Temperature-dependent elasticity of DNA, RNA, and hybrid double helices

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60461373%3A22310%2F24%3A43929607" target="_blank" >RIV/60461373:22310/24:43929607 - isvavai.cz</a>

Výsledek na webu

<a href="https://www.sciencedirect.com/science/article/abs/pii/S0006349524000730" target="_blank" >https://www.sciencedirect.com/science/article/abs/pii/S0006349524000730</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1016/j.bpj.2024.01.032" target="_blank" >10.1016/j.bpj.2024.01.032</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Temperature-dependent elasticity of DNA, RNA, and hybrid double helices

Popis výsledku v původním jazyce

Nucleic acid double helices in their DNA, RNA, and DNA -RNA hybrid form play a fundamental role in biology and are main building blocks of artificial nanostructures, but how their properties depend on temperature remains poorly understood. Here, we report thermal dependence of dynamic bending persistence length, twist rigidity, stretch modulus, and twist -stretch coupling for DNA, RNA, and hybrid duplexes between 7 degrees C and 47 degrees C. The results are based on all -atom molecular dynamics simulations using different force field parameterizations. We first demonstrate that unrestrained molecular dynamics can reproduce experimentally known mechanical properties of the duplexes at room temperature. Beyond experimentally known features, we also infer the twist rigidity and twist -stretch coupling of the hybrid duplex. As for the temperature dependence, we found that increasing temperature softens all the duplexes with respect to bending, twisting, and stretching. The relative decrease of the stretch moduli is 0.003-0.004/degrees C, similar for all the duplex variants despite their very different stretching stiffness, whereas RNA twist stiffness decreases by 0.003/degrees C, and smaller values are found for the other elastic moduli. The twist -stretch couplings are nearly unaffected by temperature. The stretching, bending, and twisting stiffness all include an important entropic component. Relation of our results to the two -state model of DNA flexibility is discussed. Our work provides temperature -dependent elasticity of nucleic acid duplexes at the microsecond scale relevant for initial stages of protein binding.

Název v anglickém jazyce

Temperature-dependent elasticity of DNA, RNA, and hybrid double helices

Popis výsledku anglicky

Nucleic acid double helices in their DNA, RNA, and DNA -RNA hybrid form play a fundamental role in biology and are main building blocks of artificial nanostructures, but how their properties depend on temperature remains poorly understood. Here, we report thermal dependence of dynamic bending persistence length, twist rigidity, stretch modulus, and twist -stretch coupling for DNA, RNA, and hybrid duplexes between 7 degrees C and 47 degrees C. The results are based on all -atom molecular dynamics simulations using different force field parameterizations. We first demonstrate that unrestrained molecular dynamics can reproduce experimentally known mechanical properties of the duplexes at room temperature. Beyond experimentally known features, we also infer the twist rigidity and twist -stretch coupling of the hybrid duplex. As for the temperature dependence, we found that increasing temperature softens all the duplexes with respect to bending, twisting, and stretching. The relative decrease of the stretch moduli is 0.003-0.004/degrees C, similar for all the duplex variants despite their very different stretching stiffness, whereas RNA twist stiffness decreases by 0.003/degrees C, and smaller values are found for the other elastic moduli. The twist -stretch couplings are nearly unaffected by temperature. The stretching, bending, and twisting stiffness all include an important entropic component. Relation of our results to the two -state model of DNA flexibility is discussed. Our work provides temperature -dependent elasticity of nucleic acid duplexes at the microsecond scale relevant for initial stages of protein binding.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10610 - Biophysics

Projekt

—

Návaznosti

S - Specificky vyzkum na vysokych skolach

Rok uplatnění

2024

Kód důvěrnosti údajů

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

Název periodika

BIOPHYSICAL JOURNAL

ISSN

0006-3495

e-ISSN

1542-0086

Svazek periodika

123

Číslo periodika v rámci svazku

5

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

12

Strana od-do

572-583

Kód UT WoS článku

001208499500001

EID výsledku v databázi Scopus

2-s2.0-85184779105