Sequence dependencies of DNA deformability and hydration in the minor groove

Yonetani, Yoshiteru; Kono, Hidetoshi

DNA deformability and hydration are both sequence dependent and are essential in specific DNA sequence recognition by proteins. However, their relationship is not well understood. Here, systematic molecular dynamics simulations of the 136 DNA sequences that differ from each other in the central tetramer revealed that sequence dependence of hydration is clearly correlated with that of deformability. We show that the feature of this correlation can be explained by the following four typical cases. Most of rigid base-pair steps are highly likely to form an ordered hydration pattern composed of one water molecule bridging between the bases of distinct strands, but there are a few exceptions which favor another ordered hydration composed of two water molecules participating in the bridge construction. Steps with medium deformability can make both of the hydration patterns with frequent transition. Highly flexible steps do not have any stable hydration pattern. The detailed picture of this correlation demonstrated that motions of hydration water molecules and of DNA bases were tightly coupled with each other at the atomic level. These results are helpful to understand the entropic contribution from water molecules in protein or drug binding and could be applied for predicting the binding sites.