Healing Length and Bubble Formation in DNA

TL;DR

This paper links DNA bubble formation probability to a healing length related to base-pair defects, providing a simple way to calculate bubble sizes at various temperatures, verified through statistical modeling.

Contribution

It introduces a physical interpretation of the healing length in DNA bubbles and offers a computationally efficient method for their analysis.

Findings

Derived a relation between bubble formation probability and healing length.

Provided a simple criteria to calculate bubble sizes for any temperature.

Validated the approach with exact statistical calculations of the Peyrard-Bishop-Dauxois model.

Abstract

We have recently suggested that the probability for the formation of thermally activated DNA bubbles is, to a very good approximation, proportional to the number of soft AT pairs over a length L(n) that depend on the size $n$ of the bubble and on the temperature of the DNA. Here we clarify the physical interpretation of this length by relating it to the (healing) length that is required for the effect of a base-pair defect to become neligible. This provides a simple criteria to calculate L(n) for bubbles of arbitrary size and for any temperature of the DNA. We verify our findings by exact calculations of the equilibrium statistical properties of the Peyrard-Bishop-Dauxois model. Our method permits calculations of equilibrium thermal openings with several order of magnitude less numerical expense as compared with direct evaluations.