Force Induced DNA Melting

Abstract

When pulled along the axis, double-strand DNA undergoes a large conformational change and elongates roughly twice its initial contour length at a pulling force about 70 pN. The transition to this highly overstretched form of DNA is very cooperative. Applying force perpendicular to the DNA axis (unzipping), double-strand DNA can also be separated into two single-stranded DNA which is a fundamental process in DNA replication. We study the DNA overstretching and unzipping transition using fully atomistic molecular dynamics (MD) simulations and argue that the conformational changes of double strand DNA associated with either of the above mentioned processes can be viewed as force induced DNA melting. As the force at one end of the DNA is increased the DNA start melting abruptly/smoothly after a critical force depending on the pulling direction. The critical force fm, at which DNA melts completely decreases as the temperature of the system is increased. The melting force in case of unzipping is smaller compared to the melting force when the DNA is pulled along the helical axis. In the cases of melting through unzipping, the double-strand separation has jumps which correspond to the different energy minima arising due to different base pair sequence. The fraction of Watson-Crick base pair hydrogen bond breaking as a function of force does not show smooth and continuous behavior and consists of plateaus followed by sharp jumps.