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Imaging of Triplexes by Electron and Scanning Force Microscopy

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Part of the book series: Perspectives in Antisense Science ((DARE,volume 2))

Abstract

During the last decade numerous attempts have been made to use synthetic oligonucleotides, primarily triple-helix-forming oligonucleotides (TFO; 13), and more recently peptide nucleic acids (PNA; 4, 5) as tools for exploring DNA structure and for creating various methods for regulation of gene expression. TFOs and PNAs form triplexes with DNA, albeit of differing natures (6 and herein). It was assumed that an unusual parallel triplex, or R-DNA, is assembled as an intermediate structure during specific recombination mediated by RecA protein (7, 8). Genome analysis and labeling using various types of triplexes is an important microscopy project with great potential.

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References

  1. Beal, P. A. and Dervan, P. B. (1991). Second structural motif for recognition of DNA by oligonucleotide-directed triple-helix formation. Science 251, 1360–1363.

    Article  PubMed  CAS  Google Scholar 

  2. Hélène, C. (1991). The anti-gene strategy: control of gene expression by triplex-forming-oligonucleotides. Anticancer Drug Des. 6, 569–584.

    PubMed  Google Scholar 

  3. Thuong, N.T. and Hélène, C. (1993). Sequence-specific recognition and modification of double-helical DNA by oligonucleotides. Angew. Chem. Int. Ed. Engl. 32, 666–690.

    Article  Google Scholar 

  4. Nielsen, P. E., Egholm, M., Berg, R. H. and Buchardt, O. (1991). Sequence selective recognition of DNA by strand displacement with a thymine-substituted polyamide. Science 254, 1497–1500.

    Article  PubMed  CAS  Google Scholar 

  5. Nielsen, P. E., Egholm, M. and Burchardt, O. (1994). Peptide nucleic acid (PNA). A DNA mimic with a peptide backbone. Bioconjugate Chem. 5, 3–7.

    Article  CAS  Google Scholar 

  6. Frank-Kamenetskii, M. D. and Mirkin, S. M. (1995). Triplex DNA structures. Annu. Rev. Biochem. 64, 65–95.

    Article  PubMed  CAS  Google Scholar 

  7. Zhurkin, V. B., Raghunathan, G., Ulyanov, N.B., Camerini-Otero, R. D. and Jernigan, R. L. (1994). A parallel DNA triplex as a model for the intermediate in homologous recombination. J. Mol. Biol. 239, 181–200.

    Article  PubMed  CAS  Google Scholar 

  8. Kim, M. G., Zhurkin, V. B., Jernigan, R. L. and Camerini-Otero, R. D. (1995). Probing the structure of a putative intermediate in homologous recombination: the third strand in the parallel DNA triplex is in contact with the major groove of the duplex. J. Mol. Biol. 247, 874–889.

    Article  PubMed  CAS  Google Scholar 

  9. Le Cam, E. and Delain, E. “Nucleic acids-ligands interactions.” In Visualization of Nucleic Acids, Morel G. (Des), CRC Press Inc. Boca Raton, FL, USA. 331–356, 1995.

    Google Scholar 

  10. Bustamante, C. and Rivetti, C. (1996). Visualizing protein-nucleic acid interactions on a large scale with the scanning force microscope. Annu. Rev. Biophys. Biomol. Struct. 25, 395–429.

    Article  PubMed  CAS  Google Scholar 

  11. Brack, C. (1981). DNA electron microscopy. Crit. Rev. Biochem. 10, 113–169.

    Article  CAS  Google Scholar 

  12. Delain, E. and Le Cam, E. “The spreading of nucleic acids.” In Visualization of Nucleic Acids, Morel G. (ed.), CRC Press Inc. Boca Raton FL, USA. 35–56, 1995.

    Google Scholar 

  13. Podtelezhnikov, A.A., Kurakin, A. V., Vologodskii, A. V. and Cherny, D. I. (1994). Testing the quality of electron microscope mapping data for DNA molecules with sequence-specific ligands. Micron 25, 439–446.

    Article  PubMed  CAS  Google Scholar 

  14. Delain, E., Fourcade, A., Poulin, J.-C., Barbin, A., Coulaud, D., Le Cam, E. and Paris, E. (1992). Comparative observation of biological specimens, especially DNA and filamentous actin molecules in atomic force, tunneling and electron microscopes. Microsc. Microanal. Microsctruct. 3, 457–470.

    Article  CAS  Google Scholar 

  15. Hansma, H. G., Laney, D.E., Bezanilla, M., Sinsheimer, R. L. and Hansma, P. K. (1995). Applications for atomic force microscopy of DNA. Biophys. J. 68, 1672–1677.

    Article  PubMed  CAS  Google Scholar 

  16. Hansma, H. G., Bezanilla, M., Zenhauserm, F., Adrian, M. and Sinsheimer, R. L. (1993). Atomic force microscopy of DNA in aqueous solutions. Nucleic Acids Res. 21, 505–512.

    Article  PubMed  CAS  Google Scholar 

  17. Pfannschmidt, C., Schaper, A., Heim, G., Jovin, T. M. and Langowski, J. (1996). Sequence-specific labeling of supercoiled DNA by triple-helix formation and psoralen crosslinking. Nucleic Acids Res. 24, 1702–1709.

    Article  PubMed  CAS  Google Scholar 

  18. Schaper, A., Starink, J. P. P. and Jovin, T. M. (1994). The scanning force microscopy of DNA in air and n-propanol using new spreading agents. FEBS Lett. 355, 91–95.

    Article  PubMed  CAS  Google Scholar 

  19. Lyubchenko, Yu. L. and Sclyakhtenko, L. S. (1997). Visualization of supercoiled DNA with atomic force microscopy in situ. Proc. Natl. Acad. Sci. USA 94, 496–501.

    Article  PubMed  CAS  Google Scholar 

  20. Bustamante, C., Rivetti, C. and Keller, D. J. (1997). Scanning force microscopy under aqueous solutions. Curr. Opin. Struct. Biol. 7, 709–716.

    Article  PubMed  CAS  Google Scholar 

  21. Lee, J. S., Latimer, L. J., Haug, B. L., Pulleyblank, D.E., Skinner, D.M. and Burkholder, G. D. (1989). Triplex DNA in plasmids and chromosomes. Gene 82, 191–199.

    Article  PubMed  CAS  Google Scholar 

  22. Cherny, D. I., Malkov, V. A., Volodin, A. A. and Frank-Kamenetskii, M. D. (1993). Electron microscopy visualization of oligonucleotide binding to duplex DNA via triplex formation. J. Mol. Biol. 230, 379–383.

    Article  PubMed  CAS  Google Scholar 

  23. Cherny, D.I., Kurakin, A. V., Lyamichev, V. N., Frank-Kamenetskii, M. D., Zinkevich, V. E., Finnan, K., Egholm, M., Burchardt, O., Berg, R. H. and Nielsen, P. E. (1994). Electron microscopy studies of sequence specific recognition of duplex DNA by different ligands. J. Molec. Recognition. 7, 171–176.

    Article  Google Scholar 

  24. Svinarchuk, F., Cherny, D., Debin, A., Delain, E. and Malvy, C. (1996). A new approach to overcome potassium-mediated inhibition of triplex formation. Nucleic Acids Res. 24, 3858–3865.

    Article  PubMed  CAS  Google Scholar 

  25. Cherny, D. I., Fourcade, A., Svinarchuk, F., Nielsen, P. E., Malvy, C. and Delain, E. (1998). Analysis of various sequence-specific triplexes by electron and atomic force microscopies. Biophys. J. 74, 1015–1023.

    Article  PubMed  CAS  Google Scholar 

  26. Hansma, H. G., Revenko, I., Kim, K. and Laney, D.E. (1996). Atomic force microscopy of long and short double-stranded, single-stranded and triple-stranded nucleic acids. Nucleic Acids Res. 24, 713–720.

    Article  PubMed  CAS  Google Scholar 

  27. Hampel, K.J., Burkholder, G. D. and Lee, J. S. (1993). Plasmid dimerization mediated by triplex formation between polypyrimidine-polypurine repeats. Biochemistry 32, 1072–1077.

    Article  PubMed  CAS  Google Scholar 

  28. Lee, J. S., Ashley, C., Hampel, K. J., Bradley, R. and Scraba, D. G. (1995). A stable interaction between separated pyrimidine.purine tracts in circular DNA. J. Mol. Biol. 252, 283–288.

    Article  PubMed  CAS  Google Scholar 

  29. Stokrova, J., Vojtiskova, M. and Palecek, E. (1989). Electron microscopy of supercoiled pEJ4 DNA containing homopurine.homopyrimidine sequences. J. Biomol. Struct. Dyn. 6, 891–898.

    Article  PubMed  CAS  Google Scholar 

  30. Svinarchuk, F., Nagibneva, I., Cherny, D., Ait-Si-Ali, S., Pritchard, L. L., Robin, P., Malvy, C. and Harel-Bellan, A. (1997). Recruitment of transcription factors to the target site by triplex-forming oligonucleotides. Nucleic Acids Res. 25, 3459–3464.

    Article  PubMed  CAS  Google Scholar 

  31. Sun, J. S., de Bizemont, T., Duval-Valentin, G., Montenay-Garestier, T. and Hélène, C. (1991). Extension of the range of recognition sequences for triple helix formation by oligonucleotides containing guanines and thymines. C. R. Acad. Sci. Ser. III 313, 585–590.

    PubMed  CAS  Google Scholar 

  32. Bouziane, M., Cherny, D.I., Mouscadet, J.-F. and Auclair, C. (1996). Alternate strand DNA triple-helix-mediated inhibition of HIV-1 U5 long terminal repeat integration in vitro. J. Biol. Chem. 271, 10359–10364.

    Article  PubMed  CAS  Google Scholar 

  33. Cherny, D.I., Belotserkovskii, B. P., Frank-Kamenetskii, M. D., Egholm, M., Buchardt, O., Berg, R. H. and Nielsen, P. E. (1993). DNA unwinding upon strand-displacement binding of a thymine-substituted polyamide to double-stranded DNA. Proc. Natl. Acad. Sci. USA 90, 1667–1670.

    Article  PubMed  CAS  Google Scholar 

  34. Demidov, V. V., Cherny, D. I., Kurakin, A. V., Yavnilovich, M. V., Malkov, V. A., Frank-Kamenetskii, M. D., Sonnichsen, S. H. and Nielsen, P. E. (1994). Electron microscopy mapping of oligopurine tracts in duplex DNA by peptide nucleic acid targeting. Nucleic Acids Res. 22, 5218–5222.

    Article  PubMed  CAS  Google Scholar 

  35. Demidov, V. V., Yavnilovich, M. V. and Frank-Kamenetskii, M. D. (1997). Kinetic analysis of specificity of duplex DNA targeting by homopyrimidine peptide nucleic acid. Biophys. J. 72, 2763–2769.

    Article  PubMed  CAS  Google Scholar 

  36. Betts, L., Josey, J. A., Veal, J. M. and Jordan, D. R. (1995). A nucleic acids triple helix formed by a peptide nucleic acid-DNA complex. Science 270, 1838–1841.

    Article  PubMed  CAS  Google Scholar 

  37. Peffer, N.J., Hanvey, J. C., Bisi, J. E., Thomson, S. A., Hassman, C. F., Noble, S. A. and Babiss, L. E. (1993). Strand-invasion of duplex DNA by peptide nucleic acid oligomers. Proc. Natl. Acad. Sci. USA 90, 10648–10652.

    Article  PubMed  CAS  Google Scholar 

  38. Stasiak, A.Z., Rosselli, W. and Stasiak, A. (1991). RecA-DNA helical filaments in genetic recombination. Biochimie 73, 199–208.

    Article  PubMed  CAS  Google Scholar 

  39. Umlauf, S. W., Cox, M. M. and Inman, R. B. (1990). Triple-helical DNA pairing intermediates formed by recA protein. J. Biol. Chem. 265, 16898–16912

    PubMed  CAS  Google Scholar 

  40. Jain, S. K., Cox, M. M. and Inman, R. B. (1995). Occurrence of three-stranded DNA within a RecA protein filament. J. Biol. Chem. 270, 4943–4949.

    Article  PubMed  CAS  Google Scholar 

  41. Morel, P., Cherny, D., Ehrlich, S.D. and Cassuto, E. (1997). Recombination-dependent repair of DNA double-strand breaks with purified proteins from Escherichia coli. J. Biol. Chem. 272, 17091–17096.

    Article  PubMed  CAS  Google Scholar 

  42. Revet, B. M., Sena, E. P. and Zarling, D. A. (1993). Homologous DNA targeting with RecA protein-coated short DNA probes and electron microscope mapping on linear duplex molecules. J. Mol. Biol. 232, 779–791.

    Article  PubMed  CAS  Google Scholar 

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Cherny, D. (1999). Imaging of Triplexes by Electron and Scanning Force Microscopy. In: Malvy, C., Harel-Bellan, A., Pritchard, L.L. (eds) Triple Helix Forming Oligonucleotides. Perspectives in Antisense Science, vol 2. Springer, Boston, MA. https://doi.org/10.1007/978-1-4615-5177-5_4

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  • DOI: https://doi.org/10.1007/978-1-4615-5177-5_4

  • Publisher Name: Springer, Boston, MA

  • Print ISBN: 978-1-4613-7358-2

  • Online ISBN: 978-1-4615-5177-5

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