Stretching-force–dependent transitions in single stranded DNA

Abstract

Mechanical properties of DNA, in particular its stretch-dependent extension and loop formation properties, have been recognized as effective probes for understanding possible biochemical roles played by them in a living cell. Single stranded DNA (ssDNA), which till recently was presumed to be a simple flexible polymer continues to spring surprises. Synthetic ssDNA, like polydA (polydeoxyadenosines) have revealed an intriguing force-extension (FX) behavior exhibiting two plateaus, which is absent in polydT (polydeoxythymidines). 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 an overstretching 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, namely FX characteristics and looping behavior, quantitatively. It also predicts a weak, nonmonotonic behavior in the temperature-extension characteristic of polydA.