Symmetry and asymmetry in the unwinding of nucleic acids

The forming and melting of complementary base pairs in RNA and DNA duplexes are conformational transitions re- quired to accomplish a plethora of biological functions. Using fully atomistic simulation we have shown that RNA unwind- ing occurs by a stepwise process in which the probability of unbinding of the base on the 5’ strand is significantly higher than that on the 3’ strand [Colizzi and Bussi JACS, 2012]. The asymmetry in the RNA unwinding dynamics is compli- ant with the mechanism of helicase activity shown by proto- typical DEx(H/D) RNA helicases and could allow decipher- ing the basis of the evolutionary pressure responsible for the unwinding mechanism catalyzed by RNA-duplex processing enzymes. In this spirit and from a broader standpoint, here we use a topology-based coarse-grain model to compare and characterize the mechanism of unwinding for both DNA and RNA. The (a)symmetric behavior of the 3’- and 5’-strand could be related to the (bi)directionality observed in molecular machineries processing nucleic acids.