Snead NM, Wu X, et al. (2013) Molecular basis for improved gene silencing by Dicer substrate interfering RNA compared with other siRNA variants. Nucleic Acids Res, 41(12):6209–6221.
The accepted experimental method of gene silencing by RNA interference (RNAi) in mammals is the introduction of small interfering RNAs (siRNAs) into cells of interest. The canonical siRNA comprises a 21 bp, double-stranded RNA molecule with the strands offset to create 2 nt overhangs at the 3′ ends. However, these siRNAs suffer from various disadvantages, including RNase susceptibility, immunogenicity to the host, and nonspecific selection of the active strand, resulting in decreased potency and potential off-target effects. Researchers have been working on improving siRNA design by altering the structure or introducing chemical modifications. If the promise of RNAi-based therapeutics is to be fulfilled, more potent and target-specific siRNAs need to be developed, and research in this field is prolific. This article investigates siRNA processing and RISC assembly, comparing different canonical siRNAs to their sequence-matched Dicer-substrate siRNAs (DsiRNAs), to define the molecular basis of the contribution of these DsiRNAs to the improved performance observed in various stages of the RNAi pathway.
Product focus—RNAi applications
Dicer-Substrate RNAs (DsiRNAs)
DsiRNA (Dicer-substrate RNAs) are chemically synthesized 27mer duplex RNAs that have increased potency in RNAi experiments compared to traditional siRNAs.
Learn more about DsiRNAs and order them from the DsiRNA product page.
TriFECTa® RNAi Kit
The TriFECTa RNAi Kit contains 3 Dicer-substrate 27mer duplexes, targeting a specific gene, that are selected from a predesigned set of duplexes from the RefSeq collection of human, mouse, and rat genes in Genbank.
Learn more from TriFECTa product page.
Secondary structure prediction software
The Unafold tool is free, online, secondary structure prediction software. The program calculates the probability of single-stranded RNA or DNA folding, or hybridization between 2 single strands.
Access the UNAFold tool here.
Using DsiRNA to map pain pathways in the CNS—Research profile: Read this example of a lab using DsiRNA technology for in vivo delivery to the CNS. These synthetic 27mer duplex RNAs have increased potency in RNA interference compared to traditional 21mer siRNAs.
Small RNA therapies for cystic fibrosis—Research profile: Learn how the McCray Lab (Univ IA, USA) used DsiRNAs to develop a protocol for efficient small RNA delivery into airway epithelia. The resulting method was then used to study miRNA regulation of gene products involved in airway fluid and electrolyte transport, cellular mechanisms linked to cystic fibrosis.
In vivo delivery of aptamer–DsiRNA molecules targeting HIV-1—Citation summary: See how these scientists improve on in vivo siRNA delivery using a modified aptamer-DsiRNA (Dicer-substrate RNA; IDT) molecule to inhibit HIV-1 replication.
Author: Ellen Prediger, PhD, is a scientific writer at IDT.
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