DNA Toplogy & Topoisomerases

Biochemistry 201

Advanced Molecular Biology

January 7, 2000

Doug Brutlag

 DNA Topology Handout

DNA Topology Slides

DNA Topoisomerase Handout

DNA Topoisomerase Slides

(You must use Acrobat Reader to View Handout)

 

Topology References

  1. Bauer, W. R., Crick, F. H. C. & White, J. H. (1980). Supercoiled DNA. Scientific American 243, 118-133.
  2. Benham, C. J. (1985). Theoretical analysis of conformational equilibria in superhelical DNA. Annu. Rev. Biophys. Biophys. Chem. 14, 23-45.
  3. Benham, C. J. (1987). The influence of tertiary structural restraints on conformational transitions in superhelical DNA. Nucleic. Acids. Res. 15, 9985-9995.
  4. Crothers, D. M. (1998). DNA curvature and deformation in protein-DNA complexes: a step in the right direction [comment]. Proc Natl Acad Sci U S A, 95(26), 15163-15165.
  5. Cozzarelli, N. R. (1991). The structure and function of DNA supercoiling and catenanes. Harvey Lect, 87, 35-55.
  6. Crick, F. H. C., Wang, J. C. & Bauer, W. R. (1979). Is DNA really a double helix? J. Mol. Biol. 129, 449-457.
  7. El Hassan, M. A. and Calladine, C. R. (1998). Two distinct modes of protein-induced bending in DNA. J Mol Biol, 282(2), 331-343.
  8. Giaever, G. N., Snyder, L., & Wang, J. C. (1988). DNA supercoiling in vivo. Biophys. Chem. 29, 7-15.
  9. Rhodes D, & Klug A (1981) Sequence-dependent helical periodicity of DNA. Nature 292 (5821): 378-380 (1981)
  10. Smith, G,R, (1981). DNA supercoiling: Another level for regulating gene expression. Cell 24, 599-600.
  11. Vologodskii, A. V. and Frank-Kamenetskii, M. D. (1992). Modeling supercoiled DNA. Methods Enzymol, 211, 467-80.
  12. Wang, J. C., & Giaever, G. N. (1988). Action at a distance along a DNA. Science 240, 300-304.
  13. Wang, J. C. (1974). Interactions between twisted DNAs and enzymes: The effects of superhelical turns. J. Mol. Biol. 87, 797-816.
  14. Wang, J. C. (1979). Helical repeat of DNA in solution. Proc. Natl. Acad. Sci.. USA 76, 200-203.
  15. Wasserman, S. A., & Cozzarelli, N. R. (1986). Biochemical topology: applications to DNA recombination and replication. Science 232, 951.

Topoisomerase Structures in PDB

E. coli Topoisomerase I (N-Terminal 67,000 Dalton domain)

E. coli Topoisomerase I (C-terminal Domain)

E. coli DNA Gyrase (59 KD fragment)

Yeast Topoisomerase I (N-terminal Fragment)

Yeast Topoisomerase II (94,000 Dalton central Fragment)

Human DNA Topoisomerase Linked to DNA

DNA Topoisomerase References

  1. Andersen, A. H., Svejstrup, J. Q. and Westergaard, O. (1994). The DNA binding, cleavage, and religation reactions of eukaryotic topoisomerases I and II. Adv Pharmacol, 29, 83-101.
  2. Berger, J. M. (1998). Structure of DNA topoisomerases. Biochim Biophys Acta, 1400(1-3), 3-18.
  3. Berger JM. (1998). Type II DNA topoisomerases. Curr Opin Struct Biol. 1998 Feb;8(1):26-32.
  4. Champoux, J. J. (1994). Mechanism of catalysis by eukaryotic DNA topoisomerase I. Adv Pharmacol, 29, 71-82.
  5. Champoux, J. J. (1998). Domains of human topoisomerase I and associated functions. Prog Nucleic Acid Res Mol Biol, 60, 111-132.
  6. Cozzarelli, N. R. (1980). DNA gyrase and the supercoiling of DNA. Science 207, 953-960.
  7. Cozzarelli NR, (1980) DNA topoisomerases. Cell 22, 327-328 (1980)
  8. Drlica, K. (1992). Control of bacterial DNA supercoiling. Mol Microbiol 6(4), 425-33.
  9. Froelich-Ammon SJ, (1995)Topoisomerase poisons: harnessing the dark side of enzyme mechanism. J. Biol. Chem. 270, 21429-21432 (1995)
  10. Gupta, M., Fujimori, A. and Pommier, Y. (1995). Eukaryotic DNA topoisomerases I. Biochim Biophys Acta, 1262(1), 1-14.
  11. Holm, C., Goto, T., Wang, J. C., and Botstein, D. (1985). DNA Topoisomerase II Is Required at the Time of Mitosis in Yeast. Cell 41, 553-563.
  12. Hsieh, T. S. (1992). DNA topoisomerases. Curr Opin Cell Biol 4(3), 396-400.
  13. Hsieh, T., Lee, M. P. and Brown, S. D. (1994). Structure of eukaryotic type I DNA topoisomerase. Adv Pharmacol, 29, 191-200.
  14. Lima CD, (1994). Three-dimensional structure of the 67K N-terminal fragment of E. coli DNA topoisomerase I. Nature 367, 138-146 (1994)
  15. Lue N, Sharma A, Mondragon A, Wang JC (1995). A 26 kDa yeast DNA topoisomerase I fragment: crystallographic structure and mechanistic implications. Structure 3 (12): 1315-1322
  16. Maxwell A, (1996) Protein gates in DNA topoisomerase II. Nat. Struct. Biol. 3, 109-112.
  17. Menzel, R. and Gellert, M. (1994). The biochemistry and biology of DNA gyrase. Adv Pharmacol, 29, 39-69.
  18. Orphanides, G. and Maxwell, A. (1994). Topoisomerases. In one gate, out the other. Curr Biol, 4(11), 1006-9.
  19. Redinbo, M. R., Stewart, L., Kuhn, P., Champoux, J. J. and Hol, W. G. (1998). Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA [see comments]. Science, 279(5356), 1504-1513.
  20. Roca, J. (1995). The mechanisms of DNA topoisomerases. Trends Biochem Sci, 20(4), 156-60.
  21. Sharma, A. and Mondragon, A. (1995). DNA topoisomerases. Curr Opin Struct Biol, 5(1), 39-47.
  22. Smith, P. J. (1990). DNA topoisomerase dysfunction: a new goal for antitumor chemotherapy. Bioessays, 12(4), 167-72.
  23. Stewart, L., Redinbo, M. R., Qiu, X., Hol, W. G. and Champoux, J. J. (1998). A model for the mechanism of human topoisomerase I. [see comments]. Science, 279(5356), 1534-1541.
  24. Wang JC, (1991) DNA topoisomerases: why so many? J. Biol. Chem. 266, 6659-6662 (1991)
  25. Wang, J.C. (1982). DNA topoisomerases. Scientific American 247, 100-109.
  26. Watt, P. M. and Hickson, I. D. (1994). Structure and function of type II DNA topoisomerases. Biochem J, 303(Pt 3)), 681-95.
  27. Zhang, H., D'Arpa, P. and Liu, L. F. (1990). A model for tumor cell killing by topoisomerase poisons. Cancer Cells, 2(1), 23-7.
  28. Zijlstra, J. G., de, J. S., de, V. E. and Mulder, N. H. (1990). Topoisomerases, new targets in cancer chemotherapy. Med Oncol Tumor Pharmacother, 7(1), 11-81.