Melting behavior and different bound states in three-stranded DNA models

TL;DR

This study investigates the melting behavior of three-stranded DNA models on a Sierpinski gasket, revealing the existence of Efimov-DNA-like states and a novel mixed phase where strands are pairwise bound without three-chain contacts.

Contribution

It demonstrates the presence of Efimov-DNA-like states and a new mixed phase in three-stranded DNA models on fractal lattices, expanding understanding of DNA melting phenomena.

Findings

Efimov-DNA-like states are observed near melting.

A new mixed phase with pairwise but not three-chain binding is identified.

Efimov-DNA is a crossover, while the mixed phase is a true thermodynamic phase.

Abstract

Thermal denaturation of DNA is often studied with coarse-grained models in which native sequential base pairing is mimicked by the existence of attractive interactions only between monomers at the same position along strands (Poland and Scheraga models). Within this framework, the existence of a three strand DNA bound state in conditions where a duplex DNA would be in the denaturated state was recently predicted from a study of three directed polymer models on simplified hierarchical lattices ($d>2$) and in $1+1$ dimensions. Such phenomenon which is similar to the Efimov effect in nuclear physics was named Efimov-DNA. In this paper we study the melting of the three-stranded DNA on a Sierpinski gasket of dimensions $d<2$ by assigning extra weight factors to fork openings and closings, to induce a two-strand DNA melting. In such a context we can find again the existence of the Efimov-DNA-like state but quite surprisingly we discover also the presence of a different phase, to be called a mixed state, where the strands are pair-wise bound but without three chain contacts. Whereas the Efimov DNA turns out to be a crossover near melting, the mixed phase is a thermodynamic phase.