Conformational transitions of a DNA hairpin through transition path times

Abstract

The stochastic dynamics of zipping/unzipping transition of a DNA hairpin is theoretically investigated within the framework of generalized Langevin equation in a complex cellular environment. Analytical expressions of the distributions of transition path and first passage times are derived. The results reveal that the transition path time of DNA is shorter compared to the Kramers’s first passage time. Especially, the transition path time depicts an unexpected behavior as it decreases with an increase in the height of the barrier, while the first passage time reveals an exactly opposite trend. Both mean first passage time and mean transition path time increases with an increase in the complexity/viscoelasticity of the cellular environment due to the caging effect of the hairpin. Our results for the free energy landscape, probability density, transition path time distribution and the mean transition path time of the DNA hairpin are in good agreement with those obtained from experiments and other theoretical studies.