Effect of defects on thermal denaturation of DNA oligomers

Abstract

Effect of defects on the melting profile of short heterogeneous DNA chains is calculated using the Peyrard-Bishop Hamiltonian. On-site potential on a defect site is represented by a potential that has only a short-range repulsion and a flat part without well of the Morse potential. Stacking energy between two neigbouring pairs involving a defect site is also modified. The results are found to be in good agreement with the experiments.