Lengthscales and Cooperativity in DNA Bubble Formation

TL;DR

This paper investigates how the probability of DNA bubble formation depends on soft AT pairs and bubble size, using a statistical physics model to analyze the process relevant to genetic functions.

Contribution

It introduces a transfer integral approach to accurately analyze the Peyrard-Bishop-Dauxois model for DNA bubbles, highlighting the role of AT pairs in bubble formation.

Findings

Bubble formation probability is regulated by the number of soft AT pairs.

The size of the bubbles is comparable to the length of regions with specific AT content.

The transfer integral method effectively calculates the model's equilibrium properties.

Abstract

It appears that thermally activated DNA bubbles of different sizes play central roles in important genetic processes. Here we show that the probability for the formation of such bubbles is regulated by the number of soft AT pairs in specific regions with lengths which at physiological temperatures are of the order of (but not equal to) the size of the bubble. The analysis is based on the Peyrard- Bishop-Dauxois model, whose equilibrium statistical properties have been accurately calculated here with a transfer integral approach.