NMU Alumnus Researches DNA Mutations

Mike Carpenter '01 BS successfully defended his dissertation in chemistry on Nov. 24 at Wayne State University.  The title of his dissertation is "Studies of base flipping by the Pyrococcus species GI-H restriction modification system" and the research was conducted under the direction of  Dr. Ashok S. Bhagwat. 

I want to thank you and everyone else at the Chemistry department at NMU for making my time there such a rewarding experience. I am always telling people how great NMU is and about the quality education that I got there. Thanks a lot! - Mike

Mike’s work was the study of how bacteria prevent mutations in their DNA under different environmental conditions.  One interesting thing Mike discovered was that a particular enzyme protected the DNA at certain sites, but actually promoted mutations at an alternative site through a mechanism called “base flipping”.  Mike published five papers on this work while at Wayne State.

Mike is a Marquette native and earned a B.S. degree in biochemistry from NMU.   He is currently looking for a postdoctoral research position in structural biology and expresses thanks to the Department of Chemistry and to NMU for making his undergraduate educational experience a great one.

Mike's Research

I started out looking at protection by DNA binding proteins against spontaneous cytosine deamination. Cytosine deamination leads to uracil in DNA which is potentially mutagenic if not repaired and occurs hundreds of times per cell per day in every DNA containing cell in the human body. The rate of cytosine deamination increases with increasing temperature and we were interested in how hyperthermophiles could exist at these elevated temperatures without lethal amounts of damage to the DNA. Using an in vitro system, I showed that R.PspGI can prevent cytosine deamination when it is bound to its cognate site. In one of the controls, an unexpected increase in mutations was observed. After ruling out other possibilities, base flipping was proposed as the mechanism by which water was accessing cytosines in DNA. This prediction was confirmed by a fluorescence based assay in which the adenine base analog 2-aminopurine was used as a probe for base flipping as well as by the determination of the structure of a catalytically inactive form of R.PspGI in complex with a DNA duplex by X-ray crystallography. In addition, the first direct evidence for base flipping by an N4-cytosine methyltransferase was shown by a 2-aminopurine based fluorescence assay.

Publications

1. Samaranayake, M.; Bujnicki, J. M.; Carpenter, M.; Bhagwat, A. S., Evaluation of molecular models for the affinity maturation of antibodies: roles of cytosine deamination by AID and DNA repair. Chem Rev 2006, 106, (2), 700-19.
2. Carpenter, M.; Divvela, P.; Pingoud, V.; Bujnicki, J.; Bhagwat, A. S., Sequence-dependent enhancement of hydrolytic deamination of cytosines in DNA by the restriction enzyme PspGI. Nucl. Acids Res. 2006, 34, (13), 3762-3770.
3. Bhagwat, A. S.; Carpenter, M. A.; Bujnicki, J. M., Is AID a monomer in solution? DNA Repair (Amst) 2008, 7, (3), 349-50.
4. Carpenter, M. A.; Bhagwat, A. S., DNA base flipping by both members of the PspGI restriction-modification system. Nucleic Acids Res 2008, 36, (16), 5417-25.
5. Szczepanowski, R. H.; Carpenter, M. A.; Czapinska, H.; Zaremba, M.; Tamulaitis, G.; Siksnys, V.; Bhagwat, A. S.; Bochtler, M., Central base pair flipping and discrimination by PspGI. Nucl. Acids Res. 2008, 36, (19), 6109-6117.