Tension propagation during DNA hairpin folding

Abstract

Characterization of DNA/RNA folding dynamics is an interesting problem involving the complex force balance between the relaxation of the growing duplex and the stretched single-stranded segments. In a previous paper, we reported that the helicity plays an important role in determining the folding time for a chain of size N, where is the Flory exponent. Here we analyze this process in further detail by using molecular dynamics, with particular emphasis on tension propagation along a single strand on the unfolded segment. We directly observe that the single-strand segments are always stretched during the folding process by the tension induced by base pair formation, propagating ahead of the y?-junction. Our molecular dynamics simulations verify the existence of a stem-flower structure in the unfolded segments, with a power-law dependence of the stem length N-s on the duplex length n. For the longest hairpin structures considered, we also find that the power-law regime terminates before the first half of the folding is completed. We demonstrate that the structure?s helicity is an integral aspect of the folding dynamics by comparing our findings with those obtained from a hypothetical non-helical model.