Sufficient minimal model for DNA denaturation: Integration of harmonic scalar elasticity and bond energies

TL;DR

This paper presents a simple yet effective model combining elasticity and bond energies to analyze DNA denaturation, accurately capturing free-energy profiles and stable states, and applicable to long DNA sequences with practical computational resources.

Contribution

It introduces a minimal model integrating Gaussian network elasticity with bond energies to study DNA denaturation, accounting for bubble entropy and enabling analysis of long sequences.

Findings

Model agrees with experimental and theoretical data

Able to identify stable and meta-stable denaturation states

Applicable to long DNA sequences (200-800 base pairs)

Abstract

We study DNA denaturation by integrating elasticity -- as described by the Gaussian network model -- with bond binding energies, distinguishing between different base-pair and stacking energies. We use exact calculation, within the model, of the Helmholtz free-energy of any partial denaturation state, which implies that the entropy of all formed bubbles ("loops") is accounted for. Considering base-pair bond removal single events, the bond designated for opening is chosen by minimizing the free-energy difference for the process, over all remaining base-pair bonds. Despite of its great simplicity, for several known DNA sequences our results are in accord with available theoretical and experimental studies. Moreover, we report free-energy profiles along the denaturation pathway, which allow to detect stable or meta-stable partial denaturation states, composed of "bubbles", as local free-energy minima separated by barriers. Our approach allows to study very long DNA strands with commonly available computational power, as we demonstrate for a few random sequences in the range 200-800 base-pairs. For the latter we also elucidate the self-averaging property of the system. Implications for the well known breathing dynamics of DNA are elucidated.