Oscillatory transients in DNA hairpin unwinding: Effect of thermal and mechanical jumps.

Abstract

The nonequilibrium behavior of many bio-materials under classical jump experiments, in which the system is subject to an instantaneous increase of controlled intensive variables, is poorly studied. Here, we study the response to such jumps of a short DNA hairpin, that possesses a bubble-generating block, in which we assume an initially equilibrated DNA. In particular, we impose temperature-jump (T-jump) and force-jump (F-jump) at various strengths and follow the DNA denaturation in time. We show how partial opening states, which can be also detected in equilibrium at various temperatures and forces, are transiently populated during the equilibration process. In combined large T- and F-jumps, we demonstrate an overshoot in the opening process, in which the middle bubble re-closes transiently after its initial opening, before opening up again permanently. Such an oscillatory behavior has been previously observed in soft-matter systems, but not in DNA, and can have consequences on the intracellular opening processes of DNA.