G-Quadruplex Secondary Structure Obtained from Circular Dichroism Spectroscopy.
TLDR
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 proteinCD spectra.Abstract:
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. Principal 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.read more
Citations
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Journal ArticleDOI
A guide to computational methods for G-quadruplex prediction
TL;DR: The present review aims at providing an updated overview of the current open-source G-quadruplex prediction algorithms and straightforward examples of their implementation, and proposing other estimates which consider non-canonical sequences and/or structure propensity and stability.
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Targeting RNA G-Quadruplex in SARS-CoV-2: A Promising Therapeutic Target for COVID-19?
Chuanqi Zhao,Geng Qin,Jingsheng Niu,Jingsheng Niu,Zhao Wang,Zhao Wang,Chunyu Wang,Jinsong Ren,Jinsong Ren,Xiaogang Qu,Xiaogang Qu +10 more
TL;DR: To the authors' knowledge, this is the first evidence that PQSs in SARS-CoV-2 can form G4 structures in live cells, and their biofunctions can be regulated by G4-specific stabilizer.
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Properties and biological impact of RNA G-quadruplexes: from order to turmoil and back.
Prakash Kharel,Gertraud Becker,Vladimir B. Tsvetkov,Vladimir B. Tsvetkov,Pavel Ivanov,Pavel Ivanov +5 more
TL;DR: The landscape of rG4s within the transcriptome is reviewed, their potential impact on biological processes are focused on, and an emerging connection of these functions in human health and disease is considered.
Journal ArticleDOI
Major G-Quadruplex Form of HIV-1 LTR Reveals a (3 + 1) Folding Topology Containing a Stem-Loop
TL;DR: The NMR structure of LTR-III in K+ solution was reported, revealing the formation of a unique quadruplex–duplex hybrid consisting of a three-layer (3 + 1) G-quadruplex scaffold, a 12-nt diagonal loop containing a conserved duplex-stem, a 3-nt lateral loop, a 1-nt propeller loop, and a V-shaped loop.
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The hTERT core promoter forms three parallel G-quadruplexes.
Robert C. Monsen,Lynn DeLeeuw,William L. Dean,Robert D. Gray,T. Michael Sabo,Srinivas Chakravarthy,Jonathan B. Chaires,John O. Trent +7 more
TL;DR: It is found with certainty that the wild-type hTERT promoter sequence does not form a hairpin structure in solution, but rather folds into a compact stacked three-G-quadruplex conformation.
References
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Journal ArticleDOI
Using circular dichroism spectra to estimate protein secondary structure
TL;DR: This protocol details the basic steps of obtaining and interpreting CD data, and methods for analyzing spectra to estimate the secondary structural composition of proteins.
Journal ArticleDOI
Estimation of Protein Secondary Structure from Circular Dichroism Spectra: Comparison of CONTIN, SELCON, and CDSSTR Methods with an Expanded Reference Set
TL;DR: Analyzing protein CD spectra using all three methods should improve the reliability of predicted secondary structural fractions, and three programs are provided in CDPro software package and have been modified for easier use with the different reference sets described in this paper.
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DICHROWEB, an online server for protein secondary structure analyses from circular dichroism spectroscopic data.
Lee Whitmore,Bonnie A. Wallace +1 more
TL;DR: The DICHROWEB web server enables on-line analyses of circular dichroism (CD) spectroscopic data, providing calculated secondary structure content and graphical analyses comparing calculated structures and experimental data.
Journal ArticleDOI
Circular dichroism and conformational polymorphism of DNA
TL;DR: Here the authors review studies that provided important information about conformational properties of DNA using circular dichroic (CD) spectroscopy, which significantly participated in all basic conformational findings on DNA.
Journal ArticleDOI
Oligonucleotide interactions. 3. Circular dichroism studies of the conformation of deoxyoligonucleotides.
TL;DR: The circular dichroism (CD) spectra of the four usual deoxymononucleosides, all sixteen deoxydinucleotides, and a number of trinucleotide diphosphates have been measured as mentioned in this paper.