Multiple timescales in a model for DNA denaturation dynamics

TL;DR

This paper models DNA denaturation dynamics revealing two distinct timescales related to bubble formation and coalescence, highlighting the importance of local conservation and boundary conditions in the process.

Contribution

It introduces a Poland-Scheraga type model with local conservation of linking, demonstrating the emergence of multiple timescales in DNA denaturation dynamics.

Findings

Two characteristic timescales scale with chain length as L^{2.15} and L^{3}

Slow denaturation involves bubble formation and coalescence leading to entropic barriers

The model differs from previous approaches neglecting helical constraints

Abstract

The denaturation dynamics of a long double-stranded DNA is studied by means of a model of the Poland-Scheraga type. We note that the linking of the two strands is a locally conserved quantity, hence we introduce local updates that respect this symmetry. Linking dissipation via untwist is allowed only at the two ends of the double strand. The result is a slow denaturation characterized by two time scales that depend on the chain length $L$. In a regime up to a first characteristic time $\tau_1\sim L^{2.15}$ the chain embodies an increasing number of small bubbles. Then, in a second regime, bubbles coalesce and form entropic barriers that effectively trap residual double-stranded segments within the chain, slowing down the relaxation to fully molten configurations, which takes place at $\tau_2\sim L^3$. This scenario is different from the picture in which the helical constraints are neglected.