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Johns Hopkins University logoProgram in Molecular Biophysics
Jim StiversStivers Lab

Jim Stivers

Department of Pharmacology and Molecular Sciences
School of Medicine

B.S. 1987,?University of Washington, Seattle
Ph.D. 1993, Johns Hopkins University

314 WBSB
725 N. Wolfe Street
Baltimore, MD 21205

Office: 410-502-2758
Lab: 410-614-9644


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Our laboratory focuses on the general problem of specific molecular recognition in biological systems. Our work begins with structure, but we are very interested in pushing and extending the measurement envelope so that we obtain a fundamental understanding of the energetic basis for molecular recognition. Accordingly, we use a wide breadth of molecular, genetic and biophysical approaches that together shed light on aspects of molecular recognition that are not apparent from structural studies alone. Our long range goal is to use this understanding to design novel small molecules that alter biological pathways within a cellular environment. One approach we are developing is the high-throughput synthesis and screening of small molecule libraries directed at important targets in cancer and viral pathogenesis.

Selected Publications
Nabel, C.S., H. Jia, Y. Ye, Y. Shen, H.L. Goldschmidt, J.T. Stivers, Y. Zhang, and R.M. Kohli. (2011) AID/APOBEC deaminases disfavor modified cytosines implicated in DNA demethylation. Nature Chem. Biol. (in press)

Ye, Y., M. Stahley, J. Xu, J. Friedman, Y. Sun, J. McKnight, J. Gray, G. Bowman, and J.T. Stivers. (2012) Enzymatic excision of uracil residues in nucleosomes depends on local DNA structure and dynamics. Biochemistry (in press)

Mak, L.H., J. Knott, K.A. Scott, C. Scott, G.F. Whyte, Y. Ye, D. Mann, O. Ces, J.T. Stivers, and R. Woscholski. (2012) Arylstibonic acids are potent and isoform-selective inhibitors of Cdc25a and Cdc25b phosphatases. Bioorg. Med. Chem. (in press)

Jun, H., and J.T. Stivers. (2012) Diverse energetic effects of charge reversal mutations of poxvirus topoisomerase Ib. Biochemistry 51:2940-2949.

Schonhoft, J.D., and J.T. Stivers. (2012) Timing facilitated site transfer of an enzyme on DNA. Nature Chem. Biol. 8:205-210.

Parker, J.B., and J.T. Stivers. (2011) Dynamics of uracil and 5-fluorouracil in DNA. Biochemistry 50:612-617.

Kohli, R.M., R.W. Maul, A.F. Guminski, R.L. McClure, K.S. Gajula, H. Saribasak, M.A. McMahon, R.F. Siliciano, P.J. Gearhart, and J.T. Stivers. (2010) Local sequence targeting in the AID/APOBEC family differentially impacts retroviral restriction and antibody diversification. J. Biol. Chem. 285:40956-40964.

Friedman, J.I., M.T. McMahon, J.T. Stivers, and P.C.M. van Zijl. (2010) Indirect detection of labile solute proton spectra via the water signal using frequency-labeled exchange (FLEX) transfer. J. Am. Chem. Soc. 132:1813-1815.

Ye, Y., and J.T. Stivers. (2010) Fluorescence-based high-throughput assay for human 5-methylcytosine DNA methyltransferase 1. Anal. Biochem. 401:168-172.

Kohli, R.M., S.R. Abrams, K.S. Gajula, R.W. Maul, P.J. Gearhart, and J.T. Stivers. (2009) A portable hotspot recognition loop transfers sequence preferences from APOBEC family members to activation-induced cytidine deaminase. J. Biol. Chem. 284:22898-22904.

Friedman, J.I., A. Majumdar, and J.T. Stivers. (2009) Nontarget DNA binding shapes the dynamic landscape for enzymatic recognition of DNA damage. Nucleic Acids Res. 37:3493-3500.

Chung, S., J.B. Parker, M. Bianchet, L.M. Amzel, and J.T. Stivers. (2009) Impact of linker strain and flexibility in the design of a fragment-based inhibitor. Nature Chem. Biol. 5:407-413.

Porecha, R.H., and J.T. Stivers. (2008) Uracil DNA glycosylase uses DNA hopping and short-range sliding to trap extrahelical uracils. Proc. Natl. Acad. Sci. USA 105:10791-10796.

Parker, J.B., M.A. Bianchet, D.J. Krosky, J.I. Friedman, L.M. Amzel, and J.T. Stivers. (2007) Enzymatic capture of a transient extrahelical thymine in the search for uracil in DNA. Nature 449:433-437.

Cao, C., Y.L. Jiang, F. Song, and J.T. Stivers. (2004) Dynamic opening of DNA during the enzymatic search for a damaged base. Nat. Struct. Mol. Biol. 11:1230-1236.

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