Compensatory Mechanisms in Temperature Dependence of DNA Double Helical Structure: Bending and Elongation

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60461373%3A22310%2F20%3A43921727" target="_blank" >RIV/60461373:22310/20:43921727 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/68081707:_____/20:00524557

Výsledek na webu

<a href="https://pubs.acs.org/doi/10.1021/acs.jctc.0c00037" target="_blank" >https://pubs.acs.org/doi/10.1021/acs.jctc.0c00037</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1021/acs.jctc.0c00037" target="_blank" >10.1021/acs.jctc.0c00037</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Compensatory Mechanisms in Temperature Dependence of DNA Double Helical Structure: Bending and Elongation

Popis výsledku v původním jazyce

Changes in the structure of double-stranded (ds) DNA with temperature affect processes in thermophilic organisms and are important for nanotechnological applications. Here we investigate temperature-dependent conformational changes of dsDNA at the scale of several helical turns and at the base pair step level, inferred from extensive all-atom molecular dynamics simulations of DNA at temperatures from 7 to 47 °C. Our results suggest that, contrary to twist, the overall bending of dsDNA without A-tracts depends only very weakly on temperature, due to the mutual compensation of directional local bends. Investigating DNA length as a function of temperature, we find that the sum of distances between base pair centers (the wire length) exhibits a large expansion coefficient of ∼2 × 10-4 °C-1, similar to values reported for thermoplastic materials. However, the wire length increase with temperature is absorbed by expanding helix radius, so the length measured along the helical axis (the spring length) seems to suggest a very small negative thermal expansion coefficient. These compensatory mechanisms contribute to thermal stability of DNA structure on the biologically relevant scale of tens of base pairs and longer. Copyright © 2020 American Chemical Society.

Název v anglickém jazyce

Compensatory Mechanisms in Temperature Dependence of DNA Double Helical Structure: Bending and Elongation

Popis výsledku anglicky

Changes in the structure of double-stranded (ds) DNA with temperature affect processes in thermophilic organisms and are important for nanotechnological applications. Here we investigate temperature-dependent conformational changes of dsDNA at the scale of several helical turns and at the base pair step level, inferred from extensive all-atom molecular dynamics simulations of DNA at temperatures from 7 to 47 °C. Our results suggest that, contrary to twist, the overall bending of dsDNA without A-tracts depends only very weakly on temperature, due to the mutual compensation of directional local bends. Investigating DNA length as a function of temperature, we find that the sum of distances between base pair centers (the wire length) exhibits a large expansion coefficient of ∼2 × 10-4 °C-1, similar to values reported for thermoplastic materials. However, the wire length increase with temperature is absorbed by expanding helix radius, so the length measured along the helical axis (the spring length) seems to suggest a very small negative thermal expansion coefficient. These compensatory mechanisms contribute to thermal stability of DNA structure on the biologically relevant scale of tens of base pairs and longer. Copyright © 2020 American Chemical Society.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

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

2020

Kód důvěrnosti údajů

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

Název periodika

Journal of Chemical Theory and Computation

ISSN

1549-9618

e-ISSN

—

Svazek periodika

16

Číslo periodika v rámci svazku

4

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

7

Strana od-do

2857-2863

Kód UT WoS článku

000526313000071

EID výsledku v databázi Scopus

2-s2.0-85083544543