Effects of compound structure on carbazole dication-DNA complexes: Tests of the minor-groove complex models

Carbazole dications have shown excellent activity against opportunistic inf ections, but they are quite different in structure from previously studied unfused aromatic cations that function by targeting the DNA minor groove. I n a previous report [Tanious, F. A., Ding, D,, Patrick, D. A., Tidwell, R. R., and Wilson, W. D, (1997) Biochemistry 36, 15315-15325] we showed that, despite their fused ring structure, the carbazoles also bind in A/T sequenc es of the DNA minor groove and we proposed models for the carbazole-DNA com plexes with the carbazole nitrogen facing out of the groove for 3,6 substit uted compounds but into the groove in 2,7 carbazoles. To test and refine th e models, carbazole-N-methyl substituted derivatives have been synthesized in both the 3.6 and 2,7 series as well as a new 2,6 substituted NH derivati ve that is intermediate in structure. Footprinting results indicate a broad AT specificity of carbazole binding and a pattern in agreement with a mino r groove complex. Surface plasmon resonance biosensor analysis of carbazole binding to an oligomer with an AATT central sequence indicated that the 2, 7 NH compound has the largest binding constant. Both the 3,6 NH and NMe com pounds bind with similar equilibrium constants that are less than for the 2 ,7 NH compound. The 2,7 NMe compound has the lowest binding constant of all the carbazoles. Spectroscopic results are also similar for the two 3,6 der ivatives but are quite different for the 2,7 NH and NMe carbazole dications , Structural analysis of carbazole complexes with an AATT sequence by 2D NM R methods also supported a minor groove complex of the carbazoles in orient ations in agreement with the previously proposed models. From these results , it is clear that the fused ring carbazoles can bind strongly in the DNA m inor groove with a broad A/T specificity and that the 2,7 and 3,6 substitut ed carbazoles bind to the minor groove in opposite orientations.