Statistical Mechanics of thermal denaturation of DNA oligomers

Details Statistical Mechanics of thermal denaturation of DNA oligomers Statistical Mechanics of thermal denaturation of DNA oligomers

2004-05-07

arxiv.org/abs/cond-mat/0405135v1

Physics

Condensed Matter

Soft Condensed Matter

Appeared in Proceeding of Conference on "Liquid Crystals and other Soft materials", held at RRI, Bangalore India

Scientific paper

Double stranded DNA chain is known to have nontrivial elasticity. We study the effect of this elasticity on the denaturation profile of DNA oligomer by constraining one base pair at one end of the oligomer to remain in unstretched (or intact) state. The effect of this constraint on the denaturation profile of the oligomer has been calculated using the Peyrard-Bishop Hamiltonian. The denaturation profile is found to be very different from the free (i.e. without the constraint) oligomer. We have also examined how this constraint affects the denaturation profile of the oligomer having a segment of defect sites located at different parts of the chain.

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