Toward an Artificial Oxidative DNA Photolyase

The design, synthesis, structure, and binding affinity of two dioptic receptors for the selective
molecular recognition of the cis,syn cyclobutane pyrimidine dimer are reported. The design is based
on two 2,6-di(acetamino)pyridine recognition units that are covalently linked via triple bonds to
an anthraquinone functional spacer unit. The convergent synthesis uses a modified Sonogashira
reaction involving a zinc transmetalation as the key step. The crystal structure of one of the receptors
reveals a supramolecular 1D polymer with strong interactions mediated by shape self-complementarity, π-stacking, and hydrogen bonding between adjacent molecules. Hydrogen bonding between
adjacent strands enforces a parallel orientation, which leads to a noncentrosymmetric crystal
structure of the highly polar compound. The receptor has an association constant of Ka = 1.0 × 103
M-1 with the cis,syn pyrimidine dimer, whereas binding of the trans,syn isomer is approximately
1 order of magnitude weaker.