Login / Register Order My Items
Contact Us
800.227.0627
Contact Us Quote Order Login / Register

Antisense Oligonucleotides — ASO, SSO & Gapmers

Design, chemistries, delivery, and QC for antisense therapeutics and research tools: RNase H‑active gapmers, steric‑block SSOs, and advanced conjugates.

ISO 9001 / 13485 RUO → GMP-like scale Texas Facilities Full QC & Analytics
Overview Mechanism Chemistry Delivery QC Design Notes FAQ Speak

Overview

Bio-Synthesis designs and manufactures antisense oligonucleotides (ASOs)—including RNase H-active gapmers and steric-block SSOs—with proven chemistries (PS/PM/PN backbones; 2′-mods like 2′-OMe, 2′-F, MOE, LNA/BNA, cEt) and targeted conjugates (GalNAc, lipids, CPPs). With 45+ years of experience, ISO 9001/13485 quality systems, and RUO→GMP-like workflows, we deliver end-to-end support: sequence design, synthesis, conjugation, purification, analytical QC (HPLC/UPLC, LC-MS, UV/OD, endotoxin, residuals), formulation, and compliant documentation—scaled from discovery to preclinical supply.

From Bench to Kilo-Scale

Seamless scale-up of ASOs and SSOs—from µmol screening lots to kilogram-class batches—with ISO 9001/13485 controls and GMP-like production files.

  • µmol discovery → mmol pilots → gram/kilogram production
  • Purification tuned to chemistry (HPLC/UPLC) + full identity/purity QC (LC-MS, OD260)
  • Custom formulation, vials/plates, barcoding & documentation for tech transfer
Speak to a Scientist Explore Modifications

Bench → Kilo

RUO → GMP-like workflows

Texas facilities • ISO 9001/13485

Chemistry Toolkit

Backbone

Stabilize against nucleases and tune protein interactions.

Hide products and Notes
Modification Description Application Code
Phosphorothioate (PS) Sulfur substitution for nuclease resistance ASO/Gapmer, Antagomir [PS]
Methylphosphonate (PM) Non‑ionic methyl substitution Neutral backbone; PK/uptake trade‑off [PM]
Phosphoramidate (PN) P–N linkage variant Stability; altered RNase interactions [PN]
Boranophosphate (BPh) Boron substitution Metabolic stability; nuclease resistance [BPh]
  • PS: Partial or terminal PS common for gapmers; uniform PS typical in single‑stranded formats.
  • PM/PN: Evaluate potency vs uptake and RNase H compatibility.
  • BPh: Consider for added resistance; confirm by LC‑MS and activity assays.

Modified Sugar and Base

Increase affinity (Tm), stability, and shape activity windows.

2′‑ModsBridgedBaseOther
Hide products and Notes
Modification Description Application Code
2′‑Modifications
DNA 2′‑deoxyribose backbone (RNase H‑compatible) Gapmer cores; probes [DNA]
RNA Ribose backbone with 2′‑OH SSO, research tools [RNA]
2′‑OMe RNA 2′‑O‑methyl substitution Stability; immune attenuation [2OMe‑RNA]
2′‑MOE RNA 2′‑O‑methoxyethyl substitution Uniform SSO; anti‑miR [MOE‑RNA]
2′‑Fluoro RNA 2′‑F substitution Potency; nuclease resistance [2F‑RNA]
2′‑O‑Arabino RNA Arabino‑configured 2′‑O substitution Affinity tuning; exploration [Ara‑RNA]
2′‑O‑Propargyl RNA Alkyne at 2′‑O Click chemistry handle [2O‑PRG‑RNA]
2′‑O‑NMA RNA 2′‑O‑(N‑methylacetamide) Stability; polarity [2O‑NMA‑RNA]
Bridged Nucleic Acid
LNA (2′,4′‑BNA) Locked ribose (2′‑O,4′‑C bridge) High Tm wings; SSO [LNA]
cEt Constrained ethyl bridge Affinity/safety balance [cEt]
ENA Ethylene‑bridged nucleic acid Affinity↑ (exploratory) [ENA]
BNA‑NC (N‑Me) Amide‑bridged (N‑methyl) analog Affinity; experimental [BNA‑NC]
Base Modification
5‑Methyl dC 5‑methyl‑2′‑deoxycytidine Stability; epigenetic mimic [5Me‑dC]
5‑Methyl rC 5‑methyl‑cytidine (RNA) Stability; SSO [5Me‑rC]
N4‑Ethyl C N4‑ethyl‑cytosine Affinity tuning [N4Et‑C]
N6‑Methyl A N6‑methyl‑adenine Stability; motif studies [N6Me‑A]
2‑Amino A 2‑amino‑adenine Affinity↑; pairing studies [2NH2‑A]
8‑oxo G 8‑oxoguanine lesion analog Damage/repair studies [8oxo‑G]
7‑deaza A 7‑deaza‑adenine Structure/probing [7dz‑A]
7‑deaza G 7‑deaza‑guanine Structure/probing [7dz‑G]
Pseudouridine Ψ base (C‑glycosidic uridine) RNA stability; translation [Ψ]
Propyne dC 5‑propynyl‑dC Affinity↑; qPCR probes [Prop‑dC]
Propyne dU 5‑propynyl‑dU Affinity↑; qPCR probes [Prop‑dU]
Other Modified Base
NPPOC Photolabile base analog / group Photo‑control; caging [NPPOC]
TMO Protected base analog (TMO) Chemistry exploration [TMO]
Abasic (AP site) Non‑informational spacer Controls; structure studies [AP]
L‑DNA / L‑RNA Enantiomeric nucleic acids Nuclease resistance; decoys [L‑DNA]/[L‑RNA]
D‑ / R‑Inosine Enantiomeric inosine variants Binding/structural studies [D‑Ino]/[R‑Ino]
UNA Unlocked nucleic acid Flexibility; structure–function [UNA]
GNA Glycol nucleic acid Simplified backbone research [GNA]
2′–5′ Linked Oligonucleotides 2′–5′ internucleotide linkages Stability/pathway studies [2‑5′‑Link]
  • Gapmers: Typical 5–10 DNA gap flanked by 2–5 modified nucleotides (LNA/2′‑OMe/2′‑F) per wing.
  • SSO: Favor higher‑affinity (LNA/MOE) uniformly; no RNase H requirement.

Termini & Handles

Protect from exonucleases, enable labeling & conjugation.

Hide products and Notes
Modification Description Application Code
3′‑InvdT / 3′‑C3 Exonuclease block ASO/SSO termini [3INVdT] / [3C3]
5′‑Amino / 5′‑Thiol / 5′‑Azide Reactive handles Labeling, click chemistry [5NH2]/[5SH]/[5N3]
5′‑Phosphate Terminal phosphate Biology workflows [5P]

Targeting & Update Delivery Conjugates

Enhance biodistribution with hepatocyte targeting or hydrophobic/peptidic conjugates.

Hide products and Notes
Conjugate Description Application Code
GalNAc (tri‑antenna) ASGPR ligand Hepatocyte targeting (SC dosing) [GalNAc3]
GalNAc (tetra‑antenna) Four‑arm GalNAc Enhanced avidity for liver delivery [GalNAc4]
Mannose Mannose receptor ligand Macrophage/DC targeting [Man]
Lactose Lectin‑binding disaccharide Lectin‑mediated uptake [Lac]
Cholesterol Hydrophobic sterol Uptake enhancement [Chol]
PC‑Cholesterol Cholesterol + phosphocholine Membrane stability; liver delivery [PC‑Chol]
Tocopherol Vitamin E derivative Antioxidant stability; robustness [Toco]
DHA / EPA Omega‑3 fatty acids CNS‑leaning biodistribution; uptake [DHA]/[EPA]
Stearic / Palmitic / Oleic C18:0 / C16:0 / C18:1 fatty acids Hydrophobic anchoring [SA]/[PA]/[OA]
Diacylglycerol (DAG) Lipid anchor Membrane association; trafficking [DAG]
Squalene Highly hydrophobic terpenoid Self‑assembly into particles [SQL]
Phosphatidylethanolamine Lipid headgroup Anchoring; endosomal release [PE]
Ceramide Sphingolipid Endolysosomal trafficking [Cer]
2′‑O‑C16 A/C/G/U Hexadecyl lipidated nucleosides Membrane interaction; extrahepatic delivery [C16‑A/C/G/U]
2′‑O‑Stearyl (C18) Stearyl‑modified nucleosides Hydrophobic anchoring [C18‑2‑O‑A/C/G/U]
2′‑O‑Oleyl (C18:1) Oleyl‑modified nucleosides Delivery efficiency; flexibility [C18:1‑2‑O‑A/C/G/U]
CPPs (TAT/R9/Penetratin) Cell‑penetrating peptides Cellular delivery [CPP‑TAT]/[CPP‑R9]/[CPP‑PEN]
RGD / iRGD Integrin‑binding peptides Tumor homing and penetration [RGD]
Angiopep‑2 LRP1‑binding peptide Brain delivery across BBB [Ang2]
RVG29 Rabies glycoprotein peptide Neuron targeting [RVG29]
NLS Peptides Nuclear localization sequence Nuclear delivery (AON/SSO) [NLS]
Doxorubicin (DOX) conjugate Anthracycline payload APT/ASO drug conjugates via cleavable linkers [Drug‑DOX]
Camptothecin (CPT) conjugate Topoisomerase inhibitor Tumor‑targeted oligo conjugates [Drug‑CPT]
Methotrexate (MTX) conjugate Antimetabolite payload Folate/aptamer‑guided delivery [Drug‑MTX]
Folate Vitamin B9 derivative Folate receptor‑positive tumors [FA]
Vitamin B12 (Cobalamin) Receptor ligand Receptor‑mediated uptake [B12]
Antibody–Oligo Conjugate (AOC) mAb/oligo via maleimide/thiol or click Cell‑type‑specific delivery [AOC]
Albumin‑binding tag Serum albumin interaction PK extension [ABP]
Short PEG / TEG Hydrophilic spacer Conjugate geometry; solubility [TEG]
Cleavable Disulfide Redox‑sensitive linker Release in cytosol [SS]
Val‑Cit‑PAB Cathepsin‑cleavable linker Enzyme‑triggered release [Val‑Cit‑PAB]
Hydrazone pH‑sensitive linker Endosomal release [Hydrazone]
Photocleavable (PC) Spacer Light‑triggered linker Controlled release [PC‑Spacer]
Multivalent Trebler / Doubler 3‑ or 2‑arm scaffolds Valency increase; avidity [Trebler]/[Doubler]
PAMAM Dendrimer Branched polymer scaffold High payload density [PAMAM]
  • Placement: Prefer 3′ end with short PEG/TEG spacers to preserve activity.
  • Balance: Avoid over‑lipidation that could hinder uptake/release dynamics.

QC & Release

Analytics

Hide products and Notes
Assay Purpose Notes
LC‑MS (ESI) Mass identity Confirms full‑length product; detects major adducts
HPLC/UPLC Purity Ion‑pair RP or AEX tuned to chemistry
UV/OD260 Quantitation Standardized extinction coefficients; CoA reporting
Endotoxin (opt.) Safety (in vivo) Recommended for animal studies
Moisture/Residuals (opt.) Formulation readiness Supports stability & regulatory files
Bioburden (opt.) Microbial load Recommended for in vivo, sterile, or sensitive applications; reportable units on request.
Sodium Content (opt.) Inorganic ion content Supports formulation and buffer compatibility; report as % or ppm.
Residual Chemicals (opt.) Residual solvents/reagents Confirms process clearance of synthesis reagents and byproducts.
Time‑Scheduled Stability (opt.) Degradation & potency over time Stability at planned intervals (e.g., 1–3–6–12 months) under defined conditions.

Why Choose Bio‑Synthesis

  • 45+ years building ASO/SSO platforms that translate from in vitro to in vivo.
  • End‑to‑end: design → synthesis → conjugation (GalNAc, lipids, CPPs) → purification → QC → formulation.
  • Scale without re‑engineering — µmol screens to kilo‑class with consistent methods and files.
  • Quality you can prove — ISO 9001/13485, RUO→GMP‑like, HPLC/UPLC + LC‑MS release, optional endotoxin/residuals.
  • Targeted delivery options — GalNAc for liver and lipid/CPP strategies for extrahepatic tissues.
45+ Years
ISO 9001 / 13485
RUO → GMP‑like
Bench → Kilo

Mechanism & Formats

RNase H Gapmers (ASO)

DNA “gap” flanked by modified wings (e.g., LNA/2′‑OMe/2′‑F). Hybridization recruits RNase H to degrade target RNA.

Steric‑Block SSO

Non‑cleaving antisense (e.g., LNA/MOE) modulates splicing or blocks translation by steric hindrance—no RNase H.

Antagomirs / miRNA Inhibitors

Heavily modified single‑strands (2′‑OMe/MOE/PS; sometimes cholesterol) to inhibit miRNAs in cells or in vivo.

Design Notes

Design Notes — ASO, SSO & Gapmers

Gapmer Architecture
  • 5–10 nt DNA gap flanked by 2–5 modified nts (LNA/2′‑OMe/2′‑F) per wing.
  • Use partial or terminal PS; consider 3′ caps for exonuclease resistance.
SSO Placement
  • Target splice donor/acceptor, ESE/ESS motifs for exon inclusion/exclusion.
  • Favor LNA/MOE for uniform, high‑affinity steric blocking (no RNase H).
Delivery Strategy
  • GalNAc for hepatocytes; cholesterol/fatty acids/CPPs for extrahepatic use.
  • Add short PEG/TEG spacers to preserve activity and tune exposure.
Safety & Immunity
  • 2′‑OMe/2′‑F reduce innate immune recognition; limit heavy uniform PS.
  • Avoid high‑affinity content in seed‑like regions that can drive off‑targets.
Analytics & Readouts
  • LC‑MS, HPLC/UPLC, OD260 for release; qPCR/RT‑qPCR, splice‑switch assays for function.
  • Consider RNA‑seq for transcriptome‑wide on/off‑target assessment.
Manufacturability
  • Standardize 2–3 recipes, define QC early, choose scalable purification.
  • Document conjugate placement and spacer lengths for tech transfer.

Need help picking the optimal ASO/SSO or Gapmer design?

We’ll recommend modification patterns, gapmer dimensions, and conjugates aligned to your target and route.

Speak to a Scientist Browse All Modifications

FAQ

What’s the difference between gapmers and steric‑block SSOs?

Gapmers recruit RNase H to cleave target RNA; SSOs modulate splicing or block translation without cleavage. Choose based on biology and delivery route.

Which chemistries improve nuclease resistance?

Terminal/partial PS with 2′‑OMe/2′‑F patterning; LNA/cEt in wings for affinity. MOE is common in steric‑block designs.

Where should I place conjugates like GalNAc or cholesterol?

Prefer 3′ placement via short PEG/TEG spacer to preserve activity and control exposure.

What’s a good starting gapmer design?

5–10 DNA gap, 2–5 LNA/2′‑OMe/2′‑F per wing, terminal PS, and optional 3′ cap.

What ASO length should I start with?

Most RNase H gapmers are designed in the 14–20 nt range (with a 5–10 nt DNA gap). Steric‑block SSOs are commonly 18–25 nt. Final length should be guided by target accessibility, Tm, and off‑target analysis.

How many phosphorothioate (PS) linkages do I need?

For gapmers, terminal or partial PS is typical to balance stability and activity. Uniform PS can be used in some single‑stranded formats but may increase protein binding—evaluate empirically.

Which purification should I choose?

HPLC/UPLC is recommended for in vivo work and most SSO/gapmer programs. Desalting can be acceptable for early screening or RUO assays; we’ll recommend a route based on chemistry and use case.

How should I resuspend and store my ASO?

Use RNase‑free water or buffer (e.g., TE) to your desired concentration. Store aliquots at −20 °C (or 4 °C short‑term) and avoid repeated freeze‑thaw cycles. Protect from nucleases and light if dye‑labeled.

Can you help with target selection and off‑target assessment?

Yes—on request we can provide design support (motif screening, BLAST‑style checks, Tm estimates) and iterate on gapmer/SSO architectures to reduce off‑target risk while maintaining potency.

What information do you need for a quote?

Please share: sequence(s) 5′→3′, intended format (gapmer vs SSO), modifications (PS pattern, sugars like 2′‑OMe/2′‑F/LNA/MOE), any conjugates (GalNAc, Chol, PEG, CPP), scale, purification, and required QC.

Do you offer GMP manufacturing?

We support programs from RUO through ISO 9001/13485 with GMP‑like workflows and enhanced QC. If full GMP is required, we can discuss options and tech transfer paths.

What QC tests are available?

Standard release includes LC‑MS, HPLC/UPLC purity, and OD260. Optional tests include endotoxin, residual solvents/moisture, and method‑specific assays—all scoped to your application.

Where should I place conjugates like GalNAc or cholesterol?

Typically on the 3′ end via a short PEG/TEG spacer to preserve hybridization and tune exposure. Exact placement can be optimized per target and tissue.

Can you plate my oligos or provide custom formatting?

Yes—tubes, vials, and plates (with barcoding/labels) are available. We can standardize concentrations/volumes to streamline screening workflows.

Speak to a Scientist

Tell us about your conjugated-oligo project

Please avoid confidential details; we can arrange an NDA if needed.

You’ll receive a confirmation by email.
Email Instead

Why Choose Bio-Synthesis

Trusted by biotech leaders worldwide for over 40+ years of delivering high quality, fast and scalable synthetic biology solutions.

Greetings Researchers,

Please be advised that any information, guidelines, writeups, and oral/video/graphic content on our website are intended solely as general guidelines.
It is the researcher's sole responsibility to conduct thorough research on the designs of the products intended for their experiments before submitting
their designs to Biosynthesis for review of production feasibility.
Thank you for your understanding.

Quick Links