DNA sequence specific hydration responsible for conformational flexibility; Molecular dynamics simulation on all possible tetramer sequences

Yonetani, Yoshiteru*; Fujii, Satoshi*; Sarai, Akinori*; Kono, Hidetoshi; Go, Nobuhiro

DNA conformation and deformability depend on sequence composition. For example, it is known that a sequence containing contiguous AT steps is more deformable. The variability in DNA conformation and deformability has been believed to be one of important factors in specific recognition of DNA sequence by regulatory proteins. Several factors can be considered to yield the difference in DNA conformation and deformability among distinct DNA sequences. One is the mechanical stiffness inherent in the DNA itself, which is originated from base-pairing hydrogen interactions and base-stacking interactions. Another important factor affecting the DNA conformation and deformability is the hydration. The hydration effect is inevitable when discussing the structural properties of DNA, since DNA is physiologically surrounded by water molecules, and the structure cannot be maintained without water. A characteristic hydration pattern observed for DNA is the spine of water, which is composed of the highly ordered water molecules aligned along the floor of the minor groove. Such a hydration pattern as well as the conformation of DNA is dependent on the sequence. Consequently, the following question arises: How and to what extent does the hydration affect the sequence-dependent deformability of DNA ? To address this question, a comparative study of various DNA sequences is required. Recently, the sequence dependence of DNA conformation and deformability has been studied by MD simulations, where all possible 136 patterns for tetramer were examined. In the present work, we report further analysis of these 136 MD trajectories focused on the hydration water. We compared the both properties of DNA hydration and deformation, and found a possible relationship between them.