Statistical mechanics of coil-hairpin transition in a single stranded DNA oligomer

TL;DR

This paper models the coil-hairpin transition in single-stranded DNA using a self-avoiding walk framework, revealing a first-order transition with specific dependencies on loop length and dimensionality.

Contribution

It introduces a novel self-avoiding walk model with constraints to analyze the conformational behavior of DNA hairpins, including detailed enumeration of all possible states.

Findings

Transition is first order with large entropy change.

Unzipping rate is independent of loop length and dimensionality.

Closing rate varies significantly with loop length and space dimension.

Abstract

A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behavior of a short RNA or a single stranded DNA molecule that forms hairpin structure and calculate the properties associated with coil-hairpin transition by enumerating all possible conformations of a chain of N monomers in two and three dimensions. The first and last five monomers of the chain have been allowed to pair and form the stem of the hairpin structure while the remaining monomers can form a loop. The coil-hairpin transition is found to be first order with large entropy change. While the rate of unzipping of the hairpin stem is found to be independent of the length of the loop and the dimensionality of the space, the rate of closing varies greatly with loop length and dimensionality of the space.