Replace shRNA, make RNAi more specific.
By rethinking Gene Silencing, researchers can now knockout target genes without the off-target suppression of traditional dsRNA. Unlike shRNA, AsymmetricRNAi is designed to enhance specificity with an elegantly designed single-stranded RNA.
A New Perspective on RNAi
RNAi has become a fundamental tool in research, but it's not perfect. The ballet of enzymes and protein complexes can evoke off-target suppression, interferon and viral responses which may interfere with precise research applications.
In an effort to improve RNAi tools, we have designed a multi-mechanism, insitu-capable series of RNAi molecules that we hope will be the answer to a lot of your advanced research needs. We invite you to explore AsymmetricRNAi applications in your own research.
Eliminate Off-Target Suppression?
Since inventing our 'Asymmetric siRNA Duplex' in 2002, Oligoengine has been working to make symmetrical siRNA more specific. How? By eliminating the sense strands' ability to guide RISC and cause unwanted suppression of non-targeted genes. Our 'Asymmetric siRNA Duplex' achieved this by chemically modifying the duplex, but an insitu solution was still needed.
AsymmetricRNAi is the answer to providing transient or stable 'one-way' gene suppression.
There are no chemical modifications or consideration of unreliable 3' thermodynamics, just pure design.
Asymmetric = Specific?
Asymmetric RNAi oligos are designed to trigger the same mechanisms as their siRNA or shRNA counterparts, but they are uniquely structured and pre-processed. Why is this more specific compared to siRNA?
Subtle design options for AsymmetricRNAi determine the overall pathway and function- each with it's unique advantage.
AsymmetricRNAi relies on functional nucleotide content, loop sizes, helix formations, and mismatches to elicit the processing routine of your preferred gene suppression mechanism. These pathway/mechanism options make AsymmetricRNAi an ideal tool for contrasting various gene silencing mechanisms with your phenotype.
AsymmetricRNAi precursors are characterized by an RNA structure capable of Gene Silencing through various pre-processing steps designed to elicit specific silencing mechanisms (see below).
Regardless of mechanism, AsymmetricRNAi precursors rely on a single-stranded RNA region to ensure it's function is asymmetric and target specific.
Guiding of the ssRNA region to your target gene for direct RNase III hydrolysis or protein-complex driven catalysis is controlled by the subtle design options introduced below:
Three Model RNAi Precursors:
A-shRNA are designed for asymmetric dicer pre-processing and RISC loading This precursor is be pre-processed first by Rnt1 before loading onto the PAZ domain. The resulting sense-strand lacking siRNA-like structure is also designed to load onto RISC asymmetrically and result in cleavage of your targeted gene.
COMPARE TO: shRNA
A-siRNA precursors are RISC loading. Like classic siRNA, this option is not dicer dependent. The precursor is designed to be processed into the sense-strand lacking siRNA-like duplex by Rnt1, then loaded onto RISC silently.
COMPARE TO: siRNA
Getting Started with AsymmetricRNAi
Three model precursors, each with unique advantages.
AsymmetricRNAi oligos can be used transiently as RNA or expressed constitutively from pSUPER vectors. Either way, the first step to designing effective Asymmetric RNAi molecules against your target gene is understanding the structure-to-mechanism relationship. To help you, Oligoengine offers design assistance to optimize the two mechanisms and three pathways possible against your target of choice.
Involving Rnt1, Dicer, and RISC
Subtle design elements optional on A-RNAi molecules are responsible for the processing pathway, mechanism, or overall effect. Loop size and placement, stem length and placement all contribute to the recruiting of enzymes or proteins required for reliable function. Please review the charts and adhere to the guidelines when designing your A-RNAi molecule.
Converting Your siRNA
Your classical siRNA or shRNA can be converted easily for A-RNAi. Please use the order form to send your classical siRNA or shRNA in for conversion.
Send us your siRNA or shRNA and we'll convert it to the A-RNAi molecule eliciting the pathway/mechanisms of your choice.
RNAi Target Suppression Prediction:
Send us your target gene and we'll rapidly design the three most potent and specific RNAi sites for reliable suppression.
Oligoengine 3.0 Software:
The next version of Oligoengine will include a suite of A-RNAi design tools as well as the support data you expect from Oligoengine.
Research-Use Price List.
A-RNAi oligos are available as DNA for vectors or RNA for transient use.
DNA versions for use in pSUPER or other vectors. Note: Please specify ligation enzymes when submitting order.
|DNA for pSUPER:||price|
|A-RNAi-0001||A-shRNA (DNA Set)||$199|
|A-RNAi-0002||A-siRNA (DNA Set)||$219|
RNA versions for invitro or in vivo use.
|RNA for transient use:||price|
|A-RNAi-0005||A-shRNA (RNA, 200 nmole)||$499|
|A-RNAi-0006||A-siRNA (RNA, 200 nmole)||$599|
Any Target + pSUPER or pSUPERIOR + 18 Days.
Pick any pSUPER or pSUPERIOR vector, a target, and we will send a sequenced A-RNAi clones for $599 each.
Cloning Service Deliverables:
• All clones are sequence confirmed.
• 18 Business Day turnaround.
• Price includes all materials.
• Delivered as mini prep, ~4 µg.
Results using A-RNAi against common targets.
We invite you to use the A-RNAi tool against your target gene. Here is some data generated against common targets.
Questions and Answers
Common Questions for AsymmetricRNAi.
Can I use my classical siRNA design?
> Yes, most likely. Send it in and we'll convert it.
Does A-RNAi work with other vectors?
> Yes, you can use pSUPER or other RNAi expression vector.
Is A-RNAi guaranteed?
> We are not yet able to guarantee its use against all targets and each mechanism. For the best results, send us your targets for designing.
What is the difference between the options?
> A-RNAi comes in two forms; I, II. The difference is in the mode of action and processing pathway.
OPTION 1: This form recruits RISC for gene destruction. This is very similar to siRNA, but unlike classical shRNA, dicer is not used to process the precursor into siRNA.
OPTION II: Same as option II, but this option is designed to enable Dicer pre-processing into final RISC-recruiting form.
Can I order my oligos from another supplier?
> At the moment, A-RNAi oligos are exclusive to Oligoengine. Licenses to other suppliers will be considered in the future.
Can I order A-RNAi oligos internationally?
> Yes, Oligoengine will ship them to most countries.
AsymmetricRNAi Evaluation Sets:
These sets are for Commercial-Use license evaluations. (Academic pricing by request)
I. BASIC Evaluation Set:
Targets: Anti-p53, Anti-GFP, Anti-Luc
Contents: 5 nm RNA using A-RNAi
II. ADVANCED Evaluation Set:
Targets: Anti-HIV, Anti-Ebola, Anti-Staph(MRSA)
Contents: 5 nm RNA using A-RNAi
III. CUSTOM Evaluation Set:
Targets: Includes all of the above, plus any two targets of choice.
Contents: 5 nm RNA using A-RNAi
Streamline the licensing process by starting with the Evaluation Sets.
Academic and Non-Profit Licensing Terms
Researchers at academic and non-profit institutions are granted a limited end-user license with the purchase of each AsymmetricRNAi.
Commercial and For-Profit Licensing Terms
Use of the AsymmetricRNAi Platform by commercial pharmacuetical and biotech companies is subject to specific licensing terms.
Companies can purchase individual Evaluation Sets including AsymmetricRNAi molecules and vectors before negotiating a streamlined product use agreement. Additionally, any products, including cell lines, transgenic animals and therapeutic compounds developed using AsymmetricRNAi will be considered as licensed products and subject to a sales royalty by Halo-Bio RNAi Therapeutics Inc.
For more information, please contact OligoEngine.