Stretching force dependent transitions in single stranded DNA

TL;DR

This paper introduces a new model for single stranded DNA, specifically polydA, that explains its force-extension behavior and predicts reentrant temperature-extension phenomena, aligning with experimental data.

Contribution

A novel model combining helix-coil and overstretching transitions for polydA, accurately reproducing experimental force-extension behaviors and predicting new temperature-dependent effects.

Findings

Model reproduces experimental force-extension plateaus.

Predicts reentrant temperature-extension behavior.

Matches observed loop closing time scaling.

Abstract

Mechanical properties of DNA, in particular their stretch dependent extension and their loop formation characteristics, have been recognized as an effective probe for understanding the possible biochemical role played by them in a living cell. Single stranded DNA (ssDNA), which, till recently was presumed to be an simple flexible polymer continues to spring surprises. Synthetic ssDNA, like polydA (polydeoxyadenosines) has revealed an intriguing force-extension (FX) behavior exhibiting two plateaus, absent in polydT (polydeoxythymidines) for example. Loop closing time in polydA had also been found to scale exponentially with inverse temperature, unexpected from generic models of homopolymers. Here we present a new model for polydA which incorporates both a helix-coil transition and a over-stretching transition, accounting for the two plateaus. Using transfer matrix calculation and Monte-Carlo simulation we show that the model reproduces different sets of experimental observations, quantitatively. It also predicts interesting reentrant behavior in the temperature-extension characteristics of polydA, which is yet to be verified experimentally.