title: Relation between the change in DNA elasticity on ligand binding and the binding energetics.
abstract: The widespread use of tweezers for measurement of ligand-DNA binding parameters is based on the McGhee-von Hippel treatment of the DNA contour and persistence length as a function of concentration. The McGhee-von Hippel approach contains the basic assumption that the binding constant K is independent of the number of already bound ligands. However, the change in elasticity of DNA on binding affects the entropic part of the Gibbs free energy and, hence, the K value in a concentration-dependent manner, making the whole approach inconsistent. In the present work we show that the energetic effect of DNA stiffening on noncovalent binding of small ligands is negligible with respect to the net energy of reaction, whereas the DNA stiffening on binding of large ligands must always be considered in each particular case.
authors.affiliation: Department of Physics, Sevastopol National Technical University, Universitetskaya street 33, Sevastopol, 99053, Ukraine.
authors.forename: Viktor V
authors.initials: VV
authors.lastname: Kostjukov
authors.forename: Maxim P
authors.initials: MP
authors.lastname: Evstigneev
mesh_terms: D004247:DNA / Q000378:metabolism*; D004548:Elasticity; D008024:Ligands; D008954:Models, Biological; D013816:Thermodynamics
chemical_list: D008024:Ligands; D004247:DNA