1. ¹Department of Chemistry, Pohang University of Science and Technology, Pohang, Korea
2. ²Global Research Laboratory for RNAi Medicine, Department of Chemistry and BK21 Chemical Materials Science, Sungkyunkwan University, Suwon, Korea
3. ³Boston Biomedicals Inc., Norwood, Massachusetts, USA
4. ⁴Department of Biomedical Engineering, Dongguk University, Seoul, Korea
5. ⁵Division of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA

Correspondence: Dong-ki Lee, Global Research Laboratory for RNAi Medicine, Department of Chemistry and BK21 Chemical Materials Science, Sungkyunkwan University, Suwon, Korea. E-mail: dklee@skku.edu

Received 29 September 2008; Accepted 15 December 2008; Published online 20 January 2009.

Abstract

Small interfering RNAs (siRNAs) are short, double-stranded RNAs that mediate efficient gene silencing in a sequence-specific manner by utilizing the endogenous RNA interference (RNAi) pathway. The current standard synthetic siRNA structure harbors a 19–base-pair duplex region with 3' overhangs of 2 nucleotides (the so-called 19+2 form). However, the synthetic 19+2 siRNA structure exhibits several sequence-independent, nonspecific effects, which has posed challenges to the development of RNAi therapeutics and specific silencing of genes in research. In this study, we report on the identification of truncated siRNA backbone structures with duplex regions shorter than 19 bp (referred to as asymmetric shorter-duplex siRNAs or asiRNAs) that can efficiently trigger gene silencing in human cell lines. Importantly, this asiRNA structure significantly reduces nonspecific effects triggered by conventional 19+2 siRNA scaffold, such as sense-strand–mediated off-target gene silencing and saturation of the cellular RNAi machinery. Our results suggest that this asiRNA structure is an important alternative to conventional siRNAs for both functional genomics studies and therapeutic applications.