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Purification and Use of DNA Minicircles with Different Linking Numbers

  • Giorgio Camilloni
  • Rodolfo Negri
  • Micaela Caserta
  • Ernesto Di Mauro
Part of the Methods in Molecular Biology™ book series (MIMB, volume 94)

Abstract

The structural organization of both prokaryotic and eukaryotic chromosomes has evolved following a common principle: the need for storing the genetic information in topologically independent domains consisting of one or more genes and of all the elements required in cis for their functioning. The elements that belong to the same functional unit are topologically linked: they depend on each other and cooperate.

Keywords

Xylene Cyanole Negative Supercoiling Versus Constant Voltage Minor Groove Width Weiss Unit 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. 1.
    Burd, J. F., Wartell, R. M., Dodgson, J. B., and Wells, R.D. (1975) Transmission of stability (telestability) in deoxyribonucleic acid. Physical and enzymatic studies on the duplex block polymer d(C15·A15)·d(T15·G15). J. Biol. Chem. 250, 5109–5113.PubMedGoogle Scholar
  2. 2.
    Burd, J. F., Larson, J. E., and Wells, R. D. (1975) Further studies on telestability in DNA. The synthesis and characterization of the duplex block polymers d(C20·A10)·d(T10·G20) and d(C20·A15)·d(T15·G20) J. Biol. Chem. 250, 6002–6007.PubMedGoogle Scholar
  3. 3.
    Hogan, M., Dattagupta, N, and Crothers, D. M. (1979) Transmission of allosteric effects in DNA. Nature (Lond.) 278, 521–524.CrossRefGoogle Scholar
  4. 4.
    Carnevali, F., Caserta, M., and Di Mauro, E. (1982) Topological modifications and template activation are induced in chimaeric plasmids by inserted sequences. J. Mol. Biol. 165, 59–77.CrossRefGoogle Scholar
  5. 5.
    Carnevali, F., Caserta, M., and Di Mauro, E. (1984) Transitions in topological organization of supercoiled DNA domains as a potential regulatory mechanism. J. Biol. Chem. 259, 12,633–12,643.PubMedGoogle Scholar
  6. 6.
    Di Mauro, E., Caserta, M., Negri, R., and Carnevali, F. (1985) Activation of in vitro transcription and topology of closed DNA domains. J. Biol. Chem. 260, 152–159.PubMedGoogle Scholar
  7. 7.
    Wells, R. D. (1988) Unusual DNA structures. J. Biol. Chem. 263, 1095–1098.PubMedGoogle Scholar
  8. 8.
    Gruskin, E. A. and Rich, A. (1993) B-DNA to Z-DNA structural transitions in the SV40 enhancer: stabilization of ZDNA in negatively supercoiled DNA minicircles. Biochemistry 32, 2167–2176.PubMedCrossRefGoogle Scholar
  9. 9.
    Camilloni, G., Della Seta, F., Negri, R., Ficca, A. G., and Di Mauro, E. (1986) Structure of RNA polymerase II promoters. Conformational alterations and template properties of circularized Saccharomyces cerevisiae GAL1-GAL10 divergent promoters. EMBO J. 5, 763–771.PubMedGoogle Scholar
  10. 10.
    Della Seta, F., Camilloni, G., Venditti, S., and Di Mauro, E. (1988) The intrinsic topological information of the wild-type and of up-promoter mutations of the Saccharomyces cerevisiae alcohol dehydrogenase II regulatory region. J. Biol. Chem. 263, 15,888–15,896.PubMedGoogle Scholar
  11. 11.
    Venditti, S., Caserta, M., Di Mauro, E., and Camilloni, G. (1988) DNA conformational variations in the in vitro torsionally strained Ig κ light chain gene localize on consensus sequences. Biochim. Biophys. Acta 951, 139–148.PubMedGoogle Scholar
  12. 12.
    Drew, H. R. and Travers, A. A. (1985) DNA bending and its relation to nucleosome positioning. J. Mol. Biol. 186, 773–790.PubMedCrossRefGoogle Scholar
  13. 13.
    Lavigne, M., Kolb, A., Yeramian, E., and Buc, H. (1994) CRP fixes the rotational orientation of covalently closed DNA molecules. EMBO J. 13, 4983–4990.PubMedGoogle Scholar
  14. 14.
    Liu-Johnson, H.-N., Gartenberg, M. R., and Crothers, D. M. (1986) The DNA binding domain and bending angle of E. coli CAP protein. Cell 47, 995–1005.PubMedCrossRefGoogle Scholar
  15. 15.
    Thompson, J. F. and Landy, A. (1988) Empirical estimation of protein-induced DNA bending angles: applications to λ site-specific recombination complexes. Nucleic Acids Res. 16, 9687–9705.PubMedCrossRefGoogle Scholar
  16. 16.
    Hodges-Garcia, Y., Hagerman, P. J., and Pettijohn, D. E. (1989) DNA ring closure mediated by protein HU. J. Biol. Chem. 264, 14,621–14,623.PubMedGoogle Scholar
  17. 17.
    Paull, T. T., Haykinson, M. J., and Johnson, R.C. (1993) The non specific DNA-binding and bending proteins HMG1 and HMG2 promote the assembly of complex nucleoprotein structures. Genes. Dev. 7, 1521–1534.PubMedCrossRefGoogle Scholar
  18. 18.
    Pil, P. M., Chow, C. S., and Lippard, S. J. (1993) High-mobility-group 1 protein mediates DNA bending as determined by ring closures. Proc. Natl. Acad. Sci. USA 90, 9465–9469.PubMedCrossRefGoogle Scholar
  19. 19.
    Pabo, C. O. and Sauer, R. T. (1992) Transcription factors: structural families and principles of DNA recognition. Annu. Rev. Biochem. 61, 1053–1095.PubMedCrossRefGoogle Scholar
  20. 20.
    Travers A. A. (1989) DNA conformation and protein binding. Annu. Rev. Biochem. 58, 427–452.PubMedCrossRefGoogle Scholar
  21. 21.
    Camilloni, G., Di Martino, E., Caserta, M., and Di Mauro, E. (1988) Eukaryotic DNA topoisomerase I reaction is topology dependent. Nucleic Acids Res. 16, 7071–7085.PubMedCrossRefGoogle Scholar
  22. 22.
    Camilloni, G., Di Martino, E., Di Mauro, E., and Caserta, M. (1989) Regulation of the function of eukaryotic DNA topoisomerase I: topological conditions for inactivity. Proc. Natl. Acad. Sci. USA 86, 3080–3084.PubMedCrossRefGoogle Scholar
  23. 23.
    Caserta, M., Amadei, A., Di Mauro, E., and Camilloni, G. (1989) In vitro preferential topoisomerization of bent DNA. Nucleic Acids Res. 17, 8463–8474.PubMedCrossRefGoogle Scholar
  24. 24.
    Costanzo, G., Di Mauro, E., Salina, G., and Negri, R. (1990) Attraction, phasing and neighbour effects of histone octamers on curved DNA. J. Mol. Biol. 216, 363–374.PubMedCrossRefGoogle Scholar
  25. 25.
    Grosscheld, R., Giese, K., and Pagel, J. (1994) HMG domain proteins: architectural elements in the assembly of nucleoprotein structures. TIG 10, 94–100.CrossRefGoogle Scholar
  26. 26.
    Negri, R., Costanzo, G., Venditti, S., and Di Mauro, E. (1989) Linkage reduction allows reconstitution of nucleosomes on DNA microdomains. J. Mol. Biol. 207, 615–619.PubMedCrossRefGoogle Scholar
  27. 27.
    Duband-Goulet, I., Carot, V., Ulyanov, A. V., Douc-Rasy, S., and Prunell, A. (1992) Chromatin reconstitution on small DNA rings. IV. DNA supercoiling and nucleosome sequence preference. J. Mol. Biol. 224, 981–1001.PubMedCrossRefGoogle Scholar
  28. 28.
    Caserta, M. and Di Mauro, E. (1996) The common topological requirements for histone octamers and DNA topoisomerase I. BioEssays 18, 685–693.PubMedCrossRefGoogle Scholar
  29. 29.
    Shore, D., Langowski, J., and Baldwin, R. L. (1981) DNA flexibility studied by covalent closure of short fragments into circles. Proc. Natl. Acad. Sci USA 78, 4833–4837.PubMedCrossRefGoogle Scholar
  30. 30.
    Shore, D. and Baldwin, R. L. (1983) Energetics of DNA twisting. J. Mol. Biol. 170, 957–981.PubMedCrossRefGoogle Scholar
  31. 31.
    Shrader, T. E. and Crothers, D. M. (1990) Effects of DNA sequence and histone-histone interactions on nucleosome placement. J. Mol. Biol. 216, 69–84.PubMedCrossRefGoogle Scholar
  32. 32.
    Yocum, R. R., Hanely, S., West, R., and Ptashne, M. (1984) Use of lac Z fusions to delimit regulatory element of the inducible divergent GAL1–GAL10 promoter in S. cerevisiae. Mol. Cell. Biol. 4, 1985–1998.Google Scholar
  33. 33.
    Dugaiczyk, A., Boyer, H. W., and Goodman, H. M. (1975) Ligation of EcoRI endonuclease-generated DNA fragments into linear and circular structures. J. Mol. Biol. 96, 171–184.PubMedCrossRefGoogle Scholar
  34. 34.
    Bednar, J., Furrer, P., Stasiak, A., Dubochet, J., Egelman, E. H., and Bates A. D. (1994) The twist, writhe and overall shape of supercoiled DNA change during counterion-induced transition from a loosely to a tightly interwound superhelix. Possible implications for DNA structure in vivo. J. Mol. Biol. 235, 825–847.PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press Inc. 1999

Authors and Affiliations

  • Giorgio Camilloni
    • 1
  • Rodolfo Negri
    • 2
  • Micaela Caserta
    • 3
  • Ernesto Di Mauro
    • 1
  1. 1.Dipartimento di Genetica e Biologia MolecolareUniversitd di RomaRomaItaly
  2. 2.Centro di Studio per gli Acidi Nucleici (CNR), Dipartimento di Genetica e Biologia MolecolareUniversitá di RomaRomeItaly
  3. 3.Centro di Studio per gli Acidi Nucleici (CNR), Dipartimento di Genetica e Biologia MolecolareUniversitd di RomaRomeItaly

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