Deciphering Dickerson-Drew DNA Equilibrium beyond the BI/BII DNA Dichotomy by Interpretation of 31P NMR Parameters

Kód výsledku v 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>

Výsledek na webu

<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>

Jazyk výsledku

angličtina

Název v původním jazyce

Deciphering Dickerson-Drew DNA Equilibrium beyond the BI/BII DNA Dichotomy by Interpretation of 31P NMR Parameters

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

Deciphering Dickerson-Drew DNA Equilibrium beyond the BI/BII DNA Dichotomy by Interpretation of 31P NMR Parameters

Popis výsledku anglicky

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.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10403 - Physical chemistry

Projekt

<a href="/cs/project/GA25-15726S" target="_blank" >GA25-15726S: Prozkoumání nových forem Ramanovy optické aktivity</a><br>

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2025

Kód důvěrnosti údajů

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

Název periodika

Journal of Chemical Theory and Computation

ISSN

—

e-ISSN

1549-9626

Svazek periodika

21

Číslo periodika v rámci svazku

19

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

12

Strana od-do

10006-10017

Kód UT WoS článku

001572352900001

EID výsledku v databázi Scopus

2-s2.0-105018698135