Obtaining Quantitative Parameters of DNA-Ligand Cooperative Binding from Persistence Length Measurements

Abstract

Binding of ligands to DNA can be studied by measuring the change of the persistence length of the complex formed, in single-molecule assays. We have measured the persistence length of DNA molecule for cationic and neutral beta-cyclodextrin binding, using optical tweezers. We propose a methodology for persistence length data analysis based on a quenched disorder statistical model and describing the binding isotherm by a Hill-type equation. We obtain an expression for the effective persistence length as a function of total ligand concentration, which fits very well our data of the DNA-cationic beta-cyclodextrin and the DNA-HU protein data available in the literature. The fit returns the values of the local persistence lengths, the dissociation constant and the degree of cooperativity for both sets of data. In both cases the persistence length behaves non-monotonically as a function of total ligand concentration. We discuss some physical mechanisms for these binding processes and their interplay with DNA flexibility.ReferencesM. S. Rocha et al., J. Chem. Phys. 127 (10), 105108 (2007);J. van Noort et al., PNAS 101 (18), 6969 (2004);D. Sagi et al., J. Mol. Biol., 341, 419 (2004).Sponsors: CNPq, Fapemig, Capes, Pronex-Facepe and INCT-FCx