Duplex molecular strands based on the 3,6-diaminopyridazine hydrogen bonding motif: amplifying small-molecule self-assembly preferences through preorganization and iterative arrangement of binding residues.

Structural parameters obtained through single-crystal X-ray diffraction analysis of the one-dimensional H-bonding motif expressed by 3,6-diaminopyridazine are applied to the design of related monomeric, dimeric, and trimeric duplex molecular strands. The mode of assembly and the interstrand affinity of the oligomers are established in solution by (1)H NMR dilution experiments, isothermal titration calorimetry (ITC), and vapor pressure osmometry. Single-crystal X-ray crystallographic analysis of the dimeric diaminopyridazine 2a corroborates the intended duplex mode of assembly. Binding free energy per unimer (-DeltaG degrees /n) increases upon extension from monomer to dimer to trimer, signifying a positive cooperative effect. Micromolar binding affinity (K(d) = 1.25 +/- 0.1 microM) was determined for the duplex trimer by ITC in 1,2-dichloroethane at 20 degrees C. These data provide further insight into the structural and interactional features of synthetic duplex oligomers required for high-affinity, high-specificity binding and define new recognition elements for use in nanoscale assembly.