Stephen Kowalczykowski

InstitutionUniversity of California Davis
Address310 Briggs Hall
CA 95616
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    1. Graham JE, Marians KJ, Kowalczykowski S. Independent and Stochastic Action of DNA Polymerases in the Replisome. Cell. 2017 Jun 15; 169(7):1201-1213.e17. PMID: 28622507.
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    2. Gong Y, Handa N, Kowalczykowski S, de Lange T. PHF11 promotes DSB resection, ATR signaling, and HR. Genes Dev. 2017 01 01; 31(1):46-58. PMID: 28115467.
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    3. Bell JC, Kowalczykowski S. RecA: Regulation and Mechanism of a Molecular Search Engine: (Trends in Biochemical Sciences, June 2016, Vol. 41, No. 6, 491--507). Trends Biochem Sci. 2016 07; 41(7):646. PMID: 27283513.
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    4. Bell JC, Kowalczykowski S. RecA: Regulation and Mechanism of a Molecular Search Engine. Trends Biochem Sci. 2016 06; 41(6):491-507. PMID: 27156117.
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    5. Bell JC, Kowalczykowski S. Mechanics and Single-Molecule Interrogation of DNA Recombination. Annu Rev Biochem. 2016 Jun 02; 85:193-226. PMID: 27088880.
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    6. Rad B, Forget AL, Baskin RJ, Kowalczykowski S. Single-molecule visualization of RecQ helicase reveals DNA melting, nucleation, and assembly are required for processive DNA unwinding. Proc Natl Acad Sci U S A. 2015 Dec 15; 112(50):E6852-61. PMID: 26540728; PMCID: PMC4687592.
    7. Kowalczykowski S. An Overview of the Molecular Mechanisms of Recombinational DNA Repair. Cold Spring Harb Perspect Biol. 2015 Nov 02; 7(11). PMID: 26525148.
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    8. Bell JC, Liu B, Kowalczykowski S. Imaging and energetics of single SSB-ssDNA molecules reveal intramolecular condensation and insight into RecOR function. Elife. 2015 Sep 18; 4:e08646. PMID: 26381353; PMCID: PMC4652220.
    9. Wang AT, Kim T, Wagner JE, Conti BA, Lach FP, Huang AL, Molina H, Sanborn EM, Zierhut H, Cornes BK, Abhyankar A, Sougnez C, Gabriel SB, Auerbach AD, Kowalczykowski S, Smogorzewska A. A Dominant Mutation in Human RAD51 Reveals Its Function in DNA Interstrand Crosslink Repair Independent of Homologous Recombination. Mol Cell. 2015 Aug 06; 59(3):478-90. PMID: 26253028; PMCID: PMC4529964.
    10. Lee KY, Im JS, Shibata E, Park J, Handa N, Kowalczykowski S, Dutta A. MCM8-9 complex promotes resection of double-strand break ends by MRE11-RAD50-NBS1 complex. Nat Commun. 2015 Jul 28; 6:7744. PMID: 26215093; PMCID: PMC4525285.
    11. Chen H, Donnianni RA, Handa N, Deng SK, Oh J, Timashev LA, Kowalczykowski S, Symington LS. Sae2 promotes DNA damage resistance by removing the Mre11-Rad50-Xrs2 complex from DNA and attenuating Rad53 signaling. Proc Natl Acad Sci U S A. 2015 Apr 14; 112(15):E1880-7. PMID: 25831494; PMCID: PMC4403154.
    12. Fasching CL, Cejka P, Kowalczykowski S, Heyer WD. Top3-Rmi1 dissolve Rad51-mediated D loops by a topoisomerase-based mechanism. Mol Cell. 2015 Feb 19; 57(4):595-606. PMID: 25699708.
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    13. Morimatsu K, Kowalczykowski S. RecQ helicase and RecJ nuclease provide complementary functions to resect DNA for homologous recombination. Proc Natl Acad Sci U S A. 2014 Dec 02; 111(48):E5133-42. PMID: 25411316; PMCID: PMC4260596.
    14. Liu B, Baskin RJ, Kowalczykowski S. DNA unwinding heterogeneity by RecBCD results from static molecules able to equilibrate. Nature. 2013 Aug 22; 500(7463):482-5. PMID: 23851395; PMCID: PMC3779544.
    15. Paeschke K, Bochman ML, Garcia PD, Cejka P, Friedman KL, Kowalczykowski S, Zakian VA. Pif1 family helicases suppress genome instability at G-quadruplex motifs. Nature. 2013 May 23; 497(7450):458-62. PMID: 23657261; PMCID: PMC3680789.
    16. Cannavo E, Cejka P, Kowalczykowski S. Relationship of DNA degradation by Saccharomyces cerevisiae exonuclease 1 and its stimulation by RPA and Mre11-Rad50-Xrs2 to DNA end resection. Proc Natl Acad Sci U S A. 2013 Apr 30; 110(18):E1661-8. PMID: 23589858; PMCID: PMC3645542.
    17. Forget AL, Dombrowski CC, Amitani I, Kowalczykowski S. Exploring protein-DNA interactions in 3D using in situ construction, manipulation and visualization of individual DNA dumbbells with optical traps, microfluidics and fluorescence microscopy. Nat Protoc. 2013 Mar; 8(3):525-38. PMID: 23411634; PMCID: PMC4329291.
    18. Jensen RB, Ozes A, Kim T, Estep A, Kowalczykowski S. BRCA2 is epistatic to the RAD51 paralogs in response to DNA damage. DNA Repair (Amst). 2013 Apr 01; 12(4):306-11. PMID: 23384538; PMCID: PMC3602134.
    19. Bell JC, Plank JL, Dombrowski CC, Kowalczykowski S. Direct imaging of RecA nucleation and growth on single molecules of SSB-coated ssDNA. Nature. 2012 Nov 08; 491(7423):274-8. PMID: 23103864; PMCID: PMC4112059.
    20. Morimatsu K, Wu Y, Kowalczykowski S. RecFOR proteins target RecA protein to a DNA gap with either DNA or RNA at the 5' terminus: implication for repair of stalled replication forks. J Biol Chem. 2012 Oct 12; 287(42):35621-30. PMID: 22902627; PMCID: PMC3471720.
    21. Cejka P, Plank JL, Dombrowski CC, Kowalczykowski S. Decatenation of DNA by the S. cerevisiae Sgs1-Top3-Rmi1 and RPA complex: a mechanism for disentangling chromosomes. Mol Cell. 2012 Sep 28; 47(6):886-96. PMID: 22885009; PMCID: PMC3462259.
    22. Nimonkar AV, Dombrowski CC, Siino JS, Stasiak AZ, Stasiak A, Kowalczykowski S. Saccharomyces cerevisiae Dmc1 and Rad51 proteins preferentially function with Tid1 and Rad54 proteins, respectively, to promote DNA strand invasion during genetic recombination. J Biol Chem. 2012 Aug 17; 287(34):28727-37. PMID: 22761450; PMCID: PMC3436576.
    23. Ciccia A, Nimonkar AV, Hu Y, Hajdu I, Achar YJ, Izhar L, Petit SA, Adamson B, Yoon JC, Kowalczykowski S, Livingston DM, Haracska L, Elledge SJ. Polyubiquitinated PCNA recruits the ZRANB3 translocase to maintain genomic integrity after replication stress. Mol Cell. 2012 Aug 10; 47(3):396-409. PMID: 22704558; PMCID: PMC3613862.
    24. Yang L, Handa N, Liu B, Dillingham MS, Wigley DB, Kowalczykowski S. Alteration of ? recognition by RecBCD reveals a regulated molecular latch and suggests a channel-bypass mechanism for biological control. Proc Natl Acad Sci U S A. 2012 Jun 05; 109(23):8907-12. PMID: 22603793; PMCID: PMC3384165.
    25. Handa N, Yang L, Dillingham MS, Kobayashi I, Wigley DB, Kowalczykowski S. Molecular determinants responsible for recognition of the single-stranded DNA regulatory sequence, ?, by RecBCD enzyme. Proc Natl Acad Sci U S A. 2012 Jun 05; 109(23):8901-6. PMID: 22603794; PMCID: PMC3384139.
    26. Rad B, Kowalczykowski S. Translocation of E. coli RecQ helicase on single-stranded DNA. Biochemistry. 2012 Apr 03; 51(13):2921-9. PMID: 22409300; PMCID: PMC3330151.
    27. Forget AL, Kowalczykowski S. Single-molecule imaging of DNA pairing by RecA reveals a three-dimensional homology search. Nature. 2012 Feb 08; 482(7385):423-7. PMID: 22318518; PMCID: PMC3288143.
    28. Rad B, Kowalczykowski S. Efficient coupling of ATP hydrolysis to translocation by RecQ helicase. Proc Natl Acad Sci U S A. 2012 Jan 31; 109(5):1443-8. PMID: 22307597; PMCID: PMC3277138.
    29. Carreira A, Kowalczykowski S. Two classes of BRC repeats in BRCA2 promote RAD51 nucleoprotein filament function by distinct mechanisms. Proc Natl Acad Sci U S A. 2011 Jun 28; 108(26):10448-53. PMID: 21670257; PMCID: PMC3127913.
    30. Nimonkar AV, Genschel J, Kinoshita E, Polaczek P, Campbell JL, Wyman C, Modrich P, Kowalczykowski S. BLM-DNA2-RPA-MRN and EXO1-BLM-RPA-MRN constitute two DNA end resection machineries for human DNA break repair. Genes Dev. 2011 Feb 15; 25(4):350-62. PMID: 21325134; PMCID: PMC3042158.
    31. Cejka P, Plank JL, Bachrati CZ, Hickson ID, Kowalczykowski S. Rmi1 stimulates decatenation of double Holliday junctions during dissolution by Sgs1-Top3. Nat Struct Mol Biol. 2010 Nov; 17(11):1377-82. PMID: 20935631; PMCID: PMC2988882.
    32. Jensen RB, Carreira A, Kowalczykowski S. Purified human BRCA2 stimulates RAD51-mediated recombination. Nature. 2010 Oct 07; 467(7316):678-83. PMID: 20729832; PMCID: PMC2952063.
    33. Cejka P, Cannavo E, Polaczek P, Masuda-Sasa T, Pokharel S, Campbell JL, Kowalczykowski S. DNA end resection by Dna2-Sgs1-RPA and its stimulation by Top3-Rmi1 and Mre11-Rad50-Xrs2. Nature. 2010 Sep 02; 467(7311):112-6. PMID: 20811461; PMCID: PMC3089589.
    34. Forget AL, Kowalczykowski S. Single-molecule imaging brings Rad51 nucleoprotein filaments into focus. Trends Cell Biol. 2010 May; 20(5):269-76. PMID: 20299221; PMCID: PMC2862779.
    35. Cejka P, Kowalczykowski S. The full-length Saccharomyces cerevisiae Sgs1 protein is a vigorous DNA helicase that preferentially unwinds holliday junctions. J Biol Chem. 2010 Mar 12; 285(11):8290-301. PMID: 20086270; PMCID: PMC2832980.
    36. Amitani I, Liu B, Dombrowski CC, Baskin RJ, Kowalczykowski S. Watching individual proteins acting on single molecules of DNA. Methods Enzymol. 2010; 472:261-91. PMID: 20580968; PMCID: PMC3119597.
    37. Kemp MG, Mason AC, Carreira A, Reardon JT, Haring SJ, Borgstahl GE, Kowalczykowski S, Sancar A, Wold MS. An alternative form of replication protein a expressed in normal human tissues supports DNA repair. J Biol Chem. 2010 Feb 12; 285(7):4788-97. PMID: 19996105; PMCID: PMC2836084.
    38. Hilario J, Kowalczykowski S. Visualizing protein-DNA interactions at the single-molecule level. Curr Opin Chem Biol. 2010 Feb; 14(1):15-22. PMID: 19945909; PMCID: PMC2819561.
    39. Handa N, Morimatsu K, Lovett ST, Kowalczykowski S. Reconstitution of initial steps of dsDNA break repair by the RecF pathway of E. coli. Genes Dev. 2009 May 15; 23(10):1234-45. PMID: 19451222; PMCID: PMC2685532.
    40. Handa N, Amitani I, Gumlaw N, Sandler SJ, Kowalczykowski S. Single molecule analysis of a red fluorescent RecA protein reveals a defect in nucleoprotein filament nucleation that relates to its reduced biological functions. J Biol Chem. 2009 Jul 10; 284(28):18664-73. PMID: 19419960; PMCID: PMC2707236.
    41. Carreira A, Hilario J, Amitani I, Baskin RJ, Shivji MK, Venkitaraman AR, Kowalczykowski S. The BRC repeats of BRCA2 modulate the DNA-binding selectivity of RAD51. Cell. 2009 Mar 20; 136(6):1032-43. PMID: 19303847; PMCID: PMC2669112.
    42. Haseltine CA, Kowalczykowski S. An archaeal Rad54 protein remodels DNA and stimulates DNA strand exchange by RadA. Nucleic Acids Res. 2009 May; 37(8):2757-70. PMID: 19282450; PMCID: PMC2677860.
    43. Nimonkar AV, Sica RA, Kowalczykowski S. Rad52 promotes second-end DNA capture in double-stranded break repair to form complement-stabilized joint molecules. Proc Natl Acad Sci U S A. 2009 Mar 03; 106(9):3077-82. PMID: 19204284; PMCID: PMC2651264.
    44. Hilario J, Amitani I, Baskin RJ, Kowalczykowski S. Direct imaging of human Rad51 nucleoprotein dynamics on individual DNA molecules. Proc Natl Acad Sci U S A. 2009 Jan 13; 106(2):361-8. PMID: 19122145.
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    45. Dillingham MS, Kowalczykowski S. RecBCD enzyme and the repair of double-stranded DNA breaks. Microbiol Mol Biol Rev. 2008 Dec; 72(4):642-71, Table of Contents. PMID: 19052323; PMCID: PMC2593567.
    46. Nimonkar AV, Ozsoy AZ, Genschel J, Modrich P, Kowalczykowski S. Human exonuclease 1 and BLM helicase interact to resect DNA and initiate DNA repair. Proc Natl Acad Sci U S A. 2008 Nov 04; 105(44):16906-11. PMID: 18971343; PMCID: PMC2579351.
    47. Dillingham MS, Tibbles KL, Hunter JL, Bell JC, Kowalczykowski S, Webb MR. Fluorescent single-stranded DNA binding protein as a probe for sensitive, real-time assays of helicase activity. Biophys J. 2008 Oct; 95(7):3330-9. PMID: 18599625; PMCID: PMC2547451.
    48. Wu Y, Kantake N, Sugiyama T, Kowalczykowski S. Rad51 protein controls Rad52-mediated DNA annealing. J Biol Chem. 2008 May 23; 283(21):14883-92. PMID: 18337252; PMCID: PMC2386943.
    49. Spies M, Amitani I, Baskin RJ, Kowalczykowski S. RecBCD enzyme switches lead motor subunits in response to chi recognition. Cell. 2007 Nov 16; 131(4):694-705. PMID: 18022364; PMCID: PMC2151923.
    50. Nimonkar AV, Amitani I, Baskin RJ, Kowalczykowski S. Single molecule imaging of Tid1/Rdh54, a Rad54 homolog that translocates on duplex DNA and can disrupt joint molecules. J Biol Chem. 2007 Oct 19; 282(42):30776-84. PMID: 17704061.
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    51. Galletto R, Kowalczykowski S. RecA. Curr Biol. 2007 Jun 05; 17(11):R395-7. PMID: 17550759.
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    52. Sugiyama T, Kantake N, Wu Y, Kowalczykowski S. Rad52-mediated DNA annealing after Rad51-mediated DNA strand exchange promotes second ssDNA capture. EMBO J. 2006 Nov 29; 25(23):5539-48. PMID: 17093500; PMCID: PMC1679760.
    53. Handa N, Kowalczykowski S. A RecA mutant, RecA(730), suppresses the recombination deficiency of the RecBC(1004)D-chi* interaction in vitro and in vivo. J Mol Biol. 2007 Feb 02; 365(5):1314-25. PMID: 17141804; PMCID: PMC1847798.
    54. Wu Y, Siino JS, Sugiyama T, Kowalczykowski S. The DNA binding preference of RAD52 and RAD59 proteins: implications for RAD52 and RAD59 protein function in homologous recombination. J Biol Chem. 2006 Dec 29; 281(52):40001-9. PMID: 17040915.
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    55. Galletto R, Amitani I, Baskin RJ, Kowalczykowski S. Direct observation of individual RecA filaments assembling on single DNA molecules. Nature. 2006 Oct 19; 443(7113):875-8. PMID: 16988658.
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    56. Amitani I, Baskin RJ, Kowalczykowski S. Visualization of Rad54, a chromatin remodeling protein, translocating on single DNA molecules. Mol Cell. 2006 Jul 07; 23(1):143-8. PMID: 16818238.
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    57. Seitz EM, Kowalczykowski S. Human Rad51 protein displays enhanced homologous pairing of DNA sequences resembling those at genetically unstable loci. Nucleic Acids Res. 2006; 34(10):2847-52. PMID: 16723430; PMCID: PMC1474073.
    58. Chédin F, Handa N, Dillingham MS, Kowalczykowski S. The AddAB helicase/nuclease forms a stable complex with its cognate chi sequence during translocation. J Biol Chem. 2006 Jul 07; 281(27):18610-7. PMID: 16632468.
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    59. Wu Y, Sugiyama T, Kowalczykowski S. DNA annealing mediated by Rad52 and Rad59 proteins. J Biol Chem. 2006 Jun 02; 281(22):15441-9. PMID: 16565518.
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    60. Spies M, Kowalczykowski S. The RecA binding locus of RecBCD is a general domain for recruitment of DNA strand exchange proteins. Mol Cell. 2006 Feb 17; 21(4):573-80. PMID: 16483938.
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    61. Dillingham MS, Webb MR, Kowalczykowski S. Bipolar DNA translocation contributes to highly processive DNA unwinding by RecBCD enzyme. J Biol Chem. 2005 Nov 04; 280(44):37069-77. PMID: 16041061.
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    62. Spies M, Dillingham MS, Kowalczykowski S. Translocation by the RecB motor is an absolute requirement for {chi}-recognition and RecA protein loading by RecBCD enzyme. J Biol Chem. 2005 Nov 04; 280(44):37078-87. PMID: 16041060.
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    63. Handa N, Bianco PR, Baskin RJ, Kowalczykowski S. Direct visualization of RecBCD movement reveals cotranslocation of the RecD motor after chi recognition. Mol Cell. 2005 Mar 04; 17(5):745-50. PMID: 15749023.
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    64. Kowalczykowski S. Cancer: catalyst of a catalyst. Nature. 2005 Feb 10; 433(7026):591-2. PMID: 15703734.
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    65. Singleton MR, Dillingham MS, Gaudier M, Kowalczykowski S, Wigley DB. Crystal structure of RecBCD enzyme reveals a machine for processing DNA breaks. Nature. 2004 Nov 11; 432(7014):187-93. PMID: 15538360.
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    66. Mazina OM, Mazin AV, Nakagawa T, Kolodner RD, Kowalczykowski S. Saccharomyces cerevisiae Mer3 helicase stimulates 3'-5' heteroduplex extension by Rad51; implications for crossover control in meiotic recombination. Cell. 2004 Apr 02; 117(1):47-56. PMID: 15066281.
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    67. Spies M, Bianco PR, Dillingham MS, Handa N, Baskin RJ, Kowalczykowski S. A molecular throttle: the recombination hotspot chi controls DNA translocation by the RecBCD helicase. Cell. 2003 Sep 05; 114(5):647-54. PMID: 13678587.
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    68. Harmon FG, Brockman JP, Kowalczykowski S. RecQ helicase stimulates both DNA catenation and changes in DNA topology by topoisomerase III. J Biol Chem. 2003 Oct 24; 278(43):42668-78. PMID: 12909639.
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    69. Dillingham MS, Spies M, Kowalczykowski S. RecBCD enzyme is a bipolar DNA helicase. Nature. 2003 Jun 19; 423(6942):893-7. PMID: 12815438.
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    70. Mirshad JK, Kowalczykowski S. Biochemical characterization of a mutant RecA protein altered in DNA-binding loop 1. Biochemistry. 2003 May 20; 42(19):5945-54. PMID: 12741853.
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    71. Mirshad JK, Kowalczykowski S. Biochemical basis of the constitutive coprotease activity of RecA P67W protein. Biochemistry. 2003 May 20; 42(19):5937-44. PMID: 12741852.
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    72. Veaute X, Jeusset J, Soustelle C, Kowalczykowski S, Le Cam E, Fabre F. The Srs2 helicase prevents recombination by disrupting Rad51 nucleoprotein filaments. Nature. 2003 May 15; 423(6937):309-12. PMID: 12748645.
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    73. Morimatsu K, Kowalczykowski S. RecFOR proteins load RecA protein onto gapped DNA to accelerate DNA strand exchange: a universal step of recombinational repair. Mol Cell. 2003 May; 11(5):1337-47. PMID: 12769856.
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    74. Kantake N, Sugiyama T, Kolodner RD, Kowalczykowski S. The recombination-deficient mutant RPA (rfa1-t11) is displaced slowly from single-stranded DNA by Rad51 protein. J Biol Chem. 2003 Jun 27; 278(26):23410-7. PMID: 12697761.
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    75. Alexeev A, Mazin A, Kowalczykowski S. Rad54 protein possesses chromatin-remodeling activity stimulated by the Rad51-ssDNA nucleoprotein filament. Nat Struct Biol. 2003 Mar; 10(3):182-6. PMID: 12577053.
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    76. Mazin AV, Alexeev AA, Kowalczykowski S. A novel function of Rad54 protein. Stabilization of the Rad51 nucleoprotein filament. J Biol Chem. 2003 Apr 18; 278(16):14029-36. PMID: 12566442.
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    77. Kowalczykowski S. Molecular mimicry connects BRCA2 to Rad51 and recombinational DNA repair. Nat Struct Biol. 2002 Dec; 9(12):897-9. PMID: 12447354.
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    78. Kantake N, Madiraju MV, Sugiyama T, Kowalczykowski S. Escherichia coli RecO protein anneals ssDNA complexed with its cognate ssDNA-binding protein: A common step in genetic recombination. Proc Natl Acad Sci U S A. 2002 Nov 26; 99(24):15327-32. PMID: 12438681; PMCID: PMC137716.
    79. Stohl EA, Brockman JP, Burkle KL, Morimatsu K, Kowalczykowski S, Seifert HS. Escherichia coli RecX inhibits RecA recombinase and coprotease activities in vitro and in vivo. J Biol Chem. 2003 Jan 24; 278(4):2278-85. PMID: 12427742.
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    80. Lio YC, Mazin AV, Kowalczykowski S, Chen DJ. Complex formation by the human Rad51B and Rad51C DNA repair proteins and their activities in vitro. J Biol Chem. 2003 Jan 24; 278(4):2469-78. PMID: 12427746.
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    81. Sugiyama T, Kowalczykowski S. Rad52 protein associates with replication protein A (RPA)-single-stranded DNA to accelerate Rad51-mediated displacement of RPA and presynaptic complex formation. J Biol Chem. 2002 Aug 30; 277(35):31663-72. PMID: 12077133.
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    82. New JH, Kowalczykowski S. Rad52 protein has a second stimulatory role in DNA strand exchange that complements replication protein-A function. J Biol Chem. 2002 Jul 19; 277(29):26171-6. PMID: 12004070.
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    83. Haseltine CA, Kowalczykowski S. A distinctive single-strand DNA-binding protein from the Archaeon Sulfolobus solfataricus. Mol Microbiol. 2002 Mar; 43(6):1505-15. PMID: 11971263.
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    84. Chédin F, Kowalczykowski S. A novel family of regulated helicases/nucleases from Gram-positive bacteria: insights into the initiation of DNA recombination. Mol Microbiol. 2002 Feb; 43(4):823-34. PMID: 11929535.
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    85. Kowalczykowski S. Some assembly required. Nat Struct Biol. 2000 Dec; 7(12):1087-9. PMID: 11101884.
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    86. Kowalczykowski S. Initiation of genetic recombination and recombination-dependent replication. Trends Biochem Sci. 2000 Apr; 25(4):156-65. PMID: 10754547.
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