Small RNAs/Functional Genomics
Support and Educational Content

ReadyMade negative controls for gene silencing (RNAi) experiments

Introducing foreign RNA via transfection can affect cells in unforeseen ways, such as induction of an immune response in mammalian cells. Therefore, it is crucial to have an appropriate negative control against which one can compare experimental results in gene silencing and functional studies using DsiRNA duplexes. IDT has developed a negative control duplex (DS NC1) that does not target any part of the human, mouse, or rat transcriptomes. This duplex sequence serves as an ideal universal negative control for DsiRNA transfections in these organisms. The DS NC1 is stocked, ready to ship, and is available at 1 and 5 nmole scales.

While we recommend using the DS NC1 negative control duplex, which has been more extensively bioinformatically screened, a legacy scrambled sequence DsiRNA (DS ScrambledNeg) is also available for customers who have had success with it in their cell lines

Learn more and order from the Dicer-Substrate siRNA (DsiRNA) page. 

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.

Additional reading

Small RNA therapies for cystic fibrosis—The McCray Lab (Univ IA, USA) used DsiRNAs to develop a protocol for efficient small RNA delivery into airway epithelia. Read how their resulting method was used to study miRNA regulation of gene products involved in airway fluid and electrolyte transport, cellular mechanisms linked to cystic fibrosis.

Nanoparticle encapsulation method delivers DsiRNA to difficult-to-transfect cells—Precision NanoSystems Inc has developed unique reagents and equipment that enable the simple assembly of novel nanoparticles, resulting in greatly improved delivery of RNA payloads. Learn about use of products to deliver DsiRNAs, 27-mer siRNAs, into primary hippocampal neuron cells and neuronal cells in vivo.

Using DsiRNA to map pain pathways in the CNS—DsiRNAs (Dicer-substrate RNAs) are chemically synthesized 27mer duplex RNAs that have increased potency in RNA interference compared to traditional 21mer siRNAs. Read on for an example of a lab using this technology for in vivo delivery to the CNS.

Review other DECODED Online neslwetter articles on gene silencing and other small RNA applications.

You can also browse our DECODED Online newsletter for additional application reviews, lab tips, and citation summaries to facilitate your research.

Author: Ellen Prediger, PhD, is a scientific writer at IDT.

© 2012, 2016 Integrated DNA Technologies. All rights reserved. Trademarks contained herein are the property of Integrated DNA Technologies, Inc. or their respective owners. For specific trademark and licensing information, see


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