Viral RNA knockdown oligos

AUMsilence V+ sdASO

Name: AUMsilence V+ sdASO
Brand: AUM BioTech

Self-delivering antisense oligonucleotides for viral RNA knockdown

AUMsilence V+ sdASO taken up by an infected cell without a transfection reagent; RNase H1 cleaves the hybridized viral RNA.

AUMsilence V+ sdASO is a self-delivering antisense oligonucleotide (ASO) for viral RNA knockdown in virology research and antiviral target discovery. AUMsilence V+ sdASOs are designed against the viral RNA of an infected cell, the genome or the transcripts of an RNA virus. Knockdown of that RNA reduces viral protein production and replication.

Many viruses infect cells that are difficult to transfect with conventional methods. Transfection reagents, electroporation, or viral vectors can introduce toxicity, alter the cellular response, or require additional optimization. AUMsilence V+ sdASOs are added directly to the culture medium of the infected cells. They enter the cell without a transfection reagent, electroporation, or a viral vector.

Viral-specific design
AUMsilence V+ sdASOs are designed for viral targets.
Several viral targets in parallel
AUMsilence V+ sdASOs are designed against several viral targets at a time, so the targets are tested in parallel.

Yields and purification

Available by quote: tell us your target and we design and price it.

Prices and lead time are on the order page. Custom yields by quote.

At a glance

Class: Self-delivering antisense (sdASO)
Targets: Viral RNA knockdown
Delivery: Add to culture medium or inject in vivo.
Fluorescent label: None

In the lab

The protocol in four steps

The steps below are the AUMsilence V+ sdASO protocol's, in its own words. The full protocol carries the amounts per plate format, the tips and the troubleshooting.

Read the full protocol

Step 1
Cell preparation and viral infection
Plate cells in their optimum growth medium at appropriate density for the cell type and viral system.
Step 2
AUMsilence V+ sdASO stock preparation
Prepare AUMsilence V+ sdASO stock solution by reconstituting lyophilized ASOs at the desired concentration. If you already have a stock solution prepared, skip to Step 3.
Step 3
AUMsilence V+ sdASO delivery to cells
Add AUMsilence V+ sdASO to the cells at the desired final concentration. The recommended working range is 5-20 μM, with a starting concentration of 10 μM. The optimal concentration varies with the target gene, the RNA class (messenger RNA, microRNA or long non-coding RNA) and the cell type, and should be determined by titration for each system.
Step 4
Incubation and analysis
Incubate cells with AUMsilence V+ sdASO and analyze viral inhibition at appropriate time points.

Step 1, prepare cells and the oligonucleotide: a clear 24-well plate of pink medium, a microtube of pale blue solution with its lid open and a pipette tip reaching into its mouth, and three short beaded violet strands drawn in the air above the tube, the slide's motif for the oligonucleotide. — For research use only. Not for use in diagnostic or therapeutic procedures.
Notes
The pictures are the object pictures of AUM BioTech's workflow slide, rendered views of the objects on a white ground. None is a photograph of an experiment and none records a measurement.
Tile 04 is a schematic of the three readouts, not data. The two conditions are drawn with a modest difference to show what each readout is, and no magnitude is asserted.

Step 2, add to the culture medium: a single-channel micropipette with a violet plunger held over a 24-well plate of pink medium, its tip in one well. — For research use only. Not for use in diagnostic or therapeutic procedures.
Notes
The pictures are the object pictures of AUM BioTech's workflow slide, rendered views of the objects on a white ground. None is a photograph of an experiment and none records a measurement.
Tile 04 is a schematic of the three readouts, not data. The two conditions are drawn with a modest difference to show what each readout is, and no magnitude is asserted.

Why

Features of AUMsilence V+ sdASO

Viral-specific design
AUMsilence V+ sdASOs are designed for viral targets. Each sequence is designed against regions of the viral RNA that are highly conserved across strains and essential for viral function. Unlike conventional antiviral compounds that target proteins, these ASOs act on the viral RNA itself.
Several viral targets in parallel
AUMsilence V+ sdASOs are designed against several viral targets at a time, so the targets are tested in parallel. Silencing each can pinpoint the viral genes that are essential to replication or pathogenesis, which is what antiviral drug discovery needs.

Mechanism

Mechanism of action

Self-delivery in infected cells: AUMsilence V+ sdASOs are taken up by endocytosis in infected cells, without the need for transfection reagents or special formulations. They reach the nucleus as well as the cytoplasm. In the nucleus, RNase H1-dependent cleavage acts on nuclear RNA in the same way, so a virus replicating in either compartment is in reach.

RNase H1-mediated cleavage: AUMsilence V+ sdASOs are reverse complementary to a region of the viral RNA and hybridize to it inside the cell. RNase H1 recognizes the resulting duplex and cleaves the viral RNA, which is then degraded.

Three stages inside an infected cell, left to right. Outside the cell membrane a spiked virion floats. Inside, a viral RNA spools from a replication complex, a cluster of translucent lobes on a membrane fold, while a gapmer with a pale central gap drifts free. The gapmer is paired with the viral RNA with RNase H1, a translucent globular enzyme, on the pale gap under the one warm glow. The viral RNA is cleaved beneath it into two clean ends with the gapmer whole across the gap. At the right the free gapmer drifts whole beside two separate fragments of the viral RNA, and an idle replication complex sits dim with no strand on it. The nucleus stands at the top right and a mitochondrion at the lower center. — Stage 1
AUMsilence V+ sdASOs are taken up by endocytosis in infected cells, without the need for transfection reagents or special formulations.
Stage 2
AUMsilence V+ sdASOs hybridize to the viral RNA. RNase H1 recognizes the resulting duplex and cleaves the viral RNA.

Applications

Applications and use cases

Inhibition of viral replication
Directly target the viral RNA to prevent replication. For example, targeting the polymerase or protease genes of an RNA virus can halt replication in infected cells.
Viral gene function studies
Systematically knock down individual viral genes to understand their roles in the viral life cycle, host interaction, or pathogenesis. This can identify the viral components that are critical for infection.
Validation of antiviral targets
Before developing small-molecule drugs or another agent against a viral target, use AUMsilence V+ sdASO to validate that silencing the specific viral component prevents viral replication or spread.
Research on emerging viruses
When new viral threats emerge, AUMsilence V+ sdASOs are designed from the viral sequence, so viral mechanisms and intervention strategies are studied even before conventional antiviral compounds are available.

Every compatible cell type, 3D model, organoid and in vivo route, with the in vitro workflow.

See where it works

Experimental considerations

The recommended working range for AUMsilence V+ sdASOs is 5-20 μM.

In the literature