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Geometry of Mediating Protein Affects the Probability of Loop Formation in DNA

Neeraj J. Agrawal ^*, Ravi Radhakrishnan  and Prashant K. Purohit 

^* Chemical and Biomolecular Engineering, Bioengineering, and Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania

Correspondence: Address reprint requests to Prashant K. Purohit, E-mail: purohit{at}seas.upenn.edu.

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. We observe two important effects that seem to directly depend on the size of the enzyme: 1), the overall propensity of loop formation at any given value of the DNA contour length increases with the size of the enzyme; and 2), the contour length corresponding to the first peak as well as the first well in the probability density functions increases with the size of the enzyme. Additionally, the eigenmodes of the fluctuating shape of the looped DNA calculated from simulations and theory are in excellent agreement, and reveal that most of the fluctuations in the DNA occur in regions of low curvature.