Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes

Guanine-rich DNA sequences tend to form four-stranded G-quadruplex structures. Characteristic glycosidic conformational patterns along the G-strands, such as the 5′-syn-anti-syn-anti pattern observed with the Oxytricha nova telomeric G-quadruplexes, have been well documented. However, an explanation...

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Main Authors:	Cang, Xiaohui, Šponer, Jiří, Cheatham, Thomas E.
Format:	Online
Language:	English
Published:	Oxford University Press 2011
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105399/

id	pubmed-3105399
recordtype	oai_dc
spelling	pubmed-31053992011-06-01 Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes Cang, Xiaohui Šponer, Jiří Cheatham, Thomas E. Structural Biology Guanine-rich DNA sequences tend to form four-stranded G-quadruplex structures. Characteristic glycosidic conformational patterns along the G-strands, such as the 5′-syn-anti-syn-anti pattern observed with the Oxytricha nova telomeric G-quadruplexes, have been well documented. However, an explanation for these featured glycosidic patterns has not emerged. This work presents MD simulation and free energetic analyses for simplified two-quartet [d(GG)]4 models and suggests that the four base pair step patterns show quite different relative stabilities: syn-anti > anti-anti > anti-syn > syn-syn. This suggests the following rule: when folding, anti-parallel G-quadruplexes tend to maximize the number of syn-anti steps and avoid the unfavorable anti-syn and syn-syn steps. This rule is consistent with most of the anti-parallel G-quadruplex structures in the Protein Databank (PDB). Structural polymorphisms of G-quadruplexes relate to these glycosidic conformational patterns and the lengths of the G-tracts. The folding topologies of G2- and G4-tracts are not very polymorphic because each strand tends to populate the stable syn-anti repeat. G3-tracts, on the other hand, cannot present this repeating pattern on each G-tract. This leads to smaller energy differences between different geometries and helps explain the extreme structural polymorphism of the human telomeric G-quadruplexes. Oxford University Press 2011-05 2011-02-03 /pmc/articles/PMC3105399/ /pubmed/21296760 http://dx.doi.org/10.1093/nar/gkr031 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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	Cang, Xiaohui Šponer, Jiří Cheatham, Thomas E.
spellingShingle	Cang, Xiaohui Šponer, Jiří Cheatham, Thomas E. Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes
author_facet	Cang, Xiaohui Šponer, Jiří Cheatham, Thomas E.
author_sort	Cang, Xiaohui
title	Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes
title_short	Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes
title_full	Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes
title_fullStr	Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes
title_full_unstemmed	Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes
title_sort	explaining the varied glycosidic conformational, g-tract length and sequence preferences for anti-parallel g-quadruplexes
description	Guanine-rich DNA sequences tend to form four-stranded G-quadruplex structures. Characteristic glycosidic conformational patterns along the G-strands, such as the 5′-syn-anti-syn-anti pattern observed with the Oxytricha nova telomeric G-quadruplexes, have been well documented. However, an explanation for these featured glycosidic patterns has not emerged. This work presents MD simulation and free energetic analyses for simplified two-quartet [d(GG)]4 models and suggests that the four base pair step patterns show quite different relative stabilities: syn-anti > anti-anti > anti-syn > syn-syn. This suggests the following rule: when folding, anti-parallel G-quadruplexes tend to maximize the number of syn-anti steps and avoid the unfavorable anti-syn and syn-syn steps. This rule is consistent with most of the anti-parallel G-quadruplex structures in the Protein Databank (PDB). Structural polymorphisms of G-quadruplexes relate to these glycosidic conformational patterns and the lengths of the G-tracts. The folding topologies of G2- and G4-tracts are not very polymorphic because each strand tends to populate the stable syn-anti repeat. G3-tracts, on the other hand, cannot present this repeating pattern on each G-tract. This leads to smaller energy differences between different geometries and helps explain the extreme structural polymorphism of the human telomeric G-quadruplexes.
publisher	Oxford University Press
publishDate	2011
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105399/
_version_	1611456718468808704

Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes

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