Statistical Theory of Force Induced Unzipping of DNA

Abstract

The unzipping transition under the influence of external force of a dsDNA molecule has been studied using the Peyrard-Bishop Hamiltonian. The critical force $F_c(T)$ is found to depend on the potential parameters $k$, represents the stiffness of single strand of DNA and the potential depth $D$. We used constant extension ensemble to calculate the average force needed to stretch a base pair $y$ distance apart. A very large peak around $y=1\mathring{\mathrm{A}}$ is found. The value of $F(y)$ needed to stretch a base pair located far away from the ends of a dsDNA molecule is found twice the value of the force needed to stretch a base pair located at one of the ends to the same distance. The effect of mismatching in the base pairs on the peak height and position is investigated. The formation and behaviour of a loop of Y shape when one of the ends base pair is stretched and a bubble of ssDNA with the shape of "an eye" when a base pair far from ends is stretched are investigated.

Minor changes in figures, published version

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Cited by in corpus (20)

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• Probing the mechanical unzipping of DNA
• The probability analysis of opening of DNA
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• Dynamical versus statistical mesoscopic models for DNA denaturation
• Theoretical and Experimental Investigations of DNA Open States
• Phase diagram of mechanically stretched DNA: The salt effect
• Thermal and mechanical denaturation properties of a DNA model with three sites per nucleotide
• The thermal denaturation of Peyrard-Bishop model with an external potential
• Pulling short DNA molecules having defects on different locations
• Can a double stranded DNA be unzipped by pulling a single strand?: Phases of adsorbed DNA
• Dynamics of a bubble formed in double stranded DNA
• Free energy landscape and characteristic forces for the initiation of DNA unzipping
• Statistical mechanical model for crack growth
• Effect of genome sequence on the force-induced unzipping of a DNA molecule
• Mapping between the order of thermal denaturation and the shape of the critical line of mechanical unzipping in 1-dimensional DNA models
• DNA Unzipping Transition
• Structural Analysis of DNA molecule in a confined shell
• On the Pseudo-Schrödinger Equation approximation of the Transfer-Integral operator for 1-dimensional DNA models