Mutual interaction between adjacent dG . dC actinomycin binding sites and dA . dT netropsin binding sites on the self-complementary d(C-G-C-G-A-A-T-T-C-G-C-G) duplex in solution.

Abstract

The Watson-Crick imino protons, the backbone phosphodiester resonances, and the antibiotic exchangeable protons have been used as markers to monitor the separate and simultaneous binding of actinomycin and netropsin to the d(C-G-C-G-A-A-T-T-C-G-C-G) self-complementary duplex in aqueous solution. We demonstrate that intercalation of actinomycin at dG(3'-5')dC sites at either end of the duplex results in a conformational perturbation at the dA . dT tetranucleotide core of the dodecanucleotide duplex. Parallel studies of the groove binding of netropsin at dA . dT sites in the interior of the duplex reveal a conformational perturbation which extends to adjacent dG . dC base pairs in the dodecanucleotide duplex. The NMR markers demonstrate that the d(C-G-C-G-A-A-T-T-C-G-C-G) duplex can accommodate actinomycin and netropsin simultaneously at adjacent dG . dC and dA . dT tetranucleotide blocks along its length with some mutual interaction between neighboring antibiotic binding sites.