siRNA for mRNA knockdown
AUMsiRNA
RNA interference (RNAi) with enhanced performance
AUMsiRNA is a chemically modified small interfering RNA duplex for mRNA knockdown, designed for researchers who prefer the familiar RNAi pathway for gene silencing. Built on the AUMsilence platform, these 21-23 nucleotide duplexes carry chemical modifications that the platform both selects and positions along the sequence.
Unlike our self-delivering antisense oligonucleotide (ASO) products, AUMsiRNA operates through the well-characterized RNAi mechanism, using the cellular RNA-induced silencing complex (RISC) machinery. This suits researchers already comfortable with siRNA workflows, without changing their experimental approach.
AUMsiRNA duplexes incorporate strategic chemical modifications while maintaining compatibility with standard transfection protocols already used in the lab.
Note: Performance characteristics are sequence and cell-type dependent. Results may vary based on target gene, experimental conditions, and delivery method. Testing multiple siRNA sequences per target, with appropriate controls, is recommended.
- Familiar technology, unchanged workflow
AUMsiRNA works with established siRNA protocols without changing workflows.
- Potency and strand selection
Only one strand of the duplex should be loaded into RISC, and the duplex's thermodynamics steers which.
- Where off-target silencing comes from
Off-target silencing by an siRNA comes from its seed region rather than from the rest of the sequence.
- How long knockdown lasts
In dividing cells, duration is set by cell division rather than by the siRNA's own stability.
Yields and purification
- RPC
- 1 · 2 · 5 · 10 · 20 · 50 nmol
- HPLC
- 5 · 10 · 20 · 50 nmol
AUMsiRNA Pool, a pool of several sequences against one target, is delivered as 5, 10 or 20 nmol in total.
Prices and lead time are on the order page. Custom yields by quote.
At a glance
- Class
- Enhanced siRNA
- Targets
- mRNA knockdown by RNAi
- Delivery
- Compatible with a standard lipid-based transfection reagent or electroporation.
- Fluorescent label
- None
In the lab
Protocols for the bench
No protocol is written for this product yet. The protocols index holds the site's bench protocols.
Why
Features of AUMsiRNA
Familiar technology, unchanged workflow
AUMsiRNA works with established siRNA protocols without changing workflows. It acts through the RNA interference (RNAi) pathway and is compatible with transfection reagents and electroporation. Experiments keep their existing time points and controls.
Potency and strand selection
Only one strand of the duplex should be loaded into RISC, and the duplex's thermodynamics steers which.
Where off-target silencing comes from
Off-target silencing by an siRNA comes from its seed region rather than from the rest of the sequence.
How long knockdown lasts
In dividing cells, duration is set by cell division rather than by the siRNA's own stability.
Mechanism
RNA interference mechanism of action
1. siRNA delivery and cellular entry: AUMsiRNA duplexes are delivered into cells using standard transfection methods. The chemically modified siRNA escapes endosomes and enters the cytoplasm where it encounters the RNAi machinery.
2. RISC loading and activation: The siRNA duplex is recognized by RISC-loading complex proteins including Dicer and TRBP. Argonaute 2 (Ago2) cleaves the passenger strand, retaining only the guide strand.
3. Target recognition and cleavage: The activated RISC uses the guide strand to scan cellular mRNAs. Upon finding a complementary target, Ago2 cleaves the mRNA between nucleotides 10-11 of the guide strand, leading to mRNA degradation.
4. Catalytic turnover: After mRNA cleavage, RISC releases the cleaved fragments and remains active to find additional target mRNAs. One siRNA-programmed RISC can cleave multiple mRNA copies, amplifying the silencing effect.
- Stage 1
AUMsiRNA duplexes are delivered into cells using standard transfection methods. The chemically modified siRNA escapes endosomes and enters the cytoplasm where it encounters the RNAi machinery.
- Stage 2
The siRNA duplex is recognized by RISC-loading complex proteins including Dicer and TRBP. Argonaute 2 (Ago2) cleaves the passenger strand, retaining only the guide strand.
- Stage 3
The activated RISC uses the guide strand to scan cellular mRNAs. Upon finding a complementary target, Ago2 cleaves the mRNA between nucleotides 10-11 of the guide strand, leading to mRNA degradation.
Applications
Applications and use cases
Target validation studies
Validate candidate targets by achieving knockdown in disease-relevant cell models. A single transfection supports time-course studies of protein depletion and recovery, and how long that window stays open is set by how fast the cells divide.
Pathway analysis
Dissect complex signaling pathways by selectively silencing pathway components. Use more than one sequence against each gene. Seed-driven silencing of unintended transcripts belongs to the sequence, so a phenotype that survives two independent siRNAs is the target's rather than the seed's.
Modeling an RNA drug
Use AUMsiRNA as a research tool to model the gene silencing an RNA drug produces. What such a study reads out is the knockdown level and how long it holds in the cells it is run in.
High-content screening
Deploy in automated screening platforms for systematic gene function analysis. AUMsiRNA duplexes are transfected with the same reagents and in the same concentration range as any siRNA, so an existing screening protocol carries over.
Every compatible cell type, 3D model and organoid with the in vitro workflow, and in vivo with a delivery system.
See where it worksRNAi vs. ASO
| AUMsiRNA (RNAi) | AUMsilence | |
|---|---|---|
| Structure | Double-stranded RNA | Single-stranded DNA/RNA |
| Mechanism | RISC/Ago2 | RNase H1 |
| Cellular location | Primarily cytoplasmic | Nuclear and cytoplasmic |
| Delivery required | Yes (transfection) | No (self-delivering) |
Delivery methods and optimization
Compatible transfection approaches
Lipid-based transfection
Works with standard cationic lipid reagents. Standard practice is to transfect siRNA at 10-50 nM final concentration.
Electroporation
Used for difficult-to-transfect cells including primary T cells, neurons, and stem cells.
Nanoparticle delivery
Compatible with polymeric, lipid nanoparticle (LNP), and other delivery systems for in vivo applications.
- Concentration range: Start with 10-25 nM for most immortalized cell lines; primary cells typically require 25-50 nM
- Timing: Assess knockdown at 24, 48, and 72 hours post-transfection
- Controls: Always include appropriate negative control siRNAs with matched modifications
Transfections per vial
At 50 nM, the top of the range in standard practice, a 5 nmol vial transfects 833 wells of a 96-well plate. The same vial transfects 166 wells of a 24-well plate or 83 of a 12-well plate. The counts are against the volume in the well after a lipid transfection, the complete medium plus the siRNA and reagent dilutions. Counts are rounded down to whole wells.
| Plate | Volume in the well | 10 nM | 50 nM |
|---|---|---|---|
| 96-well | 120 μL | 4,166 | 833 |
| 24-well | 600 μL | 833 | 166 |
| 12-well | 1,200 μL | 416 | 83 |
| 6-well | 2,500 μL | 200 | 40 |
Experimental considerations
AUMsiRNA is delivered with a transfection reagent, where self-delivering antisense oligonucleotides are taken up without one. The reagent is the product's cost: transfection reagents can introduce toxicity, alter the cellular response, or require additional optimization.
Choosing between the three products
When AUMsiRNA is the choice
- Cells that transfect efficiently with a standard reagent
- High-throughput screens with automated transfection
- Established protocols with extensive literature support
When AUMsilence
sdASO is the choice - Transfection-free delivery
- Difficult-to-transfect or primary cells
- In vivo experiments
- Nuclear RNA targets
- No RISC-related off-targets
When AUMsilence
toASO is the choice - Budget as the primary concern
- Large-scale screens
- Easy-to-transfect cell lines
- Bulk quantities for training and education
- Pilot experiments
At the bench
What arrives
Compatible with a standard lipid-based transfection reagent or electroporation.
- Lead time
- 10-14 business days
- Shipping
- Products are shipped lyophilized, with priority shipping within the United States and international priority shipping elsewhere.
- Quality control
- Every oligo is strictly controlled for quality and is manufactured in an ISO 9001:2015 certified facility.
Order AUMsiRNA
The AUMsilence platform is used to identify and design efficient siRNAs. Our scientific team is available before ordering to discuss the target and the cell type.
For research use only. Not for use in diagnostic or therapeutic procedures.