Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081707%3A_____%2F23%3A00572134" target="_blank" >RIV/68081707:_____/23:00572134 - isvavai.cz</a>
Alternative codes found
RIV/00216224:14740/23:00130996 RIV/61989592:15640/23:73621693 RIV/61989100:27740/23:10254092
Result on the web
<a href="https://pubs.acs.org/doi/10.1021/acs.jcim.3c00358" target="_blank" >https://pubs.acs.org/doi/10.1021/acs.jcim.3c00358</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/acs.jcim.3c00358" target="_blank" >10.1021/acs.jcim.3c00358</a>

Result language
angličtina
Original language name
Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations
Original language description
Holliday junction (HJ) is a noncanonical four-way DNA structure with a prominent role in DNA repair, recombination, and DNA nanotechnology. By rearranging its four arms, HJ can adopt either closed or open state. With enzymes typically recognizing only a single state, acquiring detailed knowledge of the rearrangement process is an important step toward fully understanding the biological function of HJs. Here, we carried out standard all-atom molecular dynamics (MD) simulations of the spontaneous opening-closing transitions, which revealed complex conformational transitions of HJs with an involvement of previously unconsidered half-closed inter-mediates. Detailed free-energy landscapes of the transitions were obtained by sophisticated enhanced sampling simulations. Because the force field overstabilizes the closed conformation of HJs, we developed a system-specific modification which for the first time allows the observation of spontaneous opening-closing HJ transitions in unbiased MD simulations and opens the possibilities for more accurate HJ computational studies of biological processes and nanomaterials.
Czech name
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Czech description
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Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
—
OECD FORD branch
10402 - Inorganic and nuclear chemistry

Project
<a href="/en/project/GA21-23718S" target="_blank" >GA21-23718S: The fascinating physical chemistry of DNA studied by advanced computations</a><br>
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year
2023
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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