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Structure and Mechanisms of SF2 DNA Helicases

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Book cover DNA Helicases and DNA Motor Proteins

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 767))

Abstract

Effective transcription, replication, and maintenance of the genome require a diverse set of molecular machines to perform the many chemical transactions that constitute these processes. Many of these machines use single-stranded nucleic acids as templates, and their actions are often regulated by the participation of nucleic acids in multimeric structures and macromolecular assemblies that restrict access to chemical information. Superfamily II (SF2) DNA helicases and translocases are a group of molecular machines that remodel nucleic acid lattices and enable essential cellular processes to use the information stored in the duplex DNA of the packaged genome. Characteristic accessory domains associated with the subgroups of the superfamily direct the activity of the common motor core and expand the repertoire of activities and substrates available to SF2 DNA helicases, translocases, and large multiprotein complexes containing SF2 motors. In recent years, single-molecule studies have contributed extensively to the characterization of this ubiquitous and essential class of enzymes.

David C. Beyer, Mohamed Karem Ghoneim

These authors contributed equally to this work

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References

  1. Fairman-Williams ME, Guenther U-P, Jankowsky E. SF1 and SF2 helicases: family matters. Curr Opin Struct Biol. 2010;20(3):313–24.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Lohman TM, Bjornson KP. Mechanisms of helicase-catalyzed DNA unwinding. Annu Rev Biochem. 1996;65:169–214.

    Article  CAS  PubMed  Google Scholar 

  3. Lohman TM, Tomko EJ, Wu CG. Non-hexameric DNA helicases and translocases: mechanisms and regulation. Nat Rev Mol Cell Biol. 2008;9(May):391–401.

    Article  CAS  PubMed  Google Scholar 

  4. Singleton MR, Scaife S, Wigley DB. Structural analysis of DNA replication fork reversal by RecG. Cell. 2001;107(1):79–89.

    Article  CAS  PubMed  Google Scholar 

  5. Singleton MR, Dillingham MS, Wigley DB. Structure and mechanism of helicases and nucleic acid translocases. Annu Rev Biochem. 2007;76:23–50.

    Article  CAS  PubMed  Google Scholar 

  6. Singleton M. Modularity and specialization in superfamily 1 and 2 helicases. J Bacteriol. 2002;184(7):1819–26.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Delagoutte E, von Hippel PH. Helicase mechanisms and the coupling of helicases within macromolecular machines. Q Rev Biophys. 2003;36(1):1–69.

    Article  CAS  PubMed  Google Scholar 

  8. Delagoutte E, von Hippel PH. Helicase mechanisms and the coupling of helicases within macromolecular machines Part I: structures and properties of isolated helicases. Q Rev Biophys. 2002;35(4):431–78.

    Article  CAS  PubMed  Google Scholar 

  9. Myong S, Ha T. Stepwise translocation of nucleic acid motors. Curr Opin Struct Biol. 2010;20(1):121–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. von Hippel PH, Delagoutte E. A general model for nucleic acid helicases and their “coupling” within macromolecular machines. Cell. 2001;104(2):177–90.

    Article  Google Scholar 

  11. Karamanou S, Gouridis G, Papanikou E, Sianidis G, Gelis I, Keramisanou D, et al. Preprotein-controlled catalysis in the helicase motor of SecA. EMBO J. 2007;26(12):2904–14.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Petermann E, Helleday T. Pathways of mammalian replication fork restart. Nat Rev Mol Cell Biol. 2010;11(10):683–7.

    Article  CAS  PubMed  Google Scholar 

  13. Suhasini AN, Brosh RM. Mechanistic and biological aspects of helicase action on damaged DNA. Cell Cycle. 2010;9(12):2317–29.

    Article  CAS  PubMed  Google Scholar 

  14. Bochkarev A, Bochkareva E, Frappier L, Edwards AM. The crystal structure of the complex of replication protein A subunits RPA32 and RPA14 reveals a mechanism for single-stranded DNA binding. EMBO J. 1999;18(16):4498–504.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Velankar SS, Soultanas P, Dillingham MS, Subramanya HS, Wigley DB. Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism. Cell. 1999;97(1):75–84.

    Article  CAS  PubMed  Google Scholar 

  16. Pyle AM. Translocation and unwinding mechanisms of RNA and DNA helicases. Annu Rev Biophys. 2008;37:317–36.

    Article  CAS  PubMed  Google Scholar 

  17. Tanner NK, Cordin O, Banroques J, Doère M, Linder P. The Q motif: a newly identified motif in DEAD box helicases may regulate ATP binding and hydrolysis. Mol Cell. 2003;11(1):127–38.

    Article  CAS  PubMed  Google Scholar 

  18. Zhang X, Wigley DB. The “glutamate switch” provides a link between ATPase activity and ligand binding in AAA+ proteins. Nat Struct Mol Biol. 2008;15(11):1223–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Zittel MC, Keck JL. Coupling DNA-binding and ATP hydrolysis in Escherichia coli RecQ: role of a highly conserved aromatic-rich sequence. Nucleic Acids Res. 2005;33(22):6982–91.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Büttner K, Nehring S, Hopfner KP. Structural basis for DNA duplex separation by a superfamily-2 helicase. Nat Struct Mol Biol. 2007;14(7):647–52.

    Article  CAS  PubMed  Google Scholar 

  21. Atkinson J, McGlynn P. Replication fork reversal and the maintenance of genome stability. Nucleic Acids Res. 2009;37(11):3475–92.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Briggs GS, Mahdi A, Weller GR, Wen Q, Lloyd RG. Interplay between DNA replication, recombination and repair based on the structure of RecG helicase. Philos Trans R Soc Lond B Biol Sci. 2004;359(1441):49–59.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Dillingham MS, Kowalczykowski SC. A step backward in advancing DNA replication: rescue of stalled replication forks by RecG. Mol Cell. 2001;8(4):734–6.

    Article  CAS  PubMed  Google Scholar 

  24. McGlynn P, Lloyd RG. Rescue of stalled replication forks by RecG: simultaneous translocation on the leading and lagging strand templates supports an active DNA unwinding model of fork reversal and Holliday junction formation. Proc Natl Acad Sci USA. 2001;98(15):8227–34.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Buss JA, Kimura Y, Bianco PR. RecG interacts directly with SSB: implications for stalled replication fork regression. Nucleic Acids Res. 2008;36(22):7029–42.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Gregg AV, McGlynn P, Jaktaji RP, Lloyd RG. Direct rescue of stalled DNA replication forks via the combined action of PriA and RecG helicase activities. Mol Cell. 2002;9(2):241–51.

    Article  CAS  PubMed  Google Scholar 

  27. Rudolph CJ, Upton AL, Briggs GS, Lloyd RG. Is RecG a general guardian of the bacterial genome? DNA Repair. 2010;9(3):210–23.

    Article  CAS  PubMed  Google Scholar 

  28. Rudolph CJ, Mahdi AA, Upton AL, Lloyd RG. RecG protein and single-strand DNA exonucleases avoid cell lethality associated with PriA helicase activity in Escherichia coli. Genetics. 2010;186(2):473–92.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Heyer W-D. Biochemistry of eukaryotic homologous recombination. Top Curr Genet. 2007;17:95–133.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Yusufzai T, Kadonaga JT. Branching out with DNA helicases. Curr Opin Genet Dev. 2011;21(2):214–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Whitby MC. The FANCM family of DNA helicases/translocases. DNA Repair. 2010;9(3):224–36.

    Article  CAS  PubMed  Google Scholar 

  32. Wu L. Role of the BLM helicase in replication fork management. DNA Repair. 2007;6(7):936–44.

    Article  CAS  PubMed  Google Scholar 

  33. Adelman CA, Boulton SJ. Metabolism of postsynaptic recombination intermediates. FEBS Lett. 2010;584(17):3709–16.

    Article  CAS  PubMed  Google Scholar 

  34. He Y, Andersen GR, Nielsen KH. Structural basis for the function of DEAH helicases. EMBO Rep. 2010;11(3):180–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Muzzolini L, Beuron F, Patwardhan A, Popuri V, Cui S, Niccolini B, et al. Different quaternary structures of human RECQ1 are associated with its dual enzymatic activity. PLoS Biol. 2007;5(2):12.

    Article  CAS  Google Scholar 

  36. Prakash R, Krejci L, Van Komen S, Anke Schürer K, Kramer W, Sung P. Saccharomyces cerevisiae MPH1 gene, required for homologous recombination-mediated mutation avoidance, encodes a 3′ to 5′ DNA helicase. J Biol Chem. 2005;280(9):7854–60.

    Article  CAS  PubMed  Google Scholar 

  37. Nishino T, Komori K, Tsuchiya D, Ishino Y, Morikawa K. Crystal structure and functional implications of Pyrococcus furiosus hef helicase domain involved in branched DNA processing. Structure. 2005;13(1):143–53.

    Article  CAS  PubMed  Google Scholar 

  38. Nakayama H, Nakayama K, Nakayama R, Irino N, Nakayama Y, Hanawalt PC. Isolation and genetic characterization of a thymineless death-resistant mutant of Escherichia coli K12: identification of a new mutation (recQ1) that blocks the RecF recombination pathway. Mol Gen Genet. 1984;195(3):474–80.

    Article  CAS  PubMed  Google Scholar 

  39. Vindigni A, Hickson ID. RecQ helicases: multiple structures for multiple functions? HFSP J. 2009;3(3):153–64.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Bachrati CZ, Hickson ID. RecQ helicases: guardian angels of the DNA replication fork. Chromosoma. 2008;117(3):219–33.

    Article  CAS  PubMed  Google Scholar 

  41. Bernstein KA, Gangloff S, Rothstein R. The RecQ DNA helicases in DNA repair. Annu Rev Genet. 2010;44:393–417.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Wu Y, Brosh RM. Distinct roles of RECQ1 in the maintenance of genomic stability. DNA Repair. 2010;9(3):315–24.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Bernstein DA. Domain mapping of Escherichia coli RecQ defines the roles of conserved N- and C-terminal regions in the RecQ family. Nucleic Acids Res. 2003;31(11):2778–85.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Bernstein DA, Zittel MC, Keck JL. High-resolution structure of the E. coli RecQ helicase catalytic core. EMBO J. 2003;22(19):4910–21.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Vindigni A, Marino F, Gileadi O. Probing the structural basis of RecQ helicase function. Biophys Chem. 2010;149(3):67–77.

    Article  CAS  PubMed  Google Scholar 

  46. Guo R, Rigolet P, Zargarian L, Fermandjian S, Xi XG. Structural and functional characterizations reveal the importance of a zinc binding domain in Bloom’s syndrome helicase. Nucleic Acids Res. 2005;33(10):3109–24.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Liu JL, Rigolet P, Dou S-X, Wang P-Y, Xi XG. The zinc finger motif of Escherichia coli RecQ is implicated in both DNA binding and protein folding. J Biol Chem. 2004;279(41):42794–802.

    Article  CAS  PubMed  Google Scholar 

  48. Sato A, Mishima M, Nagai A, Kim S-Y, Ito Y, Hakoshima T, et al. Solution structure of the HRDC domain of human Bloom syndrome protein BLM. J Biochem. 2010;148(4):517–25.

    Article  CAS  PubMed  Google Scholar 

  49. Yang Y, Dou S-X, Xu Y-N, Bazeille N, Wang P-Y, Rigolet P, et al. Kinetic mechanism of DNA unwinding by the BLM helicase core and molecular basis for its low processivity. Biochemistry. 2010;49(4):656–68.

    Article  CAS  PubMed  Google Scholar 

  50. Yodh JG, Stevens BC, Kanagaraj R, Janscak P, Ha T. BLM helicase measures DNA unwound before switching strands and hRPA promotes unwinding reinitiation. EMBO J. 2009;28(4):405–16.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Deschavanne PJ, Harosh I. The Rad3 protein from Saccharomyces cerevisiae: a DNA and DNA:RNA helicase with putative RNA helicase activity. Mol Microbiol. 1993;7(6):831–5.

    Article  CAS  PubMed  Google Scholar 

  52. Rudolf J, Rouillon C, Schwarz-Linek U, White MF. The helicase XPD unwinds bubble structures and is not stalled by DNA lesions removed by the nucleotide excision repair pathway. Nucleic Acids Res. 2010;38(3):931–41.

    Article  CAS  PubMed  Google Scholar 

  53. White MF. Structure, function and evolution of the XPD family of iron-sulfur-containing 5′–3′ DNA helicases. Biochem Soc Trans. 2009;37(Pt 3):547–51.

    Article  CAS  PubMed  Google Scholar 

  54. Wu Y, Brosh RM. DNA helicase and helicase-nuclease enzymes with a conserved iron-sulfur cluster. Nucleic Acids Res. 2012;40(10):1–14.

    Article  CAS  Google Scholar 

  55. Wolski SC, Kuper J, Kisker C. The XPD helicase: XPanDing archaeal XPD structures to get a grip on human DNA repair. Biol Chem. 2010;391(7):761–5.

    Article  CAS  PubMed  Google Scholar 

  56. Hiom K. FANCJ: solving problems in DNA replication. DNA Repair. 2010;9(3):250–6.

    Article  CAS  PubMed  Google Scholar 

  57. Rudolf J, Makrantoni V, Ingledew WJ, Stark MJR, White MF. The DNA repair helicases XPD and FancJ have essential iron-sulfur domains. Mol Cell. 2006;23(6):801–8.

    Article  CAS  PubMed  Google Scholar 

  58. Fuss JO, Tainer JA. XPB and XPD helicases in TFIIH orchestrate DNA duplex opening and damage verification to coordinate repair with transcription and cell cycle via CAK kinase. DNA Repair. 2011;10(7):697–713.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Kuper J, Kisker C. Damage recognition in nucleotide excision DNA repair. Curr Opin Struct Biol. 2012;22(1):88–93.

    Article  CAS  PubMed  Google Scholar 

  60. Kuper J, Wolski SC, Michels G, Kisker C. Functional and structural studies of the nucleotide excision repair helicase XPD suggest a polarity for DNA translocation. EMBO J. 2012;31(2):494–502.

    Article  CAS  PubMed  Google Scholar 

  61. Fan L, Fuss JO, Cheng QJ, Arvai AS, Hammel M, Roberts V, et al. XPD helicase structures and activities: insights into the cancer and aging phenotypes from XPD mutations. Cell. 2008;133(5):789–800.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Liu H, Rudolf J, Johnson KA, McMahon S, Oke M, Carter L, et al. Structure of the DNA repair helicase XPD. Cell. 2008;133(5):801–12.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Wolski SC, Kuper J, Hänzelmann P, Truglio JJ, Croteau DL, Van Houten B, et al. Crystal structure of the FeS cluster-containing nucleotide excision repair helicase XPD. PLoS Biol. 2008;6(6):e149.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  64. Pugh RA, Honda M, Leesley H, Thomas A, Lin Y, Nilges MJ, et al. The iron-containing domain is essential in Rad3 helicases for coupling of ATP hydrolysis to DNA translocation and for targeting the helicase to the single-stranded DNA-double-stranded DNA junction. J Biol Chem. 2008;283(3):1732–43.

    Article  CAS  PubMed  Google Scholar 

  65. Pugh RA, Wu CG, Spies M. Regulation of translocation polarity by helicase domain 1 in SF2B helicases. EMBO J. 2011;31(2):1–12.

    Google Scholar 

  66. Pugh RA, Lin Y, Eller C, Leesley H, Cann IKO, Spies M. Ferroplasma acidarmanus RPA2 facilitates efficient unwinding of forked DNA substrates by monomers of FacXPD helicase. J Mol Biol. 2008;383(5):982–98.

    Article  CAS  PubMed  Google Scholar 

  67. Honda M, Park J, Pugh RA, Ha T, Spies M. Single-molecule analysis reveals differential effect of ssDNA-binding proteins on DNA translocation by XPD helicase. Mol Cell. 2009;35(5):694–703.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Spies M, Ha T. Inching over hurdles: how DNA helicases move on crowded lattices. Cell Cycle. 2010;9(9):1742–9.

    Article  CAS  PubMed  Google Scholar 

  69. Büttner K, Nehring S, Hopfner K-P. Structural basis for DNA duplex separation by a superfamily-2 helicase. Nat Struct Mol Biol. 2007;14(7):647–52.

    Article  PubMed  CAS  Google Scholar 

  70. Richards JD, Johnson KA, Liu H, McRobbie A-M, McMahon S, Oke M, et al. Structure of the DNA repair helicase hel308 reveals DNA binding and autoinhibitory domains. J Biol Chem. 2008;283(8):5118–26.

    Article  CAS  PubMed  Google Scholar 

  71. Andrews AJ, Luger K. Nucleosome structure(s) and stability: variations on a theme. Annu Rev Biophys. 2011;40:99–117.

    Article  CAS  PubMed  Google Scholar 

  72. Hargreaves DC, Crabtree GR. ATP-dependent chromatin remodeling: genetics, genomics and mechanisms. Cell Res. 2011;21(3):396–420.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Kornberg RD. Chromatin structure: a repeating unit of histones and DNA. Science. 1974;184(139):868–71.

    Article  CAS  PubMed  Google Scholar 

  74. Luger K, Mäder AW, Richmond RK, Sargent DF, Richmond TJ. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature. 1997;389(6648):251–60.

    Article  CAS  PubMed  Google Scholar 

  75. Clapier CR, Cairns BR. The biology of chromatin remodeling complexes. Annu Rev Biochem. 2009;78(1):273–304.

    Article  CAS  PubMed  Google Scholar 

  76. Ko M, Sohn DH, Chung H, Seong RH. Chromatin remodeling, development and disease. Mutat Res. 2008;647(1–2):59–67.

    Article  CAS  PubMed  Google Scholar 

  77. Liu N, Balliano A, Hayes JJ. Mechanism(s) of SWI/SNF-induced nucleosome mobilization. Chembiochem. 2010;12(2):196–204.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  78. Saha A, Wittmeyer J, Cairns BR. Chromatin remodelling: the industrial revolution of DNA around histones. Nat Rev Mol Cell Biol. 2006;7(6):437–47.

    Article  CAS  PubMed  Google Scholar 

  79. Tang L, Nogales E, Ciferri C. Structure and function of SWI/SNF chromatin remodeling complexes and mechanistic implications for transcription. Prog Biophys Mol Biol. 2010;102(2–3):122–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Mohrmann L, Verrijzer CP. Composition and functional specificity of SWI2/SNF2 class chromatin remodeling complexes. Biochim Biophys Acta. 2005;1681(2–3):59–73.

    Article  CAS  PubMed  Google Scholar 

  81. Zhang Y, Smith CL, Saha A, Grill SW, Mihardja S, Smith SB, et al. DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSC. Mol Cell. 2006;24(4):559–68.

    Article  CAS  PubMed  Google Scholar 

  82. Corona DFV, Tamkun JW. Multiple roles for ISWI in transcription, chromosome organization and DNA replication. Biochim Biophys Acta. 2004;1677(1–3):113–9.

    Article  CAS  PubMed  Google Scholar 

  83. Marfella CGA, Imbalzano AN. The Chd family of chromatin remodelers. Mutat Res. 2007;618(1–2):30–40.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Bao Y, Shen X. INO80 subfamily of chromatin remodeling complexes. Mutat Res. 2007;618(1–2):18–29.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Bianco PR, Brewer LR, Corzett M, Balhorn R, Yeh Y, Kowalczykowski SC, et al. Processive translocation and DNA unwinding by individual RecBCD enzyme molecules. Nature. 2001;409(6818):374–8.

    Article  CAS  PubMed  Google Scholar 

  86. Hopfner K-P, Michaelis J. Mechanisms of nucleic acid translocases: lessons from structural biology and single-molecule biophysics. Curr Opin Struct Biol. 2007;17(1):87–95.

    Article  CAS  PubMed  Google Scholar 

  87. Yodh JG, Schlierf M, Ha T. Insight into helicase mechanism and function revealed through single-molecule approaches. Q Rev Biophys. 2010;43(2):185–217.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Karow JK, Newman RH, Freemont PS, Hickson ID. Oligomeric ring structure of the Bloom’s syndrome helicase. Curr Biol. 1999;9(11):597–600.

    Article  CAS  PubMed  Google Scholar 

  89. Garcia PL, Bradley G, Hayes CJ, Krintel S, Soultanas P, Janscak P. RPA alleviates the inhibitory effect of vinylphosphonate internucleotide linkages on DNA unwinding by BLM and WRN helicases. Nucleic Acids Res. 2004;32(12):3771–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Betterton M, Jülicher F. Opening of nucleic-acid double strands by helicases: active versus passive opening. Phys Rev E. 2005;71(1):1–11.

    Article  CAS  Google Scholar 

  91. Dumont S, Cheng W, Serebrov V, Beran RK, Tinoco I, Pyle AM, et al. RNA translocation and unwinding mechanism of HCV NS3 helicase and its coordination by ATP. Nature. 2006;439(7072):105–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Manosas M, Xi XG, Bensimon D, Croquette V. Active and passive mechanisms of helicases. Nucleic Acids Res. 2010;38(16):5518–26.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Pan B-Y, Dou S-X, Yang Y, Xu Y-N, Bugnard E, Ding X-Y, et al. Mutual inhibition of RecQ molecules in DNA unwinding. J Biol Chem. 2010;285(21):15884–93.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Pugh RA, Honda M, Spies M. Ensemble and single-molecule fluorescence-based assays to monitor DNA binding, translocation, and unwinding by iron-sulfur cluster containing helicases. Methods. 2010;51(3):313–21.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Sontz P, Mui T, Fuss J, Tainer JA, Barton JK. DNA charge transport as a first step in coordinating the detection of lesions by repair proteins. Proc Natl Acad Sci U S A. 2012;109(6):1856–61.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Heyer W-D, Li X, Rolfsmeier M, Zhang X-P. Rad54: the Swiss Army knife of homologous recombination? Nucleic Acids Res. 2006;34(15):4115–25.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Mazin AV, Mazina OM, Bugreev DV, Rossi MJ. Rad54, the motor of homologous recombination. DNA Repair. 2010;9(3):286–302.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Ristic D, Wyman C, Paulusma C, Kanaar R. The architecture of the human Rad54–DNA complex provides evidence for protein translocation along DNA. Proc Natl Acad Sci USA. 2001;98(15):8454–60.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Amitani I, Baskin RJ, Kowalczykowski SC. Visualization of Rad54, a chromatin remodeling protein, translocating on single DNA molecules. Mol Cell. 2006;23(1):143–8.

    Article  CAS  PubMed  Google Scholar 

  100. Nimonkar AV, Amitani I, Baskin RJ, Kowalczykowski SC. Single molecule imaging of Tid1/Rdh54, a Rad54 homolog that translocates on duplex DNA and can disrupt joint molecules. J Biol Chem. 2007;282(42):30776–84.

    Article  CAS  PubMed  Google Scholar 

  101. Lewis R, Dürr H, Hopfner K-P, Michaelis J. Conformational changes of a Swi2/Snf2 ATPase during its mechano-chemical cycle. Nucleic Acids Res. 2008;36(6):1881–90.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Dürr H, Flaus A, Owen-Hughes T, Hopfner K-P. Snf2 family ATPases and DExx box helicases: differences and unifying concepts from high-resolution crystal structures. Nucleic Acids Res. 2006;34(15):4160–7.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  103. Sanchez H, Suzuki Y, Yokokawa M, Takeyasu K, Wyman C. Protein–DNA interactions in high speed AFM: single molecule diffusion analysis of human RAD54. Integr Biol. 2011;21(4):546–56.

    Google Scholar 

  104. Racki LR, Yang JG, Naber N, Partensky PD, Acevedo A, Purcell TJ, et al. The chromatin remodeller ACF acts as a dimeric motor to space nucleosomes. Nature. 2009;462(7276):1016–21.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. Blosser TR, Yang JG, Stone MD, Narlikar GJ, Zhuang X. Dynamics of nucleosome remodelling by individual ACF complexes. Nature. 2009;462(7276):1022–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Dechassa ML, Hota SK, Sen P, Chatterjee N, Prasad P, Bartholomew B. Disparity in the DNA translocase domains of SWI/SNF and ISW2. Nucleic Acids Res. 2012;40(10):4412–21.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Shundrovsky A, Smith CL, Lis JT, Peterson CL, Wang MD. Probing SWI/SNF remodeling of the nucleosome by unzipping single DNA molecules. Nat Struct Mol Biol. 2006;13(6):549–54.

    Article  CAS  PubMed  Google Scholar 

  108. Van Vugt JJFA, Ranes M, Campsteijn C, Logie C. The ins and outs of ATP-dependent chromatin remodeling in budding yeast: biophysical and proteomic perspectives. Biochim Biophys Acta. 2007;1769(3):153–71.

    Article  PubMed  CAS  Google Scholar 

  109. Lia G, Praly E, Ferreira H, Stockdale C, Tse-Dinh YC, Dunlap D, et al. Direct observation of DNA distortion by the RSC complex. Mol Cell. 2006;21(3):417–25.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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  1. Department of Biochemistry, University of Iowa Carver College of Medicine, Iowa City, IA, USA

    David C. Beyer & Maria Spies

  2. Center for Biophysics and Computational Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA

    Mohamed Karem Ghoneim

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    Maria Spies

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Beyer, D.C., Ghoneim, M.K., Spies, M. (2013). Structure and Mechanisms of SF2 DNA Helicases. In: Spies, M. (eds) DNA Helicases and DNA Motor Proteins. Advances in Experimental Medicine and Biology, vol 767. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-5037-5_3

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