What size RNA loop holds bulk solvent?

The loss in conformational entropy that results from the closure of a loop in a polymer chain has been derived in cases where the effects of discrete solvent structure inside the loop can be neglected. We show that a pronounced entropic contribution is encountered as the discrete clustering of solvent molecules inside the loop affects the conformations of the chain, forcing the orientation of individual residues. An algorithm for RNA structure prediction incorporating such effects is implemented and tested.