Antisense oligonucleotides — gapmers and steric blockers
Single-stranded phosphorothioate-rich ASOs for RNase H–mediated knockdown (gapmers) or sequence-specific binding without degradation (steric blockers). Chemistry, length and modification pattern are chosen to the target transcript, tissue and intended clinical dose.
16–22
nt gapmer core (typical)
2–5
PS linkage density bands
RNase H
gapmer mechanism
PO / 2'-MOE
steric blocker backbones
AS / IP / IV
common routes (indicative)
Gapmers vs steric blockers
Gapmers carry a central DNA or phosphorothioate DNA gap flanked by modified wings (commonly 2'-MOE or 2'-OMe). Hybridization to pre-mRNA or mRNA recruits RNase H to cleave the RNA strand while the ASO is largely spared, giving potent target reduction.
Steric blockers (including splice-switching ASOs) bind without recruiting RNase H. They block splice sites, reframe translation start, or interfere with miRNA access. Fully modified backbones (e.g. morpholino in a separate product line) or high-affinity sugar patterns support binding at lower catalytic turnover.
When to use a gapmer vs a steric blocker
Start from the biological effect you need; chemistry follows mechanism and tolerability.
| Goal | Preferred ASO class | Typical design notes |
|---|---|---|
| Lower mRNA / protein level | Gapmer | Central DNA gap 8–10 nt; 2'-MOE or cEt wings; full or partial PS backbone |
| Exon skipping / splice correction | Steric blocker | High-affinity wings; no RNase H-competent DNA gap; often uniform 2'-MOE or mixed PS |
| Translation repression (5' UTR) | Steric blocker | Shorter ASO acceptable if affinity is high; avoid RNase H recruitment at start codon |
| Upstream of miRNA site | Either | Gapmer if degradation desired; steric if occupancy alone is sufficient |
Figures are indicative industry-typical values. Lot- and project-specific data appear on the quotation and certificate of analysis.
Indicative ASO drug-substance attributes
Release tests are project-defined. Ranges reflect common therapeutic ASO programs.
Length
12–25 nt
Gapmers often 18–22 nt total
Gap
8–10 nt DNA
RNase H–competent stretch
Wings
2'-MOE, 2'-OMe or cEt
5 and 3 flanks typically symmetric
Backbone
Phosphorothioate (full or partial)
PS at terminal linkages common
Purity (RP-HPLC)
≥85–95%
Higher for GLP/GMP lots
Identity
LC-MS / MS
Mass confirms full-length modified sequence
Residual solvents
ICH Q3C
Per synthetic route
Figures are indicative industry-typical values. Lot- and project-specific data appear on the quotation and certificate of analysis.
Common ASO chemistry options
Wing chemistries
- 2'-O-methyl (2'-OMe)
- 2'-O-methoxyethyl (2'-MOE)
- constrained ethyl (cEt)
- 2'-fluoro (2'-F) in short motifs
- locked nucleic acid (LNA) in discrete positions
Backbone patterns
- Full phosphorothioate (PS)
- Partial PS with PO in selected linkages
- PS at 3' and 5' terminal linkages for nuclease resistance
Formulation-ready options
- Sodium salt (typical IV)
- Counter-ion exchange on request
- Lyophilized or solution per stability data
Typical ASO program flow
Design and in silico triage
Pick gap length, wing chemistry and PS pattern against off-target transcript homology and RNase H rules of thumb.
Research-grade synthesis and screening
Solid-phase amidite assembly, deprotection, one-step HPLC desalting or purification; cell or in vivo screening at mg scale.
Analytics lock
Confirm identity by high-resolution MS; define impurity reporting (n–1, n+1, isomers) and method suitability.
Scale-up and tox / clinical supply
Route refinement, stability, and cGMP path when the candidate advances — see NCE / CMC and GMP pages.
What you receive
- Lyophilized or liquid ASO with stated salt form and concentration
- Certificate of analysis: identity, purity, water content where applicable
- Mass spectrum and chromatogram traces on request
- Impurity summary (length variants, modification isomers) at defined reporting thresholds
- Storage and handling guidance (–20 °C typical for research material)
- Quote tied to scale, modification density and purity tier
Frequently asked questions
Gapmers include an RNase H–competent DNA gap and reduce RNA by cleavage. Steric blockers bind without recruiting RNase H and act by blocking splicing, translation or miRNA access.
Related
Backbone & Sugar Modifications
Phosphorothioate (PS) backbones and 2'- sugar patterns (2'-OMe, 2'-F, 2'-MOE, LNA) tune nuclease resistance, affinity, innate immunity and tolerability. Modification maps are applied per position during solid-phase synthesis.
View detailsPeptide & Lipid Conjugates
Oligos linked to cell-penetrating peptides (CPP), peptide-PMO (PPMO) constructs, cholesterol and other lipid anchors, and miscellaneous delivery ligands. Conjugation chemistry preserves oligo integrity while enabling uptake in muscle, CNS and other tissues beyond GalNAc-liver programs.
View detailsGalNAc Conjugates
N-acetylgalactosamine (GalNAc) ligands conjugated to siRNA, ASO or antisense payloads route uptake via asialoglycoprotein receptor (ASGPR) on hepatocytes. Tri-antennary GalNAc clusters are the dominant motif for systemic subcutaneous dosing in modern RNAi programs.
View detailsOligo NCE / CMC Development
Chemistry, manufacturing and controls for oligonucleotide new chemical entities: route scouting on solid-phase synthesizers, impurity fate studies, specification setting, stability protocols and regulatory-ready documentation — without implying a specific plant configuration.
View detailsClinical & Commercial GMP
GMP manufacturing of oligonucleotide drug substance for clinical trials and commercial supply: batch records, validated release and stability methods, change control, and documentation packages suitable for regulatory filing — described at capability level without inventing facility certifications.
View detailsReady to specify this for your program?
Share sequence, scale and documentation needs. We reply with indicative specs and a project-specific quotation.