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. 1997 Nov 15;25(22):4608–4613. doi: 10.1093/nar/25.22.4608

Opening of the extraordinarily stable mini-hairpin d(GCGAAGC).

B Jollès 1, M Réfrégiers 1, A Laigle 1
PMCID: PMC147075  PMID: 9358172

Abstract

For the purposes of the antisense strategy oligodeoxyribonucleotides can be protected against serum and cell nuclease digestion by tagging at their 3'-end with a sequence naturally forming a very stable hairpin, d(GCGAAGC). This nuclease-resistant hairpin is also known for its high thermostability. We demonstrate in this study that attachment of d(GCGAAGC) at the 3'-end of an oligodeoxyribonucleotide does not hinder hybridization of the 5'-part of this oligonucleotide to a complementary DNA strand. Moreover, the hairpin is in equilibrium between a folded and an open structure, with an energy minimum in favor of pairing if it is possible, even with mismatches.

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Selected References

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  1. Akhtar S., Agrawal S. In vivo studies with antisense oligonucleotides. Trends Pharmacol Sci. 1997 Jan;18(1):12–18. doi: 10.1016/s0165-6147(96)01002-4. [DOI] [PubMed] [Google Scholar]
  2. Bowling J. M., Bruner K. L., Cmarik J. L., Tibbetts C. Neighboring nucleotide interactions during DNA sequencing gel electrophoresis. Nucleic Acids Res. 1991 Jun 11;19(11):3089–3097. doi: 10.1093/nar/19.11.3089. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Crooke S. T. Therapeutic applications of oligonucleotides. Annu Rev Pharmacol Toxicol. 1992;32:329–376. doi: 10.1146/annurev.pa.32.040192.001553. [DOI] [PubMed] [Google Scholar]
  4. Diekmann S., Lilley D. M. The anomalous gel migration of a stable cruciform: temperature and salt dependence, and some comparisons with curved DNA. Nucleic Acids Res. 1987 Jul 24;15(14):5765–5774. doi: 10.1093/nar/15.14.5765. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Frank R., Köster H. DNA chain length markers and the influence of base composition on electrophoretic mobility of oligodeoxyribonucleotides in polyacrylamide-gels. Nucleic Acids Res. 1979;6(6):2069–2087. doi: 10.1093/nar/6.6.2069. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Hirao I., Kawai G., Yoshizawa S., Nishimura Y., Ishido Y., Watanabe K., Miura K. Most compact hairpin-turn structure exerted by a short DNA fragment, d(GCGAAGC) in solution: an extraordinarily stable structure resistant to nucleases and heat. Nucleic Acids Res. 1994 Feb 25;22(4):576–582. doi: 10.1093/nar/22.4.576. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Hirao I., Nishimura Y., Tagawa Y., Watanabe K., Miura K. Extraordinarily stable mini-hairpins: electrophoretical and thermal properties of the various sequence variants of d(GCGAAAGC) and their effect on DNA sequencing. Nucleic Acids Res. 1992 Aug 11;20(15):3891–3896. doi: 10.1093/nar/20.15.3891. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Hirao I., Yoshizawa S., Miura K. Stabilization of mRNA in an Escherichia coli cell-free translation system. FEBS Lett. 1993 Apr 26;321(2-3):169–172. doi: 10.1016/0014-5793(93)80101-y. [DOI] [PubMed] [Google Scholar]
  9. Johnston B. H. Hydroxylamine and methoxylamine as probes of DNA structure. Methods Enzymol. 1992;212:180–194. doi: 10.1016/0076-6879(92)12012-f. [DOI] [PubMed] [Google Scholar]
  10. Khan I. M., Coulson J. M. A novel method to stabilise antisense oligonucleotides against exonuclease degradation. Nucleic Acids Res. 1993 Jun 25;21(12):2957–2958. doi: 10.1093/nar/21.12.2957. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Poddevin B., Meguenni S., Elias I., Vasseur M., Blumenfeld M. Improved anti-herpes simplex virus type 1 activity of a phosphodiester antisense oligonucleotide containing a 3'-terminal hairpin-like structure. Antisense Res Dev. 1994 Fall;4(3):147–154. doi: 10.1089/ard.1994.4.147. [DOI] [PubMed] [Google Scholar]
  12. Réfrégiers M., Laigle A., Jollès B., Chinsky L. Fluorescence resonance energy transfer analysis of the degradation of an oligonucleotide protected by a very stable hairpin. J Biomol Struct Dyn. 1996 Dec;14(3):365–371. doi: 10.1080/07391102.1996.10508131. [DOI] [PubMed] [Google Scholar]
  13. Tang J. Y., Temsamani J., Agrawal S. Self-stabilized antisense oligodeoxynucleotide phosphorothioates: properties and anti-HIV activity. Nucleic Acids Res. 1993 Jun 11;21(11):2729–2735. doi: 10.1093/nar/21.11.2729. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Turner D. H. Thermodynamics of base pairing. Curr Opin Struct Biol. 1996 Jun;6(3):299–304. doi: 10.1016/s0959-440x(96)80047-9. [DOI] [PubMed] [Google Scholar]
  15. Varani G. Exceptionally stable nucleic acid hairpins. Annu Rev Biophys Biomol Struct. 1995;24:379–404. doi: 10.1146/annurev.bb.24.060195.002115. [DOI] [PubMed] [Google Scholar]
  16. Wohlrab F. Enzyme probes in vitro. Methods Enzymol. 1992;212:294–301. doi: 10.1016/0076-6879(92)12018-l. [DOI] [PubMed] [Google Scholar]
  17. Woolf T. M., Melton D. A., Jennings C. G. Specificity of antisense oligonucleotides in vivo. Proc Natl Acad Sci U S A. 1992 Aug 15;89(16):7305–7309. doi: 10.1073/pnas.89.16.7305. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Yoshizawa S., Kawai G., Watanabe K., Miura K., Hirao I. GNA trinucleotide loop sequences producing extraordinarily stable DNA minihairpins. Biochemistry. 1997 Apr 22;36(16):4761–4767. doi: 10.1021/bi961738p. [DOI] [PubMed] [Google Scholar]
  19. Yoshizawa S., Ueda T., Ishido Y., Miura K., Watanabe K., Hirao I. Nuclease resistance of an extraordinarily thermostable mini-hairpin DNA fragment, d(GCGAAGC) and its application to in vitro protein synthesis. Nucleic Acids Res. 1994 Jun 25;22(12):2217–2221. doi: 10.1093/nar/22.12.2217. [DOI] [PMC free article] [PubMed] [Google Scholar]

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