Advertisement

Locked Nucleic Acid Aptamers

  • Jan Barciszewski
  • Michael Medgaard
  • Troels Koch
  • Jens Kurreck
  • Volker A. Erdmann
Protocol
Part of the Methods in Molecular Biology™ book series (MIMB, volume 535)

Abstract

The aptamer technology has been introduced in the early 1990s. With this technique ligands for organic dyes and proteins have been identified in many research field, providing various inhibitory molecules that allow functional interference in biological systems. Aptamers can therefore be employed for various applications ranging from diagnostic to therapeutic assay formats. Locked nucleic acid aptamers (LNA-Aps) are oligonucleotides containing one or more LNA nucleotide monomers with a bicyclic furanose unit locked in an RNA mimicking sugar conformation, evolved in vitro to bind target ligands with high affinity and specificity. LNA-Aps are attractive alternatives to antibody- and small-molecule-based therapeutics due to their stability, low toxicity and immunogenecity.

Key words

LNA – locked nucleic acid LNA-As – LNA antisense LNA-Ag – LNA antigene LNA-Ap – LNA aptamer 

References

  1. 1.
    Jepsen, J.S. and Wengel, J. (2004) LNA-antisense rivals siRNA for gene silencing. Curr. Opin. Drug Discov. Devel. 7, 188–194.PubMedGoogle Scholar
  2. 2.
    Vester, B. and Wengel, J. (2004) LNA (locked nucleic acid): high-affinity targeting of complementary RNA and DNA. Biochemistry 43, 13233–13241.PubMedCrossRefGoogle Scholar
  3. 3.
    Braasch, D.A. and Corey, D.R. (2001) Locked nucleic acid (LNA): fine-tuning the recognition of DNA and RNA. Chem. Biol. 8, 1–7.PubMedCrossRefGoogle Scholar
  4. 4.
    Grunweller, A. and Hartmann, R.K. (2007) Locked nucleic Acid oligonucleotides: the next generation of antisense agents? BioDrugs 21, 235–243.PubMedCrossRefGoogle Scholar
  5. 5.
    Kaur, H., Babu, B.R. and Maiti, S. (2007) Perspectives on chemistry and therapeutic applications of Locked Nucleic Acid (LNA). Chem. Rev. 107, 4672–4697.PubMedCrossRefGoogle Scholar
  6. 6.
    Petersen, M. and Wengel, J. (2003) LNA: a versatile tool for therapeutics and genomics. Trends Biotechnol. 21, 74–81.PubMedCrossRefGoogle Scholar
  7. 7.
    Kurreck, J., Wyszko, E., Gillen, C. and Erdmann, V.A. (2002) Design of antisense oligonucleotides stabilized by locked nucleic acids. Nucleic Acids Res. 30, 1911–1918.PubMedCrossRefGoogle Scholar
  8. 8.
    Ivanova, A. and Rosch, N. (2007) The structure of LNA:DNA hybrids from molecular dynamics simulations: the effect of locked nucleotides. J. Phys. Chem. 111, 9307–9319.CrossRefGoogle Scholar
  9. 9.
    Crinelli, R., Bianchi, M., Gentilini, L., Palma, L. and Magnani, M. (2004) Locked nucleic acids (LNA): versatile tools for designing oligonucleotide decoys with high stability and affinity. Curr. Drug Targets 5, 745–752.PubMedCrossRefGoogle Scholar
  10. 10.
    Famulok, M., Hartig, J.S. and Mayer, G. (2007) Functional aptamers and aptazymes in biotechnology, diagnostics, and therapy. Chem. Rev. 107, 3715–3743.PubMedCrossRefGoogle Scholar
  11. 11.
    Famulok, M. and Mayer, G. (2005) Intramers and aptamers: applications in protein-function analyses and potential for drug screening. ChemBioChem 6, 19–26.PubMedCrossRefGoogle Scholar
  12. 12.
    Srivastava, P., Barman, J., Pathmasiri, W., Plashkevych, O., Wenska, M. and Chattopadhyaya, J. (2007) Five- and six-membered conformationally locked 2′,4′-carbocyclic ribo-thymidines: synthesis, structure, and biochemical studies. J. Am. Chem. Soc. 129, 8362–8379.PubMedCrossRefGoogle Scholar
  13. 13.
    Pasternak, A., Kierzek, E., Pasternak, K., Turner, D.H. and Kierzek, R. (2007) A chemical synthesis of LNA-2,6-diaminopurine riboside, and the influence of 2'-O-methyl-2,6-diaminopurine and LNA-2,6-diaminopurine ribosides on the thermodynamic properties of 2′-O-methyl RNA/RNA heteroduplexes. Nucleic Acids Res. 35, 4055–4063.PubMedCrossRefGoogle Scholar
  14. 14.
    Hicke, B.J., Stephens, A.W., Gould, T., Chang, Y.F., Lynott, C.K., Heil, J., Borkowski, S., Hilger, C.S., Cook, G., Warren, S. and Schmidt, P.G. (2006) Tumor targeting by an aptamer. J. Nucl. Med. 47, 668–678.PubMedGoogle Scholar
  15. 15.
    Schmidt, K.S., Borkowski, S., Kurreck, J., Stephens, A.W., Bald, R., Hecht, M., Friebe, M., Dinkelborg, L. and Erdmann, V.A. (2004) Application of locked nucleic acids to improve aptamer in vivo stability and targeting function. Nucleic Acids Res. 32, 5757–5765.PubMedCrossRefGoogle Scholar
  16. 16.
    Forster, C., Brauer, A.B., Brode, S., Schmidt, K.S., Perbandt, M., Meyer, A., Rypniewski, W., Betzel, C., Kurreck, J., Fürste, J.P. and Erdmann, V.A. (2006) Comparative crystallization and preliminary X-ray diffraction studies of locked nucleic acid and RNA stems of a tenascin C-binding aptamer. Acta Crystallogr. F 62, 665–668.CrossRefGoogle Scholar
  17. 17.
    Lebars, I., Richard, T., Di Primo, C. and Toulmé, J.J. (2007) NMR structure of a kissing complex formed between the TAR RNA element of HIV-1 and a LNA-modified aptamer. Nucleic Acids Res. 35, 6103–6114.PubMedCrossRefGoogle Scholar
  18. 18.
    Di Primo, C., Rudloff, I., Reigadas, S., Arzumanov, A.A., Gait, M.J. and Toulmé, J.J. (2007) Systematic screening of LNA/2'-O-methyl chimeric derivatives of a TAR RNA aptamer. FEBS Lett. 581, 771–774.PubMedCrossRefGoogle Scholar
  19. 19.
    Lebars, I., Richard, T., Di Primo, C. and Toulmé, J.J. (2007) LNA derivatives of a kissing aptamer targeted to the trans-activating responsive RNA element of HIV-1. Blood Cells Mol. Dis. 38, 204–209.PubMedCrossRefGoogle Scholar
  20. 20.
    Darfeuille, F., Reigadas, S., Hansen, J.B., Orum, H., Di Primo, C. and Toulmé, J.J. (2006) Aptamers targeted to an RNA hairpin show improved specificity compared to that of complementary oligonucleotides. Biochemistry 45, 12076–12082.PubMedCrossRefGoogle Scholar
  21. 21.
    Crinelli, R., Bianchi, M., Gentilini, L. and Magnani, M. (2002) Design and characterization of decoy oligonucleotides containing locked nucleic acids. Nucleic Acids Res. 30, 2435–2443.PubMedCrossRefGoogle Scholar
  22. 22.
    Crinelli, R., Bianchi, M., Gentilini, L., Palma, L., Sørensen, M.D., Bryld, T., Babu, R.B., Arar, K., Wengel, J. and Magnani, M. (2004) Transcription factor decoy oligonucleotides modified with locked nucleic acids: an in vitro study to reconcile biostability with binding affinity. Nucleic Acids Res. 32, 1874–1885.PubMedCrossRefGoogle Scholar
  23. 23.
    Virno, A., Randazzo, A., Giancola, C., Bucci, M., Cirino, G. and Mayol, L. (2007) A novel thrombin binding aptamer containing a G-LNA residue. Bioorg. Med. Chem. 15, 5710–5718.PubMedCrossRefGoogle Scholar
  24. 24.
    Brown, T. and Brown, D. J. S. (1991) Oligonucleotides and analogues. A Practical Approach, Eckstein, F. (Ed.), IRL, Oxford, 1–24.Google Scholar
  25. 25.
    Beaucage, S.L. and Caruthers, M.H. (2000) Current protocols in nucleic acid chemistry, Beaucage, S.L., Bergstrom, D.E., Herdewijn, P., and Matsuda, A. (Eds.). John Wiley, New York, pp. 3.3.1–3.3.20.Google Scholar
  26. 26.
    Pfundheller, H.M., Sørensen, A.M., Lomholt, C., Johansen, A.M., Koch, T. and Wengel, J. (2005) Locked nucleic acid synthesis. Methods Mol. Biol. 288, 127–146.PubMedGoogle Scholar
  27. 27.
    Hansen, H.F., Olsen, O. and Koch, T. (2003) New standards in LNA synthesis. Nucleosides Nucleotides Nucleic Acids 22, 1273–1275.PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Jan Barciszewski
    • 1
  • Michael Medgaard
    • 2
  • Troels Koch
    • 3
  • Jens Kurreck
    • 4
  • Volker A. Erdmann
    • 5
  1. 1.Institute of Bioorganic Chemistry of the Polish Academy of SciencesPoland
  2. 2.Santaris PharmaDenmark
  3. 3.Santaris PharmaDenmark
  4. 4.Institute for Chemistry and BiochemistryFree University Berlin, Berlin, Germany; Institute of Industrial Genetics, University of StuttgartGermany
  5. 5.Institute for Chemistry and BiochemistryFree University BerlinGermany

Personalised recommendations