Geometry of mediating protein affects the probability of loop formation in DNA.

ABSTRACT: Recent single molecule experiments have determined the probability of loop formation in DNA as a function of the DNA contour length for different types of looping proteins. The optimal contour length for loop formation as well as the probability density functions have been found to be strongly dependent on the type of looping protein used. We show, using Monte Carlo simulations and analytical calculations, that these observations can be replicated using the wormlike-chain model for double-stranded DNA if we account for the nonzero size of the looping protein. The simulations have been performed in two dimensions so that bending is the only mode of deformation available to the DNA while the geometry of the looping protein enters through a single variable which is representative of its size.

SUBMITTER: Agrawal NJ 

PROVIDER: S-EPMC2275674 | biostudies-literature | 2008 Apr

REPOSITORIES: biostudies-literature