Position-specific chemical modification of siRNAs reduces “off-target” transcript silencing (original) (raw)
- Aimee L. Jackson1,
- Julja Burchard1,
- Devin Leake2,
- Angela Reynolds2,
- Janell Schelter1,
- Jie Guo1,
- Jason M. Johnson1,
- Lee Lim1,
- Jon Karpilow2,
- Kim Nichols2,
- William Marshall2,
- Anastasia Khvorova2, and
- Peter S. Linsley1
- 1Rosetta Inpharmatics, LLC, a wholly owned subsidiary of Merck & Co., Inc., Seattle, Washington 98109, USA
- 2Dharmacon Inc., Lafayette, Colorado 80026, USA
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.
Footnotes
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.
Article published online ahead of print. Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.30706.
- Received January 20, 2006.
- Accepted March 16, 2006.
Freely available online through the open access option.
Copyright © 2006 RNA Society