Anomalous dynamics of DNA hairpin folding

TL;DR

This study uses computer simulations to reveal that DNA hairpin folding exhibits anomalous dynamics, with folding times scaling non-linearly with hairpin length due to tension-induced friction, challenging traditional zipper model predictions.

Contribution

It demonstrates that DNA hairpin folding dynamics are anomalous and provides a theoretical explanation linking tension-induced friction to non-linear scaling of folding times.

Findings

Folding time scales as N^a with a>1, specifically a=1.59.

Anomalous dynamics arise from tension-induced friction during zippering.

Results align with a simple polymer model prediction.

Abstract

By means of computer simulations of a coarse-grained DNA model we show that the DNA hairpin zippering dynamics is anomalous, i.e. the characteristic time T scales non-linearly with N, the hairpin length: T ~ N^a with a>1. This is in sharp contrast with the prediction of the zipper model for which T ~ N. We show that the anomalous dynamics originates from an increase in the friction during zippering due to the tension built in the closing strands. From a simple polymer model we get a = 1+ nu = 1.59 with nu the Flory exponent, a result which is in agreement with the simulations. We discuss transition path times data where such effects should be detected.