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Visualizing one-dimensional diffusion of proteins along DNA

Nature Structural & Molecular Biology volume 15, pages 768–774 (2008)Cite this article

Abstract

The ability of proteins to locate specific target sequences or structures among a vast excess of nonspecific DNA is a fundamental property that affects virtually all aspects of biology. Despite this importance, experimental methods have lagged behind the establishment of theoretical principles describing potential target location mechanisms. However, recent advances in single-molecule detection now allow direct visual observation of proteins diffusing along DNA. Here we present an overview of these new observations and discuss the advantages, limitations and future prospects for imaging the motion of proteins along DNA.

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Figure 1: Potential modes of target-site location.
Figure 2: Using TIRFM to visualize protein one-dimensional diffusion.
Figure 3: Comparison of in vitro versus in vivo DNA substrates.

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References

  1. Adam, G. & Delbrück, M. Reduction of dimensionality in biological diffusion processes. in Structural Chemistry and Molecular Biology (eds. Rich, A. & Davidson, N.) 198–215 (W.H. Freeman and Company, San Francisco; London, 1968).

    Google Scholar 

  2. Riggs, A.D., Bourgeois, S. & Cohn, M. The lac repressor-operator interaction. 3. Kinetic studies. J. Mol. Biol. 53, 401–417 (1970).

    Article  CAS  PubMed  Google Scholar 

  3. Berg, O.G. & Ehrenberg, M. Association kinetics with coupled three- and one-dimensional diffusion. Chain-length dependence of the association rate of specific DNA sites. Biophys. Chem. 15, 41–51 (1982).

    Article  CAS  PubMed  Google Scholar 

  4. Berg, O.G., Winter, R.B. & von Hippel, P.H. Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory. Biochemistry 20, 6929–6948 (1981).

    Article  CAS  PubMed  Google Scholar 

  5. Winter, R.B., Berg, O.G. & von Hippel, P.H. Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli lac repressor–operator interaction: kinetic measurements and conclusions. Biochemistry 20, 6961–6977 (1981).

    Article  CAS  PubMed  Google Scholar 

  6. von Hippel, P.H. & Berg, O.G. Facilitated target location in biological systems. J. Biol. Chem. 264, 675–678 (1989).

    CAS  PubMed  Google Scholar 

  7. Jack, W.E., Terry, B.J. & Modrich, P. Involvement of outside DNA sequences in the major kinetic path by which EcoRI endonuclease locates and leaves its recognition sequence. Proc. Natl. Acad. Sci. USA 79, 4010–4014 (1982).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Gowers, D.M., Wilson, G.G. & Halford, S.E. Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA. Proc. Natl. Acad. Sci. USA 102, 15883–15888 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Dowd, D.R. & Lloyd, R.S. Biological significance of facilitated diffusion in protein-DNA interactions. Applications to T4 endonuclease V-initiated DNA repair. J. Biol. Chem. 265, 3424–3431 (1990).

    CAS  PubMed  Google Scholar 

  10. Jeltsch, A., Alves, J., Wolfes, H., Maass, G. & Pingoud, A. Pausing of the restriction endonuclease EcoRI during linear diffusion on DNA. Biochemistry 33, 10215–10219 (1994).

    Article  CAS  PubMed  Google Scholar 

  11. Jeltsch, A. & Pingoud, A. Kinetic characterization of linear diffusion of the restriction endonuclease EcoRV on DNA. Biochemistry 37, 2160–2169 (1998).

    Article  CAS  PubMed  Google Scholar 

  12. Jeltsch, A., Wenz, C., Stahl, F. & Pingoud, A. Linear diffusion of the restriction endonuclease EcoRV on DNA is essential for the in vivo function of the enzyme. EMBO J. 15, 5104–5111 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. McKinney, K., Mattia, M., Gottifredi, V. & Prives, C. p53 linear diffusion along DNA requires its C terminus. Mol. Cell 16, 413–424 (2004).

    Article  CAS  PubMed  Google Scholar 

  14. Randell, J.C. & Coen, D.M. Linear diffusion on DNA despite high-affinity binding by a DNA polymerase processivity factor. Mol. Cell 8, 911–920 (2001).

    Article  CAS  PubMed  Google Scholar 

  15. Mazur, D.J., Mendillo, M.L. & Kolodner, R.D. Inhibition of Msh6 ATPase activity by mispaired DNA induces a Msh2(ATP)-Msh6(ATP) state capable of hydrolysis-independent movement along DNA. Mol. Cell 22, 39–49 (2006).

    Article  CAS  PubMed  Google Scholar 

  16. Mendillo, M.L., Mazur, D.J. & Kolodner, R.D. Analysis of the interaction between the Saccharomyces cerevisiae MSH2–MSH6 and MLH1–PMS1 complexes with DNA using a reversible DNA end-blocking system. J. Biol. Chem. 280, 22245–22257 (2005).

    Article  CAS  PubMed  Google Scholar 

  17. Gradia, S. et al. hMSH2-hMSH6 forms a hydrolysis-independent sliding clamp on mismatched DNA. Mol. Cell 3, 255–261 (1999).

    Article  CAS  PubMed  Google Scholar 

  18. Snowden, T., Acharya, S., Butz, C., Berardini, M. & Fishel, R. hMSH4-hMSH5 recognizes Holliday junctions and forms a meiosis-specific sliding clamp that embraces homologous chromosomes. Mol. Cell 15, 437–451 (2004).

    Article  CAS  PubMed  Google Scholar 

  19. Acharya, S., Foster, P.L., Brooks, P. & Fishel, R. The coordinated functions of the E. coli MutS and MutL proteins in mismatch repair. Mol. Cell 12, 233–246 (2003).

    Article  CAS  PubMed  Google Scholar 

  20. Iwahara, J., Zweckstetter, M. & Clore, G.M. NMR structural and kinetic characterization of a homeodomain diffusing and hopping on nonspecific DNA. Proc. Natl. Acad. Sci. USA 103, 15062–15067 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Iwahara, J. & Clore, G.M. Detecting transient intermediates in macromolecular binding by paramagnetic NMR. Nature 440, 1227–1230 (2006).

    Article  CAS  PubMed  Google Scholar 

  22. Schurr, J.M. The one-dimensional diffusion coefficient of proteins absorbed on DNA. Hydrodynamic considerations. Biophys. Chem. 9, 413–414 (1975).

    Article  CAS  PubMed  Google Scholar 

  23. Bagchi, B., Blainey, P.C. & Xie, X.S. Diffusion constant of a nonspecifically bound protein undergoing curvilinear motion along DNA. J. Phys. Chem. B 112, 6282–6284 (2008).

    Article  CAS  PubMed  Google Scholar 

  24. Halford, S.E. & Marko, J.F. How do site-specific DNA-binding proteins find their targets? Nucleic Acids Res. 32, 3040–3052 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Kampmann, M. Facilitated diffusion in chromatin lattices: mechanistic diversity and regulatory potential. Mol. Microbiol. 57, 889–899 (2005).

    Article  CAS  PubMed  Google Scholar 

  26. Halford, S.E. & Szczelkun, M.D. How to get from A to B: strategies for analysing protein motion on DNA. Eur. Biophys. J. 31, 257–267 (2002).

    Article  CAS  PubMed  Google Scholar 

  27. Slutsky, M. & Mirny, L.A. Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential. Biophys. J. 87, 4021–4035 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Kalodimos, C.G. et al. Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Science 305, 386–389 (2004).

    Article  CAS  PubMed  Google Scholar 

  29. Pingoud, A. & Wende, W. A sliding restriction enzyme pauses. Structure 15, 391–393 (2007).

    Article  CAS  PubMed  Google Scholar 

  30. Erie, D.A., Yang, G., Schultz, H.C. & Bustamante, C. DNA bending by Cro protein in specific and nonspecific complexes: implications for protein site recognition and specificity. Science 266, 1562–1566 (1994).

    Article  CAS  PubMed  Google Scholar 

  31. Singer, P. & Wu, C.W. Promoter search by Escherichia coli RNA polymerase on a circular DNA template. J. Biol. Chem. 262, 14178–14189 (1987).

    CAS  PubMed  Google Scholar 

  32. Bustamante, C., Guthold, M., Zhu, X. & Yang, G. Facilitated target location on DNA by individual Escherichia coli RNA polymerase molecules observed with the scanning force microscope operating in liquid. J. Biol. Chem. 274, 16665–16668 (1999).

    Article  CAS  PubMed  Google Scholar 

  33. Harada, Y. et al. Single-molecule imaging of RNA polymerase-DNA interactions in real time. Biophys. J. 76, 709–715 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Kabata, H. et al. Visualization of single molecules of RNA polymerase sliding along DNA. Science 262, 1561–1563 (1993).

    Article  CAS  PubMed  Google Scholar 

  35. Kim, J.H. & Larson, R.G. Single-molecule analysis of 1D diffusion and transcription elongation of T7 RNA polymerase along individual stretched DNA molecules. Nucleic Acids Res. 35, 3848–3858 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Wang, Y.M., Austin, R.H. & Cox, E.C. Single molecule measurements of repressor protein 1D diffusion on DNA. Phys. Rev. Lett. 97, 048302 (2006).

    Article  CAS  PubMed  Google Scholar 

  37. Graneli, A., Yeykal, C.C., Robertson, R.B. & Greene, E.C. Long-distance lateral diffusion of human Rad51 on double-stranded DNA. Proc. Natl. Acad. Sci. USA 103, 1221–1226 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Blainey, P.C., van Oijen, A.M., Banerjee, A., Verdine, G.L. & Xie, X.S. A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA. Proc. Natl. Acad. Sci. USA 103, 5752–5757 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Jiricny, J. The multifaceted mismatch-repair system. Nat. Rev. Mol. Cell Biol. 7, 335–346 (2006).

    Article  CAS  PubMed  Google Scholar 

  40. Kunkel, T.A. & Erie, D.A. DNA mismatch repair. Annu. Rev. Biochem. 74, 681–710 (2005).

    Article  CAS  PubMed  Google Scholar 

  41. Pluciennik, A. & Modrich, P. Protein roadblocks and helix discontinuities are barriers to the initiation of mismatch repair. Proc. Natl. Acad. Sci. USA 104, 12709–12713 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Obmolova, G., Ban, C., Hsieh, P. & Yang, W. Crystal structures of mismatch repair proetin MutS and its complex with a substrate DNA. Nature 407, 703–710 (2000).

    Article  CAS  PubMed  Google Scholar 

  43. Lamers, M.H. et al. The crystal structure of DNA mismatch repair protein MutS binding to a G × T mismatch. Nature 407, 711–717 (2000).

    Article  CAS  PubMed  Google Scholar 

  44. Warren, J.J. et al. Structure of the human MutSα DNA lesion recognition complex. Mol. Cell 26, 579–592 (2007).

    Article  CAS  PubMed  Google Scholar 

  45. Gorman, J. et al. Dynamic basis for one-dimensional DNA scanning by the mismatch repair complex Msh2-Msh6. Mol. Cell 28, 359–370 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Sakata-Sogawa, K. & Shimamoto, N. RNA polymerase can track a DNA groove during promoter search. Proc. Natl. Acad. Sci. USA 101, 14731–14735 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Gorski, S.A., Dundr, M. & Misteli, T. The road much traveled: trafficking in the cell nucleus. Curr. Opin. Cell Biol. 18, 284–290 (2006).

    Article  CAS  PubMed  Google Scholar 

  48. Stanford, N.P., Szczelkun, M.D., Marko, J.F. & Halford, S.E. One- and three-dimensional pathways for proteins to reach specific DNA sites. EMBO J. 19, 6546–6557 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Misteli, T. Protein dynamics: implications for nuclear architecture and gene expression. Science 291, 843–847 (2001).

    Article  CAS  PubMed  Google Scholar 

  50. Phair, R.D. et al. Global nature of dynamic protein-chromatin interactions in vivo: three-dimensional genome scanning and dynamic interaction networks of chromatin proteins. Mol. Cell. Biol. 24, 6393–6402 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Gerland, U., Moroz, J.D. & Hwa, T. Physical constraints and functional characteristics of transcription factor-DNA interaction. Proc. Natl. Acad. Sci. USA 99, 12015–12020 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Mueller, F., Wach, P. & McNally, J.G. Evidence for a common mode of transcription factor interaction with chromatin as revealed by improved quantitative FRAP. Biophys. J. 94, 3323–3339 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Elf, J., Li, G.-W. & Xie, X.S. Probing transcription factor dynamics at the single-molecule level in a living cell. Science 316, 1191–1194 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Spies, M., Amitani, I., Baskin, R.J. & Kowalczykowski, S.C. RecBCD enzyme switches lead motor subunits in response to χ recognition. Cell 131, 694–705 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Pease, P.J. et al. Sequence-directed DNA translocation by purified FtsK. Science 307, 586–590 (2005).

    Article  CAS  PubMed  Google Scholar 

  56. Seidel, R. et al. Real-time observation of DNA translocation by the type I restriction modification enzyme EcoR124I. Nat. Struct. Mol. Biol. 11, 838–843 (2004).

    Article  CAS  PubMed  Google Scholar 

  57. Cairns, B.R. Chromatin remodeling: insights and intrigue from single-molecule studies. Nat. Struct. Mol. Biol. 14, 989–996 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Schluesche, P., Stelzer, G., Piaia, E., Lamb, D.C. & Meisterernst, M. NC2 mobilizes TBP on core promoter TATA boxes. Nat. Struct. Mol. Biol. 14, 1196–1201 (2007).

    Article  CAS  PubMed  Google Scholar 

  59. Lengronne, A. et al. Cohesin relocation from sites of chromosomal loading to places of convergent transcription. Nature 430, 573–578 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Ranjith, P., Yan, J. & Marko, J.F. Nucleosome hopping and sliding kinetics determined from dynamics of single chromatin fibers in Xenopus egg extracts. Proc. Natl. Acad. Sci. USA 104, 13649–13654 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Bonnet, I. et al. Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA. Nucleic Acids Res. 36, 4118–4127 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Tafvizi, A. et al. Tumor suppressor p53 slides on DNA with low friction and high stability. Biophys. J. 95, L01–L03 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We apologize to the researchers whose contributions could not be acknowledged because of space constraints. We also thank members of the Greene laboratory for critically reading the manuscript and providing insightful comments. E.C.G. is supported by funds from the US National Institutes of Health (NIH; GM074739) and a PECASE Award from the US National Science Foundation (0544638). J.G. is supported by an NIH training grant for Cellular and Molecular Foundations of Biomedical Sciences (T32GM00879807). We thank the referees for several insightful suggestions that have been incorporated into the final version of the Review.

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  1. Department of Biological Sciences, 650 West 168th Street, Black Building Room 536, New York, 10032, New York, USA

    Jason Gorman

  2. Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street, Black Building Room 536, New York, 10032, New York, USA

    Eric C Greene

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Correspondence to Eric C Greene.

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Gorman, J., Greene, E. Visualizing one-dimensional diffusion of proteins along DNA. Nat Struct Mol Biol 15, 768–774 (2008). https://doi.org/10.1038/nsmb.1441

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