Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1988 Jul 25;16(14A):6477–6492. doi: 10.1093/nar/16.14.6477

Bent DNA structures associated with several origins of replication are recognized by a unique enzyme from trypanosomatids.

M Linial 1, J Shlomai 1
PMCID: PMC338309  PMID: 3399408

Abstract

Sequence-directed bending of the DNA double helix is a conformational variation found in both prokaryotic and eukaryotic organisms. The utilization of bent DNA structures from various sources as specific signals recognized by an enzyme is demonstrated here using a unique endonuclease purified from trypanosomatid cells. Crithidia fasciculata nicking enzyme was previously shown to recognize specifically the bent structure found in kinetoplast DNA minicircles. The binding constant measured for this specific interaction is of two orders of magnitude higher than that measured for the binding of the enzyme to a non-curved sequence. As determined by binding competition and mobility shift electrophoresis analyses, this enzyme recognizes the sequence-directed bends associated with the origins of replication of bacteriophage lambda and simian virus 40 (SV40), as well as that located within the autonomously replicating sequence (ARS1) region of the yeast S. cerevisiae.

Full text

PDF
6477

Images in this article

6487Image
on p.6487

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Anderson J. N. Detection, sequence patterns and function of unusual DNA structures. Nucleic Acids Res. 1986 Nov 11;14(21):8513–8533. doi: 10.1093/nar/14.21.8513. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bossi L., Smith D. M. Conformational change in the DNA associated with an unusual promoter mutation in a tRNA operon of Salmonella. Cell. 1984 Dec;39(3 Pt 2):643–652. doi: 10.1016/0092-8674(84)90471-9. [DOI] [PubMed] [Google Scholar]
  3. DeLucia A. L., Deb S., Partin K., Tegtmeyer P. Functional interactions of the simian virus 40 core origin of replication with flanking regulatory sequences. J Virol. 1986 Jan;57(1):138–144. doi: 10.1128/jvi.57.1.138-144.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Deb S., DeLucia A. L., Koff A., Tsui S., Tegtmeyer P. The adenine-thymine domain of the simian virus 40 core origin directs DNA bending and coordinately regulates DNA replication. Mol Cell Biol. 1986 Dec;6(12):4578–4584. doi: 10.1128/mcb.6.12.4578. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Englund P. T., DiMaio D. C., Price S. S. A nicked form of kinetoplast DNA in Leishmania tarentolae. J Biol Chem. 1977 Sep 10;252(17):6208–6216. [PubMed] [Google Scholar]
  6. Englund P. T. The replication of kinetoplast DNA networks in Crithidia fasciculata. Cell. 1978 May;14(1):157–168. doi: 10.1016/0092-8674(78)90310-0. [DOI] [PubMed] [Google Scholar]
  7. Fried M. G., Crothers D. M. Equilibrium studies of the cyclic AMP receptor protein-DNA interaction. J Mol Biol. 1984 Jan 25;172(3):241–262. doi: 10.1016/s0022-2836(84)80025-x. [DOI] [PubMed] [Google Scholar]
  8. Fried M., Crothers D. M. Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis. Nucleic Acids Res. 1981 Dec 11;9(23):6505–6525. doi: 10.1093/nar/9.23.6505. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Frischauf A. M., Lehrach H., Poustka A., Murray N. Lambda replacement vectors carrying polylinker sequences. J Mol Biol. 1983 Nov 15;170(4):827–842. doi: 10.1016/s0022-2836(83)80190-9. [DOI] [PubMed] [Google Scholar]
  10. Gourse R. L., de Boer H. A., Nomura M. DNA determinants of rRNA synthesis in E. coli: growth rate dependent regulation, feedback inhibition, upstream activation, antitermination. Cell. 1986 Jan 17;44(1):197–205. doi: 10.1016/0092-8674(86)90498-8. [DOI] [PubMed] [Google Scholar]
  11. Kitchin P. A., Klein V. A., Fein B. I., Englund P. T. Gapped Minicircles. A novel replication intermediate of kinetoplast DNA. J Biol Chem. 1984 Dec 25;259(24):15532–15539. [PubMed] [Google Scholar]
  12. Kitchin P. A., Klein V. A., Ryan K. A., Gann K. L., Rauch C. A., Kang D. S., Wells R. D., Englund P. T. A highly bent fragment of Crithidia fasciculata kinetoplast DNA. J Biol Chem. 1986 Aug 25;261(24):11302–11309. [PubMed] [Google Scholar]
  13. Koepsel R. R., Khan S. A. Static and initiator protein-enhanced bending of DNA at a replication origin. Science. 1986 Sep 19;233(4770):1316–1318. doi: 10.1126/science.3749879. [DOI] [PubMed] [Google Scholar]
  14. Koo H. S., Crothers D. M. Chemical determinants of DNA bending at adenine-thymine tracts. Biochemistry. 1987 Jun 16;26(12):3745–3748. doi: 10.1021/bi00386a070. [DOI] [PubMed] [Google Scholar]
  15. Koo H. S., Wu H. M., Crothers D. M. DNA bending at adenine . thymine tracts. Nature. 1986 Apr 10;320(6062):501–506. doi: 10.1038/320501a0. [DOI] [PubMed] [Google Scholar]
  16. Linial M., Shlomai J. A unique endonuclease from Crithidia fasciculata which recognizes a bend in the DNA helix. Specificity of the cleavage reaction. J Biol Chem. 1988 Jan 5;263(1):290–297. [PubMed] [Google Scholar]
  17. Linial M., Shlomai J. Sequence-directed bent DNA helix is the specific binding site for Crithidia fasciculata nicking enzyme. Proc Natl Acad Sci U S A. 1987 Dec;84(23):8205–8209. doi: 10.1073/pnas.84.23.8205. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Linial M., Shlomai J. The sequence-directed bent structure in kinetoplast DNA is recognized by an enzyme from Crithidia fasciculata. J Biol Chem. 1987 Nov 5;262(31):15194–15201. [PubMed] [Google Scholar]
  19. Liu-Johnson H. N., Gartenberg M. R., Crothers D. M. The DNA binding domain and bending angle of E. coli CAP protein. Cell. 1986 Dec 26;47(6):995–1005. doi: 10.1016/0092-8674(86)90814-7. [DOI] [PubMed] [Google Scholar]
  20. Marini J. C., Levene S. D., Crothers D. M., Englund P. T. Bent helical structure in kinetoplast DNA. Proc Natl Acad Sci U S A. 1982 Dec;79(24):7664–7668. doi: 10.1073/pnas.79.24.7664. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Ntambi J. M., Marini J. C., Bangs J. D., Hajduk S. L., Jimenez H. E., Kitchin P. A., Klein V. A., Ryan K. A., Englund P. T. Presence of a bent helix in fragments of kinetoplast DNA minicircles from several trypanosomatid species. Mol Biochem Parasitol. 1984 Jul;12(3):273–286. doi: 10.1016/0166-6851(84)90084-7. [DOI] [PubMed] [Google Scholar]
  22. Ross W., Shulman M., Landy A. Biochemical analysis of att-defective mutants of the phage lambda site-specific recombination system. J Mol Biol. 1982 Apr 15;156(3):505–522. doi: 10.1016/0022-2836(82)90263-7. [DOI] [PubMed] [Google Scholar]
  23. Ryder K., Silver S., DeLucia A. L., Fanning E., Tegtmeyer P. An altered DNA conformation in origin region I is a determinant for the binding of SV40 large T antigen. Cell. 1986 Mar 14;44(5):719–725. doi: 10.1016/0092-8674(86)90838-x. [DOI] [PubMed] [Google Scholar]
  24. Shlomai J., Linial M. A nicking enzyme from trypanosomatids which specifically affects the topological linking of duplex DNA circles. Purification and characterization. J Biol Chem. 1986 Dec 5;261(34):16219–16225. [PubMed] [Google Scholar]
  25. Shlomai J., Linial M. A nicking enzyme from trypanosomatids which specifically affects the topological linking of duplex DNA circles. Purification and characterization. J Biol Chem. 1986 Dec 5;261(34):16219–16225. [PubMed] [Google Scholar]
  26. Shlomai J., Zadok A. Reversible decatenation of kinetoplast DNA by a DNA topoisomerase from trypanosomatids. Nucleic Acids Res. 1983 Jun 25;11(12):4019–4034. doi: 10.1093/nar/11.12.4019. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Snyder M., Buchman A. R., Davis R. W. Bent DNA at a yeast autonomously replicating sequence. Nature. 1986 Nov 6;324(6092):87–89. doi: 10.1038/324087a0. [DOI] [PubMed] [Google Scholar]
  28. Stenzel T. T., Patel P., Bastia D. The integration host factor of Escherichia coli binds to bent DNA at the origin of replication of the plasmid pSC101. Cell. 1987 Jun 5;49(5):709–717. doi: 10.1016/0092-8674(87)90547-2. [DOI] [PubMed] [Google Scholar]
  29. Trifonov E. N. Curved DNA. CRC Crit Rev Biochem. 1985;19(2):89–106. doi: 10.3109/10409238509082540. [DOI] [PubMed] [Google Scholar]
  30. Tschumper G., Carbon J. Sequence of a yeast DNA fragment containing a chromosomal replicator and the TRP1 gene. Gene. 1980 Jul;10(2):157–166. doi: 10.1016/0378-1119(80)90133-x. [DOI] [PubMed] [Google Scholar]
  31. Zahn K., Blattner F. R. Direct evidence for DNA bending at the lambda replication origin. Science. 1987 Apr 24;236(4800):416–422. doi: 10.1126/science.2951850. [DOI] [PubMed] [Google Scholar]
  32. Zahn K., Blattner F. R. Sequence-induced DNA curvature at the bacteriophage lambda origin of replication. Nature. 1985 Oct 3;317(6036):451–453. doi: 10.1038/317451a0. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES