Mesoscopic helical models for DNA

TL;DR

This paper introduces a mesoscopic 3D Hamiltonian model for DNA that balances detail and computational efficiency, enabling the prediction of thermodynamic and structural properties of DNA in solution.

Contribution

It presents a novel intermediate mesoscopic approach and a computational method based on path integrals to model DNA's stability and flexibility.

Findings

The model accurately predicts DNA thermodynamics.

The statistical method effectively sets fluctuation amplitude.

Application results align with experimental data.

Abstract

Nucleic acids physical properties have been investigated by theoretical methods based both on fully atomistic representations and on coarse grained models, e.g. the worm-like-chain, taken from polymer physics. In this article, I present an intermediate (mesoscopic) approach and show how to build a three dimensional Hamiltonian model which accounts for the main interactions responsible for the stability of the helical molecules. While the 3D mesoscopic model yields a sufficiently detailed description of the helix at the level of the base pair, it also allows one to predict the thermodynamical and structural properties of molecules in solution. Relying on the idea that the base pair fluctuations can be conceived as trajectories, I have built a computational method based on the time dependent path integral formalism to derive the partition function. While the main features of the method are presented, I focus here in particular on a newly developed statistical method to set the maximum amplitude of the base pair fluctuations, a key parameter of the theory. Some applications to the calculation of DNA flexibility properties are discussed together with the available experimental data.