Effect of defects on thermal denaturation of DNA oligomers

Abstract

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

Pulling short DNA molecules having defects on different locations

“…Since the nature of each chain is different, the number and location of these defects may modify the melting profile of the chain in different manner. The melting temperature, T m is calculated by the peak in the specific heat as well as from θ as given in [4,13]. For pure chain, we show the melting profile of the chain in Fig.…”

“…The model considers the stretching between the corresponding bases The on-site potential for the defect in a pair is shown by square symbol and dashed (red) line. While for the bases in a pair is represented by the depth of the potential (solid line with black circle), there is no minimum of potential for the defect pair [13].…”

“…Other quantities such as the average fraction θ(= 1 − φ) of bonded (or open) base pairs can be calculated by introducing the dsDNA ensemble(dsDNAE) [8] or using the phenomenological approach [4,13]. In general, the θ is defined as,…”

“…In the absence of the complementary base on the opposite strand, the pairing between the two bases is absent. This site is called a defect site because of an absence of a stable (or non-existing) bonding between these two bases on the opposite strands [13,14]. The presence of defects in DNA is related to interesting physics and biochemistry of the molecule.…”

“…The next task is to introduce the defect in the model. We have continued from our previous approach [13] where the defect in the model was introduced via Morse potential that represent the hydrogen bonding. If a pair has a defect that means there is an absence of hydrogen bond and this feature is reflected from the absence of potential depth while retaining the repulsive part of the potential in order to avoid the crossing of two bases in a pair (see Fig.…”