Deciphering Dickerson-Drew DNA Equilibrium beyond the BI/BII DNA Dichotomy by Interpretation of 31P NMR Parameters
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F25%3A73633605" target="_blank" >RIV/61989592:15310/25:73633605 - isvavai.cz</a>
Result on the web
<a href="https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.5c01076" target="_blank" >https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.5c01076</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/acs.jctc.5c01076" target="_blank" >10.1021/acs.jctc.5c01076</a>
Alternative languages
Result language
angličtina
Original language name
Deciphering Dickerson-Drew DNA Equilibrium beyond the BI/BII DNA Dichotomy by Interpretation of 31P NMR Parameters
Original language description
DNA duplexes exist as dynamic ensembles of interconverting conformations in solution. Conventional nuclear magnetic resonance (NMR) data interpretation often simplifies this behavior by assuming one dominant structure, but multiple substates (such as different backbone conformers) can coexist. Here, we present an approach that refines the interpretation of 31P NMR data in the Dickerson-Drew DNA by integrating a nucleotide conformational classification (NtC) (Černý et al., Nucleic Acids Research 2020, 48, 6367-6381) with molecular dynamics (MD) simulations. By finely classifying backbone conformers into distinct NtC-defined states and using MD to predict their populations, we achieve a more nuanced correspondence between experimental NMR observables and DNA structure-dynamical heterogeneity. Application of this framework demonstrates a radical improvement of NMR data interpretation, thereby enhancing the reliability of deducing DNA conformational equilibria in solution.
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
<a href="/en/project/GA25-15726S" target="_blank" >GA25-15726S: Exploration of new forms of Raman optical activity</a><br>
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)
Others
Publication year
2025
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
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e-ISSN
1549-9626
Volume of the periodical
21
Issue of the periodical within the volume
19
Country of publishing house
US - UNITED STATES
Number of pages
12
Pages from-to
10006-10017
UT code for WoS article
001572352900001
EID of the result in the Scopus database
2-s2.0-105018698135