@article{ISI:000418350100041,
 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-DNAis 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 the 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 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 the S-DNA has a twist of
similar to 10 degrees which corresponds to a helical repeat length of
similar to 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 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. Published
by AIP Publishing.},
 article-number = {225102},
 author = {Garai, Ashok and Mogurampelly, Santosh and Bag, Saientan and Maiti,
Prabal K.},
 doi = {10.1063/1.4991862},
 eissn = {1089-7690},
 issn = {0021-9606},
 journal = {JOURNAL OF CHEMICAL PHYSICS},
 month = {DEC 14},
 number = {22},
 orcid-numbers = {Mogurampelly, Santosh/0000-0002-3145-4377
Maiti, Prabal/0000-0002-9956-1136
Garai, Ashok/0000-0003-4558-9528},
 researcherid-numbers = {Garai, Ashok/AAP-3926-2020
Mogurampelly, Santosh/D-3610-2011
Maiti, Prabal/B-6335-2009
Garai, Ashok/Q-5783-2018},
 times-cited = {8},
 title = {Overstretching of B-DNA with various pulling protocols: Appearance of
structural polymorphism and S-DNA},
 unique-id = {ISI:000418350100041},
 volume = {147},
 year = {2017}
}