Specific binding of the DNA repair enzyme AlkA to a pyrrolidine-based inhibitor

In the cell, DNA is continuously subjected to damage resulting from spontaneous hydrolysis, oxidation, deamination, alkylation, and errors in replication. To counter the toxic and mutagenic lesions thus produced, DNA repair enzymes are expressed in all known organisms. Whereas DNA repair was formerly viewed as an independent housekeeping function of cells, recent evidence has linked DNA repair to other essential biological processes, including progression through the cell cycle and gene transcription. Moreover, it is now firmly established that defects in DNA repair contribute directly to carcinogenesis. Despite widespread interest in the molecular basis for recognition and repair of DNA, no high-resolution structure of a DNA repair enzyme bound specifically to its target DNA has been solved. In part, this situation arises from the necessarily fleeting nature of enzyme-substrate complexes, which makes them difficult to observe. To overcome this problem, we have initiated an effort toward the design and synthesis of molecules that bind DNA repair proteins to form stable, long-lived complexes suitable for structural analysis. Here we report potent inhibition of the Escherichia coli 3-methyladenine DNA glycosylase II (AlkA) by a pyrrolidine-containing oligonucleotide, 1.