Rational selection and quantitative evaluation of antisense oligonucleotides

A. Jayaraman, S. P. Walton, M. L. Yarmush, C. M. Roth

Research output: Contribution to journalArticle

  • 25 Citations

Abstract

Antisense oligonucleotides are an attractive therapeutic option to modulate specific gene expression. However, not all antisense oligonucleotides are effective in inhibiting gene expression, and currently very few methods exist for selecting the few effective ones from all candidate oligonucleotides. The lack of quantitative methods to rapidly assess the efficacy of antisense oligonucleotides also contributes to the difficulty of discovering potent and specific antisense oligonucleotides. We have previously reported the development of a prediction algorithm for identifying high affinity antisense oligonucleotides based on mRNA-oligonucleotide hybridization. In this study, we report the antisense activity of these rationally selected oligonucleotides against three model target mRNAs (human lactate dehydrogenase A and B and rat gp130) in cell culture. The effectiveness of oligonucleotides was evaluated by a kinetic PCR technique, which allows quantitative evaluation of mRNA levels and thus provides a measure of antisense-mediated decreases in target mRNA, as occurs through RNase H recruitment. Antisense oligonucleotides that were predicted to have high affinity for their target proved effective in almost all cases, including tests against three different targets in two cell types with phosphodiester and phosphorothioate oligonucleotide chemistries. This approach may aid the development of antisense oligonucleotides for a variety of applications.

Original languageEnglish (US)
Pages (from-to)105-114
Number of pages10
JournalBiochimica et Biophysica Acta - Gene Structure and Expression
Volume1520
Issue number2
DOIs
StatePublished - Aug 30 2001
Externally publishedYes

Profile

Antisense Oligonucleotides
Oligonucleotides
Messenger RNA
Gene Expression
Gene expression
Phosphorothioate Oligonucleotides
Ribonuclease H
L-Lactate Dehydrogenase
Cell Culture Techniques
Polymerase Chain Reaction
Bile Pigments
Anthralin
Staphylococcal Pneumonia
Airway Obstruction
Cell culture
Kinetics

Keywords

  • Antisense
  • Hybridization
  • mRNA dynamics
  • Quantitative polymerase chain reaction

ASJC Scopus subject areas

  • Biochemistry
  • Genetics
  • Structural Biology
  • Biophysics

Cite this

Rational selection and quantitative evaluation of antisense oligonucleotides. / Jayaraman, A.; Walton, S. P.; Yarmush, M. L.; Roth, C. M.

In: Biochimica et Biophysica Acta - Gene Structure and Expression, Vol. 1520, No. 2, 30.08.2001, p. 105-114.

Research output: Contribution to journalArticle

Jayaraman, A.; Walton, S. P.; Yarmush, M. L.; Roth, C. M. / Rational selection and quantitative evaluation of antisense oligonucleotides.

In: Biochimica et Biophysica Acta - Gene Structure and Expression, Vol. 1520, No. 2, 30.08.2001, p. 105-114.

Research output: Contribution to journalArticle

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