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. 1976 Apr;18(1):195–204. doi: 10.1128/jvi.18.1.195-204.1976

Introduction of interrupted secondary structure in supercoiled DNA as a function of superhelix density: consideration of hairpin structures in superhelical DNA.

M Woodworth-Gutai, J Lebowitz
PMCID: PMC515538  PMID: 1255870

Abstract

PM2 DNA was prepared with different superhelical densities (sigma) in order to examine the relationship betweenn supercoiling and the occurrence of a region(s) of unpaired bases in this DNA. A previous study showed that CH3HgOH reacts with native superhelical PM2 DNA more rapidly than the nicked form II. This evaluation of binding, monitored through the change of sedimentation velocity, was repeated on PM2 DNA I with different superhelical densities. Early binding is detected by an increase in sedimentation velocity and occurs with molecules with sigma' values betwee -0.025 and -0.037. The conversion of form I to form II with the single-strand-specific endonuclease from Neurospora crassa also occurs above a sigma value of -0.025. This data strongly supports the view that supercoiling produces interrupted secondary structure. The question whether the interrupted regions remain single stranded in character or form small intrastrand hairpin regions is considered by examining which model best fits the CH3HgOH- induced sedimentation velocity changes and the standard sedimentation velocity versus the superhelical density curve for the in vitro made DNAs. The hairpin model offers the most satisfactory explanations for all the results of this and previous studies.

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Selected References

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

  1. 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]
  2. Beerman T. A., Lebowitz J. Further analysis of the altered secondary structure of superhelical DNA. Sensitivity to methylmercuric hydroxide a chemical probe for unpaired bases. J Mol Biol. 1973 Sep 25;79(3):451–470. doi: 10.1016/0022-2836(73)90398-7. [DOI] [PubMed] [Google Scholar]
  3. Brack C., Bickle T. A., Yuan R. The relation of single-stranded regions in bacteriophage PM2 supercoiled DNA to the early melting sequences. J Mol Biol. 1975 Aug 25;96(4):693–702. doi: 10.1016/0022-2836(75)90146-1. [DOI] [PubMed] [Google Scholar]
  4. Bruner R., Vinograd J. The evaluation of standard sedimentation coefficients of sodium RNA and sodium DNA from sedimentation velocity data in concentrated NaCl and CsCl solutions. Biochim Biophys Acta. 1965 Sep 6;108(1):18–29. doi: 10.1016/0005-2787(65)90104-8. [DOI] [PubMed] [Google Scholar]
  5. Chen M., Lebowitz J., Salzman N. P. Hin D restriction mapping of upaired regions in simian virus 40 superhelical DNA I: considerations regarding structure-function relationships. J Virol. 1976 Apr;18(1):211–217. doi: 10.1128/jvi.18.1.211-217.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Dean W. W., Lebowitz J. Partial alteration of secondary structure in native superhelical DNA. Nat New Biol. 1971 May 5;231(18):5–8. [PubMed] [Google Scholar]
  7. Denhardt D. T., Kato A. C. Comparison of the effect of ultraviolet radiation and ethidium bromide intercalation on the conformation of superhelical phiX174 replicative form DNA. J Mol Biol. 1973 Jul 15;77(4):479–494. doi: 10.1016/0022-2836(73)90217-9. [DOI] [PubMed] [Google Scholar]
  8. Depew D. E., Wang J. C. Conformational fluctuations of DNA helix. Proc Natl Acad Sci U S A. 1975 Nov;72(11):4275–4279. doi: 10.1073/pnas.72.11.4275. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Espejo R. T., Canelo E. S., Sinsheimer R. L. DNA of bacteriophage PM2: a closed circular double-stranded molecule. Proc Natl Acad Sci U S A. 1969 Aug;63(4):1164–1168. doi: 10.1073/pnas.63.4.1164. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Germond J. E., Vogt V. M., Hirt B. Characterization of the single-strand-specific nuclease S1 activity on double-stranded supercoiled polyoma DNA. Eur J Biochem. 1974 Apr 16;43(3):591–600. doi: 10.1111/j.1432-1033.1974.tb03446.x. [DOI] [PubMed] [Google Scholar]
  11. Gianni A. M., Smotkin D., Weinberg R. A. Murine leukemia virus: detection of unintegrated double-stranded DNA forms of the provirus. Proc Natl Acad Sci U S A. 1975 Feb;72(2):447–451. doi: 10.1073/pnas.72.2.447. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Goebel W., Helinski D. R. Nicking activity of an endonuclease. I. Transfer ribonucleic acid complex of Escherichia coli. Biochemistry. 1970 Nov 24;9(24):4793–4801. doi: 10.1021/bi00826a025. [DOI] [PubMed] [Google Scholar]
  13. Gray H. B., Jr, Upholt W. B., Vinograd J. A buoyant method for the determination of the superhelix density of closed circular DNA. J Mol Biol. 1971 Nov 28;62(1):1–19. doi: 10.1016/0022-2836(71)90127-6. [DOI] [PubMed] [Google Scholar]
  14. Guntaka R. V., Mahy B. W., Bishop J. M., Varmus H. E. Ethidium bromide inhibits appearance of closed circular viral DNA and integration of virus-specific DNA in duck cells infected by avian sarcoma virus. Nature. 1975 Feb 13;253(5492):507–511. doi: 10.1038/253507a0. [DOI] [PubMed] [Google Scholar]
  15. Jacob R. J., Lebowitz J., Printz M. P. Unpaired bases in superhelical DNA: kinetic evidence. Nucleic Acids Res. 1974 Apr;1(4):549–558. doi: 10.1093/nar/1.4.549. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. 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]
  17. Lebowitz J., Garon C. G., Chen M. C., Salzman N. P. Chemical modification of simian virus 40 DNA by reaction with a water-soluble carbodiimide. J Virol. 1976 Apr;18(1):205–210. doi: 10.1128/jvi.18.1.205-210.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Metz D. H., Brown G. L. The investigation of nucleic acid secondary structure by means of chemical modification with a carbodiimide reagent. I. The reaction between N-cyclohexyl-N'-beta-(4-methylmorpholinium)ethylcarbodiimide and model nucleotides. Biochemistry. 1969 Jun;8(6):2312–2328. doi: 10.1021/bi00834a012. [DOI] [PubMed] [Google Scholar]
  19. Morrow J. F., Berg P. Location of the T4 gene 32 protein binding site on simian virus 40 DNA. J Virol. 1973 Dec;12(6):1631–1632. doi: 10.1128/jvi.12.6.1631-1632.1973. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. 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]
  21. Olivera B. M., Lehman I. R. Linkage of polynucleotides through phosphodiester bonds by an enzyme from Escherichia coli. Proc Natl Acad Sci U S A. 1967 May;57(5):1426–1433. doi: 10.1073/pnas.57.5.1426. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Paoletti C., LePecq J. B., Lehman I. R. The use of ethidium bromide-circular DNA complexes for the fluorometric analysis of breakage and joining of DNA. J Mol Biol. 1971 Jan 14;55(1):75–100. doi: 10.1016/0022-2836(71)90282-8. [DOI] [PubMed] [Google Scholar]
  23. Pulleyblank D. E., Morgan A. R. The sense of naturally occurring superhelices and the unwinding angle of intercalated ethidium. J Mol Biol. 1975 Jan 5;91(1):1–13. doi: 10.1016/0022-2836(75)90368-x. [DOI] [PubMed] [Google Scholar]
  24. Pulleyblank D. E., Shure M., Tang D., Vinograd J., Vosberg H. P. Action of nicking-closing enzyme on supercoiled and nonsupercoiled closed circular DNA: formation of a Boltzmann distribution of topological isomers. Proc Natl Acad Sci U S A. 1975 Nov;72(11):4280–4284. doi: 10.1073/pnas.72.11.4280. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Radloff R., Bauer W., Vinograd J. A dye-buoyant-density method for the detection and isolation of closed circular duplex DNA: the closed circular DNA in HeLa cells. Proc Natl Acad Sci U S A. 1967 May;57(5):1514–1521. doi: 10.1073/pnas.57.5.1514. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Rahn R. O. Denaturation in ultraviolet-irradiated DNA. Photophysiology. 1973;8:231–255. doi: 10.1016/b978-0-12-282608-5.50014-x. [DOI] [PubMed] [Google Scholar]
  27. Reed S. I., Ferguson J., Davis R. W., Stark G. R. T antigen binds to simian virus 40 DNA at the origin of replication. Proc Natl Acad Sci U S A. 1975 Apr;72(4):1605–1609. doi: 10.1073/pnas.72.4.1605. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Upholt W. B., Gray H. B., Jr, Vinograd J. Sedimentation velocity behavior of closed circular SV40 DNA as a function of superhelix density, ionic strength, counterion and temperature. J Mol Biol. 1971 Nov 28;62(1):21–38. doi: 10.1016/0022-2836(71)90128-8. [DOI] [PubMed] [Google Scholar]

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