Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1997 Sep 1;25(17):3440–3444. doi: 10.1093/nar/25.17.3440

Sequence-specific targeting and covalent modification of human genomic DNA.

E S Belousov 1, I A Afonina 1, M A Podyminogin 1, H B Gamper 1, M W Reed 1, R M Wydro 1, R B Meyer 1
PMCID: PMC146908  PMID: 9254701

Abstract

We compare two techniques which enable selective, nucleotide-specific covalent modification of human genomic DNA, as assayed by quantitative ligation- mediated PCR. In the first, a purine motif triplex-forming oligonucleotide with a terminally appended chlorambucil was shown to label a target guanine residue adjacent to its binding site in 80% efficiency at 0.5 microM. Efficiency was higher in the presence of the triplex-stabilizing intercalator coralyne. In the second method, an oligonucleotide targeting a site containing all four bases and bearing chlorambucil on an interior base was shown to efficiently react with a specific nucleotide in the target sequence. The targeted sequence in these cases was in the DQbeta1*0302 allele of the MHC II locus.

Full Text

The Full Text of this article is available as a PDF (97.7 KB).

Selected References

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

  1. Cantor C. R., Warshaw M. M., Shapiro H. Oligonucleotide interactions. 3. Circular dichroism studies of the conformation of deoxyoligonucleotides. Biopolymers. 1970;9(9):1059–1077. doi: 10.1002/bip.1970.360090909. [DOI] [PubMed] [Google Scholar]
  2. Cheng A. J., Van Dyke M. W. Monovalent cation effects on intermolecular purine-purine-pyrimidine triple-helix formation. Nucleic Acids Res. 1993 Dec 11;21(24):5630–5635. doi: 10.1093/nar/21.24.5630. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Chiu S. K., Rao B. J., Story R. M., Radding C. M. Interactions of three strands in joints made by RecA protein. Biochemistry. 1993 Dec 7;32(48):13146–13155. doi: 10.1021/bi00211a025. [DOI] [PubMed] [Google Scholar]
  4. Duval-Valentin G., Thuong N. T., Hélène C. Specific inhibition of transcription by triple helix-forming oligonucleotides. Proc Natl Acad Sci U S A. 1992 Jan 15;89(2):504–508. doi: 10.1073/pnas.89.2.504. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Ferrin L. J., Camerini-Otero R. D. Selective cleavage of human DNA: RecA-assisted restriction endonuclease (RARE) cleavage. Science. 1991 Dec 6;254(5037):1494–1497. doi: 10.1126/science.1962209. [DOI] [PubMed] [Google Scholar]
  6. Froehler B. C., Terhorst T., Shaw J. P., McCurdy S. N. Triple-helix formation and cooperative binding by oligodeoxynucleotides with a 3'-3' internucleotide junction. Biochemistry. 1992 Feb 18;31(6):1603–1609. doi: 10.1021/bi00121a004. [DOI] [PubMed] [Google Scholar]
  7. Gamper H. B., Reed M. W., Cox T., Virosco J. S., Adams A. D., Gall A. A., Scholler J. K., Meyer R. B., Jr Facile preparation of nuclease resistant 3' modified oligodeoxynucleotides. Nucleic Acids Res. 1993 Jan 11;21(1):145–150. doi: 10.1093/nar/21.1.145. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Giovannangeli C., Diviacco S., Labrousse V., Gryaznov S., Charneau P., Helene C. Accessibility of nuclear DNA to triplex-forming oligonucleotides: the integrated HIV-1 provirus as a target. Proc Natl Acad Sci U S A. 1997 Jan 7;94(1):79–84. doi: 10.1073/pnas.94.1.79. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Gonda D. K., Shibata T., Radding C. M. Kinetics of homologous pairing promoted by RecA protein: effects of ends and internal sites in DNA. Biochemistry. 1985 Jan 15;24(2):413–420. doi: 10.1021/bi00323a026. [DOI] [PubMed] [Google Scholar]
  10. Grant K. B., Dervan P. B. Sequence-specific alkylation and cleavage of DNA mediated by purine motif triple helix formation. Biochemistry. 1996 Sep 24;35(38):12313–12319. doi: 10.1021/bi9608469. [DOI] [PubMed] [Google Scholar]
  11. Griffin L. C., Dervan P. B. Recognition of thymine adenine.base pairs by guanine in a pyrimidine triple helix motif. Science. 1989 Sep 1;245(4921):967–971. doi: 10.1126/science.2549639. [DOI] [PubMed] [Google Scholar]
  12. Havre P. A., Glazer P. M. Targeted mutagenesis of simian virus 40 DNA mediated by a triple helix-forming oligonucleotide. J Virol. 1993 Dec;67(12):7324–7331. doi: 10.1128/jvi.67.12.7324-7331.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Havre P. A., Gunther E. J., Gasparro F. P., Glazer P. M. Targeted mutagenesis of DNA using triple helix-forming oligonucleotides linked to psoralen. Proc Natl Acad Sci U S A. 1993 Aug 15;90(16):7879–7883. doi: 10.1073/pnas.90.16.7879. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Krawczyk S. H., Milligan J. F., Wadwani S., Moulds C., Froehler B. C., Matteucci M. D. Oligonucleotide-mediated triple helix formation using an N3-protonated deoxycytidine analog exhibiting pH-independent binding within the physiological range. Proc Natl Acad Sci U S A. 1992 May 1;89(9):3761–3764. doi: 10.1073/pnas.89.9.3761. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Larhammar D., Hyldig-Nielsen J. J., Servenius B., Andersson G., Rask L., Peterson P. A. Exon-intron organization and complete nucleotide sequence of a human major histocompatibility antigen DC beta gene. Proc Natl Acad Sci U S A. 1983 Dec;80(23):7313–7317. doi: 10.1073/pnas.80.23.7313. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Lee J. S., Latimer L. J., Hampel K. J. Coralyne binds tightly to both T.A.T- and C.G.C(+)-containing DNA triplexes. Biochemistry. 1993 Jun 1;32(21):5591–5597. doi: 10.1021/bi00072a014. [DOI] [PubMed] [Google Scholar]
  17. Mergny J. L., Duval-Valentin G., Nguyen C. H., Perrouault L., Faucon B., Rougée M., Montenay-Garestier T., Bisagni E., Hélène C. Triple helix-specific ligands. Science. 1992 Jun 19;256(5064):1681–1684. doi: 10.1126/science.256.5064.1681. [DOI] [PubMed] [Google Scholar]
  18. Milligan J. F., Krawczyk S. H., Wadwani S., Matteucci M. D. An anti-parallel triple helix motif with oligodeoxynucleotides containing 2'-deoxyguanosine and 7-deaza-2'-deoxyxanthosine. Nucleic Acids Res. 1993 Jan 25;21(2):327–333. doi: 10.1093/nar/21.2.327. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Nepom G. T., Erlich H. MHC class-II molecules and autoimmunity. Annu Rev Immunol. 1991;9:493–525. doi: 10.1146/annurev.iy.09.040191.002425. [DOI] [PubMed] [Google Scholar]
  20. Petrie C. R., Reed M. W., Adams A. D., Meyer R. B., Jr An improved CPG support for the synthesis of 3'-amine-tailed oligonucleotides. Bioconjug Chem. 1992 Jan-Feb;3(1):85–87. doi: 10.1021/bc00013a014. [DOI] [PubMed] [Google Scholar]
  21. Podyminogin M. A., Meyer R. B., Gamper H. B. Sequence-specific covalent modification of DNA by cross-linking oligonucleotides. Catalysis by RecA and implication for the mechanism of synaptic joint formation. Biochemistry. 1995 Oct 10;34(40):13098–13108. doi: 10.1021/bi00040a022. [DOI] [PubMed] [Google Scholar]
  22. Podyminogin M. A., Meyer R. B., Jr, Gamper H. B. RecA-catalyzed, sequence-specific alkylation of DNA by cross-linking oligonucleotides. Effects of length and nonhomologous base substitutions. Biochemistry. 1996 Jun 4;35(22):7267–7274. doi: 10.1021/bi9529465. [DOI] [PubMed] [Google Scholar]
  23. Radding C. M. Helical interactions in homologous pairing and strand exchange driven by RecA protein. J Biol Chem. 1991 Mar 25;266(9):5355–5358. [PubMed] [Google Scholar]
  24. Rigas B., Welcher A. A., Ward D. C., Weissman S. M. Rapid plasmid library screening using RecA-coated biotinylated probes. Proc Natl Acad Sci U S A. 1986 Dec;83(24):9591–9595. doi: 10.1073/pnas.83.24.9591. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Sandor Z., Bredberg A. Repair of triple helix directed psoralen adducts in human cells. Nucleic Acids Res. 1994 Jun 11;22(11):2051–2056. doi: 10.1093/nar/22.11.2051. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Takasugi M., Guendouz A., Chassignol M., Decout J. L., Lhomme J., Thuong N. T., Hélène C. Sequence-specific photo-induced cross-linking of the two strands of double-helical DNA by a psoralen covalently linked to a triple helix-forming oligonucleotide. Proc Natl Acad Sci U S A. 1991 Jul 1;88(13):5602–5606. doi: 10.1073/pnas.88.13.5602. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Vlassov V. V., Gaidamakov S. A., Zarytova V. F., Knorre D. G., Levina A. S., Nikonova A. A., Podust L. M., Fedorova O. S. Sequence-specific chemical modification of double-stranded DNA with alkylating oligodeoxyribonucleotide derivatives. Gene. 1988 Dec 10;72(1-2):313–322. doi: 10.1016/0378-1119(88)90158-8. [DOI] [PubMed] [Google Scholar]
  28. Wilson W. D., Tanious F. A., Mizan S., Yao S., Kiselyov A. S., Zon G., Strekowski L. DNA triple-helix specific intercalators as antigene enhancers: unfused aromatic cations. Biochemistry. 1993 Oct 12;32(40):10614–10621. doi: 10.1021/bi00091a011. [DOI] [PubMed] [Google Scholar]

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

RESOURCES