Dynamics of Hydrogen Bonds Coupling on the Specific DNA-Protein Interactions

TL;DR

This paper introduces a dynamical model for DNA-protein interactions emphasizing hydrogen bond coupling, which explains site-specific binding and DNA bubble formation, relevant for genetic information transfer.

Contribution

The study presents a novel Hamiltonian-based model incorporating hydrogen bond coupling to simulate DNA-protein interaction dynamics and DNA bubble propagation.

Findings

Model demonstrates breather excitations linked to DNA bubbles

Coupling dynamics influence DNA renaturation processes

Feasibility shown for hybridization modeling

Abstract

We propose a dynamical model depicting the interactions between DNA and a specific binding protein involving long range transmissions. The dynamics rely on the coupling between Hydrogen bonds formed between DNA and protein and between the base pairs because they account for site specificity of the binding. We adopt the Morse potential with coupling terms to construct the Hamiltonian. This model gives rise to a breather excitation, corresponding to the DNA bubble formation, which propagates as the carrier of genetic information. We examine the various kind of possible coupling dynamics and suggest the model feasibility in depicting the renaturation or hybridization processes.