The systematic approach to describing conformational rearrangements in G-quadruplexes

Conformational changes in DNA G-quadruplex (GQ)-forming regions affect genome function and, thus, compose an interesting research topic. Computer modelling may yield insight into quadruplex folding and rearrangement, particularly molecular dynamics simulations. Here, we show that specific parameters...

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Main Authors:	Tsvetkov, Vladimir, Pozmogova, Galina, Varizhuk, Anna
Format:	Online
Language:	English
Published:	Taylor & Francis 2016
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4867883/

id	pubmed-4867883
recordtype	oai_dc
spelling	pubmed-48678832016-05-23 The systematic approach to describing conformational rearrangements in G-quadruplexes Tsvetkov, Vladimir Pozmogova, Galina Varizhuk, Anna Original Articles Conformational changes in DNA G-quadruplex (GQ)-forming regions affect genome function and, thus, compose an interesting research topic. Computer modelling may yield insight into quadruplex folding and rearrangement, particularly molecular dynamics simulations. Here, we show that specific parameters, which are distinct from those commonly used in DNA conformational analyses, must be introduced for adequate interpretation and, most importantly, convenient visual representation of the quadruplex modelling results. We report a set of parameters that comprehensively and systematically describe GQ geometry in dynamics. The parameters include those related to quartet planarity, quadruplex twist, and quartet stacking; they are used to quantitatively characterise various types of quadruplexes and rearrangements, such as quartet distortion/disruption or deviation/bulging of a single nucleotide from the quartet plane. Our approach to describing conformational changes in quadruplexes using the new parameters is exemplified by telomeric quadruplex rearrangement, and the benefits of applying this approach to analyse other structures are discussed. Taylor & Francis 2016-04-02 2015-07-14 /pmc/articles/PMC4867883/ /pubmed/26017012 http://dx.doi.org/10.1080/07391102.2015.1055303 Text en © 2015 The Author(s). Published by Taylor & Francis http://creativecommons.org/licenses/by-nc-nd/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives License (http://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited, and is not altered, transformed, or built upon in any way.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Tsvetkov, Vladimir Pozmogova, Galina Varizhuk, Anna
spellingShingle	Tsvetkov, Vladimir Pozmogova, Galina Varizhuk, Anna The systematic approach to describing conformational rearrangements in G-quadruplexes
author_facet	Tsvetkov, Vladimir Pozmogova, Galina Varizhuk, Anna
author_sort	Tsvetkov, Vladimir
title	The systematic approach to describing conformational rearrangements in G-quadruplexes
title_short	The systematic approach to describing conformational rearrangements in G-quadruplexes
title_full	The systematic approach to describing conformational rearrangements in G-quadruplexes
title_fullStr	The systematic approach to describing conformational rearrangements in G-quadruplexes
title_full_unstemmed	The systematic approach to describing conformational rearrangements in G-quadruplexes
title_sort	systematic approach to describing conformational rearrangements in g-quadruplexes
description	Conformational changes in DNA G-quadruplex (GQ)-forming regions affect genome function and, thus, compose an interesting research topic. Computer modelling may yield insight into quadruplex folding and rearrangement, particularly molecular dynamics simulations. Here, we show that specific parameters, which are distinct from those commonly used in DNA conformational analyses, must be introduced for adequate interpretation and, most importantly, convenient visual representation of the quadruplex modelling results. We report a set of parameters that comprehensively and systematically describe GQ geometry in dynamics. The parameters include those related to quartet planarity, quadruplex twist, and quartet stacking; they are used to quantitatively characterise various types of quadruplexes and rearrangements, such as quartet distortion/disruption or deviation/bulging of a single nucleotide from the quartet plane. Our approach to describing conformational changes in quadruplexes using the new parameters is exemplified by telomeric quadruplex rearrangement, and the benefits of applying this approach to analyse other structures are discussed.
publisher	Taylor & Francis
publishDate	2016
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4867883/
_version_	1613579634093326336

The systematic approach to describing conformational rearrangements in G-quadruplexes

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