Influence of cyanine dye structure on self-aggregation and interaction with nucleic acids: A kinetic approach to TO and BO binding

Kinetics and equilibria of cyanine dyes thiazole orange (TO) and benzothiazole orange (BO) self-aggregation and binding to CTDNA are investigated in aqueous solution at 25 C and pH 7. Absorbance spectra and T-jump experiments reveal that BO forms J-aggregates while TO forms more stable H-aggregates. Fluorescence and absorbance titrations show that TO binds to DNA more tightly than BO. TO stacks externally to DNA for low polymer-to-dye concentration ratios (C-P/C-D) while dye intercalation occurs for high values of CP/CD. T-jump and stopped-flow experiments performed at high CP/CD agree with reaction scheme D+S reversible arrow D,S reversible arrow: DSI reversible arrow DSII where the precursor complex D,S evolves to a partially intercalated complex DS, which converts to the more stable intercalate DSII. Non-electrostatic forces play a major role in D,S stabilization. Last step is similar for both dyes suggesting accommodation of the common benzothiazole residue between base pairs. Experiments using poly(dA-dT)-poly(dA-dT) and poly(dG-dC)-poly(dG-dC) confirm base pair preference for TO. (c) 2007 Elsevier Inc. All rights reserved.