Both siRNA and antisense oligonucleotides (ASOs) are chemically modified single- or double-stranded nucleic acids that silence gene expression. They dominate the oligonucleotide therapeutics landscape and are often confused. Here’s a compact side-by-side.
Mechanism
siRNA: 19-21 nt double-stranded RNA. The guide strand loads into AGO2 within the RISC complex; AGO2 slices the target mRNA between guide positions 10 and 11. Catalytic — one loaded RISC can cleave many transcripts.
ASO: 12-25 nt single-stranded, chemically modified oligonucleotide. Multiple mechanisms:
- Gapmer design: DNA gap flanked by modified wings (2’-MOE, LNA) → RNase H1 binds the RNA-DNA duplex and cleaves the mRNA. Also catalytic.
- Steric-block ASO: fully modified sugar (2’-MOE, PMO); no RNase H1 recruitment. Blocks splicing, translation initiation, or miRNA binding.
- Splice-switching ASO (e.g. nusinersen for SMA, eteplirsen for DMD): steric-block that redirects pre-mRNA splicing to include or exclude a specific exon.
Chemistry
| Feature | siRNA | ASO |
|---|---|---|
| Strandedness | Double | Single |
| Backbone | Phosphodiester (with PS at ends) | Extensive PS backbone |
| 2’ sugar | 2’-OMe, 2’-F | 2’-MOE, 2’-OMe, LNA, PMO |
| Length | 19-21 nt duplex | 12-25 nt |
| Typical dose | 0.1-3 mg/kg (LNP); ≤ 1 mg/kg (GalNAc) | 5-20 mg/kg (parent PS/MOE); much lower with GalNAc-conjugation |
Delivery
siRNA requires help — the molecule is too hydrophilic and negatively charged to cross the cell membrane efficiently. Options:
- GalNAc conjugation for hepatocytes (see RNAi article).
- LNP encapsulation for systemic use (patisiran).
- Emerging conjugates for muscle, adipose, tumor.
ASOs are more forgiving. Naked PS/MOE ASOs achieve meaningful cellular uptake in many tissues after subcutaneous or intravenous dosing — no encapsulation needed. Modern ASOs are increasingly GalNAc-conjugated for the same hepatocyte-targeting benefit as siRNA.
Intrathecal ASOs (nusinersen for SMA, tofersen for SOD1-ALS) reach the CNS by direct lumbar delivery — no equivalent siRNA is approved for CNS yet.
Approved examples
siRNA (all liver-targeted): patisiran, givosiran, lumasiran, inclisiran, vutrisiran, nedosiran.
ASO (broader tissue reach):
- Fomivirsen — CMV retinitis (first approved ASO, since withdrawn).
- Mipomersen — familial hypercholesterolemia (withdrawn from most markets due to hepatotoxicity).
- Nusinersen — SMA (intrathecal, splice-switching).
- Eteplirsen, golodirsen, viltolarsen, casimersen — Duchenne muscular dystrophy (exon-skipping).
- Inotersen — hATTR amyloidosis.
- Tofersen — SOD1-ALS.
- Volanesorsen — familial chylomicronemia.
Note the pattern: ASOs get you to more tissues (muscle, CNS, systemic), while siRNA has an unmatched liver-selective platform via GalNAc.
Duration and dosing
- siRNA (GalNAc): dosed subcutaneously every 3-6 months. Extremely durable.
- ASO (GalNAc): dosed subcutaneously monthly to quarterly.
- Parent PS/MOE ASO: weekly to monthly, with variable half-life by tissue.
- Intrathecal ASO (nusinersen): four loading doses in two months, then every four months.
Off-target profiles
Both have distinct off-target signatures:
- siRNA: seed-mediated miRNA-like repression of unintended 3’ UTRs; potential innate immune activation via TLR7/8.
- ASO gapmer: RNase H1-mediated cleavage of near-match transcripts; hepatotoxicity and thrombocytopenia in some patients.
- Steric-block ASO: generally cleaner off-target profile.
Both have converged on modern chemistry (2’-OMe/2’-F for siRNA; 2’-MOE/PMO for ASO) that substantially reduces immune activation.
When to pick which
| Scenario | Preferred modality |
|---|---|
| Liver-expressed target, need durable knockdown, chronic dosing | siRNA (GalNAc) |
| CNS target (needs intrathecal delivery) | ASO |
| Skeletal muscle target, splice modulation needed | ASO (exon-skipping) |
| Systemic target beyond liver, no LNP available | ASO |
| First-in-class discovery, want the shortest path to POC | ASO (faster to development-quality candidate) |
| Need catalytic knockdown at very low dose | siRNA |
Bottom line
siRNA and ASO are complementary, not competing. In practice, drug developers pick the modality that matches the target tissue and mechanism they need — sometimes running both in parallel discovery tracks. Understanding both is table-stakes for anyone working on oligonucleotide therapeutics.
Related reading: RNAi mechanism deep-dive, mRNA vaccine technology, and circular RNA for the emerging third RNA modality.
FAQ
Q. Can an ASO and an siRNA target the same disease gene?
A. Yes, and this is happening: multiple TTR-lowering drugs (inotersen ASO, patisiran and vutrisiran siRNAs) share the same target for hATTR amyloidosis. Each modality has different dosing intervals, delivery, and side-effect profiles.
Q. Which is more potent per dose?
A. siRNA generally shows greater potency per delivered molecule because AGO2 slicing is catalytic (one guide can cleave many targets), whereas RNase H1 cleavage in ASO mechanisms is also catalytic but less processive. Chemistry and delivery matter more than mechanism for real-world potency.
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