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 1H 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
(−ΔG°/n) increases upon extension from monomer to dimer to trimer, signifying a positive cooperative
effect. Micromolar binding affinity (Kd = 1.25 ± 0.1 μM) was determined for the duplex trimer by ITC in
1,2-dichloroethane at 20 °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.