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Nucleic Acids Research, 1995, Vol. 23, No. 5 753-760
© 1995

CHEMISTRY

Site selective bis-intercalation of a homodimeric thiazole orange dye in DNA oligonucleotides

Jens Peter Jacobsen*, Jeanette B. Pedersen, Lene F. Hansen and David E. Wemmer1

Department of Chemistry, Odense University Odense M, DK-5230, Denmark 1Structural Biology Division, Lawrence Berkeley Laboratory and Department of Chemistry, University of California Berkeley, CA 94720, USA

*To whom correspondence should be addressed

Received November 24, 1994. Revised January 10, 1995. Accepted January 10, 1995.

We have used one and two dimensional 1H NMR spectroscopy 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-di-hydro-(benzo-1,3-thiazole)-2-methylidene)-quinollnium tetraiodide (TOTO), to various double stranded DNA ollgonucleotides. TOTO binds strongly to all theoligonucleotides used, but usually more than one complex is observed and exchange between different binding sites broadensthe lines In the NMR spectra. Complete precipitation occurs when TOTO Is bound to small oligonucleotides. Binding to larger oligonucleotides occurs by bis-intercalation. The 1:1 complex of TOTO with the oligonucleotide d(CCGACTGATGC):d (GCATCAGTCGG) gave only one complex that was shown to be a bis-intercalation in the CTGA:TCAG binding site. The binding to this site was also characterized by studying the TOTO complex with the d(CCGCTGAGC):d(GCTCAGCGG) oligonucleotide. NOE connectivities and molecular modelling were used to characterize the complex. The 1:1 complex of TOTO with the oligonucleotide d(CCGCTAGCG):d (CGCTAGCGG) containing a CTAG:CTAG binding site was similarly characterized by NMR. It was concluded that the binding of TOTO to larger oligonucleotides is site selective with CTAG:CTAG as the preferred binding site.


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