In cells, small interfering RNAs (siRNAs) are produced by enzymatic cleavage of long dsRNAs by the endoribonuclease Dicer. The siRNAs associate with the RNA Induced Silencing Complex (RISC) in a process that is facilitated by Dicer. Dicer-Substrate RNAi methods take advantage of the link between Dicer and RISC loading that occurs when RNAs are processed by Dicer. Traditional 21mer siRNAs are chemically synthesized RNA duplexes that mimic Dicer products and bypass the need for Dicer processing. In contrast, our Dicer-substrate RNAs (DsiRNAs) are chemically synthesized 27mer RNA duplexes that are optimized for Dicer processing and loading into the RISC complex. This results in increased potency when compared to traditional 21mer duplexes.The DsiRNA duplexes are ideal for small scale in vitro applications. Pricing includes affinity purification and each duplex is identified by ESI mass spectrometry. All QC data is provided free of charge on the IDT website.
- Predesigned DsiRNAs - DsiRNA RefSeq Library
- TriFECTa® kit
- Large-scale DsiRNAs
Predesigned DsiRNAs - DsiRNA RefSeq Library
Over 3,000,000 DsiRNAs have been designed against the approximately 25,000 genes from each of the human, mouse, rat, cow, dog, chicken, and chimp transcriptomes in the RefSeq Genbank collection: http://www.ncbi.nlm.nih.gov/RefSeq. Site selection is first performed using a proprietary algorithm that uses novel Dicer-substrate specific design rules. Sequences that pass this stage are next screened to minimize the potential for cross-hybridization and off-target effects (Smith-Waterman analysis) and sites that include known SNPs or alternatively spliced exons are eliminated. Finally, the local mRNA secondary structure is modeled to avoid areas with a high level of predicted structure.
IDT offers two types of Predesigned DsiRNA duplexes:
- Splice common: targets all known variants of a gene in RefSeq; duplexes lie only within common extons. This constitutes the bulk of the DsiRNA collection and is the correct choice for most users. 8–10 duplexes are available for each gene target.
- Splice specific: targets only exons present in specific splice forms. In some cases, the unique exon may be very small or comprise sequence unfavorable for selection of RNAi duplexes (please note that knock-down guarantees do not apply for these sites). This collection is intended for those researchers who have a specialized need to selectively target specific splice variants or isoforms.
When working with a gene target that is included in the above collection, IDT recommends using the predesigned duplexes as these include significantly more bioinformatic analysis than is possible for sequences designed in real time using the web interface design tool.
The TriFECTa kit contains three Dicer-substrate 27mer RNA duplexes that are specific for a single target gene. Duplexes are provided in individual tubes and can be used singly or pooled, if desired. The sequences are from the DsiRNA library and so include options from seven genomes : human, mouse, rat, cow, dog, chicken, and chimpanzee. TriFECTa duplexes are selected using a rational design algorithm that integrates both traditional 21mer siRNA design rules as well as new 27mer-specific criteria. Additionally, analysis is performed to ensure that the chosen sites to not target alternatively spliced exons and do not include known single-nucleotide polymorphisms. IDT guarantees that at least two of the three DsiRNA duplexes in the TriFECTa kit will give at least 70% knockdown of the target mRNA when 1) used at 10 nM concentration and assayed by quantitative RT-PCR, 2) the fluorescent transfection control duplex indicates that >90% of the cells have been transfected, and 3) the positive control works with the expected efficiency. The TriFECTa product page is available here.
The small scales are intended for use in cell culture. For in vivo use, or other applications which require larger amounts of material, please see the Large-Scale ordering product page.