Small RNAs/Functional Genomics
Support and Educational Content

Antisense Oligonucleotides (ASOs)

Antisense oligonucleotides, or ASOs, are 15–25 nt DNA sequences designed to bind complementary RNA targets, ultimately facilitating their degradation. ASO technology provided the first oligonucleotide-based approach to disrupting gene expression and has been used in knockdown experiments, target validation, drug therapy, and other applications. More recently, ASOs are used to study the role of long noncoding RNAs (lncRNAs) in gene regulation.

Many lncRNAs are localized to the nucleus. Often, lncRNA loss-of-function studies use techniques, such as RNAi, that are less effective because the nucleus contains a low amount of the required enzymes. ASOs, however, are particularly useful for studying nuclear lncRNAs, because ASOs engage RNase H—an enzyme prevalent in the nucleus that binds and cleaves DNA/RNA heteroduplexes.

IDT scientists have done extensive research on this application. See the Related reading list below for publications describing their findings.

RNase H1

RNase H1 is an endogenous nuclease that binds DNA/RNA heteroduplexes and cleaves the RNA strand, leading to degradation. For its action, cellular RNase H1 requires the heteroduplex to contain a segment of unmodified (with either native or phosphorothiate linkages) DNA that is ≥6 bases.

Modifications providing in vitro and in vivo stability

We recommend modifying your ASO sequence for increased stability and binding affinity. The most widely used modifications are phosphorothioate (PS) bonds, which are added throughout the oligonucleotide backbone to provide nuclease resistance. PS bonds have the potential to increase toxicity, which can be minimized by including an additional 2′-O-Methyl (2′OMe) RNA to create a “gapmer” ASO. DNA with these modifications display more nuclease resistance, lower toxicity, and increased hybridization affinities within cells and in vivo.

Ordering modified ASOs

To have phosphorothioate bonds added to your sequence, use an asterisk “*” between the bases.

2′-O-Methyl bases are represented with a lower case “m” in front of each base.



These oligos can be ordered with standard desalt or HPLC purification with Na+ salt exchange. The Na+ salt exchange is necessary to remove toxic salts from HPLC purification.

Click here to order IDT Antisense Oligonucleotides.

Related reading

Background educational articles

A new renaissance for antisense in the era of lncRNA—Noncoding RNAs such as lncRNAs, are much more prevalent in humans than protein-coding RNA. Find out how antisense oligonucleotides (ASO) and RNAi are being used to study the role of noncoding RNAs in gene regulation.

Tips for successful lncRNA knockdown: Design, delivery, and analysis of antisense and RNAi reagents—IDT research scientist Kim Lennox has been optimizing effective lncRNA knockdown with antisense and RNAi reagents. Read her tips for successful lncRNA knockdown.

Using antisense technologies to modulate noncoding RNA function—Learn about useful modifications and design considerations for producing effective antisense oligonucleotides.

Peer-reviewed publications from IDT scientists

Lennox KA, Behlke MA. (2015) Cellular localization of long non-coding RNAs affects silencing by RNAi more than by antisense oligonucleotides. Nucleic Acids Res, doi: 10.1093/nar/gkv1206.—IDT researchers compare the effectiveness of ASOs and RNAi to suppress lncRNAs expressed in the nucleus vs lncRNAs expressed in the cytoplasm.
Lennox KA, Owczarzy R et al. (2015) Improved performance of anti-miRNA oligonucleotides using a novel non-nucleotide modifier. Molecular Therapy—Nucleic Acids, 2:e117; doi:10.1038/mtna.2013.46.—IDT researchers identify non-nucleotide modifiers that facilitate AMO blocking of miRNA function in vitro at low nanomolar concentrations. These modified AMOs show high specificity, and have low toxicity in cell culture.

Fellow researchers using IDT ASOs in a unique application

Gao QQ, Wyatt E, et al. (2015) Reengineering a transmembrane protein to treat muscular dystrophy using exon skipping. J Clin Invest, doi:10.1172/JCI182768.—This paper describes how antisense oligonucleotides can be used for exon skipping, bypassing premature stop codons in the target RNA that carries mutations resulting in disease, and restoring reading frame disruption.

Author: Ellen Prediger, PhD, is a senior scientific writer at IDT

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