Publications
Pre-Prints
Bai G, Endres T, Kühbacher U, Greer BH, Peacock EM, Crossley MP, Sathirachinda A, Cortez D, Eichman BF, Cimprich KA (2023) HLTF Prevents G4 Accumulation and Promotes G4-induced Fork Slowing to Maintain Genome Stability. bioRxiv 2023.10.27.563641. PDF
2024
Mullins EA, Salay LE, Durie CL, Bradley NP, Jackman JE, Ohi MD, Chazin WJ*, and Eichman BF* (2024) A mechanistic model of primer synthesis from catalytic structures of DNA polymerase α–primase. Nat Struct Mol Biol https://doi.org/10.1038/s41594-024-01227-4. PDF
2023
Rua-Fernandez J, Lovejoy CA, Mehta KPM, Paulin KA, Toudji YT, Giansanti C, Eichman BF, Cortez D (2023) Self-reversal facilitates the resolution of HMCES-DNA protein crosslinks in cells. Cell Rep, 42: 113427. PDF
Cordoba JJ, Mullins EA, Salay LE, Eichman BF, and Chazin WJ (2023) Flexibility and distributive synthesis regulate RNA priming and handoff in human DNA polymerase α–primase. J Mol Biol, 435: 168330. PDF
Eichman BF (2023) Repair and tolerance of DNA damage at the replication fork: a structural perspective. Curr Opin Struct Biol, 81: 102618. PDF
Ngo K, Gittens TH, Gonzalez DI, Hatmaker EA, Plotkin S, Engle M, Friedman GA, Goldin M, Hoerr RE, Eichman BF, Rokas A, Benton ML, and Friedman KL (2023) A comprehensive map of hotspots of de novo telomere addition in Saccharomyces cerevisiae. Genetics, 224: iyad076. PDF
Dorival J and Eichman BF (2023) Human and bacterial TatD enzymes exhibit apurinic/apyrimidinic (AP) endonuclease activity. Nucleic Acids Res, 51:2838-2849. PDF
Campos LV, Greer BH, Heintzman DR, Kavlashvili T, McDonald WH, Rose KL, Eichman BF, Dewar JM (2023) RTEL1 and MCM10 overcome topological stress during vertebrate replication termination. Cell Reports, 42: 112109. PDF
2022
Paulin KA, Cortez D, Eichman BF (2022) The SOS response-associated peptidase (SRAP) domain of YedK catalyzes ring opening of abasic sites and reversal of its DNA-protein crosslink. J Biol Chem, 298: 102307. PDF
Bradley NP★, Wahl KL★, Steenwyk JL, Rokas A, Eichman BF (2022) Resistance-guided mining of bacterial genotoxins defines a family of DNA glycosylases. mBio, 13: e03297-21. PDF
Chen X★, Bradley NP★, Lu W, Wahl KL, Zhang M, Yuan H, Hou X-F, Eichman BF*, Tang G-L* (2022) Base excision repair system targeting DNA adducts of trioxacarcin/LL-D49194 antibiotics for self-resistance. Nucleic Acids Res, 50: 2417-2430. PDF
2021
Mullins EA★, Dorival J★, Tang G-L, Boger DL, and Eichman BF (2021) Structural evolution of a DNA repair self-resistance mechanism targeting genotoxic secondary metabolites. Nat Commun, 12: 6942. PDF
2020
Rodriguez AA, Wojtaszek JL, Greer B, Haldar T, Gates KS, Williams RS*, and Eichman BF* (2020) An autoinhibitory role for the GRF zinc finger domain of NEIL3 DNA glycosylase. J Biol Chem, 295: 15566-15575. PDF
Amidon KM and Eichman BF (2020) Structural biology of DNA abasic site protection by SRAP proteins. DNA Repair, 94: 102903. PDF
Bradley NP, Washburn LA, Watanabe CMH, and Eichman BF (2020) Escherichia coli YcaQ is a DNA glycosylase that unhooks interstrand crosslinks. Nucleic Acids Res., 48: 7005-7017. PDF Breakthrough Article
Bai G, Kermi C, Stoy H, Schiltz CJ, Bacal J, Zaino AM, Hadden MK, Eichman BF, Lopes M, Cimprich KA (2020) HLTF promotes fork reversal, limiting replication stress resistance and preventing multiple mechanisms of unrestrained DNA synthesis. Mol Cell, 78: 1237-1251. PDF
Nejad MI, Housh K, Rodriguez AA, Haldar T, Kathe S, Wallace SS, Eichman BF*, and Gates KS* (2020) Unhooking of an interstrand cross-link at DNA fork structures by the DNA glycosylase NEIL3. DNA Repair, 86:102752. PDF
2019
Thompson PS★, Amidon KM★, Mohni KN, Cortez D*, and Eichman BF* (2019) Protection of abasic sites during DNA replication by a stable thiazolidine protein-DNA crosslink. Nat Struct Mol Biol, 26: 613-618. PDF NEWS & VIEWS
Mullins EA, Rodriguez AA, Bradley NP, and Eichman BF (2019) Emerging roles of DNA glycosylases and the base excision repair pathway. Trends Biochem Sci, 44: 765-781. (**cover article**) PDF
Paulson CN, John K, Baxley RM, Kurniawan F, Kurahashi K, Francis R, Sobeck A, Eichman BF, Chazin WJ, Aihara H, Georg GI, Hawkinson JE, and Bielinsky AK (2019) The anti-parasitic agent suramin and several of its analogs are inhibitors of the DNA binding protein Mcm10. Open Biol, 9: 190117.
Steenwyk JL, Opulente DA, Kominek J, Shen X, Zhou X, Labella AL, Bradley NP, Eichman BF, Čadež N, Libkind D, DeVirgilio J, Hulfachor AB, Kurtzman CP, Hittinger CT*, and Rokas A*(2019) Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts. PLOS Biol, 17:e3000255. PDF
Mohni KN, Wessel SR, Zhao R, Wojciechowski AC, Luzwick JW, Layden H, Eichman BF, Thompson PS, Mehta KPM, Cortez D (2019) HMCES maintains genome integrity by shielding abasic sites in single strand DNA. Cell, 176: 144-153. PDF
2018
Warren GM, Stein RA, Mchaourab HS, and Eichman BF (2018) Movement of the RecG motor domain upon DNA binding is required for efficient DNA fork reversal. Int J Mol Sci, 19: 3049. PDF
Shi R, Shen X, Rokas A, and Eichman BF (2018) Structural biology of the HEAT-like repeat family of DNA glycosylases. BioEssays, 40: 1800133. PDF
Chavez DA, Greer BH, Eichman BF (2018) The HIRAN domain of helicase-like transcription factor positions the DNA translocase motor to drive efficient DNA fork regression. J Biol Chem, 293: 8484-94. PDF
Shi R, Mullins EA, Shen X, Lay K, Yuen P, David SS, Rokas A, Eichman BF (2018) Selective base excision repair of DNA damage by the non-base-flipping DNA glycosylase AlkC. EMBO J, 37: 63-74. PDF
2017
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 VIEWPOINT
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 F1000
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 Opin 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 Opin 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
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