Richard P. Cunningham

Richard P. Cunningham

Biological Sciences


LS 1003R

PhD, Johns Hopkins University

Richard P. Cunningham

Areas of Interest

  • Biochemistry of DNA Repair Enzymes
  • DNA Repair in Bacteria
  • Structure and function of DNA Nucleases
  • Structure and Function of DNA Glycosylases
  • Genetic and Systems Analysis of DNA Repair Pathways


  • Herting G, Barber K, Zappala MR, Cunningham RP, Burgis NE. (2010) Quantitative in vitro and in vivo characterization of the human P32T mutant ITPase Biochim Biophys Acta, 1802: 269-274. 
  • Rooney, J.P., George, A., Patil, A., Begley, U., Bessette, E., Zappala, M., Huang, X., Conklin, D.C., Cunningham, R.P. and Begley, T.J. (2009) Systems based mapping demonstrates that recovery from alkylation damage requires DNA repair, RNA processing, and translation associated networks. Genomics. 93: 42-51. 
  • Rooney JP, Patil A, Zappala MR, Conklin DS, Cunningham RP, Begley TJ. A molecular bar-coded DNA repair resource for pooled toxicogenomic screens. (2008) DNA Repair (Amst). 7: 1855-1868. 
  • Garcin, E.D., Hosfield, D.J., Desai, S. A., Haas, B.J., Björas, M., Cunningham, R.P. and Tainer J.A. (2008) DNA apurinic-apyrimidinic site binding and excision by endonuclease IV. Nat. Struct. Mol. Biol15, 515-522.
  • Rooney, J.P., Patil, A., Conklin, D.C., Cunningham, R.P., and Begley, T.J. (2008) A Molecular Bar-Coded DNA Repair Resource for Pooled Toxicogenomic Screens. DNA Repair 7, 1855-1868.
  • Burgis N.E., Cunningham R.P. (2007) Substrate specificity of RdgB protein, a deoxyribonucleoside triphosphate pyrophosphohydrolase. J. Biol. Chem. 282, 3531-3538.
  • Ocampo-Hafalla, M.T.; Chan, M.K., Altamirano, A., Basu, A.K., Ocampo, J.E.A., Cummings, A., Boorstein, R.J., Cunningham, R.P., and Teebor, G.W.(2006) Repair of thymine glycol by hNth1 and hNeil1 is modulated by base pairing and cis-trans epimerization. DNA Repair 5, 444-454.
  • Aramini J.M., Cleaver S.H., Pon R.T., Cunningham R.P., Germann M.W. (2004) Solution structure of a DNA duplex containing an alpha-anomeric adenosine: insights into substrate recognition by endonuclease IV. J Mol Biol. 338, 77-91.
  • Begley, T.J., Haas, B.J., Morales, J.C., Kool, E.T., and Cunningham, R.P. (2003) Kinetics and binding of the thymine-DNA mismatch glycosylase, Mig-Mth, with mismatch-containing DNA substrates. DNA Repair 2, 107-120. 
  • Marenstein, D.R., Chan, M.K., Altamirano, A., Basu, A.K., Boorstein, R.J., Cunningham, R. P., and Teebor, G.W. (2003) Substrate specificity of human endonuclease III (hNth1): Effect of human AP endonuclease 1 (APE1) on hNTh1 Activity. J. Biol. Chem. 278, 9005-9012. 
  • Burgis, N.E., Brucker, J, J. and Cunningham, R.P. (2003) A repair system for non-canonical purines in Escherichia coli. J. Bacteriol. 185, 3101-3110.
  • Ocampo, M.T.A., Chaung, W., Marenstein, D.R., Chan, M.K., Altamirano, A., Basu, A.K., Boorstein, R.J., Cunningham, R.P., and Teebor, G.W. (2002) Targeted deletion of mNth1 reveals a novel DNA repair enzyme activity. Mol. Cell. Biol. 22, 6111-6121. 
  • Mol, C.D., Arvai A. S., Begley, T. J., Cunningham, R. P., and Tainer, J. A. (2002) Structure and Activity of a Thermostable Thymine-DNA Glycosylase : Evidence for Base Twisting to Remove Mismatched Normal DNA Bases. J. Mol. Biol. 315,373-384. 
  • Marenstein, D.R., Ocampo, M.T., Chan, M.K., Altamirano, A., Basu, A.K., Boorstein, R.J., Cunningham, R.P., and Teebor, G.W. (2001) Stimulation of human endonuclease III by Y box-binding protein 1 (DNA-binding protein B). Interaction between a base excision repair enzyme and a transcription factor. J. Biol. Chem. 276,21242-21249. 
  • Hashimoto M, Greenberg MM, Kow YW, Hwang JT, Cunningham RP. (2001) The 2-deoxyribonolactone lesion produced in DNA by neocarzinostatin and other damaging agents forms cross-links with the base-excision repair enzyme endonuclease III. J. Am. Chem. Soc. 123,3161-3162. 
  • Chheda A.D., Teebor G.W., and Cunningham, R.P. (2000) Identification, characterization, and purification of DNA glycosylase/AP lyases by reductive crosslinking to 2'-deoxyribooligonucleotides containing specific base lesions. Methods 22,180-187. 
  • Milligan, J. R., Aguilera J. A., Nguyen, T\_T. D., Ward, J. F., Kow, Y. W., He, B. and Cunningham, R. P. (1999) Yield of DNA Strand Breaks after Base Oxidation of Plasmid DNA. Radiat. Res. 151, 334-342.
  • Begley, T. J. and Cunningham R.P. (1999) Methanobacterium thermoformicicum Thymine DNA mismatch glycosylase: conversion of an N-glycosylase to an AP lyase. Protein Engineering,12, 333-340. 
  • Haas B.J., Sandigursky, M., Tainer, J.A., Franklin, W.A. and Cunningham, R.P. (1999) Purification and characterization of Thermotoga maritima endonuclease IV; a thermostable apurinic/apyrimidinic endonuclease and 3'-repair diesterase. J. Bacteriol. 181, 2834-2839. 
  • Begley, T.J., Haas B.J., Noel, J., Shekhtman, A., Williams, W.A., and Cunningham, R.P. (1999) A new member of the endonuclease III family of DNA repair enzymes which removes methylated purines from DNA. Current Biology 9, 653-656. 
  • Bazar, L.S., Collier, G.B., Vanek, P.G., Siles, B.A., Kow, Y.W., Doetsch, P.W., Cunningham, R.P., and Chirikjian, J.G. (1999) Mutation identification DNA analysis system (MIDAS) for detection of known mutations. Electrophoresis 6, 1141-1148. 
  • Shekhtman, A., McNaughton, L., Cunningham, R.P., and Baxter, S.M. (1999) Identification of the Archaeoglobul fulgidus endonuclease III-DNA interaction surface using heteronuclear NMR methods. Structure 7, 919-930. 
  • Hosfield, D.J., Guan, Y., Haas, B.J., Cunningham, R.P., and Tainer J.A. (1999) Structure of the DNA repair enzyme endonuclease IV and its complex with DNA: double-nucleotide flipping at abasic sites and three-metal-ion catalysis. Cell 98, 397-408. 
  • Hilbert, T.P., Chaung, W., Boorstein, R.J., Cunningham, R.P., and Teebor, G.W. (1997) Cloning and expression of the cDNA encoding the human homologue of the DNA repair enzyme, Escherichia coli endonuclease III. J. Biol. Chem. 272, 6733-6740. 
  • Jen, J., Mitchell, D.L., Cunningham, R.P., Smith, C.A., Taylor, J-S., and Cleaver, J.E. (1997)Ultraviolet irradiation produces novel endonuclease III-sensitive cytosine photoproducts at dipyrimidine sites. Photobiol. Photochem. 65, 323-329. 
  • Cunningham, R.P. (1997) DNA glycosylases. Mutat. Res. 383, 189-196. 
  • Cunningham, R.P. (1997) Caretakers of the genome? Curr. Biol. 7, 576-579. 
  • Hilbert, T.P., Boorstein, R.J., Xing, D., Kung, P.H., Bolton, P.H., Cunningham, R.P. and Teebor, G.W. (1996) Purification of a mammalian homolog of E. coli endonuclease III: Identification of a calf thymus pyrimidine hydrate/thymine glycol/AP lyase by crosslinking the enzyme to a thymine glycol-containing DNA-oligonucleotide. Biochemistry 35,2505-2511. 
  • Cunningham, R.P. (1996) DNA repair: How yeast repair radical damage. Curr. Biol. 6, 1230-1233. 
  • Purmal, A.A., Rabow, L..E, Lampman, G.W., Cunningham, R.P.and Kow Y.W. (1996) A common mechanism of action for the N-glycosylase activity of DNA N-glycosylase/AP lyases from E. coli and T4. Mutat. Res. 364, 193-207. 
  • Milligan J.R., Ng J.Y., Wu C.C., Aguilera J.A., Ward J.F., Kow Y.W., Wallace S.S. and Cunningham R.P. (1996) Methylperoxyl radicals as intermediates in the damage to DNA irradiated in aqueous dimethyl sulfoxide with gamma rays. Radiat. Res. 146, 436-443. 
  • O' Handley, S., Scholes, C.P., and Cunningham, R.P. (1995) Endonuclease III interactions with DNA substrates: 1. Binding and footprinting studies with oligonucleotides containing a reduced apyrimidinic site. Biochemistry 34,2528-2536. 
  • Xing, D. Dorr, R., Cunningham, R.P., and Scholes, C.P. (1995) Endonuclease III interactions with DNA substrates: 2. The DNA repair enzyme endonuclease III binds differently to intact and to AP DNA substrates as shown by tryptophan fluorescence quenching. Biochemistry 34,2537-2544. 
  • Mol, C.D., Kuo, C-F., Thayer, MM, Cunningham, R.P. and Tainer, J.A. (1995) Structure and function of the multifunctional DNA repair enzyme exonuclease III. Nature 374,381-386. 
  • Barzilay, G., Mol, C.D. Robson, C.N. Walker, L.J. Cunningham, R.P., Tainer, J.A., and Hickson, I.D. (1995) Identification of critical active-site residues in the multifunctional human DNA repair enzyme HAP1. Nature Structural Biology 2,561-568. 
  • Thayer, M.M., Ahern, H., Xing, D., Cunningham, R.P., and Tainer, J.A. (1995) Novel DNA binding motifs in the DNA-repair enzyme endonuclease III structure. EMBO J. 14,4108-4120. 
  • Zuo, S., Boorstein, R.J., Cunningham, R.P. and Teebor, G.W. (1995) Comparison of the effects of UV irradiation on 5-methylsubstituted and unsubstituted pyrimidines in alternating Py-Pu sequences in DNA. Biochemistry 34,11582-11590. 
  • O'Donnell, R.E., Boorstein, R.J., Cunningham, R.P., and Teebor, G.W. (1994) Effect of pH and temperature on the stability of UV-induced repairable pyrimidine hydrates in DNA. Biochemistry33,9875-9880. 
  • Hatahet, Z., Kow, Y.W., Purmal, A.A., Cunningham, R.P., and Wallace, S.S. (1994) New substrates for old enzymes: 5-hydroxy-2' -deoxycytidine and 5-hydroxy-2' - deoxyuridine are substrates for Escherichia coli endonuclease III and formamidopyrimidine DNA N-glycosylase while 5-hydroxy-2, -deoxyuridine is a substrate for uracil DNA N-glycosylase. J.Biol.Chem. 269,18814-18820.