Targeting Base Excision Repair Glycosylases with DNA Containing Transition State Mimics Prepared via Click Chemistry

Area of Science:

• Biochemistry
• Molecular Biology
• Chemical Biology

Background:

• DNA glycosylases are crucial for base excision repair (BER), removing damaged DNA bases to prevent mutations.
• Compromised DNA repair is linked to diseases like cancer, neurological disorders, and aging.
• Developing high-affinity probes is essential for understanding DNA glycosylase function and designing therapeutics.

Purpose of the Study:

• To synthesize and evaluate transition state (TS) analogues as chemical biology probes for DNA glycosylases.
• To generate a library of TS mimic-containing oligonucleotides using click chemistry.
• To assess the binding affinities and preferences of BER glycosylases for these novel DNA probes.

Main Methods:

• Synthesis of oligonucleotides incorporating a propargyl-modified pyrrolidine TS mimic.
• Generation of a small library of TS mimic oligonucleotides via copper(I)-catalyzed azide-alkyne cycloaddition (click chemistry).
• Evaluation of relative binding affinities (Kd) for *Escherichia coli* MutY, bacterial Fpg, and human OGG1 (hOGG1) using DNA duplexes.

Main Results:

• All tested BER glycosylases exhibited extremely high affinities (picomolar Kd values) for the TS mimic DNA duplexes.
• Distinct binding preferences were observed for each glycosylase, indicating varied transition state stabilization.
• Fpg showed exceptional affinity for all TS mimics; MutY affinity inversely correlated with moiety size; a specific hOGG1-high affinity probe was identified.

Conclusions:

• Propargyl-TS mimic oligonucleotides synthesized via click chemistry are effective for screening BER glycosylase ligands.
• The study highlights the utility of these probes for identifying high-affinity ligands for specific BER glycosylases.
• These findings pave the way for developing targeted chemical biology tools and therapeutics for DNA repair pathways.