Determination of the stability of complexes between DNA and the thiazole orange derivatives TO6 and TOTO by surface-enhanced resonance Raman spectroscopy

Complexes of the two thiazole orange derivatives TO6 [1-(N,N′-tetramethyl-1,3-propanediaminopropyl)-4-[3-methyl-2,3-dihydro(benzo-1,3-thiazole)-2-methylidene] quinolinium triiodide] and TOTO [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] with DNA oligonucleotide strands are investigated by the use of surface-enhanced resonance Raman spectroscopy. TO6 and TOTO contain protons that are exchangeable with deuterium when dissolved in D₂O. The exchange sites can be identified by use of nuclear magnetic resonance spectroscopy. The degree of exchange observed in the surface-enhanced resonance Raman spectra is used to measure the stability of the complexes formed. TOTO forms a highly stable complex with the d(5′-CCGCTAGCG-3′): d(5′-CGCTAGCGG-3′) oligonucleotide, whereas a less stable complex is formed with d(5′-CGCGTTAACGCG-3′)₂, indicating some degree of site specificity in the binding of TOTO to DNA. TO6 does not bind strongly to any single site in the d(5′-CGCGTTAACGCG-3′)₂ oligonucleotide. © 1997 John Wiley & Sons, Inc. Biospect 3: 207–213, 1997