Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

RNA Interference01:23

RNA Interference

27.7K
RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
27.7K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Enhanced splicing modulation by NMA-modified antisense oligonucleotides.

Nucleic acids research·2026
Same author

Six-year reconviction follow-up of a medium-secure cohort.

BJPsych bulletin·2026
Same author

NPAS4 refines spatial and temporal firing in CA1 pyramidal neurons.

bioRxiv : the preprint server for biology·2026
Same author

Reduction of RAD23A extends lifespan and mitigates pathology in a mouse model of TDP-43 proteinopathy.

Nature communications·2026
Same author

Treating a Childhood Cancer Survivor With Severe Aortic and Mitral Insufficiency Using TAVR and TMVR.

JACC. Case reports·2025
Same author

Synthesis, Incorporation, and Translation Properties of Threose Nucleic Acid Modified Trinucleotide Cap Analogs.

ACS omega·2025

Related Experiment Video

Updated: Jan 6, 2026

Author Spotlight: Cost-Effective Transcriptomic Drug Screening - Unlocking New Targets
06:40

Author Spotlight: Cost-Effective Transcriptomic Drug Screening - Unlocking New Targets

Published on: February 23, 2024

1.7K

A Workflow for Transcriptome-Wide Assessment of Antisense Oligonucleotide Selectivity.

Sagar S Damle1, Andy Watt1, Steven Kuntz2

  • 1Ionis Pharmaceuticals, Carlsbad, CA, USA.

Nucleic Acid Therapeutics
|September 29, 2025
PubMed
Summary

Developing concentration-response digital gene expression (CR-DGE) allows for accurate assessment of antisense oligonucleotide (ASO) selectivity. This method enhances the identification of selective ASOs for therapeutic development.

Keywords:
ASO selectivityantisense oligonucleotideconcentration-response assaydigital gene expressionoff-target effects

More Related Videos

An Oligonucleotide-based Tandem RNA Isolation Procedure to Recover Eukaryotic mRNA-Protein Complexes
09:45

An Oligonucleotide-based Tandem RNA Isolation Procedure to Recover Eukaryotic mRNA-Protein Complexes

Published on: August 18, 2018

11.5K
In Vitro Selection of Engineered Transcriptional Repressors for Targeted Epigenetic Silencing
10:44

In Vitro Selection of Engineered Transcriptional Repressors for Targeted Epigenetic Silencing

Published on: May 5, 2023

1.8K

Related Experiment Videos

Last Updated: Jan 6, 2026

Author Spotlight: Cost-Effective Transcriptomic Drug Screening - Unlocking New Targets
06:40

Author Spotlight: Cost-Effective Transcriptomic Drug Screening - Unlocking New Targets

Published on: February 23, 2024

1.7K
An Oligonucleotide-based Tandem RNA Isolation Procedure to Recover Eukaryotic mRNA-Protein Complexes
09:45

An Oligonucleotide-based Tandem RNA Isolation Procedure to Recover Eukaryotic mRNA-Protein Complexes

Published on: August 18, 2018

11.5K
In Vitro Selection of Engineered Transcriptional Repressors for Targeted Epigenetic Silencing
10:44

In Vitro Selection of Engineered Transcriptional Repressors for Targeted Epigenetic Silencing

Published on: May 5, 2023

1.8K

Area of Science:

  • Molecular Biology
  • Genomics
  • Drug Discovery

Background:

  • Antisense oligonucleotides (ASOs), specifically gapmer ASOs, are effective in downregulating therapeutic target gene expression by recruiting RNase H1.
  • Identifying selective ASOs that target specific transcripts without affecting unintended ones is crucial but challenging due to suboptimal in silico off-target prediction.
  • Nonselective ASOs can lead to unintended gene silencing, highlighting the need for robust methods to assess ASO selectivity.

Purpose of the Study:

  • To develop and validate an experimental workflow for assessing the selectivity of gapmer antisense oligonucleotides (ASOs).
  • To improve the prediction of off-target effects and enhance the identification of selective ASOs for therapeutic applications.

Main Methods:

  • Developed a novel experimental workflow named concentration-response digital gene expression (CR-DGE).
  • CR-DGE involves treating cells with ASOs at increasing concentrations and measuring transcriptome-wide expression changes using 3'Tag-Seq.
  • Analyzed expression data to identify genes exhibiting concentration-responsive knockdown, indicating ASO activity.

Main Results:

  • CR-DGE demonstrated high reproducibility and greater sensitivity in identifying concentration-responsive genes compared to conventional single-concentration assays.
  • Application of CR-DGE to a panel of gapmer ASOs revealed a spectrum of ASO selectivity.
  • The method successfully identified genes responsive to ASO treatment in a concentration-dependent manner.

Conclusions:

  • CR-DGE is an effective tool for evaluating the selectivity of gapmer ASOs.
  • This workflow provides a valuable approach for researchers and developers in optimizing ASO-based therapeutics.
  • Enhanced assessment of ASO selectivity using CR-DGE can lead to safer and more effective gene-silencing strategies.