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

ABSTRACT: 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.

SUBMITTER: Biedermannova L 

PROVIDER: S-EPMC9344474 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature