Skip to main content
Log in

Loops in DNA: An overview of experimental and theoretical approaches

  • Focus Point
  • Published:
The European Physical Journal E Aims and scope Submit manuscript

Abstract.

DNA loop formation plays a central role in many cellular processes. The aim of this paper is to present the state of the art and open problems regarding the experimental and theoretical approaches to DNA looping. A particular attention is devoted to the effects of the protein bridge size and of protein induced sharp DNA bending on DNA loop formation enhancement.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  1. S.E. Halford, A.J. Welsh, M.D. Szczelkun, Annu. Rev. Biophys. Biomol. Struct. 33, 1 (2004).

    Article  Google Scholar 

  2. R. Schleif, Annu. Rev. Biochem. 61, 199 (1992).

    Article  Google Scholar 

  3. S. Adhya, Annu. Rev. Genet. 23, 227 (1989).

    Article  Google Scholar 

  4. T.M. Dunn, S. Hahn, S. Ogden, R.F. Schleif, Proc. Natl. Acad. Sci. U.S.A. 81, 5017 (1984).

    ADS  Google Scholar 

  5. K.S. Matthews, Microbiol. Rev. 56, 123 (1992).

    Google Scholar 

  6. M. Amouyal, L. Mortensen, H. Buc, K. Hammer, Cell 58, 545 (1989).

    Article  Google Scholar 

  7. M. Ptashne, Cold Spring Harbor Laboratory Press, 3rd edition (2004).

  8. T. Tahirov, K. Sato, E. Ichikawa-Iwata, M. Sasaki, T. Inoue-Bungo, M. Shiina, K. Kimura, S. Takata, A. Fujikawa, H. Morii, Cell 108, 57 (2002).

    Article  Google Scholar 

  9. P. Jackson, I. Mastrangelo, M. Reed, P. Tegtmeyer, G. Yardley, J. Barrett, Oncogene 16, 283 (1998).

    Article  Google Scholar 

  10. W. Su, S. Porter, S. Kustu, H. Echols, Proc. Natl. Acad. Sci. U.S.A. 87, 5504 (1990).

    ADS  Google Scholar 

  11. C. Wyman, I. Rombel, A.K. North, C. Bustamante, S. Kustu, Science 275, 1658 (1997).

    Article  Google Scholar 

  12. J.C. Becker, A. Nikroo, T. Brabletz, R.A. Reisfeld, Proc. Natl. Acad. Sci. U.S.A. 92, 9727 (1995).

    ADS  Google Scholar 

  13. B. Tolhuis, R.J. Palstra, E. Splinter, F. Grosveld, W. de Laat, Mol. Cell 10, 1453 (2002).

    Article  Google Scholar 

  14. J. Mahillon, M. Chandler, Microbiol. Mol. Biol. Rev. 62, 725 (1998).

    Google Scholar 

  15. Y. Voziyanov, S. Pathania, M. Jayaram, Nucleic Acids Res. 27, 930 (1999).

    Article  Google Scholar 

  16. A. Nagy, Genesis 26, 99 (2000).

    Article  MathSciNet  Google Scholar 

  17. D.L. Hamilton, K. Abremski, J. Mol. Biol. 178, 481 (1984).

    Article  Google Scholar 

  18. M.L. Embleton, V. Siksnys, S.E. Halford, J. Mol. Biol. 311, 503 (2001).

    Article  Google Scholar 

  19. M.L. Embleton, S.A. Williams, M.A. Watson, S.E. Halford, J. Mol. Biol. 289, 785 (1999).

    Article  Google Scholar 

  20. N.E. Murray, Microbiol. Mol. Biol. Rev. 64, 412 (2000).

    Article  Google Scholar 

  21. D. Dryden, N. Murray, D. Rao, Nucleic Acids Res. 29, 3728 (2000).

    Article  Google Scholar 

  22. L. Postow, C.D. Hardy, J. Arsuaga, N.R. Cozzarelli, Genes Dev. 18, 1766 (2004).

    Article  Google Scholar 

  23. J.R. Marsden, U.K. Laemmli, Cell 17, 849 (1979).

    Article  Google Scholar 

  24. Y.L. Lyubchenko, L.S. Shlyakhtenko, B. Chernov, R.E. Harrington, Proc. Natl. Acad. Sci. U.S.A. 88, 5331 (1991).

    ADS  Google Scholar 

  25. Z. Katiliene, E. Katilius, N.W. Woodbury, Biophys. J. 84, 4053 (2003).

    Google Scholar 

  26. L.J. Parkhurst, K.M. Parkhurst, R. Powell, J. Wu, S. Williams, Biopolymers 61, 180 (2003).

    Article  Google Scholar 

  27. S. Chatterjee, Y.N. Zhou, S. Roy, S. Adhya, Proc. Natl. Acad. Sci. U.S.A. 94, 2957 (1997).

    Article  ADS  Google Scholar 

  28. J.D. Kahn, D.M. Crothers, Proc. Natl. Acad. Sci. U.S.A. 89, 6343 (1992).

    ADS  Google Scholar 

  29. L. Ringrose, S. Chabanis, P. Angrand, C. Woodroofe, A.F. Stewart, EMBO J. 18, 6630 (1999).

    Article  Google Scholar 

  30. Q. Du, C. Smith, N. Shiffeldrim, M. Vologodskaia, A. Vologodskii, Proc. Natl. Acad. Sci. U.S.A. 102, 5397 (2005).

    Article  ADS  Google Scholar 

  31. A. Vologodskii, N.R. Cozzarelli, Biophys. J. 70, 2548 (1996).

    Google Scholar 

  32. K. Rippe, M. Guthold, P.H. von Hippe, C. Bustamante, J. Mol. Biol. 270, 125 (1997).

    Article  Google Scholar 

  33. L. Finzi, J. Gelles, Science 267, 378 (1995).

    ADS  Google Scholar 

  34. G. Lia, D. Bensimon, V. Croquette, J.-F. Allemand, D. Dunlap, D. E. Lewis, S. Adhya, L. Finzi, Proc. Natl. Acad. Sci. U.S.A. 100, 11373 (2003).

    Article  ADS  Google Scholar 

  35. D. Skoko, J. Yan, R.C. Johnson, J.F. Marko, Phys. Rev. Lett. 95, 208101 (2005).

    Article  ADS  Google Scholar 

  36. D. Shore, J. Langowski, R.L. Baldwin, Proc. Natl. Acad. Sci. U.S.A. 78, 4833 (1981).

    ADS  Google Scholar 

  37. O. Kratky, G. Porod, Rel. Trav. Chim. 68, 1106 (1949).

    Google Scholar 

  38. J. J. Hermans, R. Ullman, Physica 18, 951 (1952).

    Article  MathSciNet  ADS  Google Scholar 

  39. H.E. Daniels, Proc. R. Soc. Edinburgh, Sect. A 63, 290 (1952).

    MATH  MathSciNet  Google Scholar 

  40. W. Gobush, H. Yamakawa, W.H. Stockmayer, W.S. Magee, J. Chem. Phys. 57, 2839 (1972).

    Article  ADS  Google Scholar 

  41. H. Yamakawa, W.H. Stockmayer, J. Chem. Phys. 57, 2843 (1972).

    Article  ADS  Google Scholar 

  42. J. Shimada, H. Yamakawa, Macromolecules 17, 689 (1984).

    Article  Google Scholar 

  43. H. Yamakawa, Helical Wormlike Chains in Polymer Solutions (Springer Verlag, Berlin, 1997).

  44. R.A. Harris, J.E. Hearst, J. Chem. Phys. 44, 2595 (1966). J.E. Hearst, R.A. Harris, E. Beals, J. Chem. Phys. 45, 3106 (1966).

    Article  ADS  Google Scholar 

  45. J.B. Lagowski, J. Noolandi, B. Nickel, J. Chem. Phys. 95, 1266 (1991).

    Article  ADS  Google Scholar 

  46. B.-Y. Ha, D. Thirumalai, J. Chem. Phys. 103, 9408 (1995). J.K. Battacharjee, D. Thirumalai, J.D. Bryngelson, cond-mat/9709345 (1997).

    Article  ADS  Google Scholar 

  47. R.G. Winkler, P. Reineker, L. Harnau, J. Chem. Phys. 101, 8119 (1994). R.G. Winkler, J. Chem. Phys. 118, 2919 (2003).

    Article  ADS  Google Scholar 

  48. J. Wilhelm, E. Frey, Phys. Rev. Lett. 77, 2581 (1996).

    Article  ADS  Google Scholar 

  49. S. Stepanow, G.M. Schütz, Europhys. Lett. 60, 546 (2002). S. Stepanow, J. Phys. Condens. Matter 17, S1799 (2005).

    Article  ADS  Google Scholar 

  50. A.J. Spakowtiz, Z.-G. Wang, J. Chem. Phys. 119, 13113 (2003)

    Article  ADS  Google Scholar 

  51. H. Kleinert, A. Chervayakov, cond-mat/0503199 (2005).

  52. P.J. Hagerman, V.A. Ramadevi, J. Mol. Biol. 212, 351 (1990).

    Article  Google Scholar 

  53. D.M. Crothers, J. Drak, J.D. Kahn, S.D. Levene, Methods Enzymol. 212, 3 (1992).

    Article  Google Scholar 

  54. S.D. Levene, D.M. Crothers, J. Mol. Biol. 189, 61 (1986), J. Mol. Biol. 189, 73 (1986).

    Article  Google Scholar 

  55. M.D. Frank-Kamenetskii, A.V. Lukashin, V.V. Anshelevich, A.V. Vologodskii, J. Bimol. Struct. Dyn. 2, 1005 (1985).

    Google Scholar 

  56. T.E. Cloutier, J. Widom, Mol. Cell 14, 355 (2004).

    Article  Google Scholar 

  57. J. Yan, J.F. Marko, Phys. Rev. E 68, 011905 (2003)

    Article  ADS  Google Scholar 

  58. P.A. Wiggins, R. Phillips, P.C. Nelson, Phys. Rev. E 71, 021909 (2005).

    Article  ADS  MathSciNet  Google Scholar 

  59. B. Chakrabarti, A.J. Levine, Phys. Rev. E 71, 031905 (2005).

    Article  ADS  MathSciNet  Google Scholar 

  60. Y.O. Popov, A.V. Tkachenko, Phys. Rev. E 71, 051905 (2005).

    Article  ADS  MathSciNet  Google Scholar 

  61. P. Ranjith, P.B. Sunil Kumar, G.I. Menon, Phys. Rev. Lett. 94, 138102 (2005).

    Article  ADS  Google Scholar 

  62. Q. Du, M. Vologodskaia, H. Kuhn, M. Frank-Kamenetskii, A. Vologodskii, Biophys. J. 88, 4137 (2005).

    Article  Google Scholar 

  63. A.A. Podtelezhnikov, A.V. Vologodskii, Macromolecules 33, 2767 (2000).

    Article  Google Scholar 

  64. C. Bustamante, J.F. Marko, E.D. Siggia, S. Smith, Science 265, 1599 (1994).

    ADS  Google Scholar 

  65. J.F. Marko, E.D. Siggia, Macromolecules 28, 8759 (1995).

    Article  Google Scholar 

  66. C. Bouchiat, M.D. Wang, S.M. Block, J.-F. Allemand, T. Strick, V. Croquette, Biophys. J. 76, 409 (1999).

    Google Scholar 

  67. M. Wang, H. Yin, R. Landick, J. Gelles, S.M. Block, Biophys. J. 72, 1335 (1997).

    Google Scholar 

  68. S. Sankararaman, J. Marko, Phys. Rev. E 71, 021911 (2005)

    Article  ADS  MathSciNet  Google Scholar 

  69. N. Douarche, S. Cocco, Phys. Rev. E. 72, 061902 (2005).

    Article  ADS  MathSciNet  Google Scholar 

  70. J.M. Kulić, H. Mohrbach, V. Lobaskin, R. Thaokar, H. Schiessel, Phys. Rev. E. 72, 041905 (2005).

    Article  ADS  Google Scholar 

  71. H. Merlitz, K. Rippe, K. Klenin, J. Langowski, Biophys. J. 74, 773 (1998).

    Google Scholar 

  72. K. Rippe, P.H. von Hippel, J. Langowski, Trends Biochem. Sci. 20, 500 (1995).

    Article  Google Scholar 

  73. K. Rippe, Trends Biochem. Sci. 26, 733 (2001).

    Article  Google Scholar 

  74. V.A. Bloomfield, D.M. Crothers, J.I. Tinoco, Physical Chemistry of Nucleic Acids (Harper and Row, 1974).

  75. M. Brenowitz, A. Pickar, E. Jamison, Biochemistry 30, 5986 (1991).

    Article  Google Scholar 

  76. K. Klenin, H. Merlitz, J. Langowski, Biophys. J. 74, 780 (1998).

    Google Scholar 

  77. M. Lewis, G. Chang, N.C. Horton, M.A. Kercher, H.C. Pace, M.A. Schumacher, R.G. Brennan, P. Lu, Science 271, 1247 (1996).

    ADS  Google Scholar 

  78. A. Balaeff, L. Mahadevan, K. Schulten, Phys. Rev. Lett. 83, 4900 (1999)

    Article  ADS  Google Scholar 

  79. E. Villa, A. Balaeff, K. Schulten, Proc. Natl. Acad. Sci. U.S.A. 102, 6783 (2005).

    Article  ADS  Google Scholar 

  80. A. Hanke, R. Metzler, Biophys. J. 85, 167 (2003).

    ADS  Google Scholar 

  81. S. Blumberg, A.V. Tkachenko, J.C. Meiners, Biophys. J. 88, 1692 (2005).

    Article  Google Scholar 

  82. D. Garrivier, B. Fourcade, Europhys. Lett. 49, 390 (2000).

    Article  ADS  Google Scholar 

  83. J. Rudnick, R. Bruinsma, Biophys. J. 76, 1725 (1999).

    Article  Google Scholar 

  84. J.F. Marko, E. Siggia, Biophys. J. 73, 2173 (1997).

    Google Scholar 

  85. S. Jun, J. Bechhoefer, B.-Y. Ha, Europhys. Lett. 64, 420 (2003).

    Article  ADS  Google Scholar 

  86. A. Dua, B. Cherayl, J. Chem. Phys. 117, 7765 (2002)

    Article  ADS  Google Scholar 

  87. S. Sankararaman, J.F. Marko, Phys. Rev. Lett. 95, 078104 (2005).

    Article  ADS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to S. Cocco.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Allemand, J.F., Cocco, S., Douarche, N. et al. Loops in DNA: An overview of experimental and theoretical approaches. Eur. Phys. J. E 19, 293–302 (2006). https://doi.org/10.1140/epje/i2005-10073-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1140/epje/i2005-10073-y

PACS.

Navigation