Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning

Kód výsledku v IS VaVaI

RIV/61989592:15310/14:33152187 - isvavai.cz

Nalezeny alternativní kódy

RIV/68081707:_____/14:00430484 RIV/61388963:_____/14:00430484 RIV/00216224:14740/14:00076810

Výsledek na webu

http://nar.oxfordjournals.org/content/42/11/7383.full.pdf+html

DOI - Digital Object Identifier

10.1093/nar/gku338

Jazyk výsledku

angličtina

Název v původním jazyce

Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning

Popis výsledku v původním jazyce

A-tracts are functionally important DNA sequences which induce helix bending and have peculiar structural properties. While A-tract structure has been qualitatively well characterized, their mechanical properties remain controversial. A-tracts appear structurally rigid and resist nucleosome formation, but seem flexible in DNA looping. In this work, we investigate mechanical properties of symmetric A(n)T(n) and asymmetric A(2n) tracts for n = 3, 4, 5 using two types of coarse-grained models. The first model represents DNA as an ensemble of interacting rigid bases with non-local quadratic deformation energy, the second one treats DNA as an anisotropically bendable and twistable elastic rod. Parameters for both models are inferred from microsecond long, atomic-resolution molecular dynamics simulations. We find that asymmetric A-tracts are more rigid than the control G/C-rich sequence in localized distortions relevant for nucleosome formation, but are more flexible in global bending and tw

Název v anglickém jazyce

Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning

Popis výsledku anglicky

A-tracts are functionally important DNA sequences which induce helix bending and have peculiar structural properties. While A-tract structure has been qualitatively well characterized, their mechanical properties remain controversial. A-tracts appear structurally rigid and resist nucleosome formation, but seem flexible in DNA looping. In this work, we investigate mechanical properties of symmetric A(n)T(n) and asymmetric A(2n) tracts for n = 3, 4, 5 using two types of coarse-grained models. The first model represents DNA as an ensemble of interacting rigid bases with non-local quadratic deformation energy, the second one treats DNA as an anisotropically bendable and twistable elastic rod. Parameters for both models are inferred from microsecond long, atomic-resolution molecular dynamics simulations. We find that asymmetric A-tracts are more rigid than the control G/C-rich sequence in localized distortions relevant for nucleosome formation, but are more flexible in global bending and tw

Druh

J_x - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)

CEP obor

BO - Biofyzika

OECD FORD obor

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Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2014

Kód důvěrnosti údajů

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

Název periodika

Nucleic Acids Research

ISSN

0305-1048

e-ISSN

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Svazek periodika

42

Číslo periodika v rámci svazku

11

Stát vydavatele periodika

GB - Spojené království Velké Británie a Severního Irska

Počet stran výsledku

12

Strana od-do

7383-7394

Kód UT WoS článku

000338769400055

EID výsledku v databázi Scopus

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