Kinetics of the interaction of acridine dyes with nucleic acids. An iodine-laser temperature-jump investigation

Abstract

The intercalation reaction of 9-aminoacridine, acriflavine, acridine orange, proflavine and ethodin into nucleic acids has been studied kinetically using the iodine-laser temperature-jump (ILTJ) technique with fluorescence detection, avoiding interference by transient electric fields. If the interaction with calf-thymus DNA (AT-rich) is considered, two main groups of dyes may be distinguished: 9-aminoacridine, acriflavine and acridine orange showed a linear correlation of the reciprocal relaxation times with DNA phosphate concentration, while proflavine and ethodin were characterized by a levelling off of the relaxation times at large DNA concentrations. On the other hand, proflavine and ethodin showed a linear dependence when Micrococcus lysodeikticus DNA (GC-rich) was used. A model for the interpretation of the experimental results has been proposed which assumes two main types of binding sites, related to GC- or AT-base pairs, for intercalation and a two-step mechanism in both cases. Rapid external binding precedes insertion between base pairs. The outer complex appears to be mainly electrostatic when attached to GC-sites, while it is much stronger with AT-sites. The nature of this extra stabilization has been discussed, together with structure–mechanism relationships.