Unfolding and unzipping of single-stranded DNA by stretching

TL;DR

This paper presents a theoretical framework for understanding how single-stranded DNA responds to stretching, revealing phase transitions and crossovers that depend on the molecule's elastic properties and hairpin loop energetics.

Contribution

It introduces a versatile theoretical approach to study ssDNA mechanics, incorporating basepairing effects with various chain elasticity models, and highlights the sensitivity of unzipping behavior to hairpin loop energetics.

Findings

Stretching curve shows unfolding phase transition and unzipping crossover.

Variation in unzipping crossover width depends on hairpin loop energetics.

The theory applies to different chain models, revealing universal and model-dependent features.

Abstract

We present a theoretical study of single-stranded DNA under stretching. Within the proposed framework, the effects of basepairing on the mechanical response of the molecule can be studied in combination with an arbitrary underlying model of chain elasticity. In a generic case, we show that the stretching curve of ssDNA exhibits two distinct features: the second-order "unfolding" phase transition, and a sharp crossover, reminiscent of the first-order "unzipping" transition in dsDNA. We apply the theory to the particular cases of Worm-like Chain (WLC) and Freely-Joint Chain (FJC) models, and discuss the universal and model--dependent features of the mechanical response of ssDNA. In particular, we show that variation of the width of the unzipping crossover with interaction strength is very sensitive to the energetics of hairpin loops. This opens a new way of testing the elastic properties of ssDNA.