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Nucleic Acids Research, 2000, Vol. 28, No. 15 2862-2865
© 2000 Oxford University Press

Identification of sequence motifs in oligonucleotides whose presence is correlated with antisense activity

O. V. Matveeva*, A. D. Tsodikov1, M. Giddings, S. M. Freier2, J. R. Wyatt2, A. N. Spiridonov3, S. A. Shabalina4, R. F. Gesteland and J. F. Atkins

Department of Human Genetics, University of Utah, 15N 2030E Room 7410, Salt Lake City, UT 84112-5330, USA, 1Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA, 2Isis Pharmaceuticals, Carlsbad, CA 92008, USA, 3IHS, Ithaca, NY 14853, USA and 4National Center for Biotechnology Information, NLM, NIH, Bethesda, MD 20814, USA

Design of antisense oligonucleotides targeting any mRNA can be much more efficient when several activity-enhancing motifs are included and activity-decreasing motifs are avoided. This conclusion was made after statistical analysis of data collected from >1000 experiments with phosphorothioate-modified oligonucleotides. Highly significant positive correlation between the presence of motifs CCAC, TCCC, ACTC, GCCA and CTCT in the oligonucleotide and its antisense efficiency was demonstrated. In addition, negative correlation was revealed for the motifs GGGG, ACTG, AAA and TAA. It was found that the likelihood of activity of an oligonucleotide against a desired mRNA target is sequence motif content dependent.

* To whom correspondence should be addressed. Tel: +1 801 581 5191; Fax: +1 801 585 3910; Email: olgam@howard.genetics.utah.edu


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