A Theoretical Consideration of the Influence of Selective Binding of Small Ligands on DNA Helix-Coil Transition

Abstract

The influence of small ligands on DNA helix-coil transition is considered theoretically. The ligands are supposed to interact with DNA base pairs reversibly and selectively. The long-range ligand-ligand interactions are taken into account. Simple formulae are derived for calculation of melting curve alteration induced by ligand binding. The proposed theoretical approach requires neither knowledge of nucleotide sequence nor long computation time.

Statistical–mechanical lattice models for protein–DNA binding in chromatin

“…Exact analytical solutions such as the McGhee-von Hippel formula are widely used for the description of in vitro binding experiments. More specific and more general solutions also exist, which consider cooperative interactions between proteins (Zasedatelev et al, 1971), polarity of protein-protein interactions (Nechipurenko et al, 1979;Wolfe and Meehan, 1992), competitions between specific and nonspecific binding on a short DNA oligomer (Tsodikov et al, 2001), electrostatic interactions between the molecules upon binding to the DNA (Rouzina and Bloomfield, 1997), ligand-induced double-helix melting (Lando, 1994), adsorptive phase transitions (Lando and Teif, 2000) DNA condensation induced by binding of multivalent counterions (Maltsev et al, 2006;Teif, 2005) and binding of flexible branched oligopolymers (Horsky, 2008;Nishio and Shimizu, 2005).…”