Overstretching of B-DNA with various pulling protocols: Appearance of structural polymorphism and S-DNA

TL;DR

This study uses molecular dynamics simulations to explore how different pulling protocols induce structural polymorphism in overstretched B-DNA, revealing the formation of S-DNA and other structural states with detailed molecular insights.

Contribution

It provides a detailed molecular understanding of DNA overstretching mechanisms and characterizes the structural polymorphism of S-DNA under various pulling protocols.

Findings

S-DNA forms under OS3 protocol with ~10° twist

Force-induced melting occurs under OS5 protocol

Higher free energy barrier observed for SE protocol

Abstract

We report a structural polymorphism of the S-DNA when a canonical B-DNA is stretched under different pulling protocols and provide a fundamental molecular understanding of the DNA stretching mechanism. Extensive all atom molecular dynamics simulations reveal a clear formation of S-DNA when the B-DNA is stretched along the 3' directions of the opposite strands (OS3) and is characterized by the changes in the number of H-bonds, entropy and free energy. Stretching along 5' directions of the opposite strands (OS5) leads to force induced melting form of the DNA. Interestingly, stretching along the opposite ends of the same strand (SS) leads to a coexistence of both the S- and melted M-DNA structures. We also do the structural characterization of the S-DNA by calculating various helical parameters. We find that S-DNA has a twist of ~10 degrees which corresponds to helical repeat length of ~ 36 base pairs in close agreement with the previous experimental results. Moreover, we find that the free energy barrier between the canonical and overstretched states of DNA is higher for the same termini (SE) pulling protocol in comparison to all other protocols considered in this work. Overall, our observations not only reconcile with the available experimental results qualitatively but also enhance the understanding of different overstretched DNA structures.