Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1992 Feb 11;20(3):467–473. doi: 10.1093/nar/20.3.467

The recognition of DNA cleavage sites by porcine spleen topoisomerase II.

H W Huang 1, J K Juang 1, H J Liu 1
PMCID: PMC310409  PMID: 1311075

Abstract

The cutting sites specificity of topoisomerase II from porcine spleen were determined by a modified Sanger's DNA sequencing method. The topoisomerase II prefers to cut DNA at the 3' side of A and leave 5' protruding end with two staggering bases. Through the free energy analysis for DNA duplex, we also found that the topoisomerase II seemed cut DNA preferably at energetically unstable regions. So it is concluded that the specific DNA cutting by porcine spleen topoisomerase II has two structural recognition factors: one is to localize around the energetically unstable region and another is to act at the 3' side of A base.

Full text

PDF
467

Images in this article

468Image
on p.468
469Image
on p.469
470Image
on p.470

Selected References

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

  1. Andersen A. H., Christiansen K., Zechiedrich E. L., Jensen P. S., Osheroff N., Westergaard O. Strand specificity of the topoisomerase II mediated double-stranded DNA cleavage reaction. Biochemistry. 1989 Jul 25;28(15):6237–6244. doi: 10.1021/bi00441a015. [DOI] [PubMed] [Google Scholar]
  2. Bae Y. S., Kawasaki I., Ikeda H., Liu L. F. Illegitimate recombination mediated by calf thymus DNA topoisomerase II in vitro. Proc Natl Acad Sci U S A. 1988 Apr;85(7):2076–2080. doi: 10.1073/pnas.85.7.2076. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Borer P. N., Dengler B., Tinoco I., Jr, Uhlenbeck O. C. Stability of ribonucleic acid double-stranded helices. J Mol Biol. 1974 Jul 15;86(4):843–853. doi: 10.1016/0022-2836(74)90357-x. [DOI] [PubMed] [Google Scholar]
  4. Capranico G., Kohn K. W., Pommier Y. Local sequence requirements for DNA cleavage by mammalian topoisomerase II in the presence of doxorubicin. Nucleic Acids Res. 1990 Nov 25;18(22):6611–6619. doi: 10.1093/nar/18.22.6611. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Capranico G., Zunino F., Kohn K. W., Pommier Y. Sequence-selective topoisomerase II inhibition by anthracycline derivatives in SV40 DNA: relationship with DNA binding affinity and cytotoxicity. Biochemistry. 1990 Jan 16;29(2):562–569. doi: 10.1021/bi00454a033. [DOI] [PubMed] [Google Scholar]
  6. Chen G. L., Yang L., Rowe T. C., Halligan B. D., Tewey K. M., Liu L. F. Nonintercalative antitumor drugs interfere with the breakage-reunion reaction of mammalian DNA topoisomerase II. J Biol Chem. 1984 Nov 10;259(21):13560–13566. [PubMed] [Google Scholar]
  7. Chiba M., Shimizu H., Fujimoto A., Nashimoto H., Ikeda H. Common sites for recombination and cleavage mediated by bacteriophage T4 DNA topoisomerase in vitro. J Biol Chem. 1989 Aug 5;264(22):12785–12790. [PubMed] [Google Scholar]
  8. Chow K. C., Macdonald T. L., Ross W. E. DNA binding by epipodophyllotoxins and N-acyl anthracyclines: implications for mechanism of topoisomerase II inhibition. Mol Pharmacol. 1988 Oct;34(4):467–473. [PubMed] [Google Scholar]
  9. Dale R. M., Arrow A. A rapid single-stranded cloning, sequencing, insertion, and deletion strategy. Methods Enzymol. 1987;155:204–214. doi: 10.1016/0076-6879(87)55017-0. [DOI] [PubMed] [Google Scholar]
  10. Earnshaw W. C., Heck M. M. Localization of topoisomerase II in mitotic chromosomes. J Cell Biol. 1985 May;100(5):1716–1725. doi: 10.1083/jcb.100.5.1716. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Freier S. M., Kierzek R., Jaeger J. A., Sugimoto N., Caruthers M. H., Neilson T., Turner D. H. Improved free-energy parameters for predictions of RNA duplex stability. Proc Natl Acad Sci U S A. 1986 Dec;83(24):9373–9377. doi: 10.1073/pnas.83.24.9373. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Garger S. J., Griffith O. M., Grill L. K. Rapid purification of plasmid DNA by a single centrifugation in a two-step cesium chloride-ethidium bromide gradient. Biochem Biophys Res Commun. 1983 Dec 28;117(3):835–842. doi: 10.1016/0006-291x(83)91672-8. [DOI] [PubMed] [Google Scholar]
  13. Gasser S. M., Laemmli U. K. The organisation of chromatin loops: characterization of a scaffold attachment site. EMBO J. 1986 Mar;5(3):511–518. doi: 10.1002/j.1460-2075.1986.tb04240.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Holm C., Goto T., Wang J. C., Botstein D. DNA topoisomerase II is required at the time of mitosis in yeast. Cell. 1985 Jun;41(2):553–563. doi: 10.1016/s0092-8674(85)80028-3. [DOI] [PubMed] [Google Scholar]
  15. Hunt C., Morimoto R. I. Conserved features of eukaryotic hsp70 genes revealed by comparison with the nucleotide sequence of human hsp70. Proc Natl Acad Sci U S A. 1985 Oct;82(19):6455–6459. doi: 10.1073/pnas.82.19.6455. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Juang J. K., Huang H. W., Chen C. M., Liu H. J. A new compound, withangulatin A, promotes type II DNA topoisomerase-mediated DNA damage. Biochem Biophys Res Commun. 1989 Mar 31;159(3):1128–1134. doi: 10.1016/0006-291x(89)92226-2. [DOI] [PubMed] [Google Scholar]
  17. Juang J. K., Liu H. J. The effect of DMSO on natural DNA conformation in enhancing transcription. Biochem Biophys Res Commun. 1987 Aug 14;146(3):1458–1464. doi: 10.1016/0006-291x(87)90813-8. [DOI] [PubMed] [Google Scholar]
  18. Kudritskaya Z. G., Danilov V. I. Quantum mechanical study of bases interactions in various associates in atomic dipole approximation. J Theor Biol. 1976 Jul 7;59(2):303–318. doi: 10.1016/0022-5193(76)90172-7. [DOI] [PubMed] [Google Scholar]
  19. Lee M. P., Sander M., Hsieh T. S. Single strand DNA cleavage reaction of duplex DNA by Drosophila topoisomerase II. J Biol Chem. 1989 Aug 15;264(23):13510–13518. [PubMed] [Google Scholar]
  20. Liu L. F., Rowe T. C., Yang L., Tewey K. M., Chen G. L. Cleavage of DNA by mammalian DNA topoisomerase II. J Biol Chem. 1983 Dec 25;258(24):15365–15370. [PubMed] [Google Scholar]
  21. Mierendorf R. C., Pfeffer D. Sequencing of RNA transcripts synthesized in vitro from plasmids containing bacteriophage promoters. Methods Enzymol. 1987;152:563–566. doi: 10.1016/0076-6879(87)52062-6. [DOI] [PubMed] [Google Scholar]
  22. Mirkovitch J., Gasser S. M., Laemmli U. K. Scaffold attachment of DNA loops in metaphase chromosomes. J Mol Biol. 1988 Mar 5;200(1):101–109. doi: 10.1016/0022-2836(88)90336-1. [DOI] [PubMed] [Google Scholar]
  23. Mirkovitch J., Mirault M. E., Laemmli U. K. Organization of the higher-order chromatin loop: specific DNA attachment sites on nuclear scaffold. Cell. 1984 Nov;39(1):223–232. doi: 10.1016/0092-8674(84)90208-3. [DOI] [PubMed] [Google Scholar]
  24. Pommier Y., Cockerill P. N., Kohn K. W., Garrard W. T. Identification within the simian virus 40 genome of a chromosomal loop attachment site that contains topoisomerase II cleavage sites. J Virol. 1990 Jan;64(1):419–423. doi: 10.1128/jvi.64.1.419-423.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Sander M., Hsieh T. S. Drosophila topoisomerase II double-strand DNA cleavage: analysis of DNA sequence homology at the cleavage site. Nucleic Acids Res. 1985 Feb 25;13(4):1057–1072. doi: 10.1093/nar/13.4.1057. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Sander M., Hsieh T. Double strand DNA cleavage by type II DNA topoisomerase from Drosophila melanogaster. J Biol Chem. 1983 Jul 10;258(13):8421–8428. [PubMed] [Google Scholar]
  27. Sperry A. O., Blasquez V. C., Garrard W. T. Dysfunction of chromosomal loop attachment sites: illegitimate recombination linked to matrix association regions and topoisomerase II. Proc Natl Acad Sci U S A. 1989 Jul;86(14):5497–5501. doi: 10.1073/pnas.86.14.5497. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Spitzner J. R., Chung I. K., Muller M. T. Eukaryotic topoisomerase II preferentially cleaves alternating purine-pyrimidine repeats. Nucleic Acids Res. 1990 Jan 11;18(1):1–11. doi: 10.1093/nar/18.1.1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Tabor S., Richardson C. C. DNA sequence analysis with a modified bacteriophage T7 DNA polymerase. Proc Natl Acad Sci U S A. 1987 Jul;84(14):4767–4771. doi: 10.1073/pnas.84.14.4767. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Turner D. H., Sugimoto N., Freier S. M. RNA structure prediction. Annu Rev Biophys Biophys Chem. 1988;17:167–192. doi: 10.1146/annurev.bb.17.060188.001123. [DOI] [PubMed] [Google Scholar]
  31. Udvardy A., Schedl P., Sander M., Hsieh T. S. Topoisomerase II cleavage in chromatin. J Mol Biol. 1986 Sep 20;191(2):231–246. doi: 10.1016/0022-2836(86)90260-3. [DOI] [PubMed] [Google Scholar]
  32. Uemura T., Tanagida M. Mitotic spindle pulls but fails to separate chromosomes in type II DNA topoisomerase mutants: uncoordinated mitosis. EMBO J. 1986 May;5(5):1003–1010. doi: 10.1002/j.1460-2075.1986.tb04315.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Wang J. C. DNA topoisomerases. Annu Rev Biochem. 1985;54:665–697. doi: 10.1146/annurev.bi.54.070185.003313. [DOI] [PubMed] [Google Scholar]

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

RESOURCES