Water plays an important role in stabilizing DNA structure and in mediating its interactions. In our work, we utilize crystallographic data to compile the average hydration patterns around biomolecules - proteins [1,2,3] and nucleic acids [4,5,6]. Recently, we investigated hydration of DNA as a function of its conformation and sequence. We analyzed hydration of DNA dinucleotides from an ensemble of 2,727 non-redundant DNA chains containing 41,853 dinucleotides and 316,265 associated first-shell water molecules [6].
The dinucleotides were classified into categories based on their 16 sequences and the previously determined structural classes, so called nucleotide conformers (NtCs). The construction of hydrated dinucleotide building blocks allowed dinucleotide hydration to be calculated as probability of water density distributions. Peaks in the water densities - Hydration Sites (HSs) - uncovered the interplay between the base and the sugar- phosphate hydration in the context of sequence and structure.
Here, we present the overview of these results and the potential application of the the hydrated building blocks for the prediction of DNA hydration. The data for the hydrated building blocks and the predictions are available for browsing and visualization at the website watlas.datmos.org/watna.