Kinetics for exchange of the imino protons of the d(C-G-C-G-A-A-T-T-C-G-C-G) double helix in complexes with the antibiotics netropsin and/or actinomycin

Abstract

The lifetimes for exchange of the amino protons in the dodecanucleotide d(C-G-C-G-A-A-T-T-C-G-C-G) upon binding of netropsin and/or actinomycin were measured by proton NMR experiments. At high temperature these lifetimes measured the lifetimes for opening of the base pairs in the double helix. Comparison of the opening rates in the dodecamer with those in the complex with netropsin (which binds at the -A-A-T-T- sequence) showed that there is a large kinetic stabilization of the A .cntdot. T base pairs at the binding site and a significant stabilization of the G .cntdot. C base pairs adjacent to the netropsin binding site. For the complex with actinomycin, which intercalates at the G-C sites in the double strand, the lifetimes of the base pairs at the binding site increase upon binding of actinomycin; the A .cntdot. T base pairs in the central core are slightly kinetically destabilized by the actinomycin binding. The activation energies for exchange of the imino protons were measured in the complexes and indicate that the mechanism for exchange of the imino protons is individual base-pair opening, where one base pair opens independently of the others. The effects of drug binding on the dynamics of individual base pairs in a double-stranded helix are discussed.