title: On binding of DNA-bending proteins to DNA minicircles.
abstract: We present a theoretical study of binding of DNA-bending proteins to circular DNA, using computer simulations of the wormlike chain model of DNA. We find that the binding affinity is affected by the bending elasticity and the conformational entropy of the polymer and that while protein adsorption is identical on open and closed long DNA molecules, there is significant enhancement of binding on DNA minicircles, compared to their linear counterparts. We also find that the ratio of the radii of gyration of open and closed chains depends on protein concentration for short DNA molecules. Experimental tests of our predictions are proposed.
authors.affiliation: Department of Physics and Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel. shlomed.uni@gmail.com
authors.forename: Shlomi
authors.initials: S
authors.lastname: Medalion
authors.forename: Yitzhak
authors.initials: Y
authors.lastname: Rabin
mesh_terms: D001665:Binding Sites; D004270:DNA, Circular / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D013816:Thermodynamics
chemical_list: D004270:DNA, Circular; D004268:DNA-Binding Proteins