Position-specific chemical modification of siRNAs reduces “off-target” transcript silencing
Abstract
Transfected siRNAs regulate numerous transcripts sharing limited complementarity to the RNA duplex. This unintended (“off-target”) silencing can hinder the use of RNAi to define gene function. Here we describe position-specific, sequence-independent chemical modifications that reduced silencing of partially complementary transcripts by all siRNAs tested. Silencing of perfectly matched targets was unaffected by these modifications. The chemical modification also reduced off-target phenotypes in growth inhibition studies. Key to the modification was 2′-O-methyl ribosyl substitution at position 2 in the guide strand, which reduced silencing of most off-target transcripts with complementarity to the seed region of the siRNA guide strand. The sharp position dependence of 2′-O-methyl ribosyl modification contrasts with the broader position dependence of base-pair substitutions within the seed region, suggesting a role for position 2 of the guide strand distinct from its effects on pairing to target transcripts.
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Footnotes
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Reprint requests to: Aimee L. Jackson, Rosetta Inpharmatics, 401 Terry Avenue N, Seattle, WA 98109, USA; e-mail: aimee_jackson{at}merck.com; fax: (206) 802-6388.
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Article published online ahead of print. Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.30706.
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- Received January 20, 2006.
- Accepted March 16, 2006.
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Freely available online through the open access option.
- Copyright © 2006 RNA Society