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

Biophysical Journal
Neeraj J AgrawalP K Purohit

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. 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...Continue Reading

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Citations

Jul 3, 2009·Physical Biology·Kevin B TowlesPhilip C Nelson
Jun 3, 2010·The European Physical Journal. E, Soft Matter·N B BeckerR Everaers
Aug 15, 2014·Nucleic Acids Research·Tung T Le, Harold D Kim
Feb 15, 2012·Acta Biomaterialia·David Argudo, Prashant K Purohit
Apr 12, 2016·Methods : a Companion to Methods in Enzymology·Jiyoun JeongHarold D Kim
Aug 7, 2013·Journal of Nanotechnology in Engineering and Medicine·Portonovo S AyyaswamyRavi Radhakrishnan
Jan 15, 2011·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Ludovica Cotta-Ramusino, John H Maddocks
May 14, 2016·Physical Review. E·James T Waters, Harold D Kim
Aug 15, 2015·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Gary R MarpleShravan Veerapaneni

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