THE INTERCALATING DYE COMPLEXES WITH PARALLEL '-D(CATGCTAACT)-L-D(AGTTAGCATG)-L-D(CATGCTAACT)-3' AND ANTIPARALLEL 5'-D(A)(10)-L-D(T)(10)-L-D(T)(10)-3' DNA TRIPLEXES

We have shown earlier that oligonucleotides 5'-d(CATGCTAACT)-L-d(AGTTA GCATG)-L-(CATGCTAACT)-3' (parARB) and 5'-d(A)(10)-L-d(T)(10)-L-d(T)(10 )-3' (antiATT), where L = pO(CH2CH2O)(3)p, form intramolecular paralle l and antiparallel triplexes, respectively. In this work, ethidium bro mide (EtBr) and acridine orange (AO) complexes with parARB and antiATT were studied and compared with their double-stranded homologs 5'-d(CA TGCTAACT)-L-d(AGTTAGCATG)-3' (antiAR) and 5'-d(A)(10)-L-d(T)(10)-3' (a ntiA/T), respectively. The EtBr polarized fluorescence assay was used to calculate the hydrodynamic volumes of the oligonucleotides under st udy, and mainly intramolecular structures were found in the physiologi cal solution. A tenfold increase in the EtBr fluorescence quantum yiel d and lifetime, as well as a threefold increase of the same parameters for AO observed upon their binding to parARb and antiATT, were indica tive of the ligand intercalation. The binding constants (K) for EtBr a nd AO complexes with parARB and antiATT were calculated to be markedly higher than those for antiAR and antiA/T, respectively. The effect of EtBr and AO on the tripler thermal stability was studied. The UV melt ing curves of EtBr-parARB, AO-parARB, and AO-antiATT were biphasic. Th e melting temperature (T-m) of the low-temperature tripler-to-duplex t ransition for parAB and antiATT depended on the amount of intercalated dye molecules and increased up to two intercalator molecules per trip ler. A further increase in the EtBr and AO concentrations resulted in a sharp decrease in T-m of the triplexes under investigation. The ther modynamic parameters of the tripler-to-duplex and the duplex-to-open-s trand transitions were calculated.