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ASO, SSO & Gapmer Oligonucleotide Manufacturing

Advanced antisense oligonucleotide synthesis with scalable chemistry, purification, analytical QC and documentation support from discovery through kilo-class production.

Bench → Kilo Production ISO 9001:2015 / ISO 13485:2016 U.S. Facilities - Texas HPLC/UPLC • LC-MS • CoA RUO → GLP/GMP-Aligned Support
Build a Scale-Up Plan Choose ASO Platform
Overview Bench to Kilo ASO Platforms Chemistry Toolkit Workflow QC Applications FAQ Contact Recommended Reading
Overview & Manufacturing Pathway

Manufacturable Antisense Designs, Not Just Research Oligos

ASO, SSO and gapmer oligonucleotides are RNA-targeting constructs used for RNase H-mediated knockdown, splice modulation, steric blocking and therapeutic-development research. The strongest programs are designed from the beginning around chemistry, mechanism, manufacturability, purification, analytics and scale.

Bio-Synthesis supports advanced antisense oligonucleotide programs across PS DNA, 2′-OMe, 2′-F, 2′-MOE, LNA/BNA/cEt, terminal caps, GalNAc, lipid, peptide and other conjugation strategies. Our focus is practical: keep the design biologically effective while making the production route scalable from early discovery through gram and kilo-class supply.

Programs can include RNase H-active gapmers, steric-blocking ASOs, splice-switching SSOs, advanced modifications, conjugation, purification, release QC and documentation from discovery screening to kilo-class supply.

Bench-to-Kilo Manufacturing Pathway

Move from sequence screening to manufacturable antisense oligonucleotide supply with scale-matched purification, analytics and project files.

01

Discovery Screens

µmol lots, multiple sequences, rapid design iteration, basic purity and identity QC.

02

Lead Confirmation

Higher-purity lots, final chemistry pattern, conjugate position and functional controls.

03

Pilot Production

mg to gram supply, scalable purification route and method consistency review.

04

Gram / Kilo-Class

Large-scale synthesis, optimized purification, in-process controls and release files.

05

Tech Transfer Ready

CoA, analytical package, formulation, packaging, labeling and documentation support.

µmol

Screening lots

mg–g

Pilot supply

Kilo

Production pathway

QC

HPLC/UPLC + LC-MS

Platform Selection

Choose the Right Antisense Platform

Organize the page around mechanism first. Gapmers, SSOs and steric blockers require different chemistry, length, purification and analytical expectations.

Gapmer ASO

RNase H

Designed with modified wings and a central DNA gap to recruit RNase H for RNA degradation.

  • Common 14–22 nt designs
  • LNA/BNA/cEt or 2′-MOE wings
  • Central DNA gap for RNase H
  • PS backbone and terminal protection

Splice-Switching SSO

Splicing

Steric-blocking designs that redirect exon inclusion, exon skipping or splice correction without RNase H cleavage.

  • Often 18–30 nt depending on target
  • 2′-MOE, 2′-OMe, PMO, PNA or LNA options
  • Exon/intron motif targeting
  • Delivery strategy reviewed early

Steric-Blocking ASO

Blocker

Designed to bind RNA and block translation, processing, protein binding or RNA structure without cleavage.

  • Fully or highly modified formats
  • No central DNA gap required
  • Affinity and mismatch tuning
  • Useful for non-cleaving mechanisms
Chemistry Architecture

Modification Strategy for Potency, Stability and Scale

The best chemistry is not always the most complex chemistry. The best chemistry is the one that supports the mechanism, survives the application environment and can be manufactured consistently.

ASO / SSO / Gapmer Chemistry Selection

Use this table as a starting framework before final sequence review, purification selection and scale planning.

Common antisense oligonucleotide chemistry options.

Chemistry Primary Role Best Fit Manufacturing Note
Phosphorothioate (PS) Nuclease resistance, exposure and protein interaction tuning ASO, gapmer, SSO terminal or full-backbone designs Define partial vs full PS pattern early for scale consistency
2′-OMe / 2′-F Stability, immune-signal reduction and RNA-binding support SSO, siRNA-like designs, aptamer/ASO hybrids Good for systematic screening and manufacturable patterns
2′-MOE Balanced stability, affinity and steric-blocking behavior SSO and gapmer wings Widely used in therapeutic-style ASO optimization
LNA / BNA / cEt High-affinity binding and shorter potent designs Gapmer wings, high-affinity ASO, probe-like constructs Use selectively to manage off-target binding and synthesis complexity
PMO / PNA Neutral, highly nuclease-resistant steric blocking Splice modulation and difficult steric-blocking targets Plan delivery, solubility and analytical strategy early
GalNAc / Lipid / Peptide Targeting, uptake and tissue-exposure strategy Liver targeting, extrahepatic delivery and receptor-mediated uptake Conjugate placement and linker length must be documented

Design Guide by Function

Preserve the current useful guidance, but make it faster to scan.

Need RNase H cleavage
Gapmer with central DNA gap
Need splice modulation
SSO / PMO / PNA / 2′-MOE
Need serum stability
PS + 2′ chemistry + end caps
Need high affinity
LNA/BNA/cEt placement
Need liver targeting
GalNAc-conjugated ASO
Need extrahepatic delivery
Lipid, peptide or ligand conjugate
Need scale-up
Standardize chemistry and purification early
Need release package
Contact Bio-Synthesis for method-specific or bundled QC requests
Chemistry Toolkit

ASO Chemistry Toolkit: What Bio-Synthesis Offers

These are listed as serviceable chemistry options, not just design concepts. The tab layout keeps the page organized while preserving the detailed live-site toolkit information.

Explore available antisense modifications, conjugates and delivery chemistries →

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]
Category Modification Description Application Code
2′ Mods DNA 2′-deoxyribose backbone, RNase H-compatible Gapmer cores, probes [DNA]
2′ Mods RNA Ribose backbone with 2′-OH SSO, research tools [RNA]
2′ Mods 2′-OMe RNA 2′-O-methyl substitution Stability; immune attenuation [2OMe-RNA]
2′ Mods 2′-MOE RNA 2′-O-methoxyethyl substitution Uniform SSO; anti-miR [MOE-RNA]
2′ Mods 2′-Fluoro RNA 2′-F substitution Potency; nuclease resistance [2F-RNA]
2′ Mods 2′-O-Arabino RNA Arabino-configured 2′-O substitution Affinity tuning; exploration [Ara-RNA]
2′ Mods 2′-O-Propargyl RNA Alkyne at 2′-O Click chemistry handle [2O-PRG-RNA]
2′ Mods 2′-O-NMA RNA 2′-O-(N-methylacetamide) Stability; polarity [2O-NMA-RNA]
Bridged LNA / 2′,4′-BNA Locked ribose with 2′-O,4′-C bridge High-Tm wings; SSO [LNA]
Bridged cEt Constrained ethyl bridge Affinity / safety balance [cEt]
Bridged ENA Ethylene-bridged nucleic acid Affinity increase; exploratory [ENA]
Bridged BNA-NC (N-Me) Amide-bridged N-methyl analog Affinity; experimental [BNA-NC]
Base 5-Methyl dC 5-methyl-2′-deoxycytidine Stability; epigenetic mimic [5Me-dC]
Base 5-Methyl rC 5-methyl-cytidine RNA Stability; SSO [5Me-rC]
Base N4-Ethyl C N4-ethyl-cytosine Affinity tuning [N4Et-C]
Base N6-Methyl A N6-methyl-adenine Stability; motif studies [N6Me-A]
Base 2-Amino A 2-amino-adenine Affinity increase; pairing studies [2NH2-A]
Base 8-oxo G 8-oxoguanine lesion analog Damage / repair studies [8oxo-G]
Base 7-deaza A 7-deaza-adenine Structure / probing [7dz-A]
Base 7-deaza G 7-deaza-guanine Structure / probing [7dz-G]
Base Pseudouridine C-glycosidic uridine base RNA stability; translation [Ψ]
Base Propyne dC 5-propynyl-dC Affinity increase; qPCR probes [Prop-dC]
Base Propyne dU 5-propynyl-dU Affinity increase; qPCR probes [Prop-dU]
Other NPPOC Photolabile base analog / group Photo-control; caging [NPPOC]
Other TMO Protected base analog Chemistry exploration [TMO]
Other Abasic AP site Non-informational spacer Controls; structure studies [AP]
Other L-DNA / L-RNA Enantiomeric nucleic acids Nuclease resistance; decoys [L-DNA]/[L-RNA]
Other D-/R-Inosine Enantiomeric inosine variants Binding / structural studies [D-Ino]/[R-Ino]
Other UNA Unlocked nucleic acid Flexibility; structure-function [UNA]
Other GNA Glycol nucleic acid Simplified backbone research [GNA]
Other 2′–5′ Linked Oligonucleotides 2′–5′ internucleotide linkages Stability / pathway studies [2-5′-Link]
Modification Description Application Code
3′-InvdT / 3′-C3 Exonuclease-blocking terminal caps ASO / SSO termini [3INVdT] / [3C3]
5′-Amino Reactive amine handle Labeling, conjugation, surface attachment [5NH2]
5′-Thiol Reactive thiol handle Maleimide coupling, gold surfaces, protein/peptide conjugation [5SH]
5′-Azide Click-ready azide handle Click chemistry and bioorthogonal conjugation [5N3]
5′-Phosphate Terminal phosphate Biology workflows [5P]
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 / dendritic-cell targeting [Man]
Lactose Lectin-binding disaccharide Lectin-mediated uptake [Lac]
Cholesterol Hydrophobic sterol Uptake enhancement [Chol]
PC-Cholesterol Cholesterol plus 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 for AON / SSO [NLS]
Doxorubicin (DOX) Anthracycline payload Aptamer / ASO drug conjugates with cleavable linkers [Drug-DOX]
Camptothecin (CPT) Topoisomerase inhibitor Tumor-targeted oligo conjugates [Drug-CPT]
Methotrexate (MTX) 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 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 Spacer Light-triggered linker Controlled release [PC-Spacer]
Trebler / Doubler 3- or 2-arm scaffolds Valency increase; avidity [Trebler]/[Doubler]
PAMAM Dendrimer Branched polymer scaffold High payload density [PAMAM]
Production Workflow

Integrated Workflow for Scalable ASO Programs

A strong page should make customers feel that Bio-Synthesis can manage the entire path, not only synthesize an oligo.

01

Sequence & Target Review

Target transcript, isoforms, splice sites, GC content, off-target risk and manufacturability review.

02

Chemistry Pattern

Define gapmer wings, DNA gap, PS pattern, steric-blocking chemistry, caps and conjugate placement.

03

Synthesis & Conjugation

Solid-phase oligo synthesis plus GalNAc, lipid, peptide, PEG, clickable or other conjugation strategies.

04

Purification Route

HPLC, UPLC, IEX/RP methods, PAGE or custom purification matched to chemistry and scale.

05

Analytical QC

LC-MS identity, analytical HPLC/UPLC purity, OD260 quantitation and optional endotoxin/residual testing.

06

Formulation & Format

Dry, solution, tubes, vials, plates, barcoding, normalized concentration and custom packaging.

07

Documentation

CoA, analytical reports, batch records, chain-of-custody and tech-transfer support.

08

Scale-Up Continuity

Move from screening to pilot and gram/kilo production with consistent methods and files.

Quality & Release

QC and Release Testing for Development-Ready Supply

Start with the QC package that matches your project stage. The detailed release menu is available below as a collapsible reference, so the page stays shorter while still showing the depth of what Bio-Synthesis can support.

Common QC Packages by Stage

Use these examples as starting points. Final release criteria can be customized.

Screening Lots
OD260, analytical purity, optional MS identity
Lead Confirmation
HPLC/UPLC purity, LC-MS, CoA and sequence-specific documentation
In Vivo Research
LC-MS, HPLC/UPLC, OD260, endotoxin and optional bioburden
Conjugated Oligos
Identity, purity, conjugate confirmation and residual chemical review
Formulated Lots
Moisture, sodium/counterion, pH, solubility and stability support
Gram / Kilo Lots
Scale-matched release files, batch documentation and optional custom panels
Stability Programs
Time-scheduled stability under defined storage and stress conditions
Not Listed?
Contact Bio-Synthesis for method-specific or bundled QC requests

Expanded QC & Release Menu

Bio-Synthesis offers more than basic identity and purity testing. If a required assay is not listed, contact us for a custom bundled panel.

Expanded QC and release testing options for ASO, SSO and gapmer supply.

Assay / Service Purpose Notes
LC-MS / ESI-MS Mass identity confirmation Confirms full-length product and detects major adducts or truncation-related species.
Analytical HPLC / UPLC Purity and impurity profile Ion-pair RP, AEX or chemistry-matched method depending on backbone and conjugate.
UV / OD260 Quantitation Amount and concentration Standardized extinction coefficient calculation with CoA reporting.
MALDI-TOF MS Identity confirmation Optional or alternative mass confirmation for selected oligo formats.
Endotoxin In vivo safety support Recommended for animal studies, in vivo research and sensitive biological applications.
Bioburden Microbial load Recommended for in vivo, sterile, formulation or sensitive-use applications; reportable units on request.
Sodium Content Inorganic ion content Supports formulation and buffer compatibility; report as percentage or ppm when requested.
Counterion / Salt Content Counterion composition Useful for formulation, solubility, lyophilization and downstream compatibility.
Water / Moisture Content Moisture and dry-state readiness Supports stability, storage and formulation readiness for larger-scale lots.
Residual Chemicals Residual solvents, reagents and byproducts Confirms process clearance of synthesis reagents, solvents and conjugation byproducts.
pH Analysis Solution compatibility Useful for solution formats, formulation buffers and stability studies.
Solubility Testing Formulation and handling Recommended for lipidated, conjugated, hydrophobic or high-concentration oligos.
Time-Scheduled Stability Degradation and potency over time Stability testing at planned intervals such as 1, 3, 6 and 12 months under defined conditions.
Purity by PAGE / CE Orthogonal separation Optional for long, structured, highly modified or difficult-to-resolve constructs.
Conjugate Ratio / Payload Confirmation Conjugation verification For GalNAc, lipid, peptide, PEG, dye, drug, antibody or other conjugated oligos.
Formulation / Fill-Finish Support Final format readiness Dry, solution, tubes, vials, plates, barcoded labels and custom packaging options.
Custom / Bundled Panel Project-specific release package If the assay is not listed, contact us. Custom QC panels can be built around your program.
Related Services

Related Oligonucleotide Services

These links help customers move from ASO/SSO concept to specialized product workflows.

ASO

Custom ASO Synthesis

Gapmer and steric-blocking ASO platforms.

Explore →

Gap

Gapmer ASO Synthesis

LNA, BNA, cEt and PS gapmers.

Explore →

SSO

Splice-Switching Oligos

Exon skipping and splice correction.

Explore →

Stab

Nuclease Resistance

Stability chemistry for in vivo research.

Explore →

Del

Cellular Uptake & Delivery

Peptide, lipid and ligand delivery strategies.

Explore →

BioC

Oligo Bioconjugation

GalNAc, peptide, lipid, PEG and click conjugation.

Explore →

Pur

Oligo Purification

HPLC, UPLC, IEX and PAGE workflows.

Explore →

QC

Oligo Release QC

LC-MS, purity testing and documentation.

Explore →

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.
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.
More FAQ'sAll FAQ's
Contact & Quote Request

Build Your ASO Scale-Up Plan

Format Gapmer, SSO, steric-block ASO
Sequence 5′→3′ and target transcript
Chemistry PS, MOE, LNA/BNA, cEt
Scale µmol, mg, gram, kilo
QC LC-MS, HPLC/UPLC, CoA
Delivery GalNAc, lipid, peptide, PEG
Bench to Kilo Production

Need ASO, SSO or gapmer supply that can scale?

Share your sequence, target, ASO format, modification pattern, conjugation strategy, scale, purity, QC and documentation needs. Bio-Synthesis can help build a practical pathway from discovery lots to pilot, gram and kilo-class production.
Request a Quote Speak to a Scientist

Need help before quoting?

Email: info@biosyn.com
Phone: 800-227-0627 (US/CAN)
Phone: +001-972-420-8505 (INT)
Tx

Scale-Up Focus

Designed for customers who need a consistent route from research screening to large production lots.

µmol mg gram kilo CoA
QC

Production Package

Purification, LC-MS, analytical purity, quantitation, labeling, packaging and documentation support.

HPLC/UPLC LC-MS OD260 Batch File QC
Recommended Reading

Recommended Reading & Literature References

Use this section to support scientific credibility while keeping the commercial message focused on scale-up production. Include Bio-Synthesis-cited work where Bio-Synthesis oligonucleotides or gapmer constructs were used.

  1. Bio-Synthesis cited in ASO/gapmer research: IGF1R-targeted delivery of a bridged nucleic acid oligonucleotide for triple-negative breast cancer. NAR Cancer, 2025. The paper reports BNA–DNA–BNA gapmer phosphorothioates and peptide conjugates assembled using oligonucleotide synthesis and click chemistry by Bio-Synthesis, Inc., Lewisville, TX.
  2. Bennett CF, Swayze EE. RNA targeting therapeutics: molecular mechanisms of antisense oligonucleotides as a therapeutic platform. Annual Review of Pharmacology and Toxicology. 2010;50:259–293.
  3. Deleavey GF, Damha MJ. Designing chemically modified oligonucleotides for targeted gene silencing. Chemistry & Biology. 2012;19(8):937–954.
  4. Prakash TP. An overview of sugar-modified oligonucleotides for antisense therapeutics. Chemistry & Biodiversity. 2011;8(9):1616–1641.
  5. Egli M, Manoharan M. Chemistry, structure and function of approved oligonucleotide therapeutics. Nucleic Acids Research. 2023;51(6):2529–2573.
  6. Summerton J, Weller D. Morpholino antisense oligomers: design, preparation, and properties. Antisense Nucleic Acid Drug Development. 1997;7(3):187–195.
  7. Obika S, Uneda T, Sugimoto T, et al. 2′-O,4′-C-methylene bridged nucleic acid (2′,4′-BNA): synthesis and triplex-forming properties. Bioorganic & Medicinal Chemistry. 2001;9(4):1001–1011.

Suggested page note: Recommended reading is provided for scientific background. Final ASO, SSO and gapmer design should be evaluated within the target transcript, mechanism, chemistry placement, delivery strategy, purification method and release QC plan.

Why Choose Bio-Synthesis

Trusted by biotech leaders worldwide for over 45+ 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.

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