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Author: search.filters.author.Singh, NavinSubject: search.filters.subject.DNA unzipping

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    Force induced unzipping of dsDNA: The solvent effect
    (Physics Express, 2013) Singh, Navin
    The salt concentration of the solution plays an important role in the stabilization of double stranded DNA (dsDNA) molecule. In our work, the Hamiltonian in Peyrard-Bishop Dauxois (PBD) model of a heterogeneous chain has been modified with a stabilizing solvent interaction term. This term strengthens the base pair dissociation energy and stabilizes the hydrogen bonds between complementary strands of dsDNA. To study the effect of salt concentration we have modified the potentials appearing in this model. We investigated the influence of salt concentration on the force required to unzip the chain. The force induced unzipping is studied in both constant extension ensemble (CEE) and constant force ensemble (CFE). We found that the results are independent of choice of the ensembles and are in good agreement with the experimental results
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    Phase diagram of mechanically stretched DNA: The salt effect
    (Elsevier, 2013-05) Singh, Navin
    The cations, in the form of salt, present in a solution containing DNA play a crucial role in the opening of the two strands of DNA. We use a simple non-linear model and investigate the role of these cations on the mechanical unzipping of DNA. The Hamiltonian is modified to incorporate the solvent effect and the presence of these cations in the solution. We calculate the melting temperature as well as the critical force that is required to unzip the DNA molecule as a function of salt concentration of the solution. The phase diagrams are found to be in close agreement with the experimental phase diagrams.
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    Effect of salt concentration on the stability of heterogeneous DNA
    (Elsevier, 2015-02) Singh, Navin
    We study the role of cations on the stability of double stranded DNA (dsDNA) molecules. It is known that the two strands of double stranded DNA (dsDNA) have negative charge due to phosphate group. Cations in the form of salt in the solution, act as shielding agents thereby reducing the repulsion between these strands. We study several heterogeneous DNA molecules. We calculate the phase diagrams for DNA molecules in thermal as well as in force ensembles using Peyrard–Bishop–Dauxois (PBD) model. The dissociation and the stacking energies are the two most important factors that play an important role in the DNA stability. With suitable modifications in the model parameters we investigate the role of cation concentration on the stability of different heterogeneous DNA molecules. The objective of this work is to understand how these cations modify the strength of different pairs or bases along the strand. The phase diagram for the force ensemble case (a dsDNA is pulled from an end) is compared with the experimental results.