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Patrick J. O'Brien, Ph.D.

Associate Professor, Biological Chemistry

B.S. Santa Clara University
Ph.D. Stanford University
Postdoctoral, Harvard Medical School

Research Profile

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

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

Selected Publications

Hedglin, M., Zhang, Y., & O'Brien, P.J. (2013) Isolating contributions from intersegmental transfer to DNA searching by alkyladenine DNA glycosylase. J. Biol. Chem, epub http://www.ncbi.nlm.nih.gov/pubmed/23839988

Admiraal, S.J. & O'Brien, P.J. (2013) DNA-N-glycosylases process novel O-glycosidic sites in DNA. Biochemistry, epub http://www.ncbi.nlm.nih.gov/pubmed/23688261

Baldwin, M.R. & O'Brien, P.J. (2012) Defining the functional footprint for recognition and repair of deaminated DNA. Nucleic Acids Res., 40, 11638-47. http://www.ncbi.nlm.nih.gov/pubmed/23074184

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. http://www.ncbi.nlm.nih.gov/pubmed/21561855

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. http://www.ncbi.nlm.nih.gov/pubmed/21491902

Hendershot, J.M., Wolfe, A.E., & O'Brien, P.J. (2011) Substitution of active site tyrosines with tryptophan alters the free energy for nucleotide flipping by human alkyladenine DNA glycosylase. Biochemistry, 50, 1864-74. http://www.ncbi.nlm.nih.gov/pubmed/21244040

Admiraal, S.J. & O'Brien, P.J. (2010) N-glycosyl bond formation catalyzed by human alkyladenine DNA glycosylase. Biochemistry, 49, 9024-6. http://www.ncbi.nlm.nih.gov/pubmed/20873830

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. http://www.ncbi.nlm.nih.gov/pubmed/20701268

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. http://www.ncbi.nlm.nih.gov/pubmed/20547483

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. http://www.ncbi.nlm.nih.gov/pubmed/20201599

Lyons, D.M. & O'Brien, P.J. (2009) Efficient recognition of an unpaired lesion by a DNA repair glycosylase. J. Am. Chem. Soc., 131, 17742-3. http://www.ncbi.nlm.nih.gov/pubmed/19924854

Wolfe, A.E. & O'Brien, P.J. (2009) Kinetic mechanism for alkyladenine DNA glycosylase-catalyzed flipping and excision of 1,N6-ethenoadenine. Biochemistry, 48, 11357-11369. http://www.ncbi.nlm.nih.gov/pubmed/19883114

Baldwin, M.R. & O'Brien, P.J. (2009) Human AP endonuclease stimulates multiple-turnover base excision by alkyladenine DNA glycosylase. Biochemistry, 48, 6022-33. http://www.ncbi.nlm.nih.gov/pubmed/19449863

Hedglin, M. & O'Brien, P.J. (2008) Human alkyladenine DNA glycosylase employs a processive search for DNA damage. Biochemistry, 47, 11434-11445. http://www.ncbi.nlm.nih.gov/pubmed/18839966

O'Brien, P.J. (2006) Catalytic promiscuity and the divergent evolution of DNA repair enzymes. Chem Rev. 106, 720-52. http://www.ncbi.nlm.nih.gov/pubmed/16464022

Pascal, J.M., O'Brien, P.J., Tomkinson, A.E. and Ellenberger, T. (2004). Human DNA ligase I completely encircles and partially unwinds nicked DNA. Nature, 432, 473-478. http://www.ncbi.nlm.nih.gov/pubmed/15565146

O’Brien, P.J. & Ellenberger, T. (2004). The Escherichia coli 3-methyladenine DNA glycosylase has a remarkably versatile active site. J. Biol. Chem., 279, 26876-26884. http://www.ncbi.nlm.nih.gov/pubmed/14688248

O’Brien, P.J. & Ellenberger, T. (2004). Dissecting the broad substrate specificity of human 3-methyladenine DNA glycosylase. J. Biol. Chem. 279, 9750-9757. http://www.ncbi.nlm.nih.gov/pubmed/15126496

O'Brien, P.J. & Ellenberger, T. (2003) Human alkyladenine DNA glycosylase uses acid-base catalysis for selective excision of damaged purines. Biochemistry. 42, 12418-12429. http://www.ncbi.nlm.nih.gov/pubmed/14567703

pjobrien@umich.edu

Office: 4220B MSRB3, Box 5606
PH: (734)647-5821

PubMed: o'brien pj

Department Affiliations

Chemical Biology Program