Propagation of elastic waves in DNA
The structure of DNA chains is thought to be made up of discrete repeating units of equal mass which are connected by massless rods of equal length. The equation of motion of each monomer unit is given for propagation of longitudinal waves along a wormlike and homopolymer assumed DNA chain. Besides the frictional force of the harmonic oscillation working on each bead they are subjected also to a Brownian force. By considering the longitudinal vibrations only and no bending a stochastic partial differential equation of second order is derived and the initial as well as the boundary conditions are specified. The standing waves along the length of the DNA polymer cause local zones of stretching and compression; local stretching of bases giving rise to kinks within the structure and consequent drug intercalation. The near neighbour exclusion phenomenon of drug intercalation may be understood also by the propagation of longitudinal sinusoidal waves along the monomer units. Local compression generates premelted regions of DNA which may give rise to conformational fluctuations of helix opening and reclosing (DNA breathing). The analysis of the equation for torsional vibrations in DNA molecule shows that in high salt concentration DNA duplex can oscillate between left handed and right handed helical conformations depending on sequences of nucleic acid bases.
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