Hydration of RNA base pairs

Abstract

The hydration patterns around the RNA Watson-Crick and non-Watson-Crick base pairs in crystals are analyzed and described. The results indicate that (i) the base pair hydration is mostly "in-plane"; (ii) eight hydration sites surround the Watson-Crick G-C and A-U base pairs, with five in the deep and three in the shallow groove, an observation which extends the characteristic isostericity of Watson-Crick pairs; (iii) while the hydration around G-C base pairs is well defined, the hydration around A-U base pairs is more diffuse; (iv) the hydration sites close to the phosphate groups are the best defined and the most recurrent ones; (v) a string of water molecules links the two shallow groove 2'-hydroxyl groups, and (vi) the water molecules fit into notches, the size and accessibility of which are almost as important as the number and strength of the hydrophilic groups lining the cavity. Residence times of water molecules at specific hydration sites, inferred from molecular dynamics simulations, are discussed in the light of present data.