Selective Recognition of Uracil and Its Derivatives Using a DNA Repair Enzyme Structural Mimic

During DNA repair, uracil DNA glycosylase (UDG) pulls unwanted uracil into its active site through hydrogen bonding and π−π stacking interactions. The reason why UDG binds only uracil tightly—and not its derivatives, such as thymine—remains unclear. In this study, we synthesized the stable, water-soluble receptor 1a as a structural mimic of the active site in UDG. Compound 1a contains a 2,6-bis(glycylamino)pyridine group, which mimics the amino acid residues of UDG that interact with uracil through a hydrogen-bonding network; it also possesses a pyrene moiety as a π−π stacking interaction element and fluorescent probe that mimics the aromatic groups (phenyl and fluorescent indolyl units) found in the active site of UDG. Receptor 1a binds selectively to uracil and derivatives (including thymine, 5-formyluracil, 5-fluorouracil, and 5-nitrouracil) and some DNA and RNA nucleosides (including thymidine and uridine) through hydrogen bonding and π−π stacking interactions. Interestingly, a plot of log Kb with respect to the values of pKa of the N(3)H units of uracil and its derivatives was linear, with a negative slope (β) of −0.24 ± 0.03. Thus, compounds featuring lower values of pKa for their N(3)H units provided greater apparent binding constants for their complexes with receptor 1a, suggesting acidity-dependent binding of uracil and its derivatives to this receptor; notably, uracil bound more tightly than did thymine. Our study provides some insight into how uracil and its derivatives in DNA are bound by DNA repair enzymes through hydrogen bonding and π−π stacking interactions.