Genome editing tools have driven a revolution and enabled the work of countless researchers across the fields of biomedical science, agriculture, biotechnology, and synthetic biology. Despite the fervor with which these technologies have been adopted, many of them suffer from key shortcomings such as unwanted DNA sequence modifications and low efficiencies for certain types of edits and in certain types of cells. This project seeks to tackle these limitations by furthering basic understanding of DNA repair mechanisms involved in the editing processes. The research will enable expansion of the current suite of genome editing tools, while simultaneously providing graduate student and postdoctoral researchers with training for successful careers in science. The project also includes a research-practice partnership with San Diego area public high schools with high enrollments of socioeconomically disadvantaged students. The students will be introduced to cutting edge genome editing technologies in a topical and approachable manner, with the goal of inciting excitement and further engagement with higher education beyond standard classroom curricula.

To alter the sequence of genomic DNA at will, genome editing tools all rely on initial introduction of damage into the DNA of live cells. “Nontraditional” genome editing tools, such as base editors and prime editors, are a class of recently developed editors that employ other types of DNA damage than double-stranded breaks to mediate the editing process. This project will use high-throughput gene knock-down strategies in combination with reporters for various base editing and prime editing outcomes to characterize the role of DNA repair genes in processing nontraditional genome editing intermediates. This effort will be complemented by computational and experimental research to determine how base editing and prime editing outcomes change in relation to different stages of the cell cycle. These studies represent the first investigations into DNA repair mechanisms employed by nontraditional genome editors, and the outcomes will advance the efficiency and precision of existing editing tools as well generate editing tools for new types of genomic modifications.

This project is jointly funded by the Genetic Mechanisms and Systems and Synthetic Biology programs of the Molecular and Cellular Biosciences Division in the Biological Sciences Directorate

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.

National Science Foundation (NSF)
Division of Molecular and Cellular Biosciences (MCB)
Application #
Program Officer
Manju Hingorani
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of California San Diego
La Jolla
United States
Zip Code