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Perspectives On DNA Looping

  • Laura Finzi
Conference paper
Part of the The IMA Volumes in Mathematics and its Applications book series (IMA, volume 150)

DNA looping is a ubiquitous regulatorymechanism which can be involved in DNA transcription, ecombination, repair, etc. Here, I will focus on protein-mediated DNA looping as a mechanism of tran-scriptional regulation. Indeed, such topological change in DNA is known to repress and/or activate many prokaryotic and viral genes [1–4] and is believed to mediate interaction between promoters and enhancers as well as insulate them in eukaryotes [5–9].

Keywords

Loop Formation Negative Supercoiling Biophysical Journal Magnetic Tweezer Lambda Repressor 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. [1]
    Schleif R. (1992). Dna Looping. Annual Review Of Biochemistry 61: 199–223.CrossRefGoogle Scholar
  2. [2]
    Dodd I.B., Shearwin K.B., and Sneppen K. (2007). Modelling transcriptional interference and DNA looping in gene regulation. Journal Of Molecular Biology 369: 1200–1213.CrossRefGoogle Scholar
  3. [3]
    Dodd I.B., Shearwin K.E., and Egan J.B. (2005). Revisited gene regulation in bacteriophage lambda. Current Opinion In Genetics & Development 15: 145–152.CrossRefGoogle Scholar
  4. [4]
    Matthews K.S. (1992). DNA LOOPING. Microbiological Reviews 56: 123–136.Google Scholar
  5. [5]
    Gaszner M. and Felsenfeld G. (2006). Insulators: exploiting transcriptional and epigenetic mechanisms. Nature Reviews Genetics 7: 703–713.CrossRefGoogle Scholar
  6. [6]
    Ameres S.L., Drueppel L., Pfleiderer K., Schmidt A., Hillen W., and Berens C. (2005). Inducible DNA-loop formation blocks transcriptional activation by an SV40 enhancer. Embo Journal 24: 358–367.CrossRefGoogle Scholar
  7. [7]
    Bondarenko V.A., Jiang Y.I., and Studitsky V.M. (2003). Rationally designed insulator-like elements can block enhancer action in vitro. Embo Journal 22: 4728–4737.CrossRefGoogle Scholar
  8. [8]
    Moreau P., Hen R., Wasylyk B., Everett R., Gaub M.P., and Chambon P. (1981). The SV40-72 base repair repeat has a striking effect on gene-expression both in SV40 and other chimeric recombinants. Nucleic Acids Research 9: 6047–6068.CrossRefGoogle Scholar
  9. [9]
    Tolhuis B., Palstra R.J., Splinter E., Grosveld F., and de Laat W. (2002). Looping and interaction between hypersensitive sites in the active beta-globin locus. Molecular Cell 10: 1453–1465.CrossRefGoogle Scholar
  10. [10]
    Finzi L. and Gelles J. (1995). Measurement Of Lactose Repressor-Mediated Loop Formation And Breakdown In Single Dna-Molecules. Science 267: 378–380.CrossRefGoogle Scholar
  11. [11]
    Finzi L. and Dunlap D. (2003). Single-molecule studies of DNA architectural changes induced by regulatory proteins. Methods Enzymol 370: 369–378.CrossRefGoogle Scholar
  12. [12]
    Nelson P.C., Zurla C., Brogioli D., Beausang J.F., Finzi L., and Dunlap D. (2006). Tethered particle motion as a diagnostic of DNA tether length. Journal Of Physical Chemistry B 110: 17260–17267.CrossRefGoogle Scholar
  13. [13]
    Lewis M. (2005). The lac repressor. Comptes Rendus Biologies 328: 521–548.CrossRefGoogle Scholar
  14. [14]
    Zurla C., Samuely T., Bertoni G., Valle F., Dietler G., Finzi L., and Dunlap D.D. (2007). Integration host factor alters LacI-induced DNA looping. Biophysical Chemistry 128: 245–252.CrossRefGoogle Scholar
  15. [15]
    Goyal S., Lillian T., Blumberg S., Meiners J.C., Meyhofer E., and Perkins N.C. (2007). Intrinsic curvature of DNA influences LacR-mediated looping. Biophysical Journal 93: 4342–4359.CrossRefGoogle Scholar
  16. [16]
    Vanzi F., Broggio C., Sacconi L., and Pavone F.S. (2006). Lac repressor hinge flexibility and DNA looping: single molecule kinetics by tethered particle motion. Nucleic Acids Research 34: 3409–3420.CrossRefGoogle Scholar
  17. [17]
    Wyman C., Grotkopp E., Bustamante C., and Nelson H.C.M. (1995). Determination Of Heat-Shock Transcription Factor-2 Stoichiometry At Looped Dna Complexes Using Scanning Force Microscopy. Embo Journal 14: 117–123.Google Scholar
  18. [18]
    Wyman C., Rombel I., North A.K., Bustamante C., and Kustu S. (1997). Unusual oligomerization required for activity of NtrC, a bacterial enhancerbinding protein. Science 275: 1658–1661.CrossRefGoogle Scholar
  19. [19]
    Podesta A., Indrieri M., Brogioli D., Manning G.S., Milani P., Guerra R., Finzi L., and Dunlap D. (2005). Positively charged surfaces increase the flexibility of DNA. Biophysical Journal 89: 2558–2563.CrossRefGoogle Scholar
  20. [20]
    Irani M.H., Orosz L., and Adhya S. (1983). A control element within a structural gene - the gal operon of Escherichia-coli. Cell 32: 783–788.CrossRefGoogle Scholar
  21. [21]
    Aki T., Choy H.E., and Adhya S. (1996). Histone-like protein HU as a specific transcriptional regulator: Co-factor role in repression of gal transcription by GAL repressor. Genes to Cells 1: 179–188.CrossRefGoogle Scholar
  22. [22]
    Geanacopoulos M., Vasmatzis G., Lewis D.E.A., Roy S., Lee B., and Adhya S. (1999). GalR mutants defective in repressosome formation. Genes & Development 13: 1251–1262.CrossRefGoogle Scholar
  23. [23]
    Choy H.E., Park S.W., Parrack P., and Adhya S. (1995). Transcription Regulation By Inflexibility Of Promoter Dna In A Looped Complex. Proceedings Of The National Academy Of Sciences Of The United States Of America 92:7327–7331.Google Scholar
  24. [24]
    Virnik K., Lyubchenko Y.L., Karymov M.A., Dahlgren P., Tolstorukov M.Y., Semsey S., Zhurkin V.B., and Adhya S. (2003). ”Antiparallel” DNA loop in gal repressosome visualized by atomic force microscopy. Journal Of Molecular Biology 334: 53–63.CrossRefGoogle Scholar
  25. [25]
    Geanacopoulos M., Vasmatzis G., Zhurkin V.B., and Adhya S. (2001). Gal repressosome contains an antiparallel DNA loop. Nature Structural Biology 8: 432–436.CrossRefGoogle Scholar
  26. [26]
    Lia G., Bensimon D., Croquette V., Allemand J.F., Dunlap D., Lewis D.E.A., Adhya S.C., and Finzi L. (2003). Supercoiling and denaturation in Gal repressor/heat unstable nucleoid protein (HU)-mediated DNA looping. Proceedings Of The National Academy Of Sciences Of The United States Of America 100: 11373–11377.Google Scholar
  27. [27]
    Strick T.R., Allemand J.F., Bensimon D., Bensimon A., and Croquette V. (1996). The elasticity of a single supercoiled DNA molecule. Science 271: 1835–1837.CrossRefGoogle Scholar
  28. [28]
    Strick T.R., Allemand J.F., Bensimon D., and Croquette V. (1998). Behavior of supercoiled DNA. Biophysical Journal 74: 2016–2028.CrossRefGoogle Scholar
  29. [29]
    Semsey S., Virnik K., and Adhya S. (2005). A gamut of loops: meandering DNA. Trends In Biochemical Sciences 30: 334–341.CrossRefGoogle Scholar
  30. [30]
    Mehta R.A. and Kahn J.D. (1999). Designed hyperstable lac repressor center dot DNA loop topologies suggest alternative loop geometries. Journal Of Molecular Biology 294: 67–77.CrossRefGoogle Scholar
  31. [31]
    Semsey S., Tolstorukov M.Y., Virnik K., Zhurkin V.B., and Adhya S. (2004). DNA trajectory in the Ga1 repressosome. Genes & Development 18: 1898–1907.CrossRefGoogle Scholar
  32. [32]
    White J.H. (1969). SELF-LINKING AND GAUSS-INTEGRAL IN HIGHER DIMENSIONS. American Journal of Mathematics 91: 693–&.Google Scholar
  33. [33]
    Lia G., Praly E., Ferreira H., Stockdale C., Tse-Dinh Y.C., Dunlap D., Croquette V., Bensimon D., and Owen-Hughes T. (2006). Direct observation of DNA distortion by the RSC complex. Mol Cell 21: 417–425.CrossRefGoogle Scholar
  34. [34]
    Ptashne M.a.G.A. (2002). Genes and Signals (Cold Spring Harbor Laboratory Press).Google Scholar
  35. [35]
    Dodd I.B., Shearwin K.E., Perkins A.J., Burr T., Hochschild A., and Egan J.B. (2004). Cooperativity in long-range gene regulation by the lambda CI repressor. Genes & Development 18: 344–354.CrossRefGoogle Scholar
  36. [36]
    Maniatis T. and Ptashne M. (1973). Multiple Repressor Binding At Operators In Bacteriophage-Lambda - (Nuclease Protection Polynucleotide Sizing Pyrimidine Tracts Supercoils E-Coli). Proceedings Of The National Academy Of Sciences Of The United States Of America 70: 1531–1535.Google Scholar
  37. [37]
    Oppenheim A.B., Kobiler O., Stavans J., Court D.L., and Adhya S. (2005). Switches in bacteriophage lambda development. Annual Review Of Genetics 39: 409–429.CrossRefGoogle Scholar
  38. [38]
    Koblan K.S. and Ackers G.K. (1992). Site-Specific Enthalpic Regulation Of Dna-Transcription At Bacteriophage-Lambda Or. Biochemistry 31: 57–65.CrossRefGoogle Scholar
  39. [39]
    Senear D.F., Brenowitz M., Shea M.A., and Ackers G.K. (1986). Energetics Of Cooperative Protein Dna Interactions - Comparison Between Quantitative Deoxyribonuclease Footprint Titration And Filter Binding. Biochemistry 25: 7344–7354.CrossRefGoogle Scholar
  40. [40]
    Jain D., Nickels B.E., Sun L., Hochschild A., and Darst S.A. (2004). Structure of a ternary transcription activation complex. Molecular Cell 13: 45–53.CrossRefGoogle Scholar
  41. [41]
    Nickels B.E., Dove S.L., Murakami K.S., Darst S.A., and Hochschild A. (2002). Protein-protein and protein-DNA interactions of sigma(70) region 4 involved in transcription activation by lambda cl. Journal Of Molecular Biology 324: 17–34.CrossRefGoogle Scholar
  42. [42]
    Revet B., von Wilcken-Bergmann B., Bessert H., Barker A., and Muller-Hill B. (1999). Four dimers of lambda repressor bound to two suitably spaced pairs of lambda operators form octamers and DNA loops over large distances. Current Biology 9: 151–154.CrossRefGoogle Scholar
  43. [43]
    Dodd I.B., Perkins A.J., Tsemitsidis D., and Egan J.B. (2001). Octamerization of lambda CI repressor is needed for effective repression of P-RM and efficient switching from lysogeny. Genes & Development 15: 3013–3022.CrossRefGoogle Scholar
  44. [44]
    Zurla C., Franzini A., Galli G., Dunlap D.D., Lewis D.E.A., Adhya S., and Finzi L. (2006). Novel tethered particle motion analysis of CI protein-mediated DNA looping in the regulation of bacteriophage lambda. Journal Of Physics-Condensed Matter 18: S225–S234.CrossRefGoogle Scholar
  45. [45]
    Liebovitch L.S., Scheurle D., Rusek M., and Zochowski M. (2001). Fractal methods to analyze ion channel kinetics. Methods 24: 359–375.CrossRefGoogle Scholar
  46. [46]
    Watkins L.P. and Yang H. (2005). Detection of intensity change points in time-resolved single-molecule measurements. Journal of Physical Chemistry B 109: 617–628.CrossRefGoogle Scholar
  47. [47]
    Marko J.F. and Siggia E.D. (1997). Driving proteins off DNA using applied tension. Biophysical Journal 73: 2173–2178.CrossRefGoogle Scholar
  48. [48]
    Strick T.R., Croquette V., and Bensimon D. (2000). Single-molecule analysis of DNA uncoiling by a type II topoisomerase. Nature 404: 901–904.CrossRefGoogle Scholar
  49. [49]
    Vologodskii A.V. and Frankkamenetskii M.D. (1992). Modeling Supercoiled Dna. Methods In Enzymology 211: 467–480.CrossRefGoogle Scholar
  50. [50]
    Vologodskii A.V., Levene S.D., Klenin K.V., Frankkamenetskii M., and Cozzarelli N.R. (1992). Conformational And Thermodynamic Properties Of Supercoiled Dna. Journal Of Molecular Biology 227: 1224–1243.CrossRefGoogle Scholar
  51. [51]
    Marko J.F. (2007). Torque and dynamics of linking number relaxation in stretched supercoiled DNA. Physical Review E 76.Google Scholar
  52. [52]
    Vologodskii A., Do Q., Shiffeldrim N., and Smith C. (2005). Microscopic mechanisms of DNA flexibility. Biophysical Journal 88: 59A–59A.Google Scholar
  53. [53]
    Levene S.D., Abola P.M., Vologodskii A.V., and Cozzarelli N.R. (1992). Studies Of Loop Closure In Supercoiled Dna.Faseb Journal 6: A222–A222.Google Scholar
  54. [54]
    Zhang Y., McEwen A.E., Crothers D.M., and Levene S.D. (2006). Statistical-mechanical theory of DNA looping. Biophysical Journal 90: 1903–1912.CrossRefGoogle Scholar
  55. [55]
    Zhang Y., McEwen A.E., Crothers D.M., and Levene S.D. (2007). Analysis of in-vivo LacR-mediated gene repression based on the mechanics of DNA looping. Biophysical Journal, 232A–232A.Google Scholar
  56. [56]
    Du Q., Kotlyar A., and Vologodskii A. (2008). Kinking the double helix by bending deformation. Nucleic Acids Research 36: 1120–1128.CrossRefGoogle Scholar
  57. [57]
    Polikanov Y.S., Bondarenko V.A., Tchernaenko V., Jiang Y.I., Lutter L.C., Vologodskii A., and Studitsky V.M. (2007). Probability of the site juxtaposition determines the rate of protein-mediated DNA looping. Biophysical Journal 93: 2726–2731.CrossRefGoogle Scholar
  58. [58]
    Lillian T.D., Goyal S., Perkins N.C., Meiners J.C., and Kahn J.D. (2007). Computational rod theory predicts experimental characteristics of DNA looping by the Lac repressor. Biophysical Journal, 416A–417A.Google Scholar
  59. [59]
    Mehta R.A. and Kahn J.D. (1999). Stability of designed Lac repressor-DNA loops. Faseb Journal 13: A1371–A1371.Google Scholar
  60. [60]
    Tolstorukov M.Y., Colasanti A.V., McCandlish D.M., Olson W.K., and Zhurkin V.B. (2007). A novel roll-and-slide mechanism of DNA folding in chromatin: Implications for nucleosome positioning. Journal of Molecular Biology 371: 725–738.CrossRefGoogle Scholar
  61. [61]
    Matsumoto A. and Olson W.K. (2006). Predicted effects of local conformational coupling and external restraints on the torsional properties of single DNA molecules. Multiscale Modeling & Simulation 5: 1227–1247.MATHCrossRefMathSciNetGoogle Scholar
  62. [62]
    Swigon D., Coleman B.D., and Olson W.K. (2006). Modeling the Lac repressor-operator assembly: The influence of DNA looping on Lac repressor conformation. Proceedings of the National Academy of Sciences of the United States of America 103: 9879–9884.Google Scholar
  63. [63]
    Czapla L., Swigon D., and Olson W.K. (2006). Sequence-dependent effects in the cyclization of short DNA. Journal of Chemical Theory and Computation 2: 685–695.CrossRefGoogle Scholar
  64. [64]
    Vilar J.M.G. (2006). Modularizing gene regulation. Molecular Systems Biology.Google Scholar
  65. [65]
    Vilar J.M.G. and Saiz L. (2006). Multiprotein DNA looping. Physical Review Letters 96.Google Scholar
  66. [66]
    Villa E. and Schulten K. (2007). Multiscale simulations of the DNA loop topologies induced by the lac repressor. Biophysical Journal, 185A–185A.Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2009

Authors and Affiliations

  1. 1.Department of PhysicsEmory UniversityAtlantaUSA

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