DNA Base Excision Repair in Chromatin

The environment contains many reactive species that can damage DNA in living organisms. Exposure to these reactive species generates an array of DNA damage lesions that alter the genetic blueprint of cells and threaten all aspects organismal function, as well as the faithful transfer of genetic information to the next generation. A variety of repair pathways have evolved to protect DNA, including base excision repair (BER) in which damaged DNA bases are removed and replaced with undamaged ones.

This project investigates how BER acts on DNA packaged by proteins into chromatin – the form DNA takes inside cells. The goal is to determine how this packaging influences DNA repair and to identify ways that cells overcome challenges associated with repairing DNA secluded within chromatin. The project will offer training opportunities to students, including undergraduates from women’s colleges, in DNA chemistry, protein biochemistry, biophysics, and molecular biology.

These skills will enable students to pursue STEM careers in research and education, and to contribute to biotechnology industries. Science outreach to middle school students is planned as well.

BER is a coordinated series of enzyme-catalyzed chemical reactions in which a damaged base in DNA is removed and replaced. A paradoxical aspect of this fundamental cellular process that still remains poorly understood is the ability of BER to repair DNA when it is packaged in chromatin, which can limit enzyme access to damaged bases. The research will employ an innovative “repair fingerprint” technique that can precisely identify locations in chromatin where BER enzymes are catalytically active as well as those that are refractory to repair.

This technique, as well as a variety of biochemistry, biophysics, and molecular biology approaches will be employed to (i) determine how DNA base flipping is controlled in packaged DNA, (ii) understand how the density of DNA packaging modulates BER, and (iii) establish the contribution of a damage sensor protein to BER in packaged DNA. The outcomes will help answer key questions regarding cellular mechanisms to overcome the packaging paradox and prevent genomic instability.

This research is funded by the Genetic Mechanisms program in the Division of Molecular and Cellular Biosciences in the Directorate of Biological Sciences.

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.