Zippering dynamics of an RNA hairpin: Role of helicity

Despite several computational studies on hairpin folding and some supporting experimental data, role of the helical geometry on hairpin folding dynamics remains mostly unexplored. We here address this question by means of extensive molecular dynamics simulations on helical and (non-helical) "ladder-like" coarse-grained models. It is known that the folding time (τ) of a thermally quenched RNA hairpin depends on the number of base pairs (N) as τ ~ N^α , where α=1+ν is found to fit the experimental data with ν≈ 0.6 (Flory exponent in three dimensions). We find that α changes from 1.6 to 1.2 ( ≈ 2ν) in three dimensions when duplex helicity is removed. Simulations in two dimensions (ν = 0.75) and with a ghost chain (ν = 0.5) further support the hypothesis α=2ν for a "ladder-like" hairpin. The contrast between the two models which have identical single-strand properties suggests that duplex dynamics is a relevant component of the folding process, hence contradicting the theoretical models focusing on the non-equilibrium behavior of the unpaired segments alone. We propose a new scaling argument for α=1+ν in helical chains and an energy argument for α ≧ 2ν.

Ref: H. Li and A. Kabakcioglu, Phys. Rev. Lett, 121(13), 138101 (2018).