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Using molecular dynamics simulations, we study the effect of pressure on thebinding propensity of small RNAs by calculating the free energy barriercorresponding to the looped out conformations of unmatched base, whichpresumably acts as the binding sites for ligands. We find that the free energyassociated with base looping out increases monotonically as the pressure isincreased. Furthermore, we calculate the mean first passage time ofconformational looping out of the base bulge using the diffusion of reactioncoordinate associated with the base flipping on the underlying free energysurface. We find that the mean first passage time associated with bulge loopingout increases slowly upon increasing pressures $P$ upto $2$~kbar but changesdramatically for $P>2$~kbar. Finally, we discuss our results in the light ofthe role of hydration shell of water around RNA.

Effect of pressure on the kinetics of bulge bases in small RNAs