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Prediction of antisense oligonucleotide efficacy by in vitro methods

Nature Biotechnology volume 16, pages 1374–1375 (1998)Cite this article

Many problems related to antisense oligonucleotide therapy, such as oligonucleotide stability or efficient delivery, are gradually being overcome through advances in oligonucleotide chemistry. One remaining challenge, however, is the apparent paucity of mRNA sites that can be targeted efficiently.

Even though oligonucleotides that are complementary to translation initiation regions sometimes are responsible for decreasing the levels of particular mRNAs or proteins, there is increasing evidence that other parts of mRNAs might be better candidates1,2,3,4. Screening of multiple oligonucleotides (often 30–50) in cells is usually required for the discovery of a few active antisense sequences. This approach has been shown to be efficient for a number of mRNAs of potential therapeutic interest2,3,4. If complicated mRNA structures with internal base pairings are responsible for the problem, then a rapid, inexpensive, and reliable in vitro method for the prediction of accessible mRNA regions would be valuable. This would allow efficient targeting by complementary oligonucleotides and could increase the speed of antisense drug discovery.

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Figure 1: Gel mobility shift assay with antisense oligonucleotides targeting various regions of C-raf mRNA.
Figure 2: Comparison of the activity in cells with the results of two in vitro assays for 20 selected antisense oligonucleotides that target C-raf mRNA.

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Acknowledgements

This work was supported in part by a joint international research grant from the Japan Health Science Foundation (grant no. K-1005, PI, Y. Nakamura) and NIH grant GM48152 to J.F.A.

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Authors and Affiliations

  1. Department of Human Genetics and Howard Hughes Medical Institute, 6160 Eccles Genetics Building, University of Utah, Salt Lake City, 84112, UT

    Olga Matveeva, Brice Felden, John F. Atkins & Raymond F. Gesteland

  2. Huntsman Cancer Center, 546 Chipeta Way, Suite 1100 ARUP, Salt Lake City, 84108 , UT

    Alexander Tsodikov

  3. Isis Pharmaceuticals, 2280 Faraday Avenue , Carlsbad, 92008, CA

    Joseph Johnston, Brett P. Monia & Susan M. Freier

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Correspondence to Olga Matveeva.

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Matveeva, O., Felden, B., Tsodikov, A. et al. Prediction of antisense oligonucleotide efficacy by in vitro methods . Nat Biotechnol 16, 1374–1375 (1998). https://doi.org/10.1038/4362

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