Journal of Biological Physics

, Volume 32, Issue 2, pp 153–168 | Cite as

Novel Polymorphism of RecA Fibrils Revealed by Atomic Force Microscopy



RecA fibrils in physiological conditions have been successfully imaged using Tapping Mode atomic force microscopy. This represents the first time images of recA have been obtained without drying, freezing and/or exposure to high vacuum conditions. While previously observed structures – the monomer, the hexamer, the short rod – were seen, a new type of fibril was also observed. This protofibril is narrower in diameter than the standard fibril, and occurs in three distinct morphologies: aperiodic, 100-nm periodic, and 150-nm periodic. In addition, much longer rods were observed, and appear curved and even circular.

Key words

RecA recombination assembly AFM 


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  1. 1.
    Roca, A.I. and Cox, M.M.: RecA Protein: Structure, Function, and Role in Recombinational DNA Repair, Prog. Nucleic Acid Res. Mol. Biol. 56 (1997), 129–223.CrossRefGoogle Scholar
  2. 2.
    Kodadek, T.: Mechanistic Parallels Between DNA Replication, Recombination and Transcription, Trends Biochem. Sci. 23 (1998), 79–83.CrossRefGoogle Scholar
  3. 3.
    Ogawa, T., et al.: Similarity of the yeast RAD51 Filament to the Bacterial RecA Filament, Science 259 (1993), 1896–1899.Google Scholar
  4. 4.
    Rashid, N., Morikawa, M. and Imanaka, T.: A RecA/RAD51 Homologue from a Hyperthermophilic Archaeon Retains the Major RecA Domain Only, Mol. Gen. Genet. 253 (1996) 397–400.CrossRefGoogle Scholar
  5. 5.
    Levin-Zaidman, S., et al.: Ordered Intracellular RecA-DNA Assemblies: A Potential Site of in Vivo RecA-mediated Activities, Proc. Natl. Acad. Sci. U. S. A. 97 (2000), 6791–6796.Google Scholar
  6. 6.
    Story, R.M., Weber, I.T. and Steitz, T.A.: The Structure of the E. coli RecA Protein Monomer and Polymer [Published Erratum appears in Nature 1992 Feb 6;355(6360):567] [see comments], Nature 355 (1992), 318–325.Google Scholar
  7. 7.
    Brenner, S.L., Zlotnick, A. and Griffith, J.D.: RecA Protein Self-Assembly. Multiple Discrete Aggregation States, J. Mol. Biol. 204 (1988), 959–972.CrossRefGoogle Scholar
  8. 8.
    Egelman, E.H. and Stasiak, A.: Structure of Helical RecA-DNA Complexes. Complexes Formed in the Presence of ATP-Gamma-S or ATP, J. Mol. Biol. 191 (1986), 677–697.CrossRefGoogle Scholar
  9. 9.
    Logan, K.M., et al.: Mutant RecA Proteins which form Hexamer-Sized Oligomers, J. Mol. Biol. 266 (1997), 306–316.Google Scholar
  10. 10.
    Neuendorf, S.K. and Cox, M.M.: Exchange of RecA Protein Between Adjacent RecA Protein-Single-Stranded DNA Complexes, J. Biol. Chem. 261 (1986), 8276–8282.Google Scholar
  11. 11.
    Williams, R.C. and Spengler, S.J.: Fibers of RecA Protein and Complexes of RecA Protein and Single-Stranded Phi X174 DNA as Visualized by Negative-Stain Electron Microscopy, J. Mol. Biol. 187 (1986), 109–118.CrossRefGoogle Scholar
  12. 12.
    Yu, X., et al.: Structural Polymorphism of the RecA Potein from the Thermophilic Bacterium Thermus Aquaticus, Biophys. J. 69 (1995), 2728–2738.Google Scholar
  13. 13.
    Amrein, M., et al.: Scanning Tunneling Microscopy of RecA-DNA Complexes Coated with a Conducting Film, Science 240 (1988), 514–516.Google Scholar
  14. 14.
    Amrein, M., et al.: Scanning Tunneling Microscopy of Uncoated RecA-DNA Complexes, Science 243 (1989), 1708–1711.Google Scholar
  15. 15.
    Morrical, S.W. and Cox, M.M.: Light Scattering Studies of the RecA Protein of Escherichia Coli: Relationship Between Free RecA Filaments and the RecA X ssDNA Complex, Biochemistry 24 (1985), 760–767.CrossRefGoogle Scholar
  16. 16.
    Ellouze, C., et al.: Evidence for Elongation of the Helical Pitch of the RecA Filament upon ATP and ADP Binding using Small-angle Neutron Scattering, Eur. J. Biochem. 233 (1995), 579–583.Google Scholar
  17. 17.
    Wilson, D.H. and Benight, A.S.: Kinetic Analysis of the Pre-equilibrium Steps in the Self-assembly of RecA Protein from Escherichia Coli, J. Biol. Chem. 265 (1990), 7351–7359.Google Scholar
  18. 18.
    Wittung, P., Norden, B. and Takahashi, M.: Secondary Structure of RecA in Solution. The Effects of Cofactor, DNA and Ionic Conditions, Eur. J. Biochem. 228 (1995), 149–154.CrossRefGoogle Scholar
  19. 19.
    Heuser, J. and Griffith, J.: Visualization of RecA Protein and its Complexes with DNA by Quick-freeze/deep-etch Electron Microscopy, J. Mol. Biol. 210 (1989), 473–484.CrossRefGoogle Scholar
  20. 20.
    Ruigrok, R.W., et al.: The Inactive form of RecA Protein: The ‘Compact’ Structure, EMBO J, 12 (1993), 9–16.Google Scholar
  21. 21.
    Ruigrok, R.W.H. and Dicapua, E.: On the Polymerization State of Reca in the Absence of DNA, Biochimie 73 (1991), 191–197.CrossRefGoogle Scholar
  22. 22.
    Timmins, P.A., Ruigrok, R.W.H. and Dicapua, E.: The Solution Structure of RecA Filaments by Small-Angle Neutron-Scattering, Biochimie 73 (1991), 227–230.CrossRefGoogle Scholar
  23. 23.
    Budzynski, D.M., Gao, X.H. and Benight, A.S.: Isolation, Characterization, and Magnesium-induced Self-association Kinetics of Discrete Aggregates of RecA Protein from Escherichia Coli, Biopolymers 38 (1996), 471–491.CrossRefGoogle Scholar
  24. 24.
    Muller, D.J., et al.: Structural Changes in Native Membrane Proteins Monitored at Subnanometer Resolution with the Atomic Force Microscope: A Review, J. Struct. Biol. 119 (1997), 149–157.Google Scholar
  25. 25.
    Muller, D.J., et al.: Observing Structure, Function and Assembly of Single Proteins by AFM, Prog. Biophys. Mol. Biol. 79 (2002), 1–43.Google Scholar
  26. 26.
    Mou, J.X., et al.: High Resolution Surface Structure of E-coli GroES Oligomer by Atomic Force Microscopy, FEBS Lett. 381 (1996), 161–164.CrossRefGoogle Scholar
  27. 27.
    Han, W.H., et al.: Kinked DNA, Nature 386 (1997), 563–563.CrossRefADSGoogle Scholar
  28. 28.
    Vesenka, J., Miller, R. and Henderson, E.: 3-Dimensional Probe Reconstruction for Atomic-force Microscopy, Rev. Sci. Instrum. 65 (1994), 2249–2251.CrossRefADSGoogle Scholar
  29. 29.
    Kuhle, A., et al.: Contrast Artifacts in Tapping Tip Atomic Force Microscopy, Appl. Phys. a-Mater, 66 (1998), S329–S332.CrossRefADSGoogle Scholar
  30. 30.
    Roca, A.I. and Cox, M.M.: The RecA Protein: Structure and Function, Crit. Rev. Biochem. Mol. Biol. 25 (1990), 415–456.CrossRefGoogle Scholar
  31. 31.
    Pollanen, M.S., et al.: Twisted Ribbon Structure of Paired Helical Filaments Revealed by Atomic-Force Microscopy, Am. J. Pathol. 144 (1994), 869–873.Google Scholar
  32. 32.
    Sattin, B.D. and Goh, M.C.: Direct Observation of the Assembly of RecA/DNA Complexes by Atomic Force Microscopy, Biophys. J. 87 (2004), 3430–3436.CrossRefGoogle Scholar

Copyright information

© Springer Science + Business Media, Inc. 2006

Authors and Affiliations

  1. 1.Department of ChemistryUniversity of TorontoTorontoCanada

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