Faculty

Patrick J. O'Brien

Associate Professor of Biological Chemistry

Ph.D., Stanford University
Postdoctoral Fellow, Harvard Medical School

Research Focus: Protein/Nucleic Acid Interactions and DNA Repair

Phone: 734.647.5821
E-mail: pjobrien@umich.edu
Fax: 734.763.4581

DNA is remarkably stable, but nonetheless suffers a wide variety of spontaneous damage. Thus, it comes as no surprise that a substantial portion of the proteome is dedicated to maintaining and repairing DNA. Work over the past several decades has identified different types of DNA damage and developed a broad picture of many different pathways for DNA repair. This work sets the foundation for understanding the biochemical and biophysical mechanisms by which DNA damage is detected and ultimately repaired. These studies will expand our understanding of carcinogenesis and the ways in which our cells safeguard against it, and culminate in a more comprehensive view of the dynamic nature of chromosomal DNA.

DNA bases are readily oxidized and alkylated in vivo and the resulting lesions are usually repaired by base excision repair (BER). The BER pathway is an excellent model system for DNA repair, because it can be reconstituted in vitro with as few as four enzymes: DNA glycosylases survey the genome and initiate repair by excising damaged bases; an abasic site-specific nuclease subsequently creates a single-stranded nick and removes the deoxyribosyl group; finally, a polymerase and a ligase act in turn to restore the DNA.

We seek to understand the biochemical and biophysical principles by which DNA is repaired, starting with relatively simple repair pathways such as BER. For all DNA repair pathways we are interested in specificity (distinguishing damaged and normal DNA) and fidelity (how efficiently the damage is repaired). The physical principles and mechanisms by which specificity and fidelity are conferred are best addressed by mechanistic analysis in vitro. Ultimately, the chemical and physical principles governing the action of BER enzymes will be more broadly applicable to other DNA repair processes, and to other DNA-templated activities such as replication. For example, the processes of locating rare sites and coordinating multi-step, multi-component pathways have features common to most DNA-templated activities. By focusing on the human proteins we hope to speed the process by which mechanistic insight leads to practical applications, such as the improvement of anticancer chemotherapies, protection from environmental carcinogens, and the development of novel antimicrobials.

 

Awards

2011-2015
Research Scholar of the American Cancer Society
2002-2004
Ruth L. Kirchstein NRSA (NIH Postdoc Fellowship)
1995-1997
National Institutes of Health Biotechnology Predoc Fellowship

 

Representative Publications

  1. Hedglin, M., O’Brien, P.J. (2010) Hopping enables a DNA repair glycosylase to efficiently search both strands and bypass a bound protein. ACS Chem. Biol. 5:427-36.

  2. Lyons, D.M., O’Brien, P.J. (2010) Human base excision repair creates a bias toward -1 frameshift mutations. J. Biol. Chem. 285:25203-12.

  3. Baldwin, M.R., O’Brien, P.J. (2010) Coordination of the initial steps of human base excision repair via nonspecific DNA binding interactions. Biochemistry 49:7879-91.

  4. Admiraal, S.J., O’Brien, P.J. (2010) N-glycosyl bond formation catalyzed by human alkyladenine DNA glycosylase. Biochemistry 49:9024-26. 

  5. Nikolova, E.N., Kim, E., Wise, A.A., O’Brien, P.J., Andricioaci, I., Al-Hashimi, H.M. (2011) Transient Hoogsteen base pairs in canonical duplex DNA. Nature 470: 498-502.

  6. Hendershot, J.M., Wolfe, A.E., O’Brien, P.J. (2011) Substitution of active site tyrosines with tryptophan alters the free energy of nucleotide flipping by human alkyladenine DNA glycosylase. Biochemistry 50:1864-74.

  7. Zhao, B., O’Brien, P.J. (2011) Kinetic mechanism for the excision of hypoxanthine by Escherichia coli AlkA and evidence for binding to DNA ends. Biochemistry 50:4350-9.

  8. Taylor, M.R., Conrad, J.A., Wahl, D.R., O’Brien, P.J. (2011) Kinetic mechanism of human DNA ligase I reveals magnesium-dependent changes in the rate-limiting step that compromise ligation efficiency. J. Biol. Chem. 286:23054-62.

 

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