Dynamics of DNA Melting

TL;DR

This paper investigates the dynamics of DNA melting, focusing on loop behavior at the denaturation transition, and proposes a method to measure the entropy exponent through single-molecule experiments.

Contribution

It introduces a scaling approach to analyze DNA loop dynamics and validates it with microscopic and toy models, suggesting experimental measurement techniques.

Findings

Asymptotic autocorrelation behavior depends on the entropy exponent c.

Scaling argument is validated with microscopic and toy models.

Proposes a method to measure the entropy exponent experimentally.

Abstract

The dynamics of loops at the DNA denaturation transition is studied. A scaling argument is used to evaluate the asymptotic behavior of the autocorrelation function of the state of complementary bases (either open or closed). The long-time asymptotic behavior of the autocorrelation function is expressed in terms of the entropy exponent, c, of a loop. The validity of the scaling argument is tested using a microscopic model of an isolated loop and a toy model of interacting loops. This suggests a method for measuring the entropy exponent using single-molecule experiments such as florescence correlation spectroscopy.