Stabilizing and destabilizing effects of intercalators on DNA triplexes

Oligonucleotide-directed tripler formation attracts much attention due to its potential usefulness in diagnostic and biotechnological applications (for review, see [1,2]). Among other aspects, the research embraces numerous studies probing the influence of intercalating ligands on tripler stability, The effect of the intercalator on tripler formation and stability is known to depend on nucleotide sequence, type of intercalator and solution conditions (for review, see [3]). The present work is aimed at determining the average number of intercalated ethidium bromide (EtBr) and acridine orange (AO) molecules leading to the most effective stabilization of triplexes, First, fluorescing complexes of intramolecular parallel (recombinant) tripler 5'-d(CATGCTAACT)-L-d(AGTTAGCATG)-L-d(CATGCTAACT)-3' (parARB) and classical antiparallel 5'-(dA)(10)-L-(dT)(10)-L-(dT)(10)-3'(antiATT) (L=-pO(CH2CH2O)(3)p-) with EtBr and AO were characterized, binding constants were obtained and compared to those for homologous DNA duplexes, Then the total EtBr and AO concentrations corresponding to an average of one, two or three intercalated molecules per oligonucleotide were estimated, Thermal denaturation of parARB and antiATT complexes with an average of one, two or three bound molecules was carried out, thermodynamic parameters of the tripler-to-duplex and duplex-to-open-strand transitions were evaluated using a three-state model, The ability of EtBr and AO to stabilize or destabilize both parallel (recombinant) and classical antiparallel triplexes was found to depend strongly on the concentration of bound intercalator, The triplexes were shown to be stabilized by intercalation of the first and second EtBr or AO molecules, while binding of the third intercalator molecule to 10 nucleotide long tripler resulted in significant tripler destabilization. (C) 1997 Federation of European Biochemical Societies.