Bis-Intercalation of Homodimeric Thiazole Orange Dye Derivatives in DNA

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Abstract
The thiazole orange dye 1,1‘-(4,4,8,8-tetramethyl-4,8-diazaundecamethylene)-bis-4-[(3-methyl-2,3-dihydro-2(3H)-benzo-1,3-thiazolylidene)methyl]quinolinium tetraiodide (TOTO) binds to double-stranded DNA (dsDNA) in a sequence selective bis-intercalation. We have examined the binding of derivatives of TOTO with different substituents on the benzothiazole ring. The analogues are the following: 1,1‘-(4,4,8,8-tetramethyl-4,8-diazaundecamethylene)-[4-[3-(benzyl-2,3-dihydro-2-(3H)-benzothiazolylidene)methyl]quinolinium]-[4-[3-(methyl-2,3-dihydro-2-(3H)-benzothiazolylidene)methyl]quinolinium]tetraiodide (TOTOBzl) and 1,1‘-(4,4,8,8-tetramethyl-4,8-diazaundecamethylene)-bis-4-[(3-ethyl-2,3-dihydro-2(3H)-benzo-1,3-thiazole)methyl]quinolinium tetraiodide (TOTOEt). In this paper, we report the synthesis of TOTOBzl and TOTOEt together with the one- and two-dimensional 1H NMR investigations of complexes between these TOTO analogues and the dsDNA oligonucleotide d(CGCTAGCG)2. Both analogues yield extremely stable complexes in which each chromophore is sandwiched between two base pairs in a (5‘-CpT-3‘):(5‘-ApG-3‘) site. The linker spans over two base pairs in the minor groove. The benzyl group in TOTOBzl and the ethyl groups in TOTOEt is pointing outward in the major groove.

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