Denaturation Patterns in Heterogeneous DNA

TL;DR

This paper uses path integral techniques to analyze the thermodynamics of heterogeneous DNA denaturation, revealing a smooth, multistep transition driven by AT-rich regions and linking microscopic fluctuations to macroscopic thermodynamic signatures.

Contribution

It introduces a path integral approach to model DNA denaturation, capturing the cooperative effects and multistep transition behavior in heterogeneous sequences.

Findings

Denaturation shows peaks in specific heat and continuous entropy growth.

Base pair opening occurs as a smooth crossover influenced by fluctuations.

AT-rich regions drive the multistep denaturation transition.

Abstract

The thermodynamical properties of heterogeneous DNA sequences are computed by path integral techniques applied to a nonlinear model Hamiltonian. The base pairs relative displacements are interpreted as time dependent paths whose amplitudes are consistent with the model potential for the hydrogen bonds between complementary strands. The portion of configuration space contributing to the partition function is determined, at any temperature, by selecting the ensemble of paths which fulfill the second law of thermodynamics. For a short DNA fragment, the denaturation is signaled by a succession of peaks in the specific heat plots while the entropy grows continuously versus $T$. Thus, the opening of the double strand with bubble formation appears as a smooth crossover due to base pair fluctuation effects which are accounted for by the path integral method. The multistep transition is driven by the AT-rich regions of the DNA fragment. The base pairs path ensemble shows an enhanced degree of cooperativity at about the same temperatures for which the specific heat peaks occur. These findings establish a link between microscopic and macroscopic signatures of the transition. The fractions of mean base pair stretchings are computed by varying the AT base pairs content and taking some threshold values for the occurrence of the molecule denaturation.