Publications

2017

Shi R, Mullins EA, Shen X, Lay K, Yuen P, David SS, Rokas A, Eichman BF (2017) Selective base excision repair of DNA damage by the non-base-flipping DNA glycosylase AlkC. EMBO J, in press. DOI 10.15252/embj.201797833   PDF

Mullins EA, Shi R, and Eichman BF (2017) Toxicity and repair of DNA adducts produced by the natural product yatakemycin. Nat Chem Biol, 13:1002-8.  PDF

Mullins EA, Warren GM, Bradley NP, and Eichman BF (2017) Structure of a DNA glycosylase that unhooks interstrand cross-links. Proc Natl Acad Sci USA, 114: 4400-4405.  PDF

2016

Parsons ZD, Bland J, Mullins EA, and Eichman BF (2016) A catalytic role for C-H/π interactions in base excision repair by Bacillus cereus DNA glycosylase AlkD. J Am Chem Soc, 138: 11485-8.  PDF

Badu-Nkansah A, Mason AC, Eichman BF, Cortez D (2016) Identification of a Substrate Recognition Domain in the Replication Stress Response Protein Zinc Finger RAN-binding Domain Containing 3 (ZRANB3). J Biol Chem, 291: 8251-7.  PDF

Meyer PA, et al (2016) Data publication with the structural biology data grid supports live analysis. Nat Commun, 7: 10882.  PDF

2015

Mullins EA, Shi R, Parsons ZD, Yuen PK, David SS, Igarashi Y, and Eichman BF (2015) The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions. Nature, 527: 254-258.  PDF   NEWS & VIEWS

Kile AC, Chavez DA, Bacal J, Eldirani S, Korzhnev DM, Bezsonova I, Eichman BF*, Cimprich KA* (2015) HLTF’s Ancient HIRAN Domain Binds 3′-DNA Ends to Drive Replication Fork Reversal. Mol Cell, 58: 1090-1100.  PDF   PREVIEW

Mullins EA, Shi R, Kotsch LA, and Eichman BF (2015) A New Family of HEAT-Like Repeat Proteins Lacking a Critical Substrate Recognition Motif Present in Related DNA Glycosylases. PLoS One, 10:e0127733.  PDF

Szulik MW, Pallan PS, Nocek B, Voehler M, Banerjee S, Brooks, SC, Joachimiak A, Egli M, Eichman BF, and Stone MP (2015) Differential stabilities and sequence-dependent base pair opening dynamics of Watson-Crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine. Biochemistry, 54:1294-305.  PDF

2014

Mason AC, Rambo RP, Greer BH, Pritchett M, Tainer JA, Cortez D, and Eichman BF (2014) A structure-specific nucleic acid-binding domain conserved among DNA repair proteins. Proc Natl Acad Sci USA, 111: 7618-7623.  PDF

Feldkamp MD, Mason AC, Eichman BF, Chazin WJ (2014) Structural analysis of RPA recruitment of the DNA damage response protein SMARCAL1. Biochemistry, 53:3052-3061.  PDF

Brooks SC, Fischer RL, Huh JH, and Eichman BF (2014) 5-methylcytosine recognition by Arabidopsis thaliana DNA glycosylases DEMETER and DML3. Biochemistry, 53: 2525-2532.  PDF

Jang H, Shin H, Eichman BF, Huh JH (2014) Excision of 5-hydroxymethylcytosine by DEMETER family DNA glycosylases. Biochem Biophys Res Commun, 446: 1067-1072. PDF

Troll CJ, Adhikary S, Mitra I, Eichman BF, and Camps M (2014) Interplay between base excision repair activity and toxicity of 3-methyladenine DNA glycosylases in an E. coli complementation system. Mutat Res, 763-764: 64-73.  PDF

Mullins EA*, Rubinson EH*, and Eichman BF (2014) The substrate binding interface of alkylpurine DNA glycosylase AlkD. DNA Repair, 13: 50-54.  PDF

Vaithiyalingam S, Arnett DR, Aggarwal A, Eichman BF, Fanning E*, and Chazin WJ* (2014) Insights into eukaryotic priming from structures of the p48 subunit of human DNA primase in pre-catalytic conformations. J Mol Biol, 426: 558-69.  PDF

2013

Rubinson EH, Christov PP, and Eichman BF (2013) Depurination of N7-methylguanine by DNA glycosylase AlkD is dependent on the DNA backbone. Biochemistry, 52:7363-7365.  PDF

Mullins EA*, Rubinson EH*, Pereira KN, Calcutt MW, Christov PP, and Eichman BF (2013) An HPLC-tandem mass spectrometry method for simultaneous detection of alkylated base excision repair products. Methods, 64: 59-66.  PDF

Du W, Josephrajan A, Adhikary S, Bowles T, Bielinsky AK, and Eichman BF (2013) Mcm10 self-association is mediated by an N-terminal coiled-coil domain. PLoS One, 8: e70518.  PDF

Bétous R, Couch FB, Mason AC, Eichman BF, Manosas M*, and Cortez D* (2013) Substrate-selective repair and restart of replication forks by DNA translocases. Cell Rep, 3: 1958-1969.  PDF

Adhikary S, Cato MC, McGary KL, Rokas A, and Eichman BF (2013) Non-productive DNA damage binding by DNA glycosylase-like protein Mag2 from Schizosaccharomyces pombe. DNA Repair, 12: 196-204.  PDF   F1000

Brooks S, Adhikary S, Rubinson EH, and Eichman BF (2013) Recent Advances in the Structural Mechanisms of DNA Glycosylases. Biochem Biophys Acta, 1834: 247-271.  (Invited review)   PDF

2012

Du W, Stauffer M, and Eichman BF (2012) Structural biology of replication initiation factor Mcm10. In MacNeill, S. (ed.), The Eukaryotic Replisome: A Guide to Protein Structure and Function. Springer Publishing Company, New York. Subcell Biochem, 62:197-216.  PDF

Shi, M., Pedchenko, V., Greer, B.H., Van Horn, W.D., Santoro, S.A., Sanders, C.R., Hudson, B.G., Eichman, B.F., Zent, R., Pozzi, A. (2012) Enhancing Integrin α1 I Domain Affinity to Ligand Potentiates Integrin α1β1-Mediated Downregulation of Collagen Synthesis. J Biol Chem, 287:35139-52.  PDF

Bétous, R., Mason, A.C., Rambo, R.P., Bansbach, C.E., Badu-Nkansah, A., Sirbu, B.M., Eichman, B.F., and Cortez, D. (2012) SMARCAL1 catalyzes fork regression and Holliday junction migration to maintain genome stability during DNA replication. Genes Dev, 26:151-62.   PDF

Rubinson, E.H. and Eichman, B.F.  (2012)  Nucleic acid recognition by tandem helical repeats. Curr Op Struct Biol, 22: 101-109.  PDF

2011

Camps, M. and Eichman, B.F. (2011) Unraveling a connection between DNA demethylation repair and cancer. Mol Cell, 44: 343-4.  PDF

Adhikary, S. and Eichman, B.F.  (2011) Analysis of substrate specificity of Schizosaccharomyces pombe Mag1 alkylpurine DNA glycosylase.  EMBO Rep, 12:1286-92.  PDF

2010

Rubinson, E.H., Spratt, T.E., Gold, B., and Eichman, B.F. (2010) An unprecedented nucleic acid capture mechanism for excision of DNA damage.  Nature, 468: 406-411.  PDF   F1000

Mok, Y.G., Uzawa, R., Lee, J., Weiner, G.M., Eichman, B.F., Fischer, R.L., Huh, J.H. (2010) Domain structure of the DEMETER 5-methylcytosine DNA glycosylase. Proc Natl Acad Sci USA, 107: 19225-19230.  PDF

Vaithiyalingam, S., Warren, E.M., Eichman, B.F.*, and Chazin, W.J.* (2010) Insights into eukaryotic DNA priming from the structure and functional interactions of the 4Fe-4S cluster domain of human DNA primase. Proc Natl Acad Sci USA, 107: 13684-13689.  PDF   F1000

Robertson, P.D., Chagot, B., Chazin, W.J.*, and Eichman, B.F.* (2010) Solution NMR structure of the C-terminal DNA binding domain of Mcm10 reveals a conserved MCM motif. J Biol Chem, 285: 22942-22949.  PDF

Rubinson, E.H., Adhikary, S., and Eichman, B.F. (2010) Structural studies of alkylpurine DNA glycosylases. In Stone, M.P. (ed.), ACS Symposium Series : Structural Biology of DNA Damage and Repair. American Chemical Society, Washington, D.C., Vol. 1041, pp. 29-45.  PDF

2004-2009

Warren, E.M., Huang, H., Fanning, E., Chazin, W.J., and Eichman, B.F. (2009) Physical interactions between Mcm10, DNA, and DNA polymerase alpha. J Biol Chem, 284: 24662-24672.  PDF

Warren, E.M., Vaithiyalingam, S., Haworth, J., Greer, B., Bielinsky, A.-K., Chazin, W.J., and Eichman, B.F. (2008)
Structural basis for DNA binding by replication initiator Mcm10. Structure, 16: 1892-1901. (**cover article**)  PDF   F1000

Bowles, T.*, Metz, A.H.*, O’Quin, J., Wawrzak, Z., and Eichman, B.F. (2008) Structure and DNA binding of alkylation response protein AidB. Proc Natl Acad Sci USA, 105: 15299-15304.  PDF

Rubinson, E.H., Metz, A.H., O’Quin, J., and Eichman, B.F. (2008) A new protein architecture for processing alkylation damaged DNA: The crystal structure of DNA glycosylase AlkD. J Mol Biol, 381: 13-23.  PDF

Robertson, P.D.*, Warren, E.M.*, Zhang, H.*, Friedman, D.B., Lary J.W., Cole, J.L., Tutter, A.V., Walter, J.C., Fanning, E., and Eichman, B.F. (2008) Domain architecture and biochemical characterization of vertebrate Mcm10. J Biol Chem, 283: 3338-3348.  PDF

Metz, A.H., Hollis, T., and Eichman, B.F. (2007) DNA damage recognition and repair by 3-methyladenine DNA glycosylase I (TAG). EMBO J, 26: 2411-2420.  PDF

Eichman, B.F. and Fanning, E. (2004) The power of pumping together; deconstructing the engine of a DNA replication machine. Cell, 119: 3-4.  PDF

Postdoctoral research with Tom Ellenberger, Harvard Medical School

Brieba, L.G., Eichman, B.F., Kokoska, R.J., Doublié, S., Kunkel, T.A., and Ellenberger, T. (2004) Structural basis for the dual coding potential of 8-oxoguanosine during nucleotide insertion and elongation by a high fidelity DNA polymerase.  EMBO J, 23: 3452-3461.  PDF

Eichman, B.F., O’Rourke, E.J., Radicella, J.P., and Ellenberger, T. (2003) Crystal structures of 3-methyladenine DNA glycosylase MagIII and the recognition of alkylated bases. EMBO J, 22: 4898-4909.  PDF   F1000

Graduate work with P. Shing Ho, Oregon State University

Eichman, B.F., Ortiz-Lombardía, M., Aymamí, J., Coll, M., and Ho, P.S. (2002) The inherent properties of DNA four-way junctions: Comparing the crystal structures of Holliday junctions. J Mol Biol, 320: 1037-1051. (**cover article**)  PDF 

Ho, P.S. and Eichman, B.F. (2001) The crystal structures of DNA Holliday junctions. Curr Op Struct Biol, 11: 302-308.  PDF

Eichman, B.F., Mooers, B.H.M., Alberti, M., Hearst, J.E., and Ho, P.S. (2001) The crystal structures of psoralen cross-linked DNA: Drug dependent formation of Holliday junctions. J Mol Biol, 308: 15-26. (**cover article**)  PDF

Vargason, J.M., Eichman, B.F., and Ho, P.S. (2000) E-DNA: An extended, eccentric structure induced by cytosine methylation and bromination. Nat Struct Biol, 7: 758-761.  PDF

Eichman, B.F., Vargason, J.M., Mooers, B.H.M., and Ho, P.S. (2000) The Holliday junction in an inverted repeat sequence: Sequence effects on the structure of four-way junctions. Proc Nat Acad Sci USA, 97: 3971-3976.  PDF

Eichman, B.F., Schroth, G.P., Basham, B., and Ho, P.S. (1999) The intrinsic structure and stability of out-of-alternation base pairs in Z-DNA. Nucleic Acids Res, 27: 543-550.  PDF

Basham, B., Eichman, B.F., and Ho, P.S. (1999) The single crystal structures of Z-DNA. In Neidle, S. (ed.), The Oxford Handbook of Nucleic Acid Structure. Oxford University Press, Oxford, UK, Vol. 1, pp. 199-252. 

Mooers, B.H.M., Eichman, B.F., and Ho, P.S. (1997) The structures and relative stabilities of d(G·G) reverse Hoogsteen, d(G·T) reverse wobble, and d(G·C) reverse Watson-Crick base-pairs in DNA crystals. J Mol Biol, 269: 796-810.  PDF