A Computational Model to Determine the Effect of Interconnecting Hydrogen Bonds in DNA Deformation

Abstract

FEM model of the double helical structure of the DNA together with the interconnecting hydrogen bonds is developed in this work. The results of the FEM model is compared with the simplistic equivalent rod model. Simulations for deformations under axial, torsional, radial and bending loading are performed. The action of enzymes on DNA can be assumed to be in the form of combination of these loadings. Normalized results of axial, torsional, radial and bending stiffness are computed. The effect of hydrogen bond stiffness on these quantities is analysed. From the results obtained it is inferred that though the hydrogen bond stiffness value has no effect on the axial and torsional stiffness, the radial and the bending stiffness are affected by the hydrogen bonds. Beyond a critical value of the bond stiffness it is observed that the bending and radial stiffness undergo a rapid change and stabilize to a higher value. The results obtained from the present work thus identify the parameter regimes of applicability ...