Collaborative Research: Evolution and Chemical Biology of Base Excision Repair

A team of scientists at two research sites, the University of California Davis and the University of Utah, will explore molecular systems that protect DNA against chemical damage. These protection systems correct and restore DNA by first identifying damaged or misplaced bases in DNA, breaking the chemical bond connecting the base to the sugar backbone, followed by replacement with undamaged DNA. The DNA glycosylase enzymes that excise damaged bases evolved early during the emergence of cellular life as evidenced by clear family relationships across all three domains: Bacteria, Eukarya, and Archaea. The project aims to illuminate the evolution and chemical mechanism for the DNA glycosylases belonging to the helix-hairpin-helix superfamily. A cross-disciplinary approach will probe these questions with methodologies spanning biochemistry, structural biology, synthetic nucleic acid chemistry, bioinformatics, and molecular evolution. The knowledge generated will provide chemical probes to study functions of DNA glycosylase in living cells and unlock biotechnological applications such as editing of bases to restore function for mutated genes. Broader impacts for the project include insights for understanding the origins of cellular life, training of the next generation of molecular scientists, and the introduction to science for first-year undergraduate students. To understand the catalytic mechanisms and evolution for Base Excision Repair (BER) DNA glycosylases, the collaborative research project will determine the structures for enzymes complexed with DNA harboring synthetic versions of substrates and reaction intermediates. The transition state intermediate will be mimicked with pyrrolidine nucleotides decorated with base-like moieties created by synthetic chemistry. DNA glycosylases from the helix-hairpin-helix superfamily will be studied including EndoIII, OGG1 and novel MutY enzymes from Archaea. The activity of DNA glycosylases from bacteria and archaea will be screened in cells by applying next-generation sequencing. Discoveries from the project will have important impacts for the field, especially illuminating convergent solutions to protect DNA from oxidative damage across evolution. Further, the project aims to develop engineered enzymes with novel functions that can be applied as biotechnology for the detection of DNA damage and DNA base editing in living cells. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.