Urea Destabilizes RNA by Forming Stacking Interactions and Multiple Hydrogen Bonds with Nucleic Acid Bases

Urea has long been used to probe the stability and folding kinetics of proteins.1 In contrast only recently it was shown that the RNA molecules that have a high propensity to misfold can be resolved using moderate amounts of urea.2 Urea titrations can also be used to probe the interactions that stabilize the folded states of RNA.2c Although the mechanism by which urea denatures proteins is now fairly well understood,3 the nature of interactions by which urea destabilizes RNA is not known. To provide a microscopic basis for the action of urea on RNA we have carried out extensive all atom molecular dynamics (MD) simulations on two RNA constructs using two urea force fields. Destabilization of RNA is due to disruption of base-pair interactions by direct hydrogen bonding of urea with the bases. The simulations also reveal a novel mechanism in which urea molecules engage in stacking interactions with the purine bases.