Molecular recognition of a thymine bulge by a high affinity, deazaguanine-based hydrogen-bonding ligandw

Single-base bulges in DNA are irregularities that may arise from replication errors or from recombination between imperfectly homologous sequences. Owing to their inherent thermodynamic instability, bulges are susceptible targets for small molecules and proteins with recognition capabilities. A number of ligands have been developed that can recognize adenine (A), guanine (G), or cytosine (C) at a DNA bulge or mismatch site. These ligands consist of a bicyclic ring system for intercalation and hydrogen-bonding groups for basespecificity. To our knowledge, there are no known ligands that bind a thymine (T) bulge in preference to the other base bulges. This may in part be attributed to its acceptor– donor–acceptor (ADA) hydrogen-bonding motif pairing weakly. Herein we introduce 7-deazaguanine (7-DeG) as a module capable of binding thymine and uracil with higher affinity than most modules containing the donor–acceptor–donor (DAD) motif. The 7-DeG unit with an intramolecularly hydrogenbonded amide group at N-2 (purine numbering) contains a rigid bicyclic structure that preorganizes the hydrogen-bond donor and acceptor groups. The rigidification occurs partly through the formation of an intramolecular hydrogen-bond with NH-1 (Fig. 1) and is clearly seen in the X-ray analysis of 1. Possibly as a result of the greater degree of preorganization, H NMR binding studies in CDCl3 reveal a comparatively high stability for the 1 U complex (Ka = 5800 M ) (Table 1). Typical diamidopyridine derivatives such as 3–4 exhibit weaker affinity toward thymine and uracil (Ka E 10 –10 M ). Other factors that may play a role in the enhanced binding exhibited by 1 include enhanced acidity or basicity of the hydrogen-bond donor and acceptor sites and the orientation of the NH-7 group.