title: Dynamic bis-intercalation of a homodimeric thiazole orange dye in DNA: evidence of intercalator creeping.
abstract: We have used one and two dimensional exchange 1H NMR spectroscopy to characterize the dynamics of 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)-quinol inium tetraiodide (TOTO), to double stranded DNA (dsDNA). The double stranded oligonucleotides used were d-(CGCTAGCG)2 (1) and d(CGCTAGCTAGCG)2 (2). TOTO binds preferentially to the (5'-CTAG-3')2 sites and forms mixtures of 1:1 and 1:2 dsDNA-TOTO complexes with 2 in ratios dependent on the relative amount of TOTO and the oligonucleotide in the sample. The dynamic exchange between preferential binding sites in the case of a 2:1 1-TOTO mixture is an intermolecular exchange process between two binding sites on different oligonucleotides. In the case of the 1:1 2-TOTO complex an intramolecular exchange process occur between two different binding sites on the same strand. Both processes were studied. The results demonstrate the ability of TOTO to migrate along a dsDNA strand in an intramolecular exchange process. The migration process ("creeping") along the DNA strand is 6 times faster than the rate of intermolecular exchange between sites in two different oligonucleotides.
authors.affiliation: Department of Chemistry, Odense University, Denmark.
authors.forename: J
authors.initials: J
authors.lastname: Faridi
authors.forename: K E
authors.initials: KE
authors.lastname: Nielsen
authors.forename: P C
authors.initials: PC
authors.lastname: Stein
authors.forename: J P
authors.initials: JP
authors.lastname: Jacobsen
mesh_terms: D052160:Benzothiazoles; D004247:DNA / Q000737:chemistry*; D005456:Fluorescent Dyes; D007364:Intercalating Agents; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D011804:Quinolines; D013844:Thiazoles
chemical_list: D052160:Benzothiazoles; D005456:Fluorescent Dyes; D007364:Intercalating Agents; D009838:Oligodeoxyribonucleotides; D011804:Quinolines; D013844:Thiazoles; C051000:thiazole orange; D004247:DNA