Measured and calculated CD spectra of G‐quartets stacked with the same or opposite polarities

Gray, David B.; Wen, Jin-Der; Gray, Carla W.; Repges, Rudolf; Repges, Charlotte; Raabe, Gerhard; Fleischhauer, Jörg

doi:10.1002/chir.20455

Cited by 219 publications

(210 citation statements)

References 72 publications

(115 reference statements)

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“…A better understanding of the various factors that contribute to the specific patterns of CD spectra is required before CD data alone can be used to determine quadruplex topology unambiguously (Gray et al, 2008). Until such data are available, the results obtained from CD spectra must be analyzed with caution and other biophysical methods should be used to confirm quadruplex formation.…”

Section: Circular Dichroism Spectroscopy (Cd)mentioning

confidence: 99%

How to study G-quadruplex structures

Małgowska¹,

Gudanis²,

Teubert³

et al. 2012

bta

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All guanine-rich DNA and RNA molecules tend to fold into inter-and intra-molecular structures called G-quadruplexes. The core of a G-quadruplex is composed of at least two adjacent G-tetrads stabilized by monovalent cations. While it has been suggested that there could potentially be over 375 000 quadruplex forming sequences in the human genome alone, only a small number of three-dimensional G-quadruplex structures are known. More structural data are needed to explain their presence and function in vivo. We offer here a short review of experimental methods commonly used to determine G-quadruplex topologies.

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Section: Circular Dichroism Spectroscopy (Cd)mentioning

confidence: 99%

How to study G-quadruplex structures

Małgowska¹,

Gudanis²,

Teubert³

et al. 2012

bta

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“…The shapes and signs of these basis spectra for dinucleotide guanine steps are generally consistent with the results of a simplified exciton coupling approach and more refined quantum mechanical calculations used to predict the CD spectra expected for different dinucleotide stacking orientations. [3,6,17] The basis spectrum obtained for lateral and diagonal loops are highly reminiscent of CD spectra obtained for single-stranded DNA di-and trinucleotide sequences. [18] The remaining basis spectrum for "other" has low amplitude and is nearly featureless.…”

mentioning

confidence: 91%

G-quadruplex secondary structure from circular dichroism spectroscopy

Villar‐Guerra

Trent

Chaires

2017

Preprint

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A curated library of circular dichroism spectra of 23 G-quadruplexes of known structure was built and analyzed. The goal of this study was to use this reference library to develop an algorithm to derive quantitative estimates of the secondary structure content of quadruplexes from their experimental CD spectra. Principle component analysis and singular value decomposition were used to characterize the reference spectral library. CD spectra were successfully fit to obtain estimates of the amounts of base steps in anti-anti, syn-anti or anti-syn conformations, in diagonal or lateral loops or in other conformations. The results show that CD spectra of nucleic acids can be analyzed to obtain quantitative structural information about secondary structure content in an analogous way to methods used to analyze protein CD spectra.peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission.The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/184390 doi: bioRxiv preprint first posted online Sep. 4, 2017; 2 Circular dichroism (CD) spectroscopy is a primary tool for the characterization of Gquadruplex (G4) structures. G-quadruplexes are functionally important genomic elements that form at specific locations in an orchestrated manner throughout the cell cycle. [1] Different G4 structures, arising from differences in G-quartet stacking, strand segment orientation and loop arrangements, display unique CD spectral signatures. [2] Qualitative rules-of-thumb have evolved that associate CD spectral features with particular G4 topologies, namely parallel (≈264 nm max, ≈245 nm min), antiparallel (≈295 max, ≈260 min) or "hybrid" (or 3+1) (≈295 max, ≈260 max, ≈245 min). [3] [4] [5] [6] [7] While some exceptions to these rules have been noted, they are generally accepted for the characterization and validation of quadruplex formation in potential quadruplex forming sequences.CD spectroscopy is widely used for the quantitative determination of the secondary structural content of proteins. Over several decades, reference libraries assembled for this purpose have grown in content and a number of analytical algorithms have evolved that now make the quantitative analysis of protein spectra by CD fairly routine. Such is not the case for nucleic acids. For duplex DNA, CD is used primarily in a qualitative way to distinguish common secondary structures (e.g., B-, A-and Z-forms) and is particularly valuable for monitoring changes in secondary structure in titration, binding or thermal denaturation experiments. [2] A recent chemometric analysis of nucleic acid CD spectra was used to classify nucleic acid structures using a library of sequences and structures that expanded the range of topologies to include multistranded triplex and quadruplex forms. [8] As of yet no quantitative analysis has been attempted for nucleic acids that is analogous to the approach used to quantify CD spectra of proteins to obtain more detailed structural information. The goal of this study is to...

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“…[23,24] The spectra displayed the expected negative (Na + , K + ) and positive (Ba 2+ ) Cotton effects, with a zero-crossing at l = 300 nm in the region of the AcG chromophore. Evidence for H-bonding and cation binding was obtained from the shifts in the vibrational band of n C=O, G from 1700 to 1680 cm À1 , which was observed in the FTIR spectra of G-quadruplexes, while the n C=O band of external acetyl moieties at 1750 cm À1 did not shift (Supporting Information, Figure S2 b).…”

mentioning

confidence: 97%