Nucleic minor groove

Other commonly used dyes include Hoechst 33258 and DAPI (4/,6-diamidino-2-phenylindole), both of which show selectivity towards poly A-T sequences. This selectivity limits the utility of these dyes as generic transducers in sensor applications. These dyes associate with double-stranded nucleic acids in a groove-binding motif, more specifically, via binding in the minor groove of B-DNA [41]. 

L. J., Clark, G.R., Martin, R.F., White, J. Structures of m-iodo Hoechst-DNA complexes in crystals with reduced solvent content implications for minor groove binder dmg design. Nucleic Acids Res. 2000, 28, 1252-1258 (b) 1QV8, 1QV4 Martin, R. F., Broadhurst, S., Reum,... 

Hoechst 33258 binds to the minor groove of double-stranded DNA with a preference for the A-T sequence (Pjura et al. 1987). Interaction between DNA and proteins very often induces structural modifications in both interacting molecules. Such modifications in DNA can be characterized with 2-aminopurine (2AP), which is a highly fluorescent isomer of adenine. 2AP does not alter the DNA structure. It forms a base pair with thymine and can be selectively excited, since its absorption is red-shifted compared to that of nucleic acids and aromatic amino acids. In addition, its fluorescence is sensitive to the conformational change that occurs within the DNA (Rachofsky et al. 2001). 

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