Molecular dynamics and Raman optical activity spectra reveal nucleotide conformation ratios in solution

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388963%3A_____%2F23%3A00570656" target="_blank" >RIV/61388963:_____/23:00570656 - isvavai.cz</a>

Alternative codes found

RIV/61989592:15310/23:73618529 RIV/00216208:11320/23:10464179 RIV/60461373:22340/23:43926680

Result on the web

<a href="https://doi.org/10.1039/D2CP05756E" target="_blank" >https://doi.org/10.1039/D2CP05756E</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1039/d2cp05756e" target="_blank" >10.1039/d2cp05756e</a>

Result language

angličtina

Original language name

Molecular dynamics and Raman optical activity spectra reveal nucleotide conformation ratios in solution

Original language description

Nucleotide conformational flexibility affects their biological functions. Although the spectroscopy of Raman optical activity (ROA) is well suited to structural analyses in aqueous solutions, the link between the spectral shape and the nucleotide geometry is not fully understood. We recorded the Raman and ROA spectra of model nucleotides (rAMP, rGMP, rCMP, and dTMP) and interpreted them on the basis of molecular dynamics (MD) combined with density functional theory (DFT). The relation between the sugar puckering, base conformation and spectral intensities is discussed. Hydrogen bonds between the sugar's C3′ hydroxyl and the phosphate groups were found to be important for the sugar puckering. The simulated spectra correlated well with the experimental data and provided an understanding of the dependence of the spectral shapes on conformational dynamics. Most of the strongest spectral bands could be assigned to vibrational molecular motions. Decomposition of the experimental spectra into calculated subspectra based on arbitrary maps of free energies provided experimental conformer populations, which could be used to verify and improve the MD predictions. The analyses indicate some flaws of common MD force fields, such as being unable to describe the fine conformer distribution. Also the accuracy of conformer populations obtained from the spectroscopic data depends on the simulations, improvement of which is desirable for gaining a more detailed insight in the future. Improvement of the spectroscopic and computational methodology for nucleotides also provides opportunities for its application to larger nucleic acids.

Czech name

—

Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10403 - Physical chemistry

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

Publication year

2023

Confidentiality

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

Name of the periodical

Physical Chemistry Chemical Physics

ISSN

1463-9076

e-ISSN

1463-9084

Volume of the periodical

25

Issue of the periodical within the volume

11

Country of publishing house

GB - UNITED KINGDOM

Number of pages

11

Pages from-to

8198-8208

UT code for WoS article

000945121700001

EID of the result in the Scopus database

2-s2.0-85149820017