Stretching of a single-stranded DNA: Evidence for structural transition

TL;DR

This paper investigates the force-extension behavior of single-stranded DNA, revealing a structural transition evidenced by a multi-step plateau in the force-extension curve, which cannot be explained solely by base stacking interactions.

Contribution

The study introduces a model incorporating helix formation and phosphate distance changes, providing a qualitative explanation for experimental force-extension features of ssDNA.

Findings

Force-extension curves differ between poly(dA) and poly(dT)

Base stacking alone does not explain experimental data

Structural transition indicated by multi-step plateau in F-x curve

Abstract

Recent experiments have shown that the force-extension (F-x) curve for single-stranded DNA (ssDNA) consisting only of adenine [poly(dA)] is significantly different from thymine [poly(dT)]. Here, we show that the base stacking interaction is not sufficient to describe the F-x curves as seen in the experiments. A reduction in the reaction co-ordinate arising from the formation of helix at low forces and an increase in the distance between consecutive phosphates of unstacked bases in the stretched state at high force in the proposed model, qualitatively reproduces the experimentally observed features. The multi-step plateau in the F-x curve is a signature of structural change in ssDNA.