Molecular Dynamics Simulation of Supercoiled DNA Rings
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Abstract
DNA supercoiling is a widespread
phenomenon in biology. Here we
introduce a coarse-grained DNA model and study supercoiled DNA rings
via a rigid body molecular dynamics simulation. Our model allows us
to investigate these structures in more detail than previously. The
simulations are performed on rings of one to six kilobase pairs length
and are compared to available experimental data and former simulation
studies. The current study provides new additional information about
some of the geometrical parameters of the supercoiled DNA rings. It
also shows how enforcing a supercoiled DNA ring to two-dimensional
space changes its geometrical parameters. Finally, our molecular dynamics
method allows us to observe some dynamical effects like the creation
and movement of supercoiled branches