How to Choose Optimal Antisense Targets in an mRNA

  • Bernhard Schu
  • Heinrich Brinkmeier
Part of the Perspectives in Antisense Science book series (DARE, volume 4)


One of the major challenges of an antisense experiment is the identification of sequences within the target RNA, which are accessible by an antisense oligonucleotide. Three-dimensional folding of the RNA results in both inaccessible segments in the inner part of the RNA molecule and double stranded regions. The folding of RNAs may prevent many oligonucleotides from reaching their complementary regions (Branch, 1998). While it is impossible to predict accessible target sites for antisense oligonucleotides from computer-aided models of RNA-structure (Fig.2), combinatorial screening is a promising approach to search for such sequences. The identification of the most active antisense oligonucleotide however remains empirical and has to be performed in translation arrest assays and in cell culture. Sequences with well-known non-antisense effects have to be avoided. Finally, stringent controls are required to prove an antisense-mediated mechanism of action.


Antisense Oligonucleotide Xenopus Oocyte Optimal Target Rabbit Reticulocyte Lysate Sense Oligonucleotide 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Bader R, Brugger H, Hinz M, Rembe C, Hofer EP, Seliger H. A rapid method for the preparation of a one dimensional sequence-overlapping oligonucleotide library. Nucleot Nucleos 1997; 16: 835–842CrossRefGoogle Scholar
  2. Branch AD. A hitchhiker’s guide to antisense and nonantisense biochemical pathways. Hepatology 1996; 24: 1517–1529PubMedCrossRefGoogle Scholar
  3. Branch AD. A good antisense molecule is hard to find. Trends Biochem Sci 1998; 23: 45–50PubMedCrossRefGoogle Scholar
  4. Brinkmeier H, Schu B, Seliger H, Kurz LL, Buchholz C, Rudel R. Antisense oligonucleotides discriminating between two muscular Na+ channel isoforms. Biochem Biophys Res Commun 1997; 234: 235–241PubMedCrossRefGoogle Scholar
  5. Boiziau C, Kurfurst R, Cazenave C, Roig V, Thuong NT, Toulme JJ. Inhibition of translation initiation by antisense oligonucleotides via an RNase-H independent mechanism. Nucleic Acids Res 1991; 19: 1113–1119PubMedCrossRefGoogle Scholar
  6. Cazenave C, Stein CA, Loreau N, Thuong NT, Neckers LM, Subasinghe C, Helene C, Cohen JS, Toulme JJ. Comparative inhibition of rabbit globin mRNA translation by modified antisense oligodeoxynucleotides. Nucleic Acids Res 1989; 17: 4255–4273PubMedCrossRefGoogle Scholar
  7. Donis Keller H. Site specific enzymatic cleavage of RNA. Nucleic Acids Res 1979; 7: 179–192CrossRefGoogle Scholar
  8. Lima WF, Brown DV, Fox M, Hanecak R, Bruice TW. Combinatorial screening and rational optimization for hybridization to folded hepatitis C virus RNA of oligonucleotides with biological antisense activity. J Biol Chem 1997; 272: 626–638PubMedCrossRefGoogle Scholar
  9. Logel J, Dill D, Leonard S. Synthesis of cRNA probes from PCR-generated DNA. Biotechniques 1992; 13: 604–610PubMedGoogle Scholar
  10. Milner N, Mir KU, Southern EM. Selecting effective antisense reagents on combinatorial oligonucleotide arrays. Nat Biotechnol 1997; 15: 537–541PubMedCrossRefGoogle Scholar
  11. Protocols and Application Guide. 1996. Promega CorporationGoogle Scholar
  12. Sambrook J, Fritsch EF, Maniatis T. Molecular cloning: a laboratory manual. 1987. Cold Spring Habor Laboratory Press, New YorkGoogle Scholar
  13. Shuttleworth J, Colman A. Antisense oligonucleotide-directed cleavage of mRNA in xenopus oocytes and eggs. EMBO J 1988;7: 427–434PubMedGoogle Scholar
  14. Schena M (ed). DNA Microarrays: A Practical Approach. IRL press, 1999 (in press).Google Scholar
  15. Snyder RD, Edwards ML. Effects of polyamine analogs on the extent and fidelity of in vitro polypeptide synthesis. Biochem Biophys Res Commun 1991; 176: 1383–1392PubMedCrossRefGoogle Scholar
  16. Stein CA. Does antisense exist? Nat Med 1995; 1: 1119–1121PubMedCrossRefGoogle Scholar
  17. Zühlke, RD, Zhang HJ, Joho RH. Xenopus oocytes: a system for expression cloning and structure-function studies of ion channels and receptors. Method Neurosci 1995; 25: 67–89CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 1999

Authors and Affiliations

  • Bernhard Schu
    • 1
  • Heinrich Brinkmeier
    • 1
  1. 1.Department of General PhysiologyUniversity of UlmUlmGermany

Personalised recommendations