Explaining the striking difference in twist-stretch coupling between DNA and RNA: A comparative molecular dynamics analysis

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60461373%3A22310%2F15%3A43900546" target="_blank" >RIV/60461373:22310/15:43900546 - isvavai.cz</a>

Alternative codes found

RIV/61388963:_____/15:00454236 RIV/00216208:11310/15:10315433

Result on the web

<a href="http://nar.oxfordjournals.org/content/43/21/10143.full" target="_blank" >http://nar.oxfordjournals.org/content/43/21/10143.full</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1093/nar/gkv1028" target="_blank" >10.1093/nar/gkv1028</a>

Result language

angličtina

Original language name

Explaining the striking difference in twist-stretch coupling between DNA and RNA: A comparative molecular dynamics analysis

Original language description

Double stranded helical DNA and RNA are flexible molecules that can undergo global conformational fluctuations. Their bending, twisting and stretching deformabilities are of similar magnitude. However, recent single-molecule experiments revealed a striking qualitative difference indicating an opposite sign for the twist-stretch couplings of dsDNA and dsRNA [Lipfert et al. 2014. Proc. Natl. Acad. Sci. U.S.A. 111, 15408] that is not explained by existing models. Employing unconstrained Molecular Dynamics (MD) simulations we are able to reproduce the qualitatively different twist-stretch coupling for dsDNA and dsRNA in semi-quantitative agreement with experiment. Similar results are also found in simulations that include an external torque to induce over-or unwinding of DNA and RNA. Detailed analysis of the helical deformations coupled to twist indicate that the interplay of helical rise, base pair inclination and displacement from the helix axis upon twist changes are responsible for the different twist-stretch correlations. Overwinding of RNA results in more compact conformations with a narrower major groove and consequently reduced helical extension. Overwinding of DNA decreases the size of the minor groove and the resulting positive base pair inclination leads to a slender and more extended helical structure.

Czech name

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Czech description

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Type

J_x - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)

CEP classification

BO - Biophysics

OECD FORD branch

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Project

<a href="/en/project/GA14-21893S" target="_blank" >GA14-21893S: Nanomechanics of RNA and DNA structural motifs</a><br>

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2015

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Nucleic Acids Research

ISSN

0305-1048

e-ISSN

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Volume of the periodical

43

Issue of the periodical within the volume

21

Country of publishing house

GB - UNITED KINGDOM

Number of pages

14

Pages from-to

10143-10156

UT code for WoS article

000366410900016

EID of the result in the Scopus database

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