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    DNA denaturation in ionic solution
    (AIP, 2016-05) Singh, Navin
    Salt or cations, present in solution play an important role in DNA denaturation and folding kinetics of DNA helix. In this work we study the thermal melting of double stranded DNA (dsDNA) molecule using Peyrard Bishop Dauxois (PBD) model. We modify the potential of H-bonding between the bases of the complimentary strands to introduce the salt and solvent effect. We choose different DNA sequences having different contents of GC pairs and calculate the melting temperatures. The melting temperature increases logarithmically with the salt concentration of the solution. The more GC base pairs in the chain enhance the stability of DNA chain at a fix salt concentration. The obtained results are in good accordance with experimental findings.
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    Molecular crowding effects on stability of DNA double helix
    (AIP, 2016-05) Singh, Navin
    Cellular environmental conditions critically affect the structure and stability of double stranded DNA (dsDNA) molecule. It is known that 20-30% of the total volume of the cell is occupied by the molecular crowders. The presence of these crowders, reduces the free space available to the base pairs of a DNA molecule, hence the movement of base pair is restricted. Here, we study the thermal opening of dsDNA molecule using Peyrard Bishop Dauxois (PBD) model. The presence of crowders in the model, that mimic those found in the cell nucleus, is realized through the potential term. Using the equilibrium statistical calculations, we find melting profile and melting probabilities of the chain. The opening of DNA molecule in the presence of these crowders is shown through the density plots. This study reveals that the stability of dsDNA molecule is influenced by entropic as well as enthalpic effects and is more stable in the crowded environment.
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    DNA melting in the presence of molecular crowders
    (RSC, 2017-07) Singh, Navin
    We study the opening of double stranded DNA (dsDNA) in the presence of molecular crowders using the Peyrard–Bishop–Dauxois (PBD) model. It is a known fact that about 15–20% of the total volume of a cell is occupied by molecular crowders. The presence of crowders in the model is represented through the potential depth in the Morse potential. Using equilibrium statistical calculations we find the melting profile and the melting probabilities of the chain. We found that the melting temperature, Tm, increases in the presence of a crowder. This is due to the fact that the crowders occupy a substantial amount of the system volume and hence reduce the free volume available to the DNA molecule. This restricts the free movement of base pairs and hence the DNA molecule, which results in an increase in the melting temperature of the DNA molecule. We also find a correlation between the melting temperature and the crowder density of the solution. The power law behaviour shows that the melting temperature scales linearly with the crowder density. At a given density, a higher density of crowder may suppress the free movement in the DNA molecule, which will increase Tm. Although the temperature changes occurring in vitro seem to be smaller than those observed in this work, the results demonstrate interesting features of the opening of DNA molecules in crowded environments.