. Both the case of non competitive binding of a metal complex ligand to DNA and the case of displacement by a metal complex ligand of an ethidium marker attached to the DNA are considered. This work may be applied directly to reduce experimental data produced by a spectropolarimeter (for circular or linear dichroism) or a spectrophotometer (for fluorescence or UV-Vis spectroscopy).
Automated High-Throughput Capillary Circular Dichroism and Intrinsic Fluorescence Spectroscopy for Rapid Determination of Protein Structure
Publisher: American Chemical Society (ACS)
Date: 04-10-2019
Calibration and Standardisation of Synchrotron Radiation Circular Dichroism and Conventional Circular Dichroism Spectrophotometers
Publisher: Hindawi Limited
Date: 2003
DOI: 10.1155/2003/379137
Abstract: Synchrotron radiation circular dichroism (SRCD) is an emerging technique in structural biology with particular value in protein secondary structure analyses since it permits the collection of data down to much lower wavelengths than conventional circular dichroism (cCD) instruments. Reference database spectra collected on different SRCD instruments in the future as well as current reference datasets derived from cCD spectra must be compatible. Therefore there is a need for standardization of calibration methods to ensure quality control. In this study, magnitude and optical rotation measurements on four cCD and three SRCD instruments were compared at 192.5, 219, 290 and 490 nm. At high wavelengths, all gave comparable results, however, at the lower wavelengths, some variations were observable. The consequences of these differences on the spectrum, and the calculated secondary structure, of a representative protein (myoglobin) are demonstrated. A method is proposed for standardising spectra obtained on any CD instrument, conventional or synchrotron‒based, with respect to existing and future databases.
Biophysical characterization of a protein for structure comparison: methods for identifying insulin structural changes
Publisher: Royal Society of Chemistry (RSC)
Date: 2016
DOI: 10.1039/C6AY01573E
Abstract: Combination of four well-established techniques complemented with temperature dependence for probing structural changes and detecting differences between insulin s les.
Elucidating the Binding Mechanism of a Novel Silica-Binding Peptide
Publisher: MDPI AG
Date: 18-12-2019
DOI: 10.3390/BIOM10010004
Abstract: Linker-protein G (LPG) is a bifunctional fusion protein composed of a solid-binding peptide (SBP, referred as the “linker”) with high affinity to silica-based compounds and a Streptococcus protein G (PG), which binds antibodies. The binding mechanisms of LPG to silica-based materials was studied using different biophysical techniques and compared to that of PG without the linker. LPG displayed high binding affinity to a silica surface (KD = 34.77 ± 11.8 nM), with a vertical orientation, in comparison to parent PG, which exhibited no measurable binding affinity. Incorporation of the linker in the fusion protein, LPG, had no effect on the antibody-binding function of PG, which retained its secondary structure and displayed no alteration of its chemical stability. The LPG system provided a milder, easier, and faster affinity-driven immobilization of antibodies to inorganic surfaces when compared to traditional chemical coupling techniques.
Metallohelices with activity against cisplatin-resistant cancer cells; does the mechanism involve DNA binding?
Publisher: Royal Society of Chemistry (RSC)
Date: 2013
DOI: 10.1039/C3SC51731D
Synchrotron radiation linear dichroism spectroscopy of the antibiotic peptide gramicidin in lipid membranes
Publisher: Royal Society of Chemistry (RSC)
Date: 2009
DOI: 10.1039/B902523E
Abstract: We have developed synchrotron radiation linear dichroism (SRLD) to measure the insertion of peptides into lipid bilayers, significantly improving both signal-to-noise and wavelength range over existing methods. Our wavelength cut-off is currently determined by the quality of quartz in the cell, rather than the light source, with signal quality still high at the cut-off. We demonstrate the use of a lipid probe to measure the orientation of the lipid bilayers under flow and describe the way in which this can be used to further interpret SRLD data. The antibiotic peptide gramicidin is shown to exhibit drastically different kinetic and equilibrium behaviour when interacting with lipid membranes with different properties. The charge on the membrane is of interest because of differences in charge between human and bacterial membranes. For this reason we increased the negative charge on the membrane by changing the lipid composition. Increasing negative charge in the gel phase stabilises the liposomes but changes the kinetics of peptide folding. In a gel phase with no negatively charged lipids, gramicidin does not fold well and gives a small signal that indicates a change in orientation of the tryptophan side chains over time. In the fluid phase with no negatively charged lipids, there is initially >10-fold greater peptide signal relative to the gel phase indicating a highly folded and ordered gramicidin backbone. This is followed by liposome disruption. In the gel phase with negatively charged lipids the liposomes are resistant to disruption by gramicidin and exhibit different folding kinetics depending on membrane composition. In the fluid phase with negatively charged lipids there is little signal from either the peptide or the lipid probe indicating that the liposomes have been disrupted by the gramicidin in the time it takes to make the first measurement.
Molecular Recognition of a Three‐Way DNA Junction by a Metallosupramolecular Helicate
Publisher: Wiley
Date: 06-03-2006
Geometry determination for ALn systems: principles and application
Publisher: Elsevier BV
Date: 06-1988
Elucidating protein secondary structure with circular dichroism and a neural network
Publisher: Wiley
Date: 05-10-2013
DOI: 10.1002/JCC.23456
Abstract: Circular dichroism spectroscopy is a quick method for determining the average secondary structures of proteins, probing their interactions with their environment, and aiding drug discovery. This article describes the development of a self-organising map structure-fitting methodology named secondary structure neural network (SSNN) to aid this process and reduce the level of expertise required. SSNN uses a database of spectra from proteins with known X-ray structures prediction of structures for new proteins is then possible. It has been designed as 3 units: SSNN1 takes spectra for known proteins, clusters them into a map, and SSNN2 creates a matching structure map. SSNN3 places unknown spectra on the map and gives them structure vectors. SSNN3 output illustrates the process and results obtained. We detail the strengths and weaknesses of SSNN and compare it with widely accepted structure fitting programs. Current input format is Δε per amino acid residue from 240 to 190 nm in 1 nm steps for the known and unknown proteins and a vector summarizing the secondary structure elements of the known proteins. The format is readily modified to include input data with, for ex le, extended wavelength ranges or different assignment of secondary structures. SSNN can be used either pretrained with a reference set from the CDPro web site (direct application of SSNN3, with the provided output from SSNN1 and SSNN2) or all three modules can be used as required. SSNN3 is available trained (with the reference set of the 48-spectra set used in this work complemented by five additional spectra) at www2.warwick.ac.uk/fac/sci/chemistry/research/arodger/arodgergroup/research_intro/instrumentation/ssnn/.
Tetramerization of ZapA is required for FtsZ bundling
Publisher: Portland Press Ltd.
Date: 09-01-2013
DOI: 10.1042/BJ20120140
Abstract: Prokaryotic cell ision is a highly orchestrated process requiring the formation of a wide range of biomolecular complexes, perhaps the most important of these involving the prokaryotic tubulin homologue FtsZ, a fibre-forming GTPase. FtsZ assembles into a ring (the Z-ring) on the inner surface of the inner membrane at the site of cell ision. The Z-ring then acts as a recruitment site for at least ten other proteins which form the ision apparatus. One of these proteins, ZapA, acts to enhance lateral associations between FtsZ fibres to form bundles. Previously we have expressed, purified and crystallized ZapA and demonstrated that it exists as a tetramer. We also showed that ZapA binds to FtsZ polymers, strongly promoting their bundling, while inhibiting FtsZ GTPase activity by inducing conformational changes in the bound nucleotide. In the present study we investigate the importance of the tetramerization of ZapA on its function. We generated a number of mutant forms of ZapA with the aim of disrupting the dimer–dimer interface. We show that one of these mutants, I83E, is fully folded and binds to FtsZ, but is a constitutive dimer. Using this mutant we show that tetramerization is a requirement for both FtsZ bundling and GTPase modulation activities.
Positively charged gold–silver nanostar enabled molecular characterization of cancer associated extracellular vesicles
Publisher: Royal Society of Chemistry (RSC)
Date: 2020
DOI: 10.1039/D0AY01770A
Abstract: Direct surface-enhanced Raman scattering (SERS) has contributed to characterizing extracellular vesicles (EVs) by providing molecular signatures.
An Estrogen–Platinum Terpyridine Conjugate: DNA and Protein Binding and Cellular Delivery
Publisher: Wiley
Date: 19-10-2006
Abstract: A platinum metal complex in which terpyridine joins estradiol (via an ethynyl link) to a platinum with a labile ligand (chloride) has been designed, synthesised and its X-ray crystal structure determined. The aim of this work was to link a targeting motif (in this case estrogen) to a metal-based biomolecule recognition unit (the platinum moiety). The target molecule: 17alpha-[4'-ethynyl-2,2':6',2'-terpyridine]-17beta-estradiol platinum(II) chloride (PtEEtpy) has been shown to bind to both human and bovine serum albumin (SA) and to DNA. FTICR mass spectrometry shows that the bimolecular units are in each case linked through coordination to the platinum with displacement of the chloride ligand. Circular dichroism indicates that a termolecular entity involving PtEEtpy, SA and DNA is formed. A range of electrospray mass spectrometry experiments showed that the PtEEtpy complex breaks and forms coordination bonds relatively easily. A whole cell estrogen receptor assay in an estrogen receptor positive cell (MCF-7) confirms binding of both EEtpy and PtEEtpy to the estrogen receptor in cells. The work demonstrates the concept of linking a targeting moiety (in this case estrogen) to a DNA binding agent.
A DNA‐Binding Copper(I ) Metallosupramolecular Cylinder that Acts as an Artificial Nuclease
Publisher: Wiley
Date: 06-06-2006
Abstract: The DNA binding of a dicationic pyridylimine-based dicopper(I) metallosupramolecular cylinder is reported together with its ability to act as an artificial nuclease. The cylinder binds strongly to DNA more strongly than the spherical dication [Ru(phen)(3)](2+) (phen=1,10-phenanthroline), but more weakly than the corresponding tetracationic cylinders. DNA coiling effects are not observed with this dication, in contrast to the situation with the previously reported tetracationic cylinder involving a similar ligand. Linear dichroism (LD) data suggests that the dicopper cylinder binds in a different orientation from that of the tetracationic iron cylinder. Furthermore, the dicopper cylinder shows DNA-cleavage activity in the presence of peroxide. Of particular note is that the cylinder displays a marked and unusual ability to cleave both DNA strands at the same site, probably reflecting its dinuclear nature and possibly its mode of binding to the DNA.
Characterizing the Assembly of the Sup35 Yeast Prion Fragment, GNNQQNY: Structural Changes Accompany a Fiber-to-Crystal Switch
Publisher: Elsevier BV
Date: 2010
Multifaceted Studies of the DNA Interactions and In Vitro Cytotoxicity of Anticancer Polyaromatic Platinum(II) Complexes.
Publisher: Wiley
Date: 24-05-2016
Abstract: This study reports a detailed biophysical analysis of the DNA binding and cytotoxicity of six platinum complexes (PCs). They are of the type [Pt(PL )(SS-dach)]Cl2 , where PL is a polyaromatic ligand and SS-dach is 1S,2S-diaminocyclohexane. The DNA binding of these complexes was investigated using six techniques including ultraviolet and fluorescence spectroscopy, linear dichroism, synchrotron radiation circular dichroism, isothermal titration calorimetry and mass spectrometry. This portfolio of techniques has not been extensively used to study the interactions of such complexes previously each assay provided unique insight. The in vitro cytotoxicity of these compounds was studied in ten cell lines and compared to the effects of their R,R enantiomers activity was very high in Du145 and SJ-G2 cells, with some submicromolar IC50 values. In terms of both DNA affinity and cytotoxicity, complexes of 5,6-dimethyl-1,10-phenanthroline and 2,2'-bipyridine exhibited the greatest and least activity, respectively, suggesting that there is some correlation between DNA binding and cytotoxicity.
Absorbance Spectroscopy: Spectral Artifacts and Other Sources of Error
Publisher: Springer Berlin Heidelberg
Date: 2018
Hyper-Truncated Glycans Augment the Activity of Neutrophil Granule Myeloperoxidase
Publisher: Cold Spring Harbor Laboratory
Date: 25-07-2020
DOI: 10.1101/2020.07.24.219956
Abstract: Myeloperoxidase (MPO) plays essential roles in neutrophil-mediated immunity via the generation of reactive oxidation products. Complex carbohydrates decorate MPO at discrete sites, but their functional relevance remain elusive. To this end, we have characterised the structure-biosynthesis-activity relationship of neutrophil MPO (nMPO). Mass spectrometry demonstrated that nMPO carries both characteristic under-processed and hyper-truncated glycans. Occlusion of the Asn355/Asn391-glycosylation sites and the Asn323-/Asn483-glycans, located in the MPO dimerisation zone, was found to affect the local glycan processing, thereby providing a molecular basis of the site-specific nMPO glycosylation. Native mass spectrometry, mass photometry, and glycopeptide profiling revealed significant molecular complexity of diprotomeric nMPO arising from heterogeneous glycosylation, oxidation, chlorination and polypeptide truncation variants, and a previously unreported low-abundance monomer. Longitudinal profiling of maturing, mature, granule-separated, and pathogen-stimulated neutrophils demonstrated that nMPO is dynamically expressed during granulopoiesis, unevenly distributed across granules and degranulated upon activation. We also show that proMPO-to-MPO maturation occurs during early/mid-stage granulopoiesis. While similar global MPO glycosylation was observed across conditions, the conserved Asn355-/Asn391-sites displayed elevated glycan hyper-truncation, which correlated with higher enzyme activities of MPO in distinct granule populations. Enzymatic trimming of the Asn355-/Asn391-glycans recapitulated the activity gain and showed that nMPO carrying hyper-truncated glycans at these positions exhibits increased thermal stability, polypeptide accessibility, and ceruloplasmin-mediated inhibition potential relative to native nMPO. Finally, structural modelling revealed that hyper-truncated Asn355-glycans positioned in the MPO-ceruloplasmin interface are critical for uninterrupted inhibition. Here, through an innovative and comprehensive approach, we report novel functional roles of MPO glycans, providing new insight into neutrophil-mediated immunity. Myeloperoxidase (MPO) is an important microbicidal glycoprotein critical for fighting pathogens. We report, for the first time, the intriguingly complex relationship between glycobiology and MPO immune function by demonstrating that uncommon and strategically positioned hyper-truncated glycans both elevate the activity and the inhibition potential of this pathogen-combating enzyme. We have used a multifaceted approach employing integrated biomolecular analytics to generate new insights into the sugar code of MPO. The findings described in this study improve our understanding of key innate immune processes and may guide future glycoengineering efforts aiming to generate therapeutically relevant recombinant MPO products with tuneable activity and inhibition potential tailored to biomedical applications involving persisting and severe pathogen infections.
Antimicrobial activity of ruthenium-based intercalators
Publisher: Elsevier BV
Date: 03-2011
DOI: 10.1016/J.EJPS.2010.12.004
Abstract: Multidrug resistance of bacterial pathogens is a major problem and there is a clear need for the development of new types of antibiotics. Here we investigated the antimicrobial activity of ruthenium(II) based DNA-intercalating complexes. These complexes were found to have no activity in vitro against the Gram-negative bacterium Escherichia coli, but the complexes were clearly active against the Gram-positive bacteria Bacillus subtilis and Staphylococcus aureus. In vivo activity has also been demonstrated for one of the compounds using a simple infection model, the nematode Caenorhabditis elegans. Importantly, this also showed that the compound tested was not toxic to the nematodes.
UV-Visible Absorption Spectroscopy, Biomacromolecular Applications
Publisher: Elsevier
Date: 2017
DNA structure control by polycationic species: Polyamine, cobalt ammines, and di-metallo transition metal chelates
Publisher: Wiley
Date: 2000
DOI: 10.1002/(SICI)1520-636X(2000)12:4<221::AID-CHIR9>3.0.CO;2-3
Circular Dichroism Spectroscopy for the Study of Protein-Ligand Interactions
Publisher: Humana Press
Date: 2005
DOI: 10.1385/1-59259-912-5:343
Abstract: Circular dichroism (CD) is the difference in absorption of left and right circularly polarized light, usually by a solution containing the molecules of interest. A signal is only measured for chiral molecules such as proteins. A CD spectrum provides information about the bonds and structures responsible for this chirality. When a small molecule (or ligand) binds to a protein, it acquires an induced CD (ICD) spectrum through chiral perturbation to its structure or electron rearrangements. The wavelengths of this ICD are determined by the ligand's own absorption spectrum, and the intensity of the ICD spectrum is determined by the strength and geometry of its interaction with the protein. Thus, ICD can be used to probe the binding of ligands to proteins. This chapter outlines protein CD and ICD, together with some of the issues relating to experimental design and implementation.
Fluorescence detected linear dichroism spectroscopy: A selective and sensitive probe for fluorophores in flow-oriented systems.
Publisher: Wiley
Date: 03-01-2018
DOI: 10.1002/CHIR.22795
Abstract: Fluorescence detection typically enhances sensitivity and selectivity for fluorescent analytes. The potential for combining fluorescence detection with flow orientation of the s le in the normal configuration of linear dichroism experiments is explored in this work by measuring the fluorescence emitted from flow-orientated DNA-bound ligands and M13 bacteriophage. Data for ethidium bromide, Hoechst 33258, and 4,6-diamidino-2-phenyindole are presented. The theoretical basis of the technique is also presented for instruments running in both the fixed direct-current mode, which is the normal operation mode of circular dichroism spectropolarimeters, and also in fixed high-tension voltage mode. The role of the stray light reaching the detector that results in a spectral shape in fixed direct current mode that resembles the shape of a linear dichroism spectrum, rather than the expected reduced linear dichroism, is also explored.
Assembly Pathway of a Designed α-Helical Protein Fiber
Publisher: Elsevier BV
Date: 04-2010
Flow Linear Dichroism of Some Prototypical Proteins
Publisher: American Chemical Society (ACS)
Date: 28-08-2009
DOI: 10.1021/JA902662E
Abstract: Flow linear dichroism (LD) spectroscopy provides information on the orientation of molecules in solution and hence on the relative orientation of parts of molecules. Long molecules such as fibrous proteins can be aligned in Couette flow cells and characterized using LD. We have measured using Couette flow and calculated from first principles the LD of proteins representing prototypical secondary structure classes: a self-assembling fiber and tropomyosin (all-alpha-helical), FtsZ (an alphabeta protein), an amyloid fibril (beta-sheet), and collagen [poly(proline)II helices]. The combination of calculation and experiment allows elucidation of the protein orientation in the Couette flow and the orientation of chromophores within the protein fibers.
Exploiting Thermoresponsive Polymers to Modulate Lipophilicity: Interactions With Model Membranes
Publisher: Wiley
Date: 15-03-2012
Abstract: Upon heating above their lower critical solution temperature (LCST) poly[oligo(ethyleneglycol)methacrylate]s (POEGMA) were shown to undergo a shift in their partition coefficient triggering aqueous to organic phase transfer, which indicated their potential to partition into cell membranes upon application of an external stimulus. Fluorescence-based assays indicated that the LCST transition did not induce lysis of model phospholipid vesicles but did promote fusion, as confirmed by dynamic light scattering. Membrane perturbation assays and linear dichroism spectroscopy investigations suggest that POEGMAs above their transition temperatures can interact with, or insert into, membranes. These findings will help develop the application of responsive polymers in drug delivery.
Looking at long molecules in solution: what happens when they are subjected to Couette flow?
Publisher: Royal Society of Chemistry (RSC)
Date: 2006
DOI: 10.1039/B604810M
Abstract: Knowing the structure of a molecule is one of the keys to deducing its function in a biological system. However, many biomacromolecules are not amenable to structural characterisation by the powerful techniques often used namely NMR and X-ray diffraction because they are too large, or too flexible or simply refuse to crystallize. Long molecules such as DNA and fibrous proteins are two such classes of molecule. In this article the extent to which flow linear dichroism (LD) can be used to characterise the structure and function of such molecules is reviewed. Consideration is given to the issues of fluid dynamics and light scattering by such large molecules. A range of applications of LD are reviewed including (i) fibrous proteins with particular attention being given to actin (ii) a far from comprehensive discussion of the use of LD for DNA and DNA-ligand systems (iii) LD for the kinetics of restriction digestion of circular supercoiled DNA and (iv) carbon nanotubes to illustrate that LD can be used on any long molecules with accessible absorption transitions.
Simulations of DNA Coiling around a Synthetic Supramolecular Cylinder That Binds in the DNA Major Groove
Publisher: Wiley
Date: 12-04-2006
Abstract: In this work we present the results of a molecular simulation study of the interaction between a tetracationic bis iron(II) supramolecular cylinder, [Fe2(C25H20N4)3]4+, and DNA. This supramolecular cylinder has been shown to bind in the major groove of DNA and to induce dramatic coiling of the DNA. The simulations have been designed to elucidate the interactions that lead the cylinder to target the major groove and that drive the subsequent DNA conformational changes. Three sets of multi-nanosecond simulations have been performed: one of the uncomplexed d(CCCCCTTTTTCC) d(GGAAAAAGGGGG) dodecamer one of this DNA complexed with the cylinder molecule and one of this DNA complexed with a neutralised version of the cylinder. Coiling of the DNA was observed in the DNA-cylinder simulations, giving insight into the molecular level nature of the supramolecular coiling observed experimentally. The cylinder charge was found not to be essential for the DNA coiling, which implies that the DNA response is moderated by the short range interactions that define the molecular shape. Cylinder charge did, however, affect the integrity of the DNA duplex, to the extent that, under some circumstances, the tetracationic cylinder induced defects in the DNA base pairing at locations adjacent to the cylinder binding site.
Calculations of flow-induced orientation distributions for analysis of linear dichroism spectroscopy
Publisher: Royal Society of Chemistry (RSC)
Date: 2013
DOI: 10.1039/C3SM27419E
Polyhedral rearrangements in clusters
Publisher: Elsevier BV
Date: 1988
Anthracene-modified oligonucleotides as fluorescent DNA mismatch sensors: discrimination between various base-pair mismatches
Publisher: Informa UK Limited
Date: 03-2011
UV Absorbance Spectroscopy of Biological Macromolecules
Publisher: Springer Berlin Heidelberg
Date: 2018
Symmetry selection rules for reaction mechanisms: application to metal-ligand isomerizations [Erratum to document cited in CA108(8):63334f]
Publisher: American Chemical Society (ACS)
Date: 08-1988
DOI: 10.1021/IC00289A035
Supramolecular Nucleoside-Based Gel: Molecular Dynamics Simulation and Characterization of Its Nanoarchitecture and Self-Assembly Mechanism
Publisher: American Chemical Society (ACS)
Date: 14-05-2018
Flow oriented linear dichroism to probe protein orientation in membrane environments
Publisher: Royal Society of Chemistry (RSC)
Date: 2002
DOI: 10.1039/B205080N
Drug Self-Assembly on DNA: Sequence Effects withtrans-bis-(4-N-methylpyridiniumyl)diphenyl Porphyrin and Hoechst 33258
Publisher: Informa UK Limited
Date: 2000
DOI: 10.1080/07391102.2000.10506639
Abstract: Abstract Self assembly in biological systems is increasingly being recognised as an important phenomenon. We have examined two model systems: the cationic meso-substituted free base porphyrin derivative frans-bis-(4-N-methylpyridiniumyl)diphenyl porphyrin (t-H(2)P) and Hoechst 33258 (Hoechst) both of which were known to assemble on DNA. t-H(2)P self-assembles in solution under appropriate conditions, whereas Hoechst does not. By varying ionic strength and ligand: DNA mixing ratios, these features together with their different steric constraints have led to quite different DNA binding behaviour. Hoechst on poly[d(A-T)](2) stacks across the major groove, probably after filling its well established monomeric minor groove binding mode. By way of contrast the Hoechst oly[d(G-C)](2) self-assembled aggregates involve partially intercalated molecules stacking in the major groove. The binding mode adopted by t-H(2)P with poly[d(A-T)](2) and poly[d(G-C)](2) appears to be kinetically controlled and to be determined by the pre-existence of monomer binding and/or ligand stacks in solution. With poly[d(A-T)](2) the modes adopted both involve displacing the DNA bases to be more parallel than perpendicular to the helix axis. One is probably based on porphyrin intercalation and the other on minor groove binding. Resonance light scattering, linear dichroism, circular dichroism, normal absorption and fluorescence spectroscopies have been used to characterise the self-assembly in these systems.
Volatile C8 compounds and pseudomonads influence primordium formation ofAgaricus bisporus
Publisher: Informa UK Limited
Date: 09-2009
DOI: 10.3852/07-194
Abstract: Primordium formation of Agaricus bisporus depends on the presence of a casing layer containing stimulatory bacteria and on sufficient air exchange. The influence of specific pseudomonad populations and volatile organic compounds (VOC) on primordium formation of A. bisporus was studied in microcosm cultures. VOC produced by A. bisporus mycelium were predominantly C8 compounds, some of which could inhibit primordium formation, with 1-octen-3-ol being most inhibitory. A VOC produced by the rye grain substrate, 2-ethyl-1-hexanol, on which A. bisporus was grown also inhibited primordium formation. 2-Ethyl-1-hexanol and 1-octen-3-ol were metabolized by pseudomonad populations and adsorbed by activated charcoal, with both modes of removal enabling primordium formation in the casing. Removal of VOC by ventilation also enabled primordium formation to occur under axenic conditions. The presence of 2-ethyl-1-hexanol and 1-octen-3-ol in the microcosms resulted in higher total bacterial and pseudomonad populations in the casing. The stimulatory effects of the casing and its microbiota and air exchange on primordium formation of A. bisporus at least partly are due to the removal of inhibitory C8 compounds produced by the mycelium and its substrate. Monitoring and controlling the levels of these inhibitory VOC in mushroom culture should enable primordium formation of A. bisporus to be more efficiently and precisely controlled.
Irreducible Representations for Cyclic, Dihedral and Cubic Point Groups
Publisher: CSIRO Publishing
Date: 1987
DOI: 10.1071/CH9871035
Abstract: A method for deriving the matrix irreducible representations for cyclic, dihedral and cubic groups purely from the structure of the group multiplication table is presented. Full irreducible representations for D∞h and O are given, from which those for all cyclic, dihedral and cubic groups can simply be derived.
Symmetry selection rules for reaction mechanisms: a practical formulation for the generation of symmetry-allowed mechanisms and applications
Publisher: American Chemical Society (ACS)
Date: 1987
DOI: 10.1021/J100285A041
An Escherichia coli twin‐arginine signal peptide switches between helical and unstructured conformations depending on the hydrophobicity of the environment
Publisher: Wiley
Date: 24-07-2003
DOI: 10.1046/J.1432-1033.2003.03710.X
Abstract: The Tat system catalyzes the transport of folded globular proteins across the bacterial plasma membrane and the chloroplast thylakoid. It recognizes cleavable signal peptides containing a critical twin-arginine motif but little is known of the overall structure of these peptides. In this report, we have analyzed the secondary structure of the SufI signal peptide, together with those of two nonfunctional variants in which the region around the twin-arginine, RRQFI, is replaced by KKQFI or RRQAA. Circular dichroism studies show that the SufI peptide exists as an unstructured peptide in aqueous solvent with essentially no stable secondary structure. In membrane-mimetic environments such as SDS micelles or water/trifluoroethanol, however, the peptide adopts a structure containing up to about 40% alpha-helical content. Secondary structure predictions and molecular modelling programs strongly suggest that the helical region begins at, or close to, the twin-arginine motif. Studies on the thermal stability of the helix demonstrate a sharp transition between the unstructured and helical states, suggesting that the peptide exists in one of two distinct states. The two nonfunctional peptides exhibit almost identical spectra and properties to the wild-type SufI peptide, indicating that it is the arginine sidechains, and not their contribution to the helical structure, that are critical in this class of peptide.
Inside Back Cover: Os2–Os4 Switch Controls DNA Knotting and Anticancer Activity (Angew. Chem. Int. Ed. 31/2016)
Publisher: Wiley
Date: 06-06-2016
Insight into the Mechanism of Action and Peptide‐Membrane Interactions of Aib‐Rich Peptides: Multitechnique Experimental and Theoretical Analysis
Publisher: Wiley
Date: 24-02-2021
Abstract: The increase in resistant bacterial strains necessitates the identification of new antimicrobial molecules. Antimicrobial peptides (AMPs) are an attractive option because of evidence that bacteria cannot easily develop resistance to AMPs. The peptaibols, a class of naturally occurring AMPs, have shown particular promise as antimicrobial drugs, but their development has been hindered by their mechanism of action not being clearly understood. To explore how peptaibols might interact with membranes, circular dichroism, vibrational circular dichroism, linear dichroism, Raman spectroscopy, Raman optical activity, neutron reflectivity and molecular dynamics simulations have been used to study a small library of peptaibol mimics, the Aib‐rich peptides. All the peptides studied quickly partitioned and oriented in membranes, and we found evidence of chiral interactions between the phospholipids and membrane‐embedded peptides. The protocols presented in this paper open new ground by showing how chiro‐optical spectroscopies can throw light on the mechanism of action of AMPs.
Linear dichroism of biomolecules: which way is up?
Publisher: Elsevier BV
Date: 10-2004
DOI: 10.1016/J.SBI.2004.08.005
Abstract: Understanding the organization of molecules in naturally occurring ordered arrays (e.g. membranes, protein fibres and DNA strands) is of great importance to understanding biological function. Unfortunately, few biophysical techniques provide detailed structural information on these non-crystalline systems. UV, visible and IR linear dichroism have the potential to provide such information. Recent advances in technology and simulations allow this potential to be fulfilled, and can now provide a detailed understanding of the molecular mechanisms of such fundamental biological processes as amyloid fibre formation and membrane protein folding.
Antimicrobial activity of an iron triple helicate
Publisher: Elsevier BV
Date: 05-2009
DOI: 10.1016/J.IJANTIMICAG.2008.10.031
Abstract: The prevalence of antibiotic resistance has resulted in the need for new approaches to be developed to combat previously easily treatable infections. Here we investigated the potential of the synthetic metallomolecules [Fe(2)L(3)](4+) and [Cu(2)(L')(2)](2+) as antibacterial agents. Both molecules have been shown to bind DNA [Fe(2)L(3)](4+) binds in the major groove and causes DNA coiling, whilst [Cu(2)(L')(2)](2+) can act as an artificial nuclease. The work described here shows that only [Fe(2)L(3)](4+) is bactericidal for Bacillus subtilis and Escherichia coli. We demonstrate that [Fe(2)L(3)](4+) binds bacterial DNA in vivo and, strikingly, that it kills B. subtilis cells very rapidly.
Secondary Structure Transitions for a Family of Amyloidogenic, Antimicrobial Uperin 3 Peptides in Contact with Sodium Dodecyl Sulfate.
Publisher: Wiley
Date: 2022
Abstract: Secondary structure changes are an inherent part of antimicrobial (AMP) and amyloidogenic peptide activity, especially in close proximity to membranes, and impact the peptides' function and dysfunction roles. The formation, and stability of α-helical components are regarded as essential 'intermediates' for both these functions. To illuminate the conformational transitions leading to amyloid formation we use short cationic AMPs, from an Australian toadlet, Uperoleia mjobergii, (Uperin 3 family, U3) and assess the impact on secondary structural elements in the presence of a membrane mimetic surfactant, sodium dodecyl sulfate (SDS). Specifically, Uperin 3.x, where x=4, 5, 6 wild-type peptides and position seven variants for each, R7A or K7A, were investigated using a combination of experimental and simulation approaches. In water, U3 peptides remain largely unstructured as random coils, with the addition of salts initiating structural transitions leading to assembly towards amyloid. Solution NMR data show that an unstructured U3.5 wt peptide transitions in the presence of SDS to a well-defined α-helical structure that spans nearly the entire sequence. Circular dichroism (CD) and ThT fluorescence studies show that all six U3 peptides aggregate in solution, albeit with vastly varying rates, and a dynamic equilibrium between soluble aggregates rich in either α-helices or β-sheets may exist in solution. However, the addition of SDS leads to a rapid disaggregation for all peptides and stabilisation of predominantly α-helical content in all the U3 peptides. Molecular dynamics (MD) simulations show that the adsorption of U3.5 wt/R7A peptides onto the SDS micelle is driven by Coulombic attraction between peptide cationic residues and the negatively charged sulfate head-groups on SDS. Simulating the interactions of various kinds of β-sheet dimers (of both U3.5 wt and its variant U3.5 R7A) with SDS micelles confirmed β-sheet content decreases in the dimers after their attachment to the SDS micelle. Adsorbed peptides interact favourably with the hydrophobic core of the micelle, promoting intramolecular hydrogen bonds leading to stabilisation of the α-helical structure in peptides, and resulting in a corresponding decrease in intermolecular hydrogen bonds responsible for β-sheets.
Chiral discrimination in mobile phases for HPLC
Publisher: Elsevier BV
Date: 05-2002
Absorption Spectroscopy to Indicate Macromolecule Structural Changes
Publisher: Springer Berlin Heidelberg
Date: 2018
Sequence-Dependent Oligomerization of the Neu Transmembrane Domain Suggests Inhibition of “Conformational Switching” by an Oncogenic Mutant
Publisher: American Chemical Society (ACS)
Date: 10-03-2010
DOI: 10.1021/BI902087V
Abstract: Membrane-spanning epidermal growth factor receptor ErbB2 is of key importance in cell ision, in which a dimeric complex of the protein is responsible for tyrosine kinase activation following ligand binding. The rat homologue of this receptor (Neu) is prone to a valine to glutamic acid mutation in the transmembrane domain (TM), resulting in permanent activation and oncogenesis. In this study, the TM domains of Neu and the corresponding oncogenic mutant Neu*, which contains a V to E mutation at position 664 in the TM domain, have been analyzed to improve our understanding of the structural effects of the oncogenic V(664)E mutation. Building on previous work, we have focused here on understanding the sequence dependence of TM helix-helix interactions and any differences in behavior upon introduction of the V(664)E mutation. Using a variety of biochemical and biophysical methods, we find that the rat Neu TM domain forms strong oligomers and, similar to previous observations for the human ErbB2 TM domain, the oncogenic mutation results in a reduced level of self-association. Our data also strongly indicate that the proto-oncogenic Neu TM domain can adopt multiple (at least two) oligomeric conformations in the membrane, possibly corresponding to the active and inactive forms of the receptor, and can "switch" between the two. Further, the oncogenic Neu* mutant appears to inhibit this "conformational switching" of TM dimers, as we observe that dimerization of the Neu* TM domain in the Escherichia coli inner membrane strongly favors a single conformation stabilized by an IXXXV motif (I(659)-XXX-V(663)) originally identified by site-specific infrared spectroscopic studies.
An external quality assurance trial to assess mass spectrometry protein testing facilities for identifying multiple human peptides
Publisher: Springer Science and Business Media LLC
Date: 05-08-2019
DOI: 10.1007/S00216-019-02047-Y
Abstract: The application of proteomic liquid chromatography mass spectrometry (LC-MS) for identifying proteins and peptides associated with human disease is rapidly growing in clinical diagnostics. However, the ability to accurately and consistently detect disease-associated peptides remains clinically uncertain. Variability in diagnostic testing occurs in part due to the absence of appropriate reference testing materials and standardised clinical guidelines for proteomic testing. In addition, multiple proteomic testing pipelines have not been fully assessed through external quality assurance (EQA). This trial was therefore devised to evaluate the performance of a small number of mass spectrometry (MS) testing facilities to (i) evaluate the EQA material for potential usage in a proteomic quality assurance program, and to (ii) identify key problem areas associated with human peptide testing. Five laboratories were sent six peptide reference testing s les formulated to contain a total of 35 peptides in differing ratios of light (natural) to heavy (labelled) peptides. Proficiency assessment of laboratory data used a modified approach to similarity and dissimilarity testing that was based on Bray-Curtis and Sorensen indices. Proficiency EQA concordant consensus values could not be derived from the assessed data since none of the laboratories correctly identified all reference testing peptides in all s les. However, the produced data may be reflective of specific inter-laboratory differences for detecting multiple peptides since no two testing pipelines used were the same for any laboratory. In addition, laboratory feedback indicated that peptide filtering of the reference material was a common key problem area prior to analysis. These data highlight the importance of an EQA programme for identifying underlying testing issues so that improvements can be made and confidence for clinical diagnostic analysis can be attained.
A molecular mechanics study of spermine complexation to DNA: a new model for sperm ine-poly(dG-dC) binding
Publisher: The Royal Society
Date: 22-05-1991
Abstract: Molecular mechanics calculations of the binding of spermine to a number of solvated DNA helices have led to the development of a new model for spermine complexation. The structural details of the complexes formed with d(GCGCGCGCGC)2 and d(ATATATATAT)2 decamers allowed a rationalization of the observed experimental differences for binding to these two helices. For d(ATATATATAT)2 it was concluded that spermine remains in a cross-major groove binding site. Conversely, for d(GCGCGCGCGC)2 spermine reorientation via specific ligand-base-pair hydrogen-bond formation allows complexation along the major groove. The solvent plays an important role in differentiating the two binding modes. A mechanism of spermine complexation to natural DNA is postulated from these results. Past experimental data are also considered in the context of the new model.
Viscometric functions and rheo-optical properties of dilute polymer solutions: Comparison of FENE-Fraenkel dumbbells with rodlike models
Publisher: Elsevier BV
Date: 11-2020
Coordination of iron ions in the form of histidinyl dinitrosyl complexes does not prevent their genotoxicity
Publisher: Elsevier BV
Date: 11-2012
DOI: 10.1016/J.BMC.2012.09.032
Abstract: Formation of dinitrosyl iron complexes (DNICs) was observed in a wide spectrum of pathophysiological conditions associated with overproduction of NO. To gain insight into the possible genotoxic effects of DNIC, we examined the interaction of histidinyl dinitrosyl iron complexes (HIS-DNIC) with DNA by means of circular dichroism. Formation of DNIC was monitored by EPR and FT/IR spectroscopy. Vibrational bands for aquated HIS-DNIC are reported. Dichroism results indicate that HIS-DNIC changes the conformation of the DNA in a dose-dependent manner in 10mM phosphate buffer (pH 6). Increase of the buffer pH or ionic strength decreased the effect. Comparison of HIS-DNIC DNA interaction with the effect of hydrated Fe(2+) ion revealed many similarities. The importance of iron ions in HIS-DNIC induced genotoxicity is confirmed by plasmid nicking assay. Treatment of pUC19 plasmid with 1μM HIS-DNIC did not affect the plasmid supercoiling. Higher concentrations of HIS-DNIC induced single strand breaks. The effect was completely abrogated by addition of deferoxamine, a specific strong iron chelator. Our data reveal that formation of HIS-DNIC does not prevent DNA from iron-induced damage and imply that there is no direct interrelationship between iron-NO coordination and their mutual toxicity modulation.
Detection of Pathogenic Bacteria Using a Homogeneous Immunoassay Based on Shear Alignment of Virus Particles and Linear Dichroism
Publisher: American Chemical Society (ACS)
Date: 12-12-2011
DOI: 10.1021/AC201544H
Abstract: Biomolecular detection has for a long time depended on a relatively small number of established methodologies. Many of these depend on the detection of a ligand-antibody complex using some kind of optical technique, e.g., chemiluminescence. Before this measurement can be made, the ligand-antibody complex generally has to be separated from bulk contaminants. This process involves the implementation of a heterogeneous assay format involving immobilization of the antibody onto a solid support to enable washing of the unbound ligand. This approach has a number of inherent issues including being slow and complex and requiring the use of expensive reagents. In this paper, we demonstrate how we have harnessed a biologically inspired nanoparticle to provide the basis for a homogeneous assay which requires no immobilization. The method relies on using fluid shear flow to align a fiber-like nanoparticle formed from a filamentous virus, M13, combined with a ligand-specific antibody. This renders the particle visible to linear dichroic spectroscopy, which provides an easily interpretable signal. The addition of the target ligand (in this case Escherichia coli O157) leads to the formation of a nanoparticle-ligand particle that is unable to align, leading to the perturbation of the linear dichroism signal.
Minimising sample volume and run times for circular dichroism spectroscopy
Publisher: Royal Society of Chemistry (RSC)
Date: 2022
DOI: 10.1039/D2AY00298A
Abstract: Low volume circular dichroism spectroscopy with DMV Bio-cells and Jasco MSD-462 micros ling disk.
Exploring the Potential of Molecular Spectroscopy for the Detection of Post-translational Modifications of a Stressed Biopharmaceutical Protein
Publisher: Bentham Science Publishers Ltd.
Date: 11-2021
DOI: 10.2174/1389203722666210916143020
Abstract: Proteins are biomolecules that consist of sequences of amino acids (primary structure) which can further interact and cause the backbone to fold into more complex arrangements (secondary and tertiary structures). Any chemical alterations of the molecules after the translation of the messenger RNA code into a protein primary sequence are known as posttranslational modifications (PTMs). PTMs may affect the protein’s functionality thus it is necessary to identify them. PTMs of particular interest to the pharmaceutical industry include deamidation, oxidation, deglycosylation and isomerization, which may occur due to environmental stressors. However, they have proved challenging to identify quickly. Electronic and vibrational spectroscopies have proved valuable tools for studying higher-order structure and stability of proteins. In this work, circular dichroism (CD), infrared absorbance (IR) and Raman spectroscopies were applied to characterize antibody (mAb NIP 228) PTMs as a result of different stressors. Mass spectrometry was used to confirm the identity of modifications including the targeted ones. Room temperature CD showed that the secondary structure was the same after all treatments, and temperature-controlled CD showed how protein stability was affected by modifications. Both Raman and IR analysis detected small differences between the reference and deglycosylated proteins, and clearly indicated the presence of other PTMs. This work required some novel computational approaches to pre-process Raman and IR spectra and a review of the band assignments for proteins existing in the literature.
Far UV Protein Circular Dichroism
Publisher: Springer Berlin Heidelberg
Date: 2018
4‐Picoline‐2,2′:6′,2″‐terpyridine‐platinum(II) — A potent intercalator of DNA
Publisher: Wiley
Date: 12-02-1996
DOI: 10.1016/0014-5793(95)01537-X
Abstract: 4-Picoloine-2,2':6',2"-terpyridine-platinum(II) is shown in a ligation assay to unwind and so intercalate into DNA. Circular dichroism is used to determine an equilibrium binding constant of approximately 2 x 10(7) M(-1) for the most stable binding mode of 4-picoline-2,2':6',2"-terpyridine-platinum(II) to poly[d(A-T)2] with a site size of about 4 base pairs, and about 1 x 10(6) M(-1) for a second binding mode with a site size of about 2 base pairs. Fluorescence spectroscopy provides further evidence for the strong equilibrium binding constant of 4-picoline-2,2':6',2"-terpyridine-platinum(II) in that it displaces ethidium bromide bound to DNA. The double positive charge on 4-picoline-2,2':6',2"-terpyridine-platinum(II), together with the intercalative binding mode is probably responsible for the large binding constant.
Design and DNA Binding of an Extended Triple‐Stranded Metallo‐supramolecular Cylinder
Publisher: Wiley
Date: 25-02-2005
Abstract: A new tetracationic triple-stranded supramolecular cylinder is prepared from a bis(pyridylimine) ligand containing a diphenylmethane and two ketimine groups in the spacer. The cylinder is longer and slightly wider than the corresponding cylinder containing just diphenylmethane spacers. Inter-strand CH...pi interactions are not observed and this affects the relay of the chiral information within the cylinder a mixture of rac and meso isomers results, with the meso isomer being the dominant solution species and characterised in the solid state by crystallography. This new cylinder does bind to DNA as confirmed by induced circular dichroism signals in both the metal-to-ligand charge transfer (MLCT) and in-ligand bands of the cylinder. Flow linear dichroism demonstrates that the cylinder binds to DNA in a specific orientation(s) and is consistent with (major) groove-binding as seen for the shorter cylinder. Some DNA bending/coiling is observed but the effect is much less dramatic than observed for the cylinder with diphenylmethane spacers confirming that coiling is not solely a consequence of the tetracationic charge, but rather is related to the precise size and shape of the cylinder.
Electronic Circular and Linear Dichroism
Publisher: Wiley
Date: 29-03-2013
DOI: 10.1002/0471440264.PST585
Abstract: Circular dichroism (CD) is the difference in absorption of light left and right circularly polarized, and linear dichroism (LD) is the difference in absorption of light linearly polarized parallel and perpendicular to an orientation axis. These polarized light spectroscopy techniques can be used to determine structural information about polymeric systems. CD spectra give information about the asymmetric character of the molecules in a solution, whereas LD gives data on relative orientations of subunits of oriented polymeric system. This article outlines what the techniques are, from where the signals originate and illustrates spectra that can be obtained and how they can be analyzed.
Probing the structure of long DNA molecules in solution using synchrotron radiation linear dichroism
Publisher: Royal Society of Chemistry (RSC)
Date: 2012
DOI: 10.1039/C1CP22371B
Abstract: Linear dichroism (LD), a spectroscopic method for aligned s les, has been used with a synchrotron radiation source to reveal insights into the structure and stability of DNA with increasing salt concentrations (thus stabilizing the base pairing) and increasing temperature while remaining below the melting point (thus destabilizing the base pairing). Measurements have been made from 350 nm to 182 nm, and the spectral changes observed quantified using a Bayesian Markov chain Monte Carlo (MCMC) algorithm, which uses statistical methods to fit to experimental data. Based on literature H-D exchange experiments, we surmise that the cause of the spectral variations is the induction of transient single stranding of tracts in the DNA polymer, particularly those with significant content of the weaker AT base pairs. More detailed analysis of the LD data will require better nucleotide transition polarization assignments.
DICD of Co(III) complexes in sugar solutions
Publisher: Elsevier BV
Date: 05-1985
Flow Linear Dichroism to Probe Binding of Aromatic Molecules and DNA to Single-Walled Carbon Nanotubes
Publisher: American Chemical Society (ACS)
Date: 20-08-2004
DOI: 10.1021/JA048720J
Abstract: Structures of carbon nanotube/ligand complexes were studied by flow linear dichroism (the differential absorption of light polarized parallel and perpendicular to the flow orientation direction) with the aim of establishing linear dichroism as a technique to study such systems. Anthracene, naphthalene, and DNA were chosen as ligands, and the potential for flow linear dichroism to probe ligands noncovalently (as well as covalently) bound to single-walled nanotubes is reported. Linear dichroism enables the determination of approximate orientations of the ligands on the carbon nanotubes.
Linear dichroism of visible-region chromophores using M13 bacteriophage as an alignment scaffold
Publisher: Royal Society of Chemistry (RSC)
Date: 2018
DOI: 10.1039/C8RA05475D
Abstract: Here we characterise four dyes and assess the complementarity of linear dichroism and FRET in biomimetic light-harvesting antennae optimisation.
Self-Assembly Mechanism for a Naphthalene−Dipeptide Leading to Hydrogelation
Publisher: American Chemical Society (ACS)
Date: 18-11-2009
DOI: 10.1021/LA903694A
Abstract: Suitably functionalized dipeptides have been shown to be effective hydrogelators. The design of the hydrogelators and the mechanism by which hydrogelation occurs are both currently not well understood. Here, we have utilized the hydrolysis of glucono-delta-lactone to gluconic acid as a means of adjusting the pH in a naphthalene-alanylvaline solution allowing the specific targeting of the final pH. In addition, this method allows the assembly process to be characterized. We show that assembly begins as charge is removed from the C-terminus of the dipeptide. The removal of charge allows lateral assembly of the molecules leading to pi-pi stacking (shown by CD) and beta-sheet formation (as shown by IR and X-ray fiber diffraction). This leads to the formation of fibrous structures. Electron microscopy reveals that thin fibers form initially, with low persistence length. Lateral association then occurs to give bundles of fibers with higher persistence length. This results in the initially weak hydrogel becoming stronger with time. The final mechanical properties of the hydrogels are very similar irrespective of the amount of GdL added rather, the time taken to achieving the final gel is determined by the GdL concentration. However, differences are observed between the networks under strain, implying that the kinetics of assembly do impart different final materials' properties. Overall, this study provides detailed understanding of the assembly process that leads to hydrogelation.
A new reference material for UV–visible circular dichroism spectroscopy
Publisher: Wiley
Date: 27-05-2008
DOI: 10.1002/CHIR.20566
Abstract: To obtain accurate and consistent measurements from circular dichroism (CD) instruments over time and from different laboratories, it is important that they are properly calibrated. The characteristics of the available reference materials are not ideal to ensure proper calibration as they typically only give peaks in one or two spectral regions, and often have issues concerning purity and stability. Currently either c hor sulfonic acid or ammonium c hor sulfonate are used. The latter can be an unstable, slightly hygroscopic secondary standard compound with only one characterized CD band. The former is the very hygroscopic primary standard for which only one enantiomer is readily available. We have synthesized a new reference material for CD, Na[Co(EDDS)].H(2)O (EDDS = N,N-ethylenediaminedisuccinic acid) which addresses these problems. It is extremely stable and available in both enantiomeric forms. The CD spectrum of Na[Co(EDDS)].H(2)O has nine distinct peaks between 180 and 599 nm. It thus fulfils the principal requirements for CD calibration chemical standards and has the potential to be used to ensure good practice in the measurement of CD data, providing two spectra of equal magnitude and opposite sign for a given concentration and path length. We have carried out an interlaboratory comparison using this material and show how it can be used to improve CD comparability between laboratories. A fitting algorithm has been developed to assess CD spectropolarimeter performance between 750 and 178 nm. This could be the basis of a formal quality control process once criteria for performance have been decided.
Circular and linear dichroism of proteins
Publisher: Royal Society of Chemistry (RSC)
Date: 2007
DOI: 10.1039/B615870F
Abstract: Circular dichroism (CD) is an important technique in the structural characterisation of proteins, and especially for secondary structure determination. The CD of proteins can be calculated from first principles using the so-called matrix method, with an accuracy which is almost quantitative for helical proteins. Thus, for proteins of unknown structure, CD calculations and experimental data can be used in conjunction to aid structure analysis. Linear dichroism (LD) can be calculated using analogous methodology and has been used to establish the relative orientations of subunits in proteins and protein orientation in an environment such as a membrane. However, simple analysis of LD data is not possible, due to overlapping transitions. So coupling the calculations and experiment is an important strategy. In this paper, the use of LD for the determination of protein orientation and how these data can be interpreted with the aid of calculations, are discussed. We review methods for the calculation of CD spectra, focusing on semiempirical and ab initio parameter sets used in the matrix method. Lastly, a new web interface for online CD and LD calculation is presented.
Is DNA a worm-like chain in Couette flow?:In search of persistence length, a critical review
Publisher: SAGE Publications
Date: 07-2009
Abstract: Persistence length is the foremost measure of DNA flexibility. Its origins lie in polymer theory which was adapted for DNA following the determination of B-DNA structure in 1953. There is no single definition of persistence length used, and the links between published definitions are based on assumptions which may, or may not be, clearly stated. DNA flexibility is affected by local ionic strength, solvent environment, bound ligands and intrinsic sequence-dependent flexibility. This article is a review of persistence length providing a mathematical treatment of the relationships between four definitions of persistence length, including: correlation, Kuhn length, bending, and curvature. Persistence length has been measured using various microscopy, force extension and solution methods such as linear dichroism and transient electric birefringence. For each experimental method a model of DNA is required to interpret the data. The importance of understanding the underlying models, along with the assumptions required by each definition to determine a value of persistence length, is highlighted for linear dichroism data, where it transpires that no model is currently available for long DNA or medium to high shear rate experiments.
Absorption Spectroscopy to Probe Ligand Binding
Publisher: Springer Berlin Heidelberg
Date: 2018
Linear Dichroism Activity of Chiral Poly(p-Aryltriazole) Foldamers
Publisher: American Chemical Society (ACS)
Date: 24-11-2021
Absolute configuration and electronic state properties of light-switch complex [Ru(phen)2dppz]2+ deduced from oriented circular dichroism in a lamellar liquid crystal host
Publisher: Elsevier BV
Date: 03-2002
Paper: A cheap yet effective chiral stationary phase for chromatographic resolution of metallo-supramolecular helicates
Publisher: Royal Society of Chemistry (RSC)
Date: 2001
DOI: 10.1039/B101970H
Expression, purification and crystallization of the cell-division protein YgfE fromEscherichia coli
Publisher: International Union of Crystallography (IUCr)
Date: 24-02-2005
Theoretical studies of the intercalation of 9-hydroxyellipticine in DNA
Publisher: Wiley
Date: 06-12-1998
DOI: 10.1002/(SICI)1097-0282(199609)39:3<309::AID-BIP4>3.0.CO;2-S
Binding geometries of triple helix selective benzopyrido [4,3-b]indole ligands complexed with double- and triple-helical polynucleotides
Publisher: Wiley
Date: 07-1997
DOI: 10.1002/(SICI)1097-0282(199707)42:1<101::AID-BIP9>3.0.CO;2-S
Symmetry selection rules for reaction mechanisms
Publisher: Elsevier BV
Date: 09-1986
A unified view of inorganic stereochemistry and stereochemical changes
Publisher: Elsevier BV
Date: 05-1994
The CD of ligand‐DNA systems. 2. Poly(dA‐dT) B‐DNA
Publisher: Wiley
Date: 09-1992
Abstract: A systematic theoretical study of the CD of [poly(dA-dT)]2 and its complexes with achiral small molecules is presented. The CD spectra of [poly(dA-dT)]2 and of poly(dA):poly(dT) are calculated for various DNA structures using the matrix method. The calculated and experimental spectra agree reasonably well for [poly(dA-dT)]2 but less well for poly(dA):poly(dT). The calculated CD spectrum of [poly(dA-dT)]2 fails to reproduce the wavelength region of 205-245 nm of the experimental spectrum. This discrepancy can be explained by a magnetic dipole allowed transition contributing significantly to the CD spectrum in this region. The induced CD of a transition moment of a molecule bound to [poly(dA-dT)]2 is also calculated. As was the case for [poly(dG-dC)]2, the induced CD of a groove bound molecule is one order of magnitude stronger than that of an intercalated molecule. The calculations also show considerable differences between pyrimidine-purine sites and purine-pyrimidine sites. Both signs and magnitudes of the CD induced into ligands bound in the minor groove agree with experimental observations.
DNA-Ligand Flow Linear Dichroism
Publisher: Springer Berlin Heidelberg
Date: 2018
Template symmetry restrictions on reaction mechanisms
Publisher: Elsevier BV
Date: 07-1991
Folding and Membrane Insertion of the Pore-Forming Peptide Gramicidin Occur as a Concerted Process
Publisher: Elsevier BV
Date: 11-2008
DOI: 10.1016/J.JMB.2008.07.091
Abstract: Many antibiotic peptides function by binding and inserting into membranes. Understanding this process provides an insight into the fundamentals of both membrane protein folding and antibiotic peptide function. For the first time, in this work, flow-aligned linear dichroism (LD) is used to study the folding of the antibiotic peptide gramicidin. LD provides insight into the combined processes of peptide folding and insertion and has the advantage over other similar techniques of being insensitive to off-membrane aggregation events. By combining LD data with conventional measurements of protein fluorescence and circular dichroism, the mechanism of gramicidin insertion is elucidated. The mechanism consists of five separately assignable steps that include formation of a water-insoluble gramicidin aggregate, dissociation from the aggregate, partitioning of peptide to the membrane surface, oligomerisation on the surface and concerted insertion and folding of the peptide to the double-helical form of gramicidin. Measurement of the rates of each step shows that although changes in the fluorescence signal cease 10 s after the initiation of the process, the insertion of the peptide into the membrane is actually not complete for a further 60 min. This last membrane insertion phase is only apparent by measurement of LD and circular dichroism signal changes. In summary, this study demonstrates the importance of multi-technique approaches, including LD, in studies of membrane protein folding.
Shape-Induced Variations in Aromatic Thiols Adsorption on Gold Nanoparticle: A Novel Method for Accurate Evaluation of Adsorbed Molecules
Publisher: American Chemical Society (ACS)
Date: 30-10-2023
The CD of ligand–DNA systems. I. Poly(dG‐dC) B‐DNA
Publisher: Wiley
Date: 12-1991
Abstract: A systematic theoretical study of the CD of double-stranded poly(dG-dC) and its complexes with small molecules is presented. The intrinsic CD of the polymer and the induced CD of a transition belonging to a molecule bound to DNA are calculated using the matrix method. The calculations show considerable differences between pyrimidine-purine and purine-pyrimidine binding sites, and we find that the induced CD of a groove bound molecule is one order of magnitude stronger than that of an intercalated molecule. The results form a sound basis for interpreting the CD of ligand-DNA systems in terms of molecular geometry, interactions, and spectroscopy.
Absorption Spectroscopy: Practical Aspects
Publisher: Springer Berlin Heidelberg
Date: 2018
Dialysis cells for controlled DNA∶drug binding studies
Publisher: Royal Society of Chemistry (RSC)
Date: 2001
DOI: 10.1039/B005972M
Abstract: An efficient small volume accurate dialysis system has been designed, built and tested for proflavine binding to DNA based upon the side by side design used in the Franz diffusion cell. In a typical experiment 3 cm3 of DNA solution is added to one side and 3 cm3 of ligand to the other with a dialysis membrane between the two sides of 1 cm in diameter, thereby minimizing the area of dialysis membrane that the solutions are in contact with.
Oxidized polyethylene films for orienting polar molecules for linear dichroism spectroscopy
Publisher: Royal Society of Chemistry (RSC)
Date: 2014
DOI: 10.1039/C3AN02322B
Abstract: Oxidized polyethylene (PE OX ) films allow for collection of much higher quality linear dichroism (LD) data than previously possible for both polar and non-polar small molecules.
Ruthenium polypyridyl complexes and their modes of interaction with DNA: Is there a correlation between these interactions and the antitumor activity of the compounds?
Publisher: Springer Science and Business Media LLC
Date: 16-12-2008
Circular dichroism of oxiranes: an independent systems/perturbation approach
Publisher: American Chemical Society (ACS)
Date: 08-1988
DOI: 10.1021/JA00226A002
Absorption Spectroscopy, the Beer-Lambert Law, and Transition Polarizations
Publisher: Springer Berlin Heidelberg
Date: 2018
The Interfacial Behaviour of Peptides Over Long Time Scales
Publisher: Elsevier BV
Date: 02-2011
Biomacromolecular Applications of UV-Visible Absorption Spectroscopy*
Publisher: Elsevier
Date: 1999
Circular Dichroism Spectroscopy: Units
Publisher: Springer Berlin Heidelberg
Date: 2018
Beyond the Discovery Void: New Targets for Antibacterial Compounds
Publisher: SAGE Publications
Date: 06-2016
DOI: 10.3184/003685016X14616130512308
Abstract: Antibiotics save many lives, but their efficacy is under threat: overprescription, population growth, and global travel all contribute to the rapid origination and spread of resistant strains. Exacerbating this threat is the fact that no new major classes of antibiotics have been discovered in the last 30 years: this is the “discovery void.” We discuss the traditional molecular targets of antibiotics as well as putative novel targets.
Morphology, energetics and growth kinetics of diphenylalanine fibres
Publisher: Royal Society of Chemistry (RSC)
Date: 2021
DOI: 10.1039/D0CP05477A
Abstract: The formation and stability of diphenylalanine fibres are studied by combining molecular dynamics simulations with microscopy and spectroscopy experiments, quantitatively detailing their morphology, energetics and growth kinetics.
Estrogen-Derived Steroidal Metal Complexes: Agents for Cellular Delivery of Metal Centers to Estrogen Receptor-Positive Cells
Publisher: American Chemical Society (ACS)
Date: 07-2001
DOI: 10.1021/IC010152A
Abstract: Targeted cellular delivery of drugs to specific tissues is an important goal in biomedical chemistry. Achieving this requires harnessing and applying molecular-level recognition events prevalent in (or specific to) the desired tissue type. Tissues rich in estrogen receptors (ERs), which include many types of breast cancer, accumulate molecules that have high binding affinities for these receptors. Therefore, molecules that (i) bind to the ER, (ii) have favorable cellular transport properties, and (iii) contain a second functionality (such as a center that may be used for diagnostic imaging or medical therapy) are exciting synthetic targets in the field of drug delivery. To this end, we have prepared a range of metallo-estrogens based on 17alpha-ethynylestradiol and examined their binding to the ER both as isolated receptor and in whole cell assays (ER positive MCF-7 cells). Estrogens functionalized with metal binding units are prepared by palladium-catalyzed cross-coupling reactions and a wide range of metal centers introduced readily. All the compounds prepared and tested exhibit effective binding to the estrogen receptor and are delivered across the cell membrane into MCF-7 cells. In the whole cell assays, despite their monocationic nature, the palladium and platinum complexes prepared exhibit similar (and even enhanced) receptor binding affinities compared to their corresponding neutral free ligands. It is unprecedented for a higher ER binding affinity to be observed for a cationic complex than for its metal-free ligand.
SSNN, a method for neural network protein secondary structure fitting using circular dichroism data
Publisher: Royal Society of Chemistry (RSC)
Date: 2014
DOI: 10.1039/C3AY41831F
Abstract: SSNN is a self-organising map neural network approach for estimating protein structure from circular dichroism (CD) spectra. The method for using SSNN is described here, and SSNN is compared with CDSSTR, a well-known methodology for finding secondary structures from CD. SSNN compares well with similar methodologies.
Sequence Selective Binding to the DNA Major Groove: Tris(1,10-phenanthroline) Metal Complexes Binding to Poly(dG-dC) and Poly(dA-dT)
Publisher: Informa UK Limited
Date: 08-1991
DOI: 10.1080/07391102.1991.10507891
Abstract: Molecular modelling and energy minimisation calculations that incorporate solvent effects have been used to investigate the complexation of delta and lambda-[Ru(1,10-phenanthroline]2+ to DNA. The most stable binding geometry for both enantiomers is one in which a phenanthroline chelate is positioned in the major groove. The chelate is partially inserted between neighbouring base pairs, but is not intercalated. For delta, though not for lambda, a geometry with two chelates in the major groove is only slightly less favourable. Minor groove binding is shown to be no more favourable than external electrostatic binding. The optimised geometries of the DNA/[Ru(1,10-phenanthroline]2+ complexes enable published linear dichroism spectra to be used to determine the percentage of each enantiomer in the two most favourable major groove sites. For delta 57 +/- 15% and for lambda 82 +/- 7% of bound molecules are in the partially inserted site.
Aryl substituted ruthenium bis-terpyridine complexes: intercalation and groove binding with DNA
Publisher: Elsevier BV
Date: 07-2002
DOI: 10.1016/S0162-0134(01)00423-8
Abstract: The non-covalent interaction of five novel ruthenium(II) bis-terpyridine complexes with calf thymus DNA and, where appropriate, with poly[d(G-C)](2) and poly[d(A-T)](2) is described. Each complex is functionalised with aryl tail groups in the 4' position of the terpyridine ligands ((i) 9-anthracenyl, (ii) 4,4'-biphenyl, (iii) beta-naphthyl, (iv) 9-phenanthrenyl, and (v) 1-pyrenyl). Circular dichroism and linear dichroism show that the binding of three of the complexes (phenanthrenyl, anthracenyl and pyrenyl) at low metal complex concentration is dominated by intercalation of the aryl tail groups between the DNA bases. The complex with the biphenyl tail predominantly exhibits groove binding with no significant tail intercalation. The naphthyl derivative binds both by intercalation and a non-intercalative mode even at low metal complex concentrations. At high metal complex concentrations, aggregation of the complexes on the DNA is observed. Resonance light scattering indicates that the aggregates are of low nuclearity along the groove.
Circular Dichroism and Chirality
Publisher: Springer Berlin Heidelberg
Date: 2018
Rationalisation of a mechanism for sensing single point variants in target DNA using anthracene-tagged base discriminating probes
Publisher: Royal Society of Chemistry (RSC)
Date: 2018
DOI: 10.1039/C8OB01710G
Abstract: The fluorescence sensing mechanism for identifying single base changes in target DNA strands has been established through detailed biophysical measurements.
Order-disorder transitions of cytoplasmic N-termini in the mechanisms of P-type ATPases
Publisher: Royal Society of Chemistry (RSC)
Date: 2021
DOI: 10.1039/D0FD00040J
Abstract: Circular dichroism of an H + , K + -ATPase N-terminal peptide at varying trifluoroethanol concentrations is investigated, indicating that its secondary structure is environmentally sensitive.
Carbohydrate Derivatives of the Antitumour Alkaloid 9-Hydroxyellipticine
Publisher: Wiley
Date: 2003
DOI: 10.1002/1099-0690(200301)2003:1<63::AID-EJOC63>3.0.CO;2-V
DNA Binding Studies of a New Dicationic Porphyrin. Insights into Interligand Interactions
Publisher: American Chemical Society (ACS)
Date: 14-07-2007
DOI: 10.1021/BI700293G
Abstract: Cationic porphyrins have an affinity for DNA and potential for applications in the fields of photodynamic therapy and cellular imaging. This report describes a new dicationic porphyrin, 5,15-dimethyl-10,20-di(N-methylpyridinium-4-yl)porphyrin, abbreviated H2tMe2D4. Although tetrasubstituted, H2tMe2D4 presents modest steric requirements and forms in reasonable yield by a "2+2" synthetic method. Accordingly, studies of the zinc(II)- and copper(II)-containing derivatives, Zn(tMe2D4) and Cu(tMe2D4), have also been possible. Methods used to characterize DNA-binding motifs include absorption, emission, linear, and circular dichroism spectroscopies, as well as viscometry. An unusually detailed picture of porphyrin uptake emerges. As the ratio of DNA to porphyrin increases during a typical titration, H2tMe2D4 or Cu(tMe2D4) initially aggregates on the host and then shifts to intercalative binding at close quarters before finally dispersing into non-interacting intercalation sites of the host. Emission studies of the copper(II) porphyrin have been very valuable. The existence of a measurable signal is diagnostic of intercalative binding, and the saturation behavior establishes that internalization typically monopolizes approximately three base pairs. In the moderate loading regime, emission data are most telling because dipole-dipole interactions between near-neighbor porphyrins tend to confuse other spectroscopic assays. The third ligand, Zn(tMe2D4), behaves differently in that the uptake is a strictly cooperative process. The mode of binding also varies with the base content of the DNA host. When the DNA is rich in A=T base pairs, the porphyrin remains five-coordinate and binds externally however, Zn(tMe2D4) loses its axial ligand and binds by intercalation if the host contains only G[triple bond]C base pairs.
Influence of surface shape on DNA binding of bimetallo helicates
Publisher: Elsevier BV
Date: 11-2007
DOI: 10.1016/J.JINORGBIO.2007.07.005
Abstract: In order to probe the DNA-helicate interactions responsible for the DNA binding and remarkable changes of the DNA secondary structure induced by a tetracationic bi-metallo helicate [Fe(2)(L(1))(3)](4+) (L(1)=C(25)H(20)N(4)), we have designed and synthesised derivatives with hydrophobic methyl groups at different positions on the ligand backbone. Two dimetallo helicates [Fe(2)(L(i))(3)](4+) were prepared using ligands L(3) and L(5) with the methyl substituent on, respectively, the 3 and 5 positions of the pyridyl ring thus producing a wider or slightly longer tetracationic DNA binder. UV/visible absorbance, circular and linear dichroism spectroscopies have been used to characterize the interactions of the cylinders with DNA with the aim of investigating any sequence preference or selectivity upon binding. Competitive binding studies using fluorescent dyes Hoechst 33258 (a minor groove binder), ethidium bromide (an intercalator) and a major groove binding cation (cobalt (III) hexammine) which induces the B-->Z transition have been employed to determine the binding geometries of the enantiomers of two methylated helicates (L(3) and L(5)) to DNA and compare with the data obtained previously for the unmethylated analogue (L(1)). The results demonstrate that the racemic mixtures and the resolved enantiomers of all helicates bind to DNA inducing structural changes. The overall conclusion from the effect of adding these groups to the surface of the parent helicate is that increasing the width (L(3)) reduces the DNA binding strength, the bending and coiling effect and the groove selectivity of the enantiomers compared with the parent compound. There is limited evidence to suggest a slight GC sequence preference. Lengthening the helicate (L(5)) results in DNA interactions similar to those of the parent compounds, with an increased preference of the P enantiomer for the minor groove indicating an enhancement of mode selectivity.
Viscosity of aqueous DNA solutions determined using dynamic light scattering
Publisher: Royal Society of Chemistry (RSC)
Date: 2011
DOI: 10.1039/C1AN15475C
Abstract: Viscosity is a key parameter for characterising the behaviour of liquids and their flow. It is, however, difficult to measure precisely, reproducibly and accurately for aqueous solutions on a micro-litre volume scale, which is what is usually needed for biological s les. We report the development of a new method for measuring dynamic viscosity by measuring dynamic light scattering (DLS) data for a range of particles of well-defined size. Most applications of DLS involve determining particle size for s les of known viscosity. We inverted the usual protocol and endeavoured to determine viscosity for s les of known particle size. Viscosity measurements for water and aqueous solutions of calf thymus DNA made using DLS were compared with those from a U-tube viscometer. The styrene particles, frequently used as particle size standards, gave unsatisfactory results for our DNA s les as did C-6 derivatized silica and positively charged amino polystyrene microspheres. However, negatively charged carboxylate polystyrene microspheres particles readily gave accurate viscosity measurements over a range of temperatures (0-100 °C). The s le volume required depends on the cuvette used to measure DLS, but can be performed with s les sizes ranging from 40 to 3000 μL. The s le can then be recovered for subsequent experiments. The DLS method is simple to perform at different temperatures and provides data of accuracy significantly above that of a U-tube viscometer. Our results also indicate a way forward to account accurately for solution viscosity in the normal applications of DLS to particle size determination by including the appropriate non-interacting particles as an internal standard.
Sensitive and Direct DNA Mutation Detection by Surface-Enhanced Raman Spectroscopy Using Rational Designed and Tunable Plasmonic Nanostructures
Publisher: American Chemical Society (ACS)
Date: 30-03-2020
Molecular Features of CoIII Tetra- and Pentammines Affect Their Influence on DNA Structure
Publisher: Wiley
Date: 09-2001
DOI: 10.1002/1099-0682(200109)2001:9<2311::AID-EJIC2311>3.0.CO;2-E
Validation of new microvolume Couette flow linear dichroism cells
Publisher: Royal Society of Chemistry (RSC)
Date: 2005
DOI: 10.1039/B506149K
Abstract: Long molecules such as fibrous proteins are particularly difficult to characterise structurally. We have recently designed a microvolume Couette flow linear dichroism (LD) cell whose s le volume is only 20-40 microL in contrast to previous cells where the volume of s le required has typically been of the order of 1000-2000 microL. This brings the s le requirements of LD to a level where it can be used for biological s les. Since LD is the difference in absorption of light polarised parallel to an orientation direction and perpendicular to that direction, it is the ideal technique for determining relative orientations of subunits of e.g. fibrous proteins, DNA-drug systems, etc. For solution phase s les, Couette flow orientation, whereby the s le is sandwiched between two cylinders, one of which rotates, has proved to be the optimal technique for LD experiments in many laboratories. Our capillary microvolume LD cell has been designed using extruded quartz rods and capillaries and focusing and collecting lenses. We have developed applications with PCR products, fibrous proteins, liposome-bound membrane proteins, as well as DNA-dye systems. Despite this range of applications, to date there is nothing reported in the literature to enable one to validate the performance of Couette flow LD cells. In this paper we establish validation criteria and show that the data from the microvolume cells are reproducible, vary by less than 1% with s le reloading, follow the Beer-Lambert law, and have signals linear in voltage over a wide voltage range. The microvolume cell data are consistent with those from the large-volume cells for DNA s les. Surprisingly, upon extending the wavelength range by adding the intercalator ethidium bromide, the spectra in the microvolume and large-volume cells differ by a wavelength dependent orientation parameter. This wavelength variation was concluded to be the result of Taylor-vortices in the large-volume cells which have inner rotating cylinders in our laboratory. Thus the microvolume LD cells can be concluded to provide better data than our large-volume LD cells, though the latter are still to be preferred for titration series as it is extremely difficult to add s le to the capillary cells without introducing artefacts.
Enantiomeric resolution of supramolecular helicates with different surface topographies
Publisher: Royal Society of Chemistry (RSC)
Date: 2007
DOI: 10.1039/B614093A
Abstract: The enantiomeric resolution of an extended range of di-metallo supramolecular triple-helical molecules are reported. The ligands for all complexes are symmetric with two units containing an aryl group linked via an imine bond to a pyridine. Alkyl substituents have been attached in different positions on the ligand backbone. Previous work on the parent compound, whose molecular formula is [Fe(2)(C(25)H(20)N(4))(3)]Cl4, showed that it could be resolved into enantiomerically pure solutions using cellulose and 20 mM aqueous sodium chloride. In this work a range of mobile phases have been investigated to see if the separation and speed of elution could be increased and the amount of NaCl co-eluted with the compounds decreased. Methanol, ethanol and acetonitrile were considered, together with aqueous NaCl : organic mixtures. Effective separation was most often achieved when using 90% acetonitrile : 10% 20 mM NaCl (aq) w/v, which gives scope for scaling up to incorporate the use of HPLC. The overall most efficient (i.e. fastest) separation was generally achieved where the cellulose column was packed with 20 mM NaCl (aq) and the column first eluted with 100% acetonitrile, then with 75% ethanol : 25% 20 mM NaCl (aq) until the M enantiomer had fully eluted and finally with 90% acetonitrile : 10% 20 mM NaCl (aq) until the P enantiomer had been collected. The sequence of eluents ensured minimum NaCl accompanying the enantiomers and minimum total solvent being required to elute the enantiomers, especially the second one, from the column. No helicate with a methyl group on the imine bond could be resolved and methyl groups on the pyridine rings also have an adverse effect on resolution.
Principles of bonding and reactivity in transition metal cluster compounds
Publisher: Elsevier BV
Date: 05-1988
Symmetry rules for the determination of the intercalation geometry of host/systems using circular dichroism: a symmetry-adapted coupled-oscillator model
Publisher: American Chemical Society (ACS)
Date: 07-1983
DOI: 10.1021/JA00352A007
Capillary circular dichroism
Publisher: Wiley
Date: 2010
DOI: 10.1002/CHIR.20878
Abstract: Circular dichroism (CD) has become an increasingly important tool in the study of biological molecules as it enables structural information to be obtained nondestructively on solution-phase s les. However, s le requirements for CD are often seen as being too high with protein backbone measurements in standard cuvettes typically requiring ∼100-300 μL of 0.1 mg/ml protein. To address this issue, we have designed a new form of CD s le holder, which reduces the s le requirements of the technique by two orders of magnitude, with a s le requirement of less than 3 μl. This s le saving has been achieved through the use of extruded quartz capillaries, the s le being held within the internal diameter of the quartz capillary through capillary action. The extruded quartz capillaries exhibit remarkably little birefringence, although still transmitting high energy UV circularly polarized light. The optics associated with capillaries were investigated. A configuration has been adopted with the light beam of the spectrophotometer being focused in front of the front face of the capillary using a biconvex lens and advantage being taken of the additional focusing effect of the capillary itself. The focusing is vital to the low wavelength performance of the cell, where we have acquired reliable data down to 180 nm using a Jasco J-815 spectrophotometer. The system performance was validated with Na[Co(EDDS)].H(2)O (EDDS = N,N-ethylenediaminedisuccinic acid), concanavalin A, lysozyme, and progesterone.
LD spectroscopy of natural and synthetic biomaterials
Publisher: Royal Society of Chemistry (RSC)
Date: 2010
DOI: 10.1039/B912917K
Abstract: The structural characterization of biomaterials is challenging because they are usually too large for NMR or high resolution mass spectrometry and not well-enough structured for X-ray crystallography. Structural characterization and kinetic analysis for such systems thus has to proceed by collecting complementary data from a wide range of different techniques. This tutorial review describes how linear dichroism, a polarized absorbance spectroscopy technique applied to oriented molecular systems, can be used to provide useful data on biomaterials. In particular LD can provide information about relative orientations of sub-units of biomaterials and orientations of the whole biomaterial with respect to an orientation axis. An outline of linear dichroism and a summary of the artifacts to be avoided are followed by a description of how Couette flow linear dichroism has been used for a range of biomaterial systems including: DNA DNA:ligand systems cytoskeletal fibrous proteins synthetic protein fibres membrane proteins in liposomes bacteriophage carbon nanotubes and peptidoglycan systems.
Tetraaza[14]macrocyclic Transition Metal Complexes as DNA Intercalators
Publisher: Wiley
Date: 08-01-2015
d-d Transitions of Co(III) Complexes Studied by Associated Induced Circular Dichroism
Publisher: Elsevier BV
Date: 12-1986
A DICD (dispersion-induced circular dichroism) and normal absorption study of the n → π* carbonyl transition for the isoelectronic substituent series −CH3, −NH2, −OH
Publisher: Elsevier BV
Date: 1988
Geometrical and orientational isomers in clusters
Publisher: Elsevier BV
Date: 1990
An androgenic steroid delivery vector that imparts activity to a non-conventional platinum(ii) metallo-drug
Publisher: Royal Society of Chemistry (RSC)
Date: 2010
DOI: 10.1039/C0DT00838A
Abstract: A range of androgen conjugates with non-conventional platinum(II) complexes have been synthesised with the aim of targeting tumour cells since many display elevated levels of the androgen receptor. The androgenic platinum conjugates are delivered into selected cells with improved efficiency (when compared to their non-steroidal analogues). The act of conjugating an androgen to a platinum(II) complex resulted in synergistic effects between the metallic centre and the steroidal ligand, creating highly potent platinum(II) complexes from the inactive components.
Fluorescence detected linear dichroism of small molecules oriented on polyethylene film
Publisher: Royal Society of Chemistry (RSC)
Date: 2018
DOI: 10.1039/C8AN01588K
Abstract: We demonstrate that by measuring the fluorescence emission data during a linear dichroism measurement, one obtains additional information on the exited state properties and interactions of oriented molecules in the solid state.
Circular and Linear Dichroism Spectroscopy for the Study of Protein–Ligand Interactions
Publisher: Humana Press
Date: 2013
DOI: 10.1007/978-1-62703-398-5_8
Abstract: Circular dichroism (CD) is the difference in absorption of left and right circularly polarized light, usually by a solution containing the molecules of interest. A non-zero signal for solutions is only measured for chiral molecules such as proteins whose mirror image is not superposable on the original molecule. A CD spectrum provides information about the bonds and structures responsible for the chirality. When a small molecule (or ligand) binds to a protein, it acquires an induced CD (ICD) spectrum through chiral perturbation to its structure or electron rearrangements (transitions). The wavelengths of this ICD are determined by the ligand's own absorption spectrum, and the intensity of the ICD spectrum is determined by the strength and geometry of its interaction with the protein. Thus, ICD can be used to probe the binding of ligands to proteins. This chapter contains an outline of how to perform protein CD and ICD experiments, together with some of the issues relating to experimental design and implementation. Addition of a quarter wave plate to a CD spectropolarimeter converts it to a linear dichroism (LD) spectrometer. When protein s les are aligned either in flow (as for fibers or membrane proteins in liposomes) or on surfaces the orientations of ligands with respect to the protein backbone or other subunits can be determined.
Synthesis and cytotoxicity of dinuclear complexes containing ruthenium(ii) bipyridyl units linked by a bis(pyridylimine) ligand
Publisher: Royal Society of Chemistry (RSC)
Date: 2008
DOI: 10.1039/B711080D
Abstract: Enantiopure dinuclear ruthenium polypyridyl complexes of the form [Ru(2)(LL)(4)L(1)](PF(6))(4) (LL = 2,2'-bipyridine (bpy) or 1,10-phenanthroline (phen) L(1)= C(25)H(20)N(4) a bis(pyridylimine) ligand containing a diphenylmethane spacer) have been synthesized using the chiral building blocks cis-[Ru(bpy)(2)(py)(2)](2+) and cis-[Ru(phen)(2)(py)(2)](2+). These dinuclear ruthenium complexes have been characterised using NMR, mass spectrometry, UV-visible absorbance, circular dichroism and linear dichroism. The compounds exhibit good photo and thermal stability. The extinction coefficient for the bpy complex at 478 nm is epsilon(478) = 15,700 mol(-1) cm(-1) dm(3) and for the phen complex is epsilon(478) = 24,900 mol(-1) cm(-1) dm(3). Both complexes have their longest wavelength (metal to ligand charge transfer) transition predominantly x/y (short axis)-polarised while the transitions at shorter wavelength are a mixture of x/y and z-polarisations, similar to both the copper helicate and iron triple helicate studied previously. Cytotoxicity studies reveal that the compounds are dramatically less active against cancer cell lines than the recently reported supramolecular cylinders prepared from the same bis(pyridylimine) ligand.
Synthetic metallomolecules as agents for the control of DNA structure
Publisher: Royal Society of Chemistry (RSC)
Date: 2007
DOI: 10.1039/B609495C
Abstract: This tutorial review summarises B-DNA structure and metallomolecule binding modes and illustrates some DNA structures induced by molecules containing metallic cations. The effects of aquated metal ions, cobalt amines, ruthenium octahedral metal complexes, metallohelicates and platinum complexes such as cis-platin are discussed alongside the techniques of NMR, X-ray crystallography, gel electrophoresis, circular dichroism, linear dichroism and molecular dynamics. The review will be of interest to people interested in both DNA structure and roles of metallomolecules in biological systems.
Linear dichroism for the detection of single base pair mutationsElectronic supplementary information (ESI) available: Figures S1–S4. See http://www.rsc.org/suppdata/cc/b1/b107830p/
Publisher: Royal Society of Chemistry (RSC)
Date: 08-11-2001
DOI: 10.1039/B107830P
Abstract: Flow linear dichroism is shown to be able to detect single base mismatches in a polymerase chain reaction (PCR) limers from exon 10 of the human beta-glucocerebrosidase gene (associated with Gaucher disease) over a kilobase long with no post PCR manipulation.
FtsZ Fiber Bundling Is Triggered by a Conformational Change in Bound GTP
Publisher: Elsevier BV
Date: 11-2004
New Approaches to Stretched Film Sample Alignment and Data Collection for Vibrational Linear Dichroism
Publisher: American Chemical Society (ACS)
Date: 28-09-2023
Gas chromatography: an investigative tool in multiple allergies to essential oils
Publisher: Wiley
Date: 11-2002
DOI: 10.1034/J.1600-0536.2002.470506.X
Abstract: Essential or fragrant oils are volatile odourous mixtures of organic chemical compounds that are widely used in aromatherapy and in the perfume industry. Because of their frequent use, allergy to essential oils is being increasingly recognized. We report 2 cases of multiple allergies to essential oils in professional aromatherapists. Gas chromatography/mass spectrometry was used to analyse the oils in order to identify a common allergen responsible for the contact dermatitis. In both the cases, alpha- and beta-pinene were found to be the most common constituent in the oils and thus appeared to be key allergens. alpha-pinene was confirmed as an allergen on repeat patch testing with pure alpha-pinene in both cases. 12 controls tested were negative for the same. Gas chromatography-mass spectrometry was found to be an extremely useful tool that could be utilized in investigating multiple allergies to essential oils.
DNA as a Catalyst and Catalytic Template for the Racemisation of Metal Tris-Phenanthroline Complexes
Publisher: Wiley
Date: 2002
DOI: 10.1002/1099-0682(20021)2002:1<49::AID-EJIC49>3.0.CO;2-8
The association of defensin HNP-2 with negatively charged membranes: A combined fluorescence and linear dichroism study
Publisher: Elsevier BV
Date: 04-2016
DOI: 10.1016/J.BBAMEM.2016.01.014
Abstract: The association of defensin HNP-2 with negatively charged membranes has been studied using a new approach that combines fluorescence and linear dichroism (LD) spectroscopies with simulated LD spectra in order to characterise the binding kinetics and bound configurations of the peptide. Binding to membranes composed of mixtures of diacylglycerophosphocholines (PC) with either diacylglycerophosphoglycerol (PG) or diacylglycerophosphoserine (PS) was conducted at lipid:peptide ratios that yielded binding, but not membrane fusion. HNP-2 association with membranes under these conditions was a 2 stage-process, with both stages exhibiting first order kinetics. The fast initial step, with a half-life of 3 min. Conversion between the states was estimated to have an enthalpy of activation of approximately 10 kJ mol(-1) and an entropy of activation of -0.2 kJ K mol(-1). LD spectra corresponding to each of the membrane bound states were generated by non-linear regression using a standard kinetic model. These spectra are interpreted in comparison with spectra calculated using the program Dichrocalc and reveal that the peptide associates with membranes in a small number of stable configurations. All of these configurations have a significant proportion of β-sheet structure residing in the plane of the membrane. Two configurations support structures previously proposed for defensins in membranes.
Experimental and Theoretical Polarized Raman Linear Difference Spectroscopy of Small Molecules with a New Alignment Method Using Stretched Polyethylene Film
Publisher: American Chemical Society (ACS)
Date: 11-01-2012
DOI: 10.1021/AC202432E
Abstract: This paper reports the development of the new technique of Raman linear difference (RLD) spectroscopy and its application to small molecules: anthracene and nucleotides adenosine-5'-monophosphate, thymidine-5'-monophosphate, guanosine-5'-monophosphate, and cytidine-5'-monophosphate. In this work we also present a new alignment method for Raman spectroscopy where stretched polyethylene films are used as the matrix. Raman spectra using light polarized along the orientation direction and perpendicular to it are reported. The polyethylene (PE) film spectra are consistent with powder s les and films deposited on quartz. RLD spectra determined from the difference of the parallel and perpendicular polarized light Raman spectra are also reported. The equations describing RLD are derived, and RLD spectra of anthracene and thymidine are calculated from these equations using Density Functional Theory and assuming perfect orientation of the s les. Because of the wealth of spectroscopic information in the vibrational spectra of biomolecules together with our ability to calculate spectra as a function of orientation, we conclude that RLD has the potential to provide structural information for biological s les that currently cannot be extracted from any other method.
Generalized selection rules: An augmentation procedure for the determination of symmetry invariants
Publisher: Elsevier BV
Date: 08-1985
Spectroscopic Identification of Binding Modes of Anthracene Probes and DNA Sequence Recognition†
Publisher: Wiley
Date: 2006
Spectroscopic assignment of d-d transitions of achiral metal complexes using circular dichroism: DICD of cobalt(III) complexes in sugar solutions
Publisher: American Chemical Society (ACS)
Date: 06-1985
DOI: 10.1021/JA00298A010
Spectroscopic and thermodynamic studies of conformational changes in long, natural messenger ribonucleic acid molecules
Publisher: Royal Society of Chemistry (RSC)
Date: 1996
DOI: 10.1039/AC9963300117
Antiproliferative Activity of G-Quartet-Forming Oligonucleotides with Backbone and Sugar Modifications
Publisher: American Chemical Society (ACS)
Date: 20-02-2002
DOI: 10.1021/BI0119520
Abstract: Oligonucleotide-based therapies have considerable potential in cancer, viral, and cardiovascular disease therapies. However, it is becoming clear that the biological effects of oligonucleotides are not solely due to the intended sequence-specific interactions with nucleic acids. Oligonucleotides are also capable of interacting with numerous cellular proteins owing to their polyanionic character or specific secondary structure. We have examined the antiproliferative activity, protein binding, and G-quartet formation of a series of guanosine-rich oligonucleotides, which are analogues of GRO29A, a G-quartet forming, growth-inhibitory oligonucleotide, whose effects we have previously described [Bates P. J., Kahlon, J. B., Thomas, S. D., Trent, J. O., and Miller, D. M. (1999) J. Biol. Chem. 274, 26369-26377]. The GRO29A analogues include phosphorothioate (PS29A), 2'-O-methyl RNA (MR29A), and mixed DNA/2'-O-methyl RNA (MRdG29A) oligonucleotides. We demonstrate by UV spectroscopy that all of the modified analogues form stable structures, which are consistent with G-quartet formation. We find that the phosphorothioate and mixed DNA/2'-O-methyl analogues are able to significantly inhibit proliferation in a number of tumor cell lines, while the 2'-O-methyl RNA has no significant effects. Similar to the original oligonucleotide, GRO29A, the growth inhibitory oligonucleotides were able to compete with the human telomere sequence oligonucleotide for binding to a specific cellular protein. The less active MR29A does not compete significantly for this protein. On the basis of molecular modeling of the oligonucleotide structures, it is likely that the inactivity of MR29A is due to the differences in the groove structure of the quadruplex formed by this oligonucleotide. Interestingly, all GRO29A analogues, including an unmodified DNA phosphodiester oligonucleotide, are remarkably resistant to nuclease degradation in the presence of serum-containing medium, indicating that secondary structure plays an important role in biological stability. The remarkable stability and strong antiproliferative activity of these oligonucleotides confirm their potential as therapeutic agents.
SOMSpec as a General Purpose Validated Self-Organising Map Tool for Rapid Protein Secondary Structure Prediction From Infrared Absorbance Data
Publisher: Frontiers Media SA
Date: 27-01-2022
DOI: 10.3389/FCHEM.2021.784625
Abstract: A protein’s structure is the key to its function. As protein structure can vary with environment, it is important to be able to determine it over a wide range of concentrations, temperatures, formulation vehicles, and states. Robust reproducible validated methods are required for applications including batch-batch comparisons of biopharmaceutical products. Circular dichroism is widely used for this purpose, but an alternative is required for concentrations above 10 mg/mL or for solutions with chiral buffer components that absorb far UV light. Infrared (IR) protein absorbance spectra of the Amide I region (1,600–1700 cm −1 ) contain information about secondary structure and require higher concentrations than circular dichroism often with complementary spectral windows. In this paper, we consider a number of approaches to extract structural information from a protein infrared spectrum and determine their reliability for regulatory and research purpose. In particular, we compare direct and second derivative band-fitting with a self-organising map (SOM) approach applied to a number of different reference sets. The self-organising map (SOM) approach proved significantly more accurate than the band-fitting approaches for solution spectra. As there is no validated benchmark method available for infrared structure fitting, SOMSpec was implemented in a leave-one-out validation (LOOV) approach for solid-state transmission and thin-film attenuated total reflectance (ATR) reference sets. We then tested SOMSpec and the thin-film ATR reference set against 68 solution spectra and found the average prediction error for helix (α + 3 10 ) and β -sheet was less than 6% for proteins with less than 40% helix. This is quantitatively better than other available approaches. The visual output format of SOMSpec aids identification of poor predictions. We also demonstrated how to convert aqueous ATR spectra to and from transmission spectra for structure fitting. Fourier self-deconvolution did not improve the average structure predictions.
Bayesian inference assessment of protein secondary structure analysis using circular dichroism data – how much structural information is contained in protein circular dichroism spectra?
Publisher: Royal Society of Chemistry (RSC)
Date: 2021
DOI: 10.1039/D0AY01645D
Abstract: Bayesian modelling capturing uncertainty and correlations in circular dichroism (CD) spectra suggests it is not possible to identify more than 3 distinct secondary structure classes from CD spectra above 175 nm.
Molecular Recognition of a Three‐Way DNA Junction by a Metallosupramolecular Helicate
Publisher: Wiley
Date: 06-02-2006
Interaction between Polysialic Acid and the MARCKS-ED Peptide at the Molecular Level
Publisher: American Chemical Society (ACS)
Date: 15-05-2020
Interaction between a DNA oligonucleotide and a dinuclear iron(II) supramolecular cylinder; an NMR and molecular dynamics study
Publisher: Springer Science and Business Media LLC
Date: 09-2002
DOI: 10.1007/S00775-002-0354-2
Abstract: A tetracationic supramolecular cylinder, [Fe(2)L(3)](4+) (L=C(25)H(20)N(4)), with a triple-helical architecture, is just the right size to fit into the major groove of DNA but too big to fit into the minor groove. A detailed NMR spectroscopic analysis supported by molecular dynamics (MD) calculations shows unambiguously the close fit between the cylinder and a duplex oligonucleotide, [d(GACGGCCGTC)(2)]. Furthermore, only the left-handed enantiomer of the cylinder seems to fit the groove geometry. With both free and complexed species of [Fe(2)L(3)](4+) and DNA in solution, the NMR spectra are too complicated for a detailed structure determination. Based on differences in chemical shifts and extensive MD calculations, a realistic qualitative picture of the DNA-cylinder adduct is presented. Several sets of chemical shifts assigned to the protons of the three ligand strands in the cylinder indicate that the iron complex situated in the major groove exhibits restricted rotation on the NMR timescale around the cylindrical axis. The NMR NOE data support a model where the cylinder undergoes both a translational and rotational oscillation in the major groove. The results of an NOE restrained MD calculation indicates that the cylinder induces a 40 degrees bend of the double helix, in accordance with linear dichroism measurements. Other distinct features to be noticed are the very low value of the helical twist (16 degrees) induced at the G(4)C(5) step.
A model of membrane contraction predicting initiation and completion of bacterial cell division
Publisher: Oxford University Press (OUP)
Date: 2013
DOI: 10.1039/C3IB20273A
Abstract: Bacterial cell ision involves a complex and dynamic sequence of events whereby polymers of the protein FtsZ assemble at the ision plane and rearrange to achieve the goal of contracting the cell membrane at the site of cell ision, thus iding the parent cell into two daughter cells. We present a mathematical model (which we refer to as CAM-FF: Critical Accumulation of Membrane-bound FtsZ Fibres) of the assembly of the contractile ring in terms of the accumulation of short linear polymers of FtsZ that associate and dissociate from the cell membrane. In prokaryotes, the biochemical function of FtsZ is thought to underpin the assembly and at least the initial kinetic force of ring contraction. Our model extends earlier work of Surovtsev et al. [PLoS Comput. Biol., 2008, 4, e1000102] by adding (i) the kinetics of FtsZ accumulation on cell membrane anchor proteins and (ii) the physical forces required to deform the cell against its surface tension. Moreover, we provide a more rigorous treatment of intracellular diffusion and we revise some of the model parameter values in light of the experimental evidence now available. We derive a critical contraction parameter which links the chemical population dynamics of membrane-bound FtsZ molecules to the force of contraction. Using this parameter as a tool to predict the ability of the cell to initiate ision, we are able to predict the ision outcome in cells depleted of key FtsZ-binding proteins.
DNA-Ligand Circular Dichroism
Publisher: Springer Berlin Heidelberg
Date: 2018
Effect of bridging ligand structure on the thermal stability and DNA binding properties of iron(ii) triple helicates
Publisher: Royal Society of Chemistry (RSC)
Date: 2009
DOI: 10.1039/B822039E
Abstract: Triple helical di-iron complexes, readily prepared through interaction of iron(II) ions with imine-based ligands, are cylinder-shaped tetracations comparable in size and shape to common protein DNA recognition units. They have a strong tendency to coil DNA, and have recently been found to induce formation of three-way junctions in palindromic oligonucleotides. To introduce potential H bond acceptor units onto the surface of triple-helicates, new iron(II) complexes have been synthesized in which the central linking unit in the bridging ligand is S or O, instead of CH(2). The DNA binding properties of these new metallo-helicates were studied using UV-vis spectroscopy and circular and linear dichroism. Results show that the three iron triple helicates bind the DNA in a similar way but that the stability of the triple helicate unit is decreased with the O linked bridging ligand.
Beginners guide to circular dichroism
Publisher: Portland Press Ltd.
Date: 26-03-2021
DOI: 10.1042/BIO_2020_105
Abstract: Circular dichroism (CD) is used to give information about the chirality or handedness of molecular systems. It is particularly widely applied to determine the secondary structure of proteins such as biopharmaceutical products.
Biophysical and biological properties of quadruplex oligodeoxyribonucleotides
Publisher: Oxford University Press (OUP)
Date: 15-04-2003
DOI: 10.1093/NAR/GKG316
Abstract: Single-stranded guanosine-rich oligodeoxyribonucleotides (GROs) have a propensity to form quadruplex structures that are stabilized by G-quartets. In addition to intense speculation about the role of G-quartet formation in vivo, there is considerable interest in the therapeutic potential of quadruplex oligonucleotides as aptamers or non-antisense antiproliferative agents. We previously have described several GROs that inhibit proliferation and induce apoptosis in cancer cell lines. The activity of these GROs was related to their ability to bind to a specific cellular protein (GRO-binding protein, which has been tentatively identified as nucleolin). In this report, we describe the physical properties and biological activity of a group of 12 quadruplex oligonucleotides whose structures have been characterized previously. This group includes the thrombin-binding aptamer, an anti-HIV oligonucleotide, and several quadruplexes derived from telomere sequences. Thermal denaturation and circular dichroism (CD) spectropolarimetry were utilized to investigate the stability, reversibility and ion dependence of G-quartet formation. The ability of each oligonucleotide to inhibit the proliferation of cancer cells and to compete for binding to the GRO-binding protein was also examined. Our results confirm that G-quartet formation is essential for biological activity of GROs and show that, in some cases, quadruplex structures formed in the presence of potassium ions are significantly more active than those formed in the presence of sodium ions. However, not all quadruplex structures exhibit antiproliferative effects, and the most accurate factor in predicting biological activity was the ability to bind to the GRO-binding protein. Our data also indicate that the CD spectra of quadruplex oligonucleotides may be more complex than previously thought.
DNA Interactions of Monofunctional Organometallic Ruthenium(II) Antitumor Complexes in Cell-free Media
Publisher: American Chemical Society (ACS)
Date: 06-09-2003
DOI: 10.1021/BI034933U
Abstract: Modifications of natural DNA in a cell-free medium by antitumor monodentate Ru(II) arene compounds of the general formula [(eta(6)-arene)Ru(en)Cl](+) (arene = biphenyl, dihydroanthracene, tetrahydroanthracene, p-cymene, or benzene en = ethylenediamine) were studied by atomic absorption, melting behavior, transcription mapping, circular and linear dichroism, plasmid unwinding, competitive ethidium displacement, and differential pulse polarography. The results indicate that these complexes bind preferentially to guanine residues in double-helical DNA. The data are consistent with DNA binding of the complexes containing biphenyl, dihydroanthracene, or tetrahydroanthracene ligands that involves combined coordination to G N7 and noncovalent, hydrophobic interactions between the arene ligand and DNA, which may include arene intercalation and minor groove binding. In contrast, the single hydrocarbon rings in the p-cymene and benzene ruthenium complexes cannot interact with double-helical DNA by intercalation. Interestingly, the adducts of the complex containing p-cymene ligand, which has methyl and isopropyl substituents, distort the conformation and thermally destabilize double-helical DNA distinctly more than the adducts of the three multiring ruthenium arene compounds. It has been suggested that the different character of conformational alterations induced in DNA, and the resulting thermal destabilization, may affect differently further "downstream" effects of damaged DNA and consequently may result in different biological effects of this new class of metal-based antitumor compounds. The results point to a unique profile of DNA binding for Ru(II) arene compounds, suggesting that a search for new anticancer compounds based on this class of complexes may also lead to an altered profile of biological activity in comparison with that of metal-based antitumor drugs already used in the clinic or currently on clinical trials.
Circular dichroism for secondary structure determination of proteins with unfolded domains using a self-organising map algorithm SOMSpec
Publisher: Royal Society of Chemistry (RSC)
Date: 2021
DOI: 10.1039/D1RA02898G
Abstract: Circular dichroism secondary structure fitting by analysing derandomized spectra using the SOMSpec approach then regenerating data for the original spectrum.
Generalized selection rules for circular dichroism: a symmetry-adapted perturbation model for magnetic dipole allowed transitions
Publisher: Elsevier BV
Date: 11-1986
Infrared absorbance spectroscopy of aqueous proteins: Comparison of transmission and ATR data collection and analysis for secondary structure fitting
Publisher: Wiley
Date: 20-07-2018
DOI: 10.1002/CHIR.23002
Polymerase Chain Reaction on a Viral Nanoparticle
Publisher: American Chemical Society (ACS)
Date: 07-2015
DOI: 10.1021/ACSSYNBIO.5B00034
Abstract: The field of synthetic biology includes studies that aim to develop new materials and devices from biomolecules. In recent years, much work has been carried out using a range of biomolecular chassis including α-helical coiled coils, β-sheet amyloids and even viral particles. In this work, we show how hybrid bionanoparticles can be produced from a viral M13 bacteriophage scaffold through conjugation with DNA primers that can template a polymerase chain reaction (PCR). This unprecedented ex le of a PCR on a virus particle has been studied by flow aligned linear dichroism spectroscopy, which gives information on the structure of the product as well as a new protototype methodology for DNA detection. We propose that this demonstration of PCR on the surface of a bionanoparticle is a useful addition to ways in which hybrid assemblies may be constructed using synthetic biology.
Hairpin-Shaped Heterometallic Luminescent Lanthanide Complexes for DNA Intercalative Recognition
Publisher: American Chemical Society (ACS)
Date: 24-07-2003
DOI: 10.1021/JA029886S
Abstract: Luminescent Ln-Pt2 metallohairpin complexes have been developed, and their intercalative recognition with DNA has been demonstrated with linear dichroism spectroscopy. The heterotrimetallic complexes were formed in a one-step reaction, by assembly of an aminopolycarboxylate ligand, a platinum terpyridine unit, and the lanthanide salt. The metallohairpin complexes bear a neutral lanthanide moiety and two positively charged platinum-containing intercalating units. The Nd(III) analogues are luminescent in the near infrared, and this near-IR luminescence is retained upon binding to DNA. The DNA recognition was demonstrated by linear dichroism spectroscopy. The linear dichroism spectra suggested that the complexes bind perpendicular to the DNA helical axis, confirming intercalative recognition accompanied by dramatic stiffening of DNA, which suggests bis-intercalation of the complex.
Circular Dichroism and Linear Dichroism
Publisher: Wiley
Date: 13-01-2014
DOI: 10.1002/9780470027318.A5402.PUB2
Abstract: Circular dichroism (CD) is the difference in absorption, A, of left and right circularly polarized light, Equation (1): For randomly oriented systems such as solutions of molecules, only chiral molecules will show any CD intensity corresponding to their absorption bands. Chiral molecules are those molecules that cannot be superposed on their mirror images. Chiral is derived from the Greek word χϵιρ meaning hand, hence the alternate term for chirality, ‘handedness’. Two molecules that are mirror images of each other are often referred to as enantiomers , and equimolar mixtures of two enatiomers form a racemic mixture, which has no net CD intensity in solution. CD can be used to analyze chiral structures such as protein secondary structure in molecules and to probe interactions between chiral molecules and other molecules. Linear dichroism (LD) is the difference in absorption of light linearly polarized parallel and perpendicular to an orientation axis, Equation (2): LD can be used to provide orientation information about subunits of a molecular system such as small molecules absorbed onto stretched films, flow‐oriented DNAs and fibrous proteins, and lipid bilayer systems.
Dilute polymer solutions under shear flow: Comprehensive qualitative analysis using a bead-spring chain model with a FENE-Fraenkel spring
Publisher: Society of Rheology
Date: 13-01-2023
DOI: 10.1122/8.0000517
Abstract: Although the nonequilibrium behavior of polymer solutions is generally well understood, particularly in extensional flow, there remain several unanswered questions for dilute solutions in simple shear flow, and full quantitative agreement with experiments has not been achieved. For ex le, experimental viscosity data exhibit qualitative differences in shear-thinning exponents, the shear rate for the onset of shear-thinning, and high-shear Newtonian plateaus depending on polymer semiflexibility, contour length, and solvent quality. While polymer models are able to incorporate all of these effects through various spring force laws, bending potentials, excluded volume (EV) potentials, and hydrodynamic interaction (HI), the inclusion of each piece of physics has not been systematically matched to experimentally observed behavior. Furthermore, attempts to develop multiscale models (in the sense of representing an arbitrarily small or large polymer chain) which can make quantitative predictions are hindered by the lack of ability to fully match the results of bead-rod models, often used to represent a polymer chain at the Kuhn-step level, with bead-spring models, which take into account the entropic elasticity. In light of these difficulties, this work aims to develop a general model based on the so-called FENE-Fraenkel spring, originally formulated by Larson and co-workers [J. Chem. Phys. 124 (2006)], which can span the range from rigid rod to traditional entropic spring, as well as include a bending potential, EV, and HI. As we show, this model can reproduce, and smoothly move between, a wide range of previously observed polymer solution rheology in shear flow.
Quantitation of protein orientation in flow-oriented unilamellar liposomes by linear dichroism
Publisher: Elsevier BV
Date: 07-2006
Absorbance Spectroscopy: Overview
Publisher: Springer Berlin Heidelberg
Date: 2018
Flow Linear Dichroism of Protein–Membrane Systems
Publisher: Springer US
Date: 2021
Peptide Adsorption to Lipid Bilayers: Slow Processes Revealed by Linear Dichroism Spectroscopy
Publisher: Elsevier BV
Date: 02-2009
Micro-Volume Couette Flow Sample Orientation for Absorbance and Fluorescence Linear Dichroism
Publisher: Elsevier BV
Date: 09-2004
Intramolecular DNA Coiling Mediated by a Metallo-Supramolecular Cylinder
Publisher: Wiley
Date: 02-03-2001
DOI: 10.1002/1521-3773(20010302)40:5<879::AID-ANIE879>3.0.CO;2-X
Hyper-truncated Asn355- and Asn391-glycans modulate the activity of neutrophil granule myeloperoxidase
Publisher: Elsevier BV
Date: 2021
Structures of CUG Repeats in RNA
Publisher: Elsevier BV
Date: 09-2002
Bacterial Cell Division: Experimental and Theoretical Approaches to the Divisome
Publisher: SAGE Publications
Date: 12-2015
DOI: 10.3184/003685015X14461391862881
Abstract: Cell ision is a key event in the bacterial life cycle. It involves constriction at the midcell, so that one cell can give rise to two daughter cells. This constriction is mediated by a ring composed of fibrous multimers of the protein FtsZ. However, a host of additional factors is involved in the formation and dynamics of this “Z-ring” and this complicated apparatus is collectively known as the “ isome”. We review the literature, with an emphasis on mathematical modelling, and show how such theoretical efforts have helped experimentalists to make sense of the at times bewildering data, and plan further experiments.
FtsZ Polymer-bundling by the Escherichia coli ZapA Orthologue, YgfE, Involves a Conformational Change in Bound GTP
Publisher: Elsevier BV
Date: 05-2007
DOI: 10.1016/J.JMB.2007.03.025
Abstract: Cell ision is a fundamental process for both eukaryotic and prokaryotic cells. In bacteria, cell ision is driven by a dynamic, ring-shaped, cytoskeletal element (the Z-ring) made up of polymers of the tubulin-like protein FtsZ. It is thought that lateral associations between FtsZ polymers are important for function of the Z-ring in vivo, and that these interactions are regulated by accessory cell ision proteins such as ZipA, EzrA and ZapA. We demonstrate that the putative Escherichia coli ZapA orthologue, YgfE, exists in a dimer/tetramer equilibrium in solution, binds to FtsZ polymers, strongly promotes FtsZ polymer bundling and is a potent inhibitor of the FtsZ GTPase activity. We use linear dichroism, a technique that allows structure analysis of molecules within linear polymers, to reveal a specific conformational change in GTP bound to FtsZ polymers, upon bundling by YgfE. We show that the consequences of FtsZ polymer bundling by YgfE and alent cations are very similar in terms of GTPase activity, bundle morphology and GTP orientation and therefore propose that this conformational change in bound GTP reveals a general mechanism of FtsZ bundling.
Exploring the sequence–structure relationship for amyloid peptides
Publisher: Portland Press Ltd.
Date: 15-02-2013
DOI: 10.1042/BJ20121773
Abstract: Amyloid fibril formation is associated with misfolding diseases, as well as fulfilling a functional role. The cross-β molecular architecture has been reported in increasing numbers of amyloid-like fibrillar systems. The Waltz algorithm is able to predict ordered self-assembly of amyloidogenic peptides by taking into account the residue type and position. This algorithm has expanded the amyloid sequence space, and in the present study we characterize the structures of amyloid-like fibrils formed by three peptides identified by Waltz that form fibrils but not crystals. The structural challenge is met by combining electron microscopy, linear dichroism, CD and X-ray fibre diffraction. We propose structures that reveal a cross-β conformation with ‘steric-zipper’ features, giving insights into the role for side chains in peptide packing and stability within fibrils. The amenity of these peptides to structural characterization makes them compelling model systems to use for understanding the relationship between sequence, self-assembly, stability and structure of amyloid fibrils.
Linear Dichroism
Publisher: Springer Berlin Heidelberg
Date: 2018
Surface-enhanced Raman spectroscopy for circulating biomarkers detection in clinical diagnosis
Publisher: Elsevier
Date: 2022
Circular Dichroism and Related Spectroscopic Techniques
Publisher: Wiley
Date: 15-03-2019
A Molecular Dynamics Simulation of a Polyamine-Induced Conformational Change of DNA. A Possible Mechanism for the B to Z Transition
Publisher: Informa UK Limited
Date: 08-1992
DOI: 10.1080/07391102.1992.10508638
Abstract: A 75ps molecular dynamics simulation has been performed on a fully solvated complex of spermine with the B DNA decamer (dGdC)5.(dGdC)5. The simulation indicates a possible mechanism by which polyamines might induce the formation of a left-handed helix, the B to Z transition. Spermine was initially located in the major groove, hydrogen bonded to the helix. During the simulation the ligand migrates deeper into the DNA, maintaining strong hydrogen bonding to the central guanine bases and destroying the Watson-Crick base pairing with their respective cytosines. Significant rotation of these and other cytosine bases was observed, in part due to interactions of the helix with the aminopropyl chains of spermine. An intermediate BII conformation might be of importance in this process.
Linear dichroism as a probe of molecular structure and interactions.
Publisher: Royal Society of Chemistry (RSC)
Date: 2016
DOI: 10.1039/C6AN01771A
Abstract: Linear dichroism (LD) spectroscopy involves measuring the wavelength (or energy) dependence of the difference in absorption of light parallel and perpendicular to an orientation direction. It requires s les to have a net orientation. The aim of this review is to summarise some UV-visible linear dichroism (LD) methods that can be usefully applied to increase our understanding of biomacromolecules and their complexes that have a high aspect ratio. LD shares the advantages of most spectroscopic techniques including the fact that data collection is fairly straightforward and many s le types can be investigated. Conversely, LD shares the disadvantage that the measured signal is an average over all species in the s le on which the light beam is incident. LD mitigates this disadvantage somewhat in that only species which are oriented give a net signal. How the data can be analysed to give structural information about small molecules in stretched films and membrane systems or bound to biomacromolecules and directly about biomacromolecules such as DNA and protein fibres forms part of this review. In the UV-visible region LD often suffers noticeably from light scattering since the s les tend to be large relative to the wavelength of the incident light, so consideration is also given to data analysis challenges including removal of scattering contributions to an observed signal. Brief mention is made of fluorescence detected LD.
Design and synthesis of boron complexes as new Raman reporter molecules for sensitive SERS nanotags
Publisher: Wiley
Date: 13-11-2020
DOI: 10.1002/JRS.6020
A new method for fibrous protein analysis illustrated by application to tubulin microtubule polymerisation and depolymerisation
Publisher: Wiley
Date: 2006
DOI: 10.1002/CHIR.20305
Abstract: A thermostatted micro volume Couette cell has been designed to enable linear dichroism (LD) data to be collected at a range of temperatures. The cell is a development of the traditional Couette flow LD cell and includes the recent development of micro-volume LD (20-40 microL) coupled with the addition of a heating element, temperature probe and controller. This new micro volume Couette LD cell opens the way not only to the LD analysis of systems where s le volume is critical, but also for the LD analysis of temperature sensitive s les. The polymerization of the microtubule protein tubulin has been followed in a range of different conditions using the thermostatted micro volume Couette LD cell. The focusing lenses on the cell, which are required for the microvolume cell, have the side benefit of significantly reducing the light-scattering artifacts caused by the large size of tubulin microtubules. It is now possible to monitor real-time polymerization and depolymerization kinetics, and any structural rearrangements of chromophores within the polymer. In the case of tubulin, the LD spectra revealed a greater change in the orientation of tryptophan residues at approximately 290 nm during polymerization compared to other contributing chromophores-guanine, phenylalanine, and tyrosine. The improvements in instrumental design have also allowed LD spectra of tubulin to be collected down to approximately 230 nm (previous data have only been available from the near UV region), which means that some indication of protein backbone-orientation changes are now available. It was observed during this work that apparent LD intensity maxima are in fact artifacts when the high-tension voltage is high. The onset of such artifacts has been observed at much lower voltages with light-scattering fibrous proteins (including tubulin) than with nonscattering s les. Therefore, caution must be used when interpreting LD data collected with medium to high photomultiplier tube voltages.
A study of the secondary structure of Candida antarctica lipase B using synchrotron radiation circular dichroism measurements
Publisher: Elsevier BV
Date: 2005
Spectroscopic signatures of an Fmoc–tetrapeptide, Fmoc and fluorene
Publisher: Royal Society of Chemistry (RSC)
Date: 2013
DOI: 10.1039/C3RA41979G
Gold Nanoparticle Aggregation as a Probe of Antifreeze (Glyco) Protein-Inspired Ice Recrystallization Inhibition and Identification of New IRI Active Macromolecules
Publisher: Springer Science and Business Media LLC
Date: 26-10-2015
DOI: 10.1038/SREP15716
Abstract: Antifreeze (glyco)proteins are found in polar fish species and act to slow the rate of growth of ice crystals a property known as ice recrystallization inhibition. The ability to slow ice growth is of huge technological importance especially in the cryopreservation of donor cells and tissue, but native antifreeze proteins are often not suitable, nor easily available. Therefore, the search for new materials that mimic this function is important, but currently limited by the low-throughout assays associated with the antifreeze properties. Here 30 nm gold nanoparticles are demonstrated to be useful colorimetric probes for ice recrystallization inhibition, giving a visible optical response and is compatible with 96 well plates for high-throughout studies. This method is faster, requires less infrastructure and has easier interpretation than the currently used ‘splat’ methods. Using this method, a series of serum proteins were identified to have weak, but specific ice recrystallization inhibition activity, which was removed upon denaturation. It is hoped that high-throughput tools such as this will accelerate the discovery of new antifreeze mimics.
Polarized Light, Linear Dichroism, and Circular Dichroism
Publisher: Springer Berlin Heidelberg
Date: 2018
Shape effects on the activity of synthetic major-groove binding ligands
Publisher: Elsevier BV
Date: 03-2007
DOI: 10.1016/J.JMGM.2006.07.004
Abstract: In this work we present the results of a molecular simulation study of two different tetracationic bis iron(II) supramolecular cylinders interacting with DNA. One cylinder has been shown to bind in the major groove of DNA and to induce dramatic coiling of the DNA the second is a derivative of the first, with additional methyl groups attached so as to give a larger cylinder-radius. The simulations show that both cylinders bind strongly to the major groove of the DNA, and induce complex structural changes in A-T rich regions. Whereas the parent cylinder tends to bind along the major groove, the derivatised cylinder tends to twist so that only one end remains within the major groove. Both G-C rich and A-T rich binding sites for the derivatised cylinder are discussed.
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