Prompt Non-Stacking Binding of Actinomycin D to Hairpin Oligonucleotide HP1 and Slow Redistribution from HP1 to DNA

Abstract

Complexes of actinomycin D (AMD) and 7-amino-actinomycin D (7AAMD) with model hairpin oligonucleotide HP1 and various types of DNA in aqueous solutions were investigated by steady-state, polarized, time-resolved and stopped-flow fluorimetry, and photometry. Prompt non-stacking binding of the actinomycins inside HP1 was observed. No energy transfer from nucleotides to 7AAMD in the complex was detected, most likely because of the absence of stacking intercalation. Complex formation of AMD or 7AAMD and HP1 was followed by the transition from a random flexible conformation of the hairpin to a more compact rigid structure, and subsequently to hypochromism. Strong competition between AMD and 7AAMD for a cavity in HP1 was observed. The decrease in the 7AAMD emission after addition of DNA to the 7AAMD/HP1 complex indicates that actinomycins can be redistributed from HP1 to DNA, i.e. hairpin oligonucleotides can serve as molecular carriers of actinomycins.