A lattice polymer study of DNA renaturation dynamics

Abstract

DNA renaturation is the recombination of two complementary single strands to form adouble helix. It is experimentally known that renaturation proceeds through theformation of a double-stranded nucleus of several base pairs (the rate limitingstep) followed by a much faster zippering. We consider a lattice polymer modelundergoing Rouse dynamics and focus on the nucleation of two diffusing strands.We study numerically the dependence of various nucleation rates on the strandlengths and on an additional local nucleation barrier. When the local barrier issufficiently high, all renaturation rates considered scale with the length as predicted byKramers’ rate theory and are also in agreement with experiments: their scalingbehavior is governed by exponents describing equilibrium properties of polymers.When the local barrier is lowered, renaturation occurs in a regime of genuinenon-equilibrium behavior and the scaling deviates from the rate theory prediction.