Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1996 Feb 1;24(3):458–463. doi: 10.1093/nar/24.3.458

Transcription-mediated binding of peptide nucleic acid (PNA) to double-stranded DNA: sequence-specific suicide transcription.

H J Larsen 1, P E Nielsen 1
PMCID: PMC145648  PMID: 8602358

Abstract

Peptide nucleic acid (PNA) forms sequence-specific (PNA)2/DNA triplexes with one strand of double-stranded DNA by strand invasion. When formed with the template strand of DNA such a (PNA)2/DNA triplex can arrest transcription elongation in vitro and can thus act as an anti-gene agent. One of the major obstacles to applying PNA as an anti-gene agent in vivo is that PNA strand invasion occurs at a very slow rate under moderate salt conditions. In the present study we show that transcription can increase the rate of sequence-specific PNA binding dramatically. Such transcription-mediated PNA binding occurs three times as efficiently when the PNA target is situated on the non- template strand as compared with the template strand. Since transcription can mediate template strand-associated (PNA)2/DNA complexes which arrest further elongation, the action of RNA polymerase results in repression of its own activity, i.e. suicide transcription. These findings are highly relevant for the possible future use of PNA as an anti-gene agent.

Full Text

The Full Text of this article is available as a PDF (112.7 KB).

Selected References

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

  1. Cherny D. Y., Belotserkovskii B. P., Frank-Kamenetskii M. D., Egholm M., Buchardt O., Berg R. H., Nielsen P. E. DNA unwinding upon strand-displacement binding of a thymine-substituted polyamide to double-stranded DNA. Proc Natl Acad Sci U S A. 1993 Mar 1;90(5):1667–1670. doi: 10.1073/pnas.90.5.1667. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Choo Y., Klug A. Designing DNA-binding proteins on the surface of filamentous phage. Curr Opin Biotechnol. 1995 Aug;6(4):431–436. doi: 10.1016/0958-1669(95)80073-5. [DOI] [PubMed] [Google Scholar]
  3. Christensen L., Fitzpatrick R., Gildea B., Petersen K. H., Hansen H. F., Koch T., Egholm M., Buchardt O., Nielsen P. E., Coull J. Solid-phase synthesis of peptide nucleic acids. J Pept Sci. 1995 May-Jun;1(3):175–183. doi: 10.1002/psc.310010304. [DOI] [PubMed] [Google Scholar]
  4. Demidov V. V., Cherny D. I., Kurakin A. V., Yavnilovich M. V., Malkov V. A., Frank-Kamenetskii M. D., Sönnichsen S. H., Nielsen P. E. Electron microscopy mapping of oligopurine tracts in duplex DNA by peptide nucleic acid targeting. Nucleic Acids Res. 1994 Dec 11;22(24):5218–5222. doi: 10.1093/nar/22.24.5218. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Demidov V. V., Yavnilovich M. V., Belotserkovskii B. P., Frank-Kamenetskii M. D., Nielsen P. E. Kinetics and mechanism of polyamide ("peptide") nucleic acid binding to duplex DNA. Proc Natl Acad Sci U S A. 1995 Mar 28;92(7):2637–2641. doi: 10.1073/pnas.92.7.2637. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Demidov V., Frank-Kamenetskii M. D., Egholm M., Buchardt O., Nielsen P. E. Sequence selective double strand DNA cleavage by peptide nucleic acid (PNA) targeting using nuclease S1. Nucleic Acids Res. 1993 May 11;21(9):2103–2107. doi: 10.1093/nar/21.9.2103. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Egholm M., Christensen L., Dueholm K. L., Buchardt O., Coull J., Nielsen P. E. Efficient pH-independent sequence-specific DNA binding by pseudoisocytosine-containing bis-PNA. Nucleic Acids Res. 1995 Jan 25;23(2):217–222. doi: 10.1093/nar/23.2.217. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Hanvey J. C., Peffer N. J., Bisi J. E., Thomson S. A., Cadilla R., Josey J. A., Ricca D. J., Hassman C. F., Bonham M. A., Au K. G. Antisense and antigene properties of peptide nucleic acids. Science. 1992 Nov 27;258(5087):1481–1485. doi: 10.1126/science.1279811. [DOI] [PubMed] [Google Scholar]
  9. Hélène C. Sequence-selective recognition and cleavage of double-helical DNA. Curr Opin Biotechnol. 1993 Feb;4(1):29–36. doi: 10.1016/0958-1669(93)90028-u. [DOI] [PubMed] [Google Scholar]
  10. Maher L. J., 3rd DNA triple-helix formation: an approach to artificial gene repressors? Bioessays. 1992 Dec;14(12):807–815. doi: 10.1002/bies.950141204. [DOI] [PubMed] [Google Scholar]
  11. Møllegaard N. E., Buchardt O., Egholm M., Nielsen P. E. Peptide nucleic acid.DNA strand displacement loops as artificial transcription promoters. Proc Natl Acad Sci U S A. 1994 Apr 26;91(9):3892–3895. doi: 10.1073/pnas.91.9.3892. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Nielsen P. E., Egholm M., Berg R. H., Buchardt O. Peptide nucleic acids (PNAs): potential antisense and anti-gene agents. Anticancer Drug Des. 1993 Feb;8(1):53–63. [PubMed] [Google Scholar]
  13. Nielsen P. E., Egholm M., Berg R. H., Buchardt O. Sequence specific inhibition of DNA restriction enzyme cleavage by PNA. Nucleic Acids Res. 1993 Jan 25;21(2):197–200. doi: 10.1093/nar/21.2.197. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Nielsen P. E., Egholm M., Berg R. H., Buchardt O. Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide. Science. 1991 Dec 6;254(5037):1497–1500. doi: 10.1126/science.1962210. [DOI] [PubMed] [Google Scholar]
  15. Nielsen P. E., Egholm M., Buchardt O. Evidence for (PNA)2/DNA triplex structure upon binding of PNA to dsDNA by strand displacement. J Mol Recognit. 1994 Sep;7(3):165–170. doi: 10.1002/jmr.300070303. [DOI] [PubMed] [Google Scholar]
  16. Nielsen P. E., Egholm M., Buchardt O. Sequence-specific transcription arrest by peptide nucleic acid bound to the DNA template strand. Gene. 1994 Nov 4;149(1):139–145. doi: 10.1016/0378-1119(94)90422-7. [DOI] [PubMed] [Google Scholar]
  17. Peffer N. J., Hanvey J. C., Bisi J. E., Thomson S. A., Hassman C. F., Noble S. A., Babiss L. E. Strand-invasion of duplex DNA by peptide nucleic acid oligomers. Proc Natl Acad Sci U S A. 1993 Nov 15;90(22):10648–10652. doi: 10.1073/pnas.90.22.10648. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Sastry S. S., Hearst J. E. Studies on the interaction of T7 RNA polymerase with a DNA template containing a site-specifically placed psoralen cross-link. I. Characterization of elongation complexes. J Mol Biol. 1991 Oct 20;221(4):1091–1110. [PubMed] [Google Scholar]

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

RESOURCES