Profile

DNA damage arising from exposure to environmental toxins and cellular metabolites thwarts DNA replication and leads to genome instability, cell death, and diseases including cancer. This laboratory uses the tools of structural biology and biochemistry to investigate molecular mechanisms of proteins involved in repairing DNA damage and maintaining replication fork progression. Current work focuses on base excision repair of DNA alkylation damage by DNA glycosylases and repair of stalled replication forks by structure-specific DNA translocases. The long-term goals are to understand the fundamental processes underlying genome maintenance and to develop new therapeutic strategies that target genetic diseases.

Publications

The following timeline graph is generated from all co-authored publications.

Featured publications are shown below:

  1. A Catalytic Role for C-H/π Interactions in Base Excision Repair by Bacillus cereus DNA Glycosylase AlkD. Parsons ZD, Bland JM, Mullins EA, Eichman BF (2016) J Am Chem Soc 138(36): 11485-8
    › Primary publication · 27571247 (PubMed) · PMC5034759 (PubMed Central)
  2. Data publication with the structural biology data grid supports live analysis. Meyer PA, Socias S, Key J, Ransey E, Tjon EC, Buschiazzo A, Lei M, Botka C, Withrow J, Neau D, Rajashankar K, Anderson KS, Baxter RH, Blacklow SC, Boggon TJ, Bonvin AM, Borek D, Brett TJ, Caflisch A, Chang CI, Chazin WJ, Corbett KD, Cosgrove MS, Crosson S, Dhe-Paganon S, Di Cera E, Drennan CL, Eck MJ, Eichman BF, Fan QR, Ferré-D'Amaré AR, Fromme JC, Garcia KC, Gaudet R, Gong P, Harrison SC, Heldwein EE, Jia Z, Keenan RJ, Kruse AC, Kvansakul M, McLellan JS, Modis Y, Nam Y, Otwinowski Z, Pai EF, Pereira PJ, Petosa C, Raman CS, Rapoport TA, Roll-Mecak A, Rosen MK, Rudenko G, Schlessinger J, Schwartz TU, Shamoo Y, Sondermann H, Tao YJ, Tolia NH, Tsodikov OV, Westover KD, Wu H, Foster I, Fraser JS, Maia FR, Gonen T, Kirchhausen T, Diederichs K, Crosas M, Sliz P (2016) Nat Commun : 10882
    › Primary publication · 26947396 (PubMed) · PMC4786681 (PubMed Central)
  3. Identification of a Substrate Recognition Domain in the Replication Stress Response Protein Zinc Finger Ran-binding Domain-containing Protein 3 (ZRANB3). Badu-Nkansah A, Mason AC, Eichman BF, Cortez D (2016) J Biol Chem 291(15): 8251-7
    › Primary publication · 26884333 (PubMed) · PMC5414104 (PubMed Central)
  4. The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions. Mullins EA, Shi R, Parsons ZD, Yuen PK, David SS, Igarashi Y, Eichman BF (2015) Nature 527(7577): 254-8
    › Primary publication · 26524531 (PubMed) · PMC4896645 (PubMed Central)
  5. HLTF's Ancient HIRAN Domain Binds 3' DNA Ends to Drive Replication Fork Reversal. Kile AC, Chavez DA, Bacal J, Eldirany S, Korzhnev DM, Bezsonova I, Eichman BF, Cimprich KA (2015) Mol Cell 58(6): 1090-100
    › Primary publication · 26051180 (PubMed) · PMC4475461 (PubMed Central)
  6. A structure-specific nucleic acid-binding domain conserved among DNA repair proteins. Mason AC, Rambo RP, Greer B, Pritchett M, Tainer JA, Cortez D, Eichman BF (2014) Proc Natl Acad Sci U S A 111(21): 7618-23
    › Primary publication · 24821763 (PubMed) · PMC4040553 (PubMed Central)
  7. Structural analysis of replication protein A recruitment of the DNA damage response protein SMARCAL1. Feldkamp MD, Mason AC, Eichman BF, Chazin WJ (2014) Biochemistry 53(18): 3052-61
    › Primary publication · 24730652 (PubMed) · PMC4020579 (PubMed Central)
  8. 5-methylcytosine recognition by Arabidopsis thaliana DNA glycosylases DEMETER and DML3. Brooks SC, Fischer RL, Huh JH, Eichman BF (2014) Biochemistry 53(15): 2525-32
    › Primary publication · 24678721 (PubMed) · PMC4004242 (PubMed Central)
  9. Insights into eukaryotic primer synthesis from structures of the p48 subunit of human DNA primase. Vaithiyalingam S, Arnett DR, Aggarwal A, Eichman BF, Fanning E, Chazin WJ (2014) J Mol Biol 426(3): 558-69
    › Primary publication · 24239947 (PubMed) · PMC3946992 (PubMed Central)
  10. An HPLC-tandem mass spectrometry method for simultaneous detection of alkylated base excision repair products. Mullins EA, Rubinson EH, Pereira KN, Calcutt MW, Christov PP, Eichman BF (2013) Methods 64(1): 59-66
    › Primary publication · 23876937 (PubMed) · PMC3812247 (PubMed Central)
  11. Substrate-selective repair and restart of replication forks by DNA translocases. Bétous R, Couch FB, Mason AC, Eichman BF, Manosas M, Cortez D (2013) Cell Rep 3(6): 1958-69
    › Primary publication · 23746452 (PubMed) · PMC3700663 (PubMed Central)
  12. Non-productive DNA damage binding by DNA glycosylase-like protein Mag2 from Schizosaccharomyces pombe. Adhikary S, Cato MC, McGary KL, Rokas A, Eichman BF (2013) DNA Repair (Amst) 12(3): 196-204
    › Primary publication · 23273506 (PubMed) · PMC4008723 (PubMed Central)
  13. Recent advances in the structural mechanisms of DNA glycosylases. Brooks SC, Adhikary S, Rubinson EH, Eichman BF (2013) Biochim Biophys Acta 1834(1): 247-71
    › Primary publication · 23076011 (PubMed) · PMC3530658 (PubMed Central)
  14. SMARCAL1 catalyzes fork regression and Holliday junction migration to maintain genome stability during DNA replication. Bétous R, Mason AC, Rambo RP, Bansbach CE, Badu-Nkansah A, Sirbu BM, Eichman BF, Cortez D (2012) Genes Dev 26(2): 151-62
    › Primary publication · 22279047 (PubMed) · PMC3273839 (PubMed Central)
  15. Nucleic acid recognition by tandem helical repeats. Rubinson EH, Eichman BF (2012) Curr Opin Struct Biol 22(1): 101-9
    › Primary publication · 22154606 (PubMed) · PMC3766767 (PubMed Central)
  16. Analysis of substrate specificity of Schizosaccharomyces pombe Mag1 alkylpurine DNA glycosylase. Adhikary S, Eichman BF (2011) EMBO Rep 12(12): 1286-92
    › Primary publication · 21960007 (PubMed) · PMC3245690 (PubMed Central)
  17. Domain structure of the DEMETER 5-methylcytosine DNA glycosylase. Mok YG, Uzawa R, Lee J, Weiner GM, Eichman BF, Fischer RL, Huh JH (2010) Proc Natl Acad Sci U S A 107(45): 19225-30
    › Primary publication · 20974931 (PubMed) · PMC2984145 (PubMed Central)
  18. An unprecedented nucleic acid capture mechanism for excision of DNA damage. Rubinson EH, Gowda AS, Spratt TE, Gold B, Eichman BF (2010) Nature 468(7322): 406-11
    › Primary publication · 20927102 (PubMed) · PMC4160814 (PubMed Central)
  19. Insights into eukaryotic DNA priming from the structure and functional interactions of the 4Fe-4S cluster domain of human DNA primase. Vaithiyalingam S, Warren EM, Eichman BF, Chazin WJ (2010) Proc Natl Acad Sci U S A 107(31): 13684-9
    › Primary publication · 20643958 (PubMed) · PMC2922289 (PubMed Central)
  20. Structural basis for DNA binding by replication initiator Mcm10. Warren EM, Vaithiyalingam S, Haworth J, Greer B, Bielinsky AK, Chazin WJ, Eichman BF (2008) Structure 16(12): 1892-901
    › Primary publication · 19081065 (PubMed) · PMC2636851 (PubMed Central)
  21. Structure and DNA binding of alkylation response protein AidB. Bowles T, Metz AH, O'Quin J, Wawrzak Z, Eichman BF (2008) Proc Natl Acad Sci U S A 105(40): 15299-304
    › Primary publication · 18829440 (PubMed) · PMC2563087 (PubMed Central)
  22. DNA damage recognition and repair by 3-methyladenine DNA glycosylase I (TAG). Metz AH, Hollis T, Eichman BF (2007) EMBO J 26(9): 2411-20
    › Primary publication · 17410210 (PubMed) · PMC1864966 (PubMed Central)
  23. Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase. Brieba LG, Eichman BF, Kokoska RJ, Doublié S, Kunkel TA, Ellenberger T (2004) EMBO J 23(17): 3452-61
    › Primary publication · 15297882 (PubMed) · PMC516626 (PubMed Central)
  24. Crystal structures of 3-methyladenine DNA glycosylase MagIII and the recognition of alkylated bases. Eichman BF, O'Rourke EJ, Radicella JP, Ellenberger T (2003) EMBO J 22(19): 4898-909
    › Primary publication · 14517230 (PubMed) · PMC204488 (PubMed Central)
  25. The inherent properties of DNA four-way junctions: comparing the crystal structures of holliday junctions. Eichman BF, Ortiz-Lombardía M, Aymamí J, Coll M, Ho PS (2002) J Mol Biol 320(5): 1037-51
    › Primary publication · 12126623 (PubMed) · PMC4537162 (PubMed Central)
  26. The crystal structures of DNA Holliday junctions. Ho PS, Eichman BF (2001) Curr Opin Struct Biol 11(3): 302-8
    › Primary publication · 11406378 (PubMed)
  27. The crystal structures of psoralen cross-linked DNAs: drug-dependent formation of Holliday junctions. Eichman BF, Mooers BH, Alberti M, Hearst JE, Ho PS (2001) J Mol Biol 308(1): 15-26
    › Primary publication · 11302703 (PubMed)
  28. The extended and eccentric E-DNA structure induced by cytosine methylation or bromination. Vargason JM, Eichman BF, Ho PS (2000) Nat Struct Biol 7(9): 758-61
    › Primary publication · 10966645 (PubMed)
  29. The Holliday junction in an inverted repeat DNA sequence: sequence effects on the structure of four-way junctions. Eichman BF, Vargason JM, Mooers BH, Ho PS (2000) Proc Natl Acad Sci U S A 97(8): 3971-6
    › Primary publication · 10760268 (PubMed) · PMC18126 (PubMed Central)
  30. The intrinsic structure and stability of out-of-alternation base pairs in Z-DNA. Eichman BF, Schroth GP, Basham BE, Ho PS (1999) Nucleic Acids Res 27(2): 543-50
    › Primary publication · 9862978 (PubMed) · PMC148213 (PubMed Central)
  31. The structures and relative stabilities of d(G x G) reverse Hoogsteen, d(G x T) reverse wobble, and d(G x C) reverse Watson-Crick base-pairs in DNA crystals. Mooers BH, Eichman BF, Ho PS (1997) J Mol Biol 269(5): 796-810
    › Primary publication · 9223642 (PubMed)