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.Comment: 23 pages, 9 figures, accepted for publication in J. Phys.: Condens.
Matte
