Dynamics of water around RNA

The structures and dynamics of water molecules in the DNA grooves play an important role in the biological function of DNA. As discussed later, the intercalation of the anti-cancer drug daunomycin into DNA is indeed facilitated by water molecules in the grooves. While the role of water molecules in stabilizing a DNA duplex is well known (water molecules screen the electrostatic repulsion between the negatively charged phosphate ions, form HBs with the polar atoms of the nucleic 

Hydration of the grooves is particularly relevant for AT minor grooves because the groove is both narrow and deep. Water molecules are known to form a spine of hydration along the minor grooves. Recent computer simulation studies have quantified the nature of the spine of hydration by using concepts from bulk water. Thus, one has used the tetrahedrality order parameter to demonstrate that the water molecules are indeed partly ice-like. The entropy calculation has further substantiated these observations. 

Being a single strand, RNA is more open to the interaction of water. Unfortunately there exist fewer studies of water dynamics around RNA. Here the structure is relatively less rigid and also more open, allowing water molecules to sustain stronger interactions with the nucleic acids. 

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