Mesoscopic Model for Free Energy Landscape Analysis of DNA sequences

TL;DR

This paper introduces a mesoscopic model combining DNA dynamics with a Brownian particle to analyze free energy landscapes, revealing complex structures linked to biological function in promoter sequences.

Contribution

The novel mesoscopic model enables quantification of binding site strengths and free energy differences in DNA sequences, connecting physical properties to biological activity.

Findings

Free energy landscapes show complex structures in promoter sequences.

Model successfully quantifies free energy differences of binding sites.

Analysis correlates landscape features with biological behavior.

Abstract

A mesoscopic model which allows us to identify and quantify the strength of binding sites in DNA sequences is proposed. The model is based on the Peyrard-Bishop-Dauxois model for the DNA chain coupled to a Brownian particle which explores the sequence interacting more importantly with open base pairs of the DNA chain. We apply the model to promoter sequences of different organisms. The free energy landscape obtained for these promoters shows a complex structure that is strongly connected to their biological behavior. The analysis method used is able to quantify free energy differences of sites within genome sequences.