Bis-Intercalation of a Homodimeric Thiazole Orange Dye in DNA in Symmetrical Pyrimidine-Pyrimidine-Purine-Purine Oligonucleotides

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Abstract
One-and two-dimensional 1H NMR spectroscopy were used to characterize the binding of a homodimeric thiazole orange dye, 1,1′-(4,4,8,8-tetramethyl-4,8-diaza-undecamethylene)-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 1H 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.

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