  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.
