Four nonnatural imidazole nucleosides with different substituents were synthesized and studied for their binding to a CG Watson-Crick base pair by NMR spectroscopic techniques in an aprotic solvent. Concentration and temperature dependent measurements allowed the determination of association constants, association enthalpies and entropies. Strong binding was observed with analogues carrying an ureidophenyl substituent and corresponding enthalpies of association are compatible with the anticipated formation of three hydrogen bonds to the CG base pair. In contrast, only weak binding was observed for analogues with an aminophenyl or benzamidophenyl substituent. 2D NOE measurements at low temperatures confirm the proposed binding mode for the high-affinity ligands but indicate binding interactions for the weakly bound analogues different from the expected geometry.

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A carboxyl-functionalized methylene blue (MB) derivative was synthesized and covalently coupled to three CG-rich self-complementary 2'-deoxyoligonucleotides at their 5'-end. Thermodynamic and structural details about the interactions between the dye and oligonucleotide duplexes were investigated employing ultraviolet (UV) melting and (1)H nuclear magnetic resonance (NMR) experiments. In contrast to previous findings on MB binding, no specific intercalation or binding in the minor or major groove of the double helix was found in a 100 mM NaCl buffer. Rather, proton chemical shift changes in the conjugates provide ample evidence for weak dye-DNA interactions largely through external MB stacking on the terminal base pairs.

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