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

Garai, Ashok and Mogurampelly, Santosh and Bag, Saientan and Maiti, Prabal K (2017) Overstretching of B-DNA with various pulling protocols: Appearance of structural polymorphism and S-DNA. In: JOURNAL OF CHEMICAL PHYSICS, 147 (22).

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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.

Item Type:	Journal Article
Publication:	JOURNAL OF CHEMICAL PHYSICS
Publisher:	10.1063/1.4991862
Additional Information:	Copy right for this article belongs to the AMER INST PHYSICS, 1305 WALT WHITMAN RD, STE 300, MELVILLE, NY 11747-4501 USA
Department/Centre:	Division of Physical & Mathematical Sciences > Physics
Date Deposited:	12 Jan 2018 08:59
Last Modified:	12 Jan 2018 08:59
URI:	http://eprints.iisc.ac.in/id/eprint/58695

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