Skip to main content
PMC home page
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1980 Nov;77(11):6468–6472. doi: 10.1073/pnas.77.11.6468

The inverted repeat as a recognizable structural feature in supercoiled DNA molecules.

D M Lilley
PMCID: PMC350306  PMID: 6256738

Abstract

The single-strand-specific endonuclease S1 from Aspergillus oryzae introduces highly selective cleavages into supercoiled covalently closed circular DNA molecules, but not into their previously linearized counterparts. The cleavage sites are inverted repeats of unit length between 9 and 13 base pairs, separated by a nonrepetitious 2-6 base pairs. Such regions may adopt hairpin or similar structures stabilized by the negative superhelix density and may constitute recognition sites for cellular proteins.

Full text

PDF
6471

Images in this article

6468Image
on p.6468
6469Image
on p.6469
6469Image
on p.6469
6470Image
on p.6470
6470Image
on p.6470
6471Image
on p.6471
6471Image
on p.6471
6471Image
on p.6471

Selected References

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

  1. Ando T. A nuclease specific for heat-denatured DNA in isolated from a product of Aspergillus oryzae. Biochim Biophys Acta. 1966 Jan 18;114(1):158–168. doi: 10.1016/0005-2787(66)90263-2. [DOI] [PubMed] [Google Scholar]
  2. Beard P., Morrow J. F., Berg P. Cleavage of circular, superhelical simian virus 40 DNA to a linear duplex by S1 nuclease. J Virol. 1973 Dec;12(6):1303–1313. doi: 10.1128/jvi.12.6.1303-1313.1973. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Benham C. J. Torsional stress and local denaturation in supercoiled DNA. Proc Natl Acad Sci U S A. 1979 Aug;76(8):3870–3874. doi: 10.1073/pnas.76.8.3870. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Benyajati C., Worcel A. Isolation, characterization, and structure of the folded interphase genome of Drosophila melanogaster. Cell. 1976 Nov;9(3):393–407. doi: 10.1016/0092-8674(76)90084-2. [DOI] [PubMed] [Google Scholar]
  5. Bolivar F., Rodriguez R. L., Greene P. J., Betlach M. C., Heyneker H. L., Boyer H. W., Crosa J. H., Falkow S. Construction and characterization of new cloning vehicles. II. A multipurpose cloning system. Gene. 1977;2(2):95–113. [PubMed] [Google Scholar]
  6. Camerini-Otero R. D., Felsenfeld G. A simple model of DNA superhelices in solution. Proc Natl Acad Sci U S A. 1978 Apr;75(4):1708–1712. doi: 10.1073/pnas.75.4.1708. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Campbell A. M., Jolly D. J. Light-scattering studies on supercoil unwinding. Biochem J. 1973 Jun;133(2):209–226. doi: 10.1042/bj1330209. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Cook P. R., Brazell I. A. Supercoils in human DNA. J Cell Sci. 1975 Nov;19(2):261–279. doi: 10.1242/jcs.19.2.261. [DOI] [PubMed] [Google Scholar]
  9. Davidson N. Effect of DNA length on the free energy of binding of an unwinding ligand to a supercoiled DNA. J Mol Biol. 1972 May 14;66(2):307–309. doi: 10.1016/0022-2836(72)90482-2. [DOI] [PubMed] [Google Scholar]
  10. Fuller F. B. The writhing number of a space curve. Proc Natl Acad Sci U S A. 1971 Apr;68(4):815–819. doi: 10.1073/pnas.68.4.815. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Godson G. N. Action of the single-stranded DNA specific nuclease S1 on double-stranded DNA. Biochim Biophys Acta. 1973 Apr 21;308(7):59–67. doi: 10.1016/0005-2787(73)90122-6. [DOI] [PubMed] [Google Scholar]
  12. Hossenlopp P., Oudet P., Chambon P. Animal DNA-dependent RNA polymerases. Studies on the binding of mammalian RNA polymerases AI and B to Simian virus 40 DNA. Eur J Biochem. 1974 Jan 16;41(2):397–411. doi: 10.1111/j.1432-1033.1974.tb03281.x. [DOI] [PubMed] [Google Scholar]
  13. Kato A. C., Bartok K., Fraser M. J., Denhardt D. T. Sensitivity of superhelical DNA to a single-strand specific endonuclease. Biochim Biophys Acta. 1973 Apr 21;308(7):68–78. doi: 10.1016/0005-2787(73)90123-8. [DOI] [PubMed] [Google Scholar]
  14. Katz L., Kingsbury D. T., Helinski D. R. Stimulation by cyclic adenosine monophosphate of plasmid deoxyribonucleic acid replication and catabolite repression of the plasmid deoxyribonucleic acid-protein relaxation complex. J Bacteriol. 1973 May;114(2):577–591. doi: 10.1128/jb.114.2.577-591.1973. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. LINN S., LEHMAN I. R. AN ENDONUCLEASE FROM NEUROSPORA CRASSA SPECIFIC FOR POLYNUCLEOTIDES LACKING AN ORDERED STRUCTURE. I. PURIFICATION AND PROPERTIES OF THE ENZYME. J Biol Chem. 1965 Mar;240:1287–1293. [PubMed] [Google Scholar]
  16. Lescure B., Chestier A., Yaniv M. Transcription of polyoma virus DNA in vitro. II. Transcription of superhelical and linear polyoma DNA by RNA polymerase II. J Mol Biol. 1978 Sep 5;124(1):73–85. doi: 10.1016/0022-2836(78)90148-1. [DOI] [PubMed] [Google Scholar]
  17. Lilley D. M., Houghton M. The interaction of RNA polymerase II from wheat with supercoiled and linear plasmid templates. Nucleic Acids Res. 1979 Feb;6(2):507–523. doi: 10.1093/nar/6.2.507. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Lim V. I., Mazanov A. L. Tertiary structure for palindromic regions of DNA. FEBS Lett. 1978 Apr 1;88(1):118–123. doi: 10.1016/0014-5793(78)80621-8. [DOI] [PubMed] [Google Scholar]
  19. Maniatis T., Jeffrey A., van deSande H. Chain length determination of small double- and single-stranded DNA molecules by polyacrylamide gel electrophoresis. Biochemistry. 1975 Aug 26;14(17):3787–3794. doi: 10.1021/bi00688a010. [DOI] [PubMed] [Google Scholar]
  20. Maxam A. M., Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977 Feb;74(2):560–564. doi: 10.1073/pnas.74.2.560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. McGavin S. Models of specifically paired like (homologous) nucleic acid structures. J Mol Biol. 1971 Jan 28;55(2):293–298. doi: 10.1016/0022-2836(71)90201-4. [DOI] [PubMed] [Google Scholar]
  22. Méchali M., de Recondo A. M., Girard M. Action of the S1 endonuclease from Aspergillus oryzae on simian virus 40 supercoiled component I DNA. Biochem Biophys Res Commun. 1973 Oct 15;54(4):1306–1320. doi: 10.1016/0006-291x(73)91130-3. [DOI] [PubMed] [Google Scholar]
  23. Oka A., Nomura N., Morita M., Sugisaki H., Sugimoto K., Takanami M. Nucleotide sequence of small ColE1 derivatives: structure of the regions essential for autonomous replication and colicin E1 immunity. Mol Gen Genet. 1979 May 4;172(2):151–159. doi: 10.1007/BF00268276. [DOI] [PubMed] [Google Scholar]
  24. Patient R. K. Characterization of in vitro transcription initiation and termination sites in Col E1 DNA. Nucleic Acids Res. 1979 Jun 25;6(8):2647–2665. doi: 10.1093/nar/6.8.2647. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Paulson J. R., Laemmli U. K. The structure of histone-depleted metaphase chromosomes. Cell. 1977 Nov;12(3):817–828. doi: 10.1016/0092-8674(77)90280-x. [DOI] [PubMed] [Google Scholar]
  26. Richardson J. P. Effects of supercoiling on transcription from bacteriophage PM2 deoxyribonucleic acid. Biochemistry. 1974 Jul 16;13(15):3164–3169. doi: 10.1021/bi00712a025. [DOI] [PubMed] [Google Scholar]
  27. Sanger F., Coulson A. R., Friedmann T., Air G. M., Barrell B. G., Brown N. L., Fiddes J. C., Hutchison C. A., 3rd, Slocombe P. M., Smith M. The nucleotide sequence of bacteriophage phiX174. J Mol Biol. 1978 Oct 25;125(2):225–246. doi: 10.1016/0022-2836(78)90346-7. [DOI] [PubMed] [Google Scholar]
  28. Sharp P. A., Sugden B., Sambrook J. Detection of two restriction endonuclease activities in Haemophilus parainfluenzae using analytical agarose--ethidium bromide electrophoresis. Biochemistry. 1973 Jul 31;12(16):3055–3063. doi: 10.1021/bi00740a018. [DOI] [PubMed] [Google Scholar]
  29. Shishido K. Relationship between S1 endonuclease-sensitivity and number of superhelical turns in a negatively-twisted DNA. FEBS Lett. 1980 Mar 10;111(2):333–336. doi: 10.1016/0014-5793(80)80821-0. [DOI] [PubMed] [Google Scholar]
  30. Shlomai J., Kornberg A. An Escherichia coli replication protein that recognizes a unique sequence within a hairpin region in phi X174 DNA. Proc Natl Acad Sci U S A. 1980 Feb;77(2):799–803. doi: 10.1073/pnas.77.2.799. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Sutcliffe J. G. Complete nucleotide sequence of the Escherichia coli plasmid pBR322. Cold Spring Harb Symp Quant Biol. 1979;43(Pt 1):77–90. doi: 10.1101/sqb.1979.043.01.013. [DOI] [PubMed] [Google Scholar]
  32. Vogelstein B., Gillespie D. Preparative and analytical purification of DNA from agarose. Proc Natl Acad Sci U S A. 1979 Feb;76(2):615–619. doi: 10.1073/pnas.76.2.615. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Vogt V. M. Purification and further properties of single-strand-specific nuclease from Aspergillus oryzae. Eur J Biochem. 1973 Feb 15;33(1):192–200. doi: 10.1111/j.1432-1033.1973.tb02669.x. [DOI] [PubMed] [Google Scholar]
  34. Wang J. C. Interactions between twisted DNAs and enzymes: the effects of superhelical turns. J Mol Biol. 1974 Aug 25;87(4):797–816. doi: 10.1016/0022-2836(74)90085-0. [DOI] [PubMed] [Google Scholar]
  35. Woodworth-Gutai M., Lebowitz J. Introduction of interrupted secondary structure in supercoiled DNA as a function of superhelix density: consideration of hairpin structures in superhelical DNA. J Virol. 1976 Apr;18(1):195–204. doi: 10.1128/jvi.18.1.195-204.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Worcel A., Burgi E. On the structure of the folded chromosome of Escherichia coli. J Mol Biol. 1972 Nov 14;71(2):127–147. doi: 10.1016/0022-2836(72)90342-7. [DOI] [PubMed] [Google Scholar]
  37. Yang H. L., Heller K., Gellert M., Zubay G. Differential sensitivity of gene expression in vitro to inhibitors of DNA gyrase. Proc Natl Acad Sci U S A. 1979 Jul;76(7):3304–3308. doi: 10.1073/pnas.76.7.3304. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES