Stacking Interactions in Denaturation of DNA Fragments

TL;DR

This paper presents a mesoscopic path integral model for DNA denaturation, linking stacking interactions and backbone stiffness to melting transition features, and introduces methods to analyze base pair opening fractions.

Contribution

It develops a novel path integral approach to model heterogeneous DNA denaturation, emphasizing the role of stacking interactions and backbone stiffness in transition behavior.

Findings

Ensemble size varies with backbone stiffness, affecting melting transition.

Melting transition is a smooth crossover starting from AT-rich regions.

Base pair opening fractions align with specific heat data, indicating multistep denaturation.

Abstract

A mesoscopic model for heterogeneous DNA denaturation is developed in the framework of the path integral formalism. The base pair stretchings are treated as one-dimensional, time dependent paths contributing to the partition function. The size of the paths ensemble, which measures the degree of cooperativity of the system, is computed versus temperature consistently with the model potential physical requirements. It is shown that the ensemble size strongly varies with the molecule backbone stiffness providing a quantitative relation between stacking and features of the melting transition. The latter is an overall smooth crossover which begins from the \emph{adenine-thymine} rich portions of the fragment. The harmonic stacking coupling shifts, along the $T$-axis, the occurrence of the multistep denaturation but it does not change the character of the crossover. The methods to compute the fractions of open base pairs versus temperature are discussed: by averaging the base pair displacements over the path ensemble we find that such fractions signal the multisteps of the transition in good agreement with the indications provided by the specific heat plots.