Knowledge-based prediction of DNA hydration using hydrated dinucleotides as building blocks

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F86652036%3A_____%2F22%3A00560262" target="_blank" >RIV/86652036:_____/22:00560262 - isvavai.cz</a>

Result on the web

<a href="https://scripts.iucr.org/cgi-bin/paper?S2059798322006234" target="_blank" >https://scripts.iucr.org/cgi-bin/paper?S2059798322006234</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1107/S2059798322006234" target="_blank" >10.1107/S2059798322006234</a>

Result language

angličtina

Original language name

Knowledge-based prediction of DNA hydration using hydrated dinucleotides as building blocks

Original language description

Water plays an important role in stabilizing the structure of DNA and mediating its interactions. Here, the hydration of DNA was analyzed in terms of dinucleotide fragments from an ensemble of 2727 nonredundant DNA chains containing 41 853 dinucleotides and 316 265 associated first-shell water molecules. The dinucleotides were classified into categories based on their 16 sequences and the previously determined structural classes known as nucleotide conformers (NtCs). The construction of hydrated dinucleotide building blocks allowed dinucleotide hydration to be calculated as the probability of water density distributions. Peaks in the water densities, known as hydration sites (HSs), uncovered the interplay between base and sugar-phosphate hydration in the context of sequence and structure. To demonstrate the predictive power of hydrated DNA building blocks, they were then used to predict hydration in an independent set of crystal and NMR structures. In ten tested crystal structures, the positions of predicted HSs and experimental waters were in good agreement (more than 40% were within 0.5 angstrom) and correctly reproduced the known features of DNA hydration, for example the 'spine of hydration' in B-DNA. Therefore, it is proposed that hydrated building blocks can be used to predict DNA hydration in structures solved by NMR and cryo-EM, thus providing a guide to the interpretation of experimental data and computer models. The data for the hydrated building blocks and the predictions are available for browsing and visualization at the website https://watlas.datmos.org/watna/.

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

10406 - Analytical 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

2022

Confidentiality

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

Name of the periodical

Acta Crystallographica Section D-Biological Crystallography

ISSN

1399-0047

e-ISSN

2059-7983

Volume of the periodical

78

Issue of the periodical within the volume

AUG 1 2022

Country of publishing house

GB - UNITED KINGDOM

Number of pages

9

Pages from-to

1032-1045

UT code for WoS article

000837045300010

EID of the result in the Scopus database

2-s2.0-85135316301