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. 1987 Dec;84(23):8205–8209. doi: 10.1073/pnas.84.23.8205

Sequence-directed bent DNA helix is the specific binding site for Crithidia fasciculata nicking enzyme.

M Linial 1, J Shlomai 1
PMCID: PMC299510  PMID: 2825181

Abstract

The sequence-directed bent structure of kinetoplast DNA minicircles specifies a unique binding site for Crithidia fasciculata nicking enzyme. Binding of the purified enzyme to the bent structure results in the formation of a tight enzyme-DNA complex that is highly specific to curved DNA. Recognition of the binding site is not determined by the nucleotide sequence at the site of binding per se but through the specific local variation in the DNA helix geometry. Both dynamic curved structures, which are generated by supercoiling, and static ones, which are sequenced-directed, could support and efficient enzyme-DNA complex formation. Binding interactions are dependent upon the degree of the helix curvature and decrease with the straightening of the binding site. DNase I protection experiments identify distinct domains of enzyme binding within the bent structure and suggest the induction of structural changes within these regions as a result of protein-DNA interactions.

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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. 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]
  4. Griffith J., Bleyman M., Rauch C. A., Kitchin P. A., Englund P. T. Visualization of the bent helix in kinetoplast DNA by electron microscopy. Cell. 1986 Aug 29;46(5):717–724. doi: 10.1016/0092-8674(86)90347-8. [DOI] [PubMed] [Google Scholar]
  5. 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]
  6. 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]
  7. 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]
  8. Kopka M. L., Yoon C., Goodsell D., Pjura P., Dickerson R. E. The molecular origin of DNA-drug specificity in netropsin and distamycin. Proc Natl Acad Sci U S A. 1985 Mar;82(5):1376–1380. doi: 10.1073/pnas.82.5.1376. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. 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]
  10. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  11. 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]
  12. 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]
  13. 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]
  14. Saucier J. M., Benard J., da Silva J., Riou G. Occurrence of a kinetoplast DNA-protein complex in Trypanosoma cruzi. Biochem Biophys Res Commun. 1981 Aug 14;101(3):988–994. doi: 10.1016/0006-291x(81)91846-5. [DOI] [PubMed] [Google Scholar]
  15. 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]
  16. 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]
  17. 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]
  18. Trifonov E. N. Curved DNA. CRC Crit Rev Biochem. 1985;19(2):89–106. doi: 10.3109/10409238509082540. [DOI] [PubMed] [Google Scholar]
  19. Wu H. M., Crothers D. M. The locus of sequence-directed and protein-induced DNA bending. Nature. 1984 Apr 5;308(5959):509–513. doi: 10.1038/308509a0. [DOI] [PubMed] [Google Scholar]
  20. 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]

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