Comprehensive Assessment of Force-Field Performance in Molecular Dynamics Simulations of DNA/RNA Hybrid Duplexes
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081707%3A_____%2F24%3A00597520" target="_blank" >RIV/68081707:_____/24:00597520 - isvavai.cz</a>
Alternative codes found
RIV/61989592:15640/24:73625496 RIV/61989100:27640/24:10255732 RIV/61989100:27740/24:10255732
Result on the web
<a href="https://pubs.acs.org/doi/10.1021/acs.jctc.4c00601" target="_blank" >https://pubs.acs.org/doi/10.1021/acs.jctc.4c00601</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/acs.jctc.4c00601" target="_blank" >10.1021/acs.jctc.4c00601</a>
Alternative languages
Result language
angličtina
Original language name
Comprehensive Assessment of Force-Field Performance in Molecular Dynamics Simulations of DNA/RNA Hybrid Duplexes
Original language description
Mixed double helices formed by RNA and DNA strands, commonly referred to as hybrid duplexes or hybrids, are essential in biological processes like transcription and reverse transcription. They are also important for their applications in CRISPR gene editing and nanotechnology. Yet, despite their significance, the hybrid duplexes have been seldom modeled by atomistic molecular dynamics methodology, and there is no benchmark study systematically assessing the force-field performance. Here, we present an extensive benchmark study of polypurine tract (PPT) and Dickerson-Drew dodecamer hybrid duplexes using contemporary and commonly utilized pairwise additive and polarizable nucleic acid force fields. Our findings indicate that none of the available force-field choices accurately reproduces all the characteristic structural details of the hybrid duplexes. The AMBER force fields are unable to populate the C3 '-endo (north) pucker of the DNA strand and underestimate inclination. The CHARMM force field accurately describes the C3 '-endo pucker and inclination but shows base pair instability. The polarizable force fields struggle with accurately reproducing the helical parameters. Some force-field combinations even demonstrate a discernible conflict between the RNA and DNA parameters. In this work, we offer a candid assessment of the force-field performance for mixed DNA/RNA duplexes. We provide guidance on selecting utilizable force-field combinations and also highlight potential pitfalls and best practices for obtaining optimal performance.
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
10403 - Physical chemistry
Result continuities
Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
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
Journal of Chemical Theory and Computation
ISSN
1549-9618
e-ISSN
1549-9626
Volume of the periodical
20
Issue of the periodical within the volume
15
Country of publishing house
US - UNITED STATES
Number of pages
13
Pages from-to
6917-6929
UT code for WoS article
001270065500001
EID of the result in the Scopus database
2-s2.0-85198951698