Bis-intercalation of a homodimeric thiazole orange dye in DNA in symmetrical pyrimidine-pyrimidine-purine-purine oligonucleotides

One- and two-dimensional H-1 NMR spectroscopy were used to characterize the binding of a homodimeric thiazole orange dye, 1,1'-(4,4,8,8-tetramethyl-4,8-diazaundecamethylene) -bis-4-(3-methyl-2,3-dihydro-(benzo-1,3-thiazole)-2-methylidene)-quinolinium tetraiodide (TOTO), to various double-stranded DNA oligonucleotides containing symmetric (5'-pyr-pyr-pu-pu-3')(2) or (5'-pu-pu-pyr-pyr-3')(2) sequences. It was found that TOTO binds preferentially to oligonucleotides containing a (5'-CTAG-3')(2) or a (5'-CCGG-3')(2) sequence, Binding to the (5'-CCGG-3')(2) sequence is less favored than to the (5'-CTAG-3')(2) sequence, The complexes of TOTO with d(CGCTAGCGCTAGCG)(2) (10) and d(CGCTAGCCGGCG):d(CGCCGGCTAGCG) (11) oligonucleotides, each containing two preferential binding sites, was also examined, In both cases TOTO forms mixtures of 1:1 and 1:2 dsDNA-TOTO complexes in ratios dependent on the relative amount of TOTO and the oligonucleotides in the sample, Binding of TOTO to the two oligonucleotides is sequence selective at the (5'-CTAG-3')(2) and (5'-CCGG-3')(2) sites, The H-1 NMR spectra of both the 1:2 complexes and the three different 1:1 complexes have been assigned, A slight negative cooperativity is observed in formation of the 1:2 complexes, The ratio between the two different 1:1 complexes formed with oligonucleotide 11 is 2.4 in favor of binding to the (5'-CTAG-3')(2) site. This is very similar to results obtained when the two sites are in different oligonucleotides, Thus the distribution of TOTO among the (5'-CTAG-3')(2) and (5'-CCGG-3')(2) sites is independent of whether the two sites are in the same or two different oligonucleotides.