Dependence on temperature and GC content of bubble length distributions in DNA

TL;DR

This study investigates how temperature and GC content influence the distribution of bubble lengths in DNA, using numerical models and Monte Carlo simulations to understand their effects on DNA stability and behavior.

Contribution

It provides new numerical insights and simple expressions describing the dependence of DNA bubble length distributions on temperature and GC content.

Findings

Bubble length distribution parameters depend on temperature and GC content.

The average bubble length varies with temperature.

The exponent c in the distribution shows temperature dependence.

Abstract

We present numerical results on the temperature dependence of the distribution of bubble lengths in DNA segments of various guanine-cytosine (GC) concentrations. Base-pair openings are described by the Peyrard-Bishop-Dauxois model and the corresponding thermal equilibrium distributions of bubbles are obtained through Monte Carlo calculations for bubble sizes up to the order of a hundred base pairs. The dependence of the parameters of bubble length distribution on temperature and the GC content is investigated. We provide simple expressions which approximately describe these relations. The variation of the average bubble length is also presented. We find a temperature dependence of the exponent c that appears in the distribution of bubble lengths. If an analogous dependence exists in the loop entropy exponent of real DNA, it may be relevant to understand overstretching in force-extension experiments.