Skip to content

Create an account and get up to 25% off.

Order

long non-coding RNA knockdown

AUMlnc sdASO

Self-delivering antisense oligonucleotides for long non-coding RNA knockdown

Species

Choose a species.

Official symbol, alias or previous symbol

Request a quoteCompare the products
AUMlnc sdASO taken up by a cell without a transfection reagent; in the nucleus, RNase H1 cleaves the hybridized long non-coding RNA.

AUMlnc sdASOs are self-delivering antisense oligonucleotides (ASOs) designed for the knockdown of long non-coding RNAs (lncRNAs). Long non-coding RNAs are a class of RNA transcripts (typically >200 nucleotides) that do not code for proteins but often regulate gene expression, chromatin state, or other cellular processes. They can localize to the nucleus or cytoplasm and have diverse functions.

AUMlnc sdASOs are built on the same AUMsilence platform and self-delivery mechanism as our other products. Long non-coding RNA is often retained in the nucleus. Many primary cells and disease-relevant models are difficult to transfect with conventional methods. Transfection reagents, electroporation, or viral vectors can introduce toxicity, alter the cellular response, or require additional optimization. AUMlnc sdASOs enter the cell without a transfection reagent, electroporation, or a viral vector. Add them to the culture medium or inject them into an animal. They reach the nucleus and induce RNase H1-mediated degradation of the lncRNA.

Yields and purification

RPC
10 · 25 · 50 · 100 nmol
HPLC
25 · 50 · 100 nmol
Labeled, HPLC
10 · 25 · 50 · 100 nmol · FAM, Cyanine 3, Cyanine 5, Cyanine 7

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

At a glance

Class
Self-delivering antisense (sdASO)
Targets
lncRNA knockdown
Delivery
Add to culture medium or inject in vivo.
Fluorescent label
FAM, Cyanine 3, Cyanine 5 or Cyanine 7

In the lab

The protocol in four steps

The steps below are the AUMlnc 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

  1. Step 1

    Cell preparation

    Plate cells in their optimum growth medium at a density appropriate for the cell type. A confluency of 50-70% at the time of treatment is typical.

  2. Step 2

    AUMlnc sdASO stock preparation

    Prepare AUMlnc sdASO stock solution by reconstituting lyophilized ASOs at the desired concentration. If you already have a stock solution prepared, skip to Step 3.

  3. Step 3

    AUMlnc sdASO delivery to cells

    Add AUMlnc 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.

  4. Step 4

    Incubation and analysis

    Incubate cells with AUMlnc sdASO and analyze knockdown at appropriate time points. Knockdown is typically observed 24 to 72 hours after treatment, depending on the cell type and the target gene. Longer time points may be required in some systems.

FigureThe workflow in cell culture, in four steps

In vitro, the four steps

  1. Step 1

    Prepare cells

    Seed the cells in a 24-well plate; the oligonucleotide waits in solution.

  2. Step 2

    Add to the medium

    Add the self-delivering oligonucleotide straight to the medium: no transfection reagent, no carrier.

  3. Step 3

    Incubate

    Incubate at 37 degrees C in 5% carbon dioxide, humidified, for the exposure time.

  4. Step 4

    Quantify knockdown

    Measure the knockdown: RT-qPCR, immunoblot, flow cytometry.

    Schematic of the three readouts, not data.

Notes
  1. 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.
  2. 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 AUMlnc sdASO

  • Knockdown in cells and in animals

    AUMlnc sdASO silences lncRNAs in cells and in animals. Historically, lncRNAs have been challenging to study because of the lack of tools to perturb them. Whether the lncRNA acts in cis (nearby on the DNA) or in trans (far away in the cell), AUMlnc sdASO is designed against the lncRNA itself.

  • Cleavage in the nucleus

    AUMlnc sdASO reaches the nucleus, where many lncRNAs act, so a nuclear transcript is cleaved rather than only blocked.

  • High specificity for lncRNA sequence

    AUMlnc sdASOs can be designed to target unique regions of the lncRNA, because lncRNAs often belong to gene families or have repetitive elements. Each sequence is scored for specificity against the transcriptome before synthesis. Off-target effects are sequence-dependent and are checked with a non-targeting control.

  • No need for genetic manipulation

    AUMlnc sdASO offers a non-genetic, reversible approach to lncRNA knockdown. This is crucial because some lncRNA genes overlap with other genes or have regulatory elements that a genomic deletion would disturb. The alternatives, CRISPR-mediated deletion of the genomic locus or CRISPR interference, can be labor-intensive, and a deletion of the locus is permanent.

Mechanism

Mechanism of action

Targeting the lncRNA: AUMlnc sdASOs typically hybridize to the lncRNA along stretches of sequence that are accessible (e.g., unstructured regions or regions not bound by proteins). Once hybridized, they form an ASO–lncRNA duplex. The DNA-like characteristics of AUMlnc sdASOs trigger RNase H1 to recognize the duplex and cleave the RNA strand. This leads to degradation of the lncRNA.

Functional blockade (steric blocking): An AUMlnc sdASO may instead be designed against a critical functional domain of the lncRNA. That domain may be a region that binds a protein partner, or the locus at which the lncRNA base-pairs with another RNA. The hybridized AUMlnc sdASO blocks the lncRNA from performing its function, even if the lncRNA is not fully degraded.

Self-delivery and nuclear uptake: AUMlnc sdASOs do not require any transfection reagent to get inside cells. They are taken up by endocytosis and reach the nucleus as well as the cytoplasm. In the nucleus, RNase H1-dependent cleavage proceeds as it does in the cytoplasm. Unlike RNA interference by siRNA, which acts mainly in the cytoplasm, AUMlnc sdASOs act on nuclear RNA.

FigureHow AUMlnc sdASO acts
Three stages in the nucleus: the gapmer crosses a nuclear pore, RNase H1 cleaves the long non-coding RNA, and the gapmer is released whole.
  1. Stage 1

    AUMlnc sdASOs do not require any transfection reagent to get inside cells. They are taken up by endocytosis and reach the nucleus as well as the cytoplasm.

  2. Stage 2

    AUMlnc sdASOs typically hybridize to the lncRNA along stretches of sequence that are accessible. Once hybridized, they form an ASO–lncRNA duplex.

  3. Stage 3

    The DNA-like characteristics of AUMlnc sdASOs trigger RNase H1 to recognize the duplex and cleave the RNA strand. This leads to degradation of the lncRNA.

Applications

Applications and use cases

  • Function of a new lncRNA

    A new lncRNA is often found by RNA sequencing or in a CRISPR screen. AUMlnc sdASO knocks it down, and the phenotype of the knockdown is screened.

  • lncRNA in cis effects

    Some lncRNAs regulate neighboring genes on the DNA (e.g., by recruiting chromatin modifiers). Using AUMlnc sdASO to degrade the lncRNA can test whether the presence of the RNA (not the act of transcription alone) is required for that regulation.

  • Target validation in disease models

    A growing number of lncRNAs are being implicated in diseases. AUMlnc sdASO is used in disease models, to see what silencing the lncRNA does.

  • Chromatin and nuclear body analysis

    AUMlnc sdASO is designed against an architectural lncRNA, such as NEAT1 for paraspeckles or MALAT1 for nuclear speckles. The effect of its loss on nuclear structure is then assessed.

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 AUMlnc sdASOs is 5-20 μM. For AUMlnc toASO, delivered with a transfection reagent, the recommended range is 50-100 nM.

Where an AUMlnc sdASO is designed to block a functional domain, the lncRNA may not be fully degraded. The effect is then assessed by a functional readout rather than by the lncRNA level.

In the literature

AUMlnc sdASO in published studies

  • Harshe et al. · Nature Communications · 2020

    Endogenous antisense RNA curbs CD39 expression in Crohn’s disease

    Self-delivering AUMsilence sdASOs against an antisense long non-coding RNA at the CD39 locus restored CD39 in Crohn's disease T cells and lowered disease activity, histology score and colon shortening in humanized mice.

    The study on this siteRead the paper

  • Nath et al. · Proceedings of the National Academy of Sciences · 2019

    Discovering long noncoding RNA predictors of anticancer drug sensitivity beyond protein-coding genes

    AUMlnc sdASOs against EGFR-AS1 and MIR205HG, added straight to the medium of two human lung cancer lines, slowed growth and shifted the EGFR isoform ratio, turning two computationally predicted erlotinib biomarkers into functional ones.

    The study on this siteRead the paper
All publications using AUM BioTech products

At the bench

Protocol, controls and what arrives

Add to culture medium or inject in vivo. The protocol, the controls and the How much to order page are written for this product.

View the protocolControls and validationHow much to orderHow to cite
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.

Related

Order AUMlnc sdASO

Sequences are designed using the AUMsilence platform. Our scientific team is available before ordering to discuss the target and the cell type.

Request a quoteHow to citeView protocols

For research use only. Not for use in diagnostic or therapeutic procedures.