Loop Dynamics in DNA Denaturation

TL;DR

This paper investigates the dynamics of DNA denaturation loops using scaling and simulations, proposing a method to measure the loop exponent c through fluorescence correlation spectroscopy.

Contribution

It introduces a novel approach combining scaling arguments and simulations to analyze DNA loop dynamics and suggests an experimental technique to determine the loop exponent c.

Findings

Autocorrelation decay relates to the loop exponent c

Method for measuring c via fluorescence correlation spectroscopy

Differences in dynamics between homopolymers and heteropolymers

Abstract

The dynamics of a loop in DNA molecules at the denaturation transition is studied by scaling arguments and numerical simulations. The autocorrelation function of the state of complementary bases (either closed or open) is calculated. The long-time decay of the autocorrelation function is expressed in terms of the loop exponent c both for homopolymers and heteropolymers. This suggests an experimental method for measuring the exponent c using florescence correlation spectroscopy.