Temperature-dependent elasticity of DNA, RNA, and hybrid double helices
The result's identifiers
Result code in 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>
Result on the web
<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>
Alternative languages
Result language
angličtina
Original language name
Temperature-dependent elasticity of DNA, RNA, and hybrid double helices
Original language description
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.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10610 - Biophysics
Result continuities
Project
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Continuities
S - Specificky vyzkum na vysokych skolach
Others
Publication year
2024
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
BIOPHYSICAL JOURNAL
ISSN
0006-3495
e-ISSN
1542-0086
Volume of the periodical
123
Issue of the periodical within the volume
5
Country of publishing house
US - UNITED STATES
Number of pages
12
Pages from-to
572-583
UT code for WoS article
001208499500001
EID of the result in the Scopus database
2-s2.0-85184779105