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 / ISO13485:2016 U.S. Facilities - Texas HPLC/UPLC • LC-MS • CoA RUO → GLP/GMP-Aligned Support

Build a Scale-Up Plan Choose ASO Platform

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Overview Bench to Kilo ASO Platforms Chemistry Toolkit Workflow QC Applications FAQ Contact 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.

Discovery Screens

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

Lead Confirmation

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

Pilot Production

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

Gram / Kilo-Class

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

Tech Transfer Ready

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

µmol

Screening lots

mg–g

Pilot supply

Kilo

Production pathway

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.

Sequence & Target Review

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

Chemistry Pattern

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

Synthesis & Conjugation

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

Purification Route

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

Analytical QC

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

Formulation & Format

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

Documentation

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

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 →

Oligo Release QC

LC-MS, purity testing and documentation.

Explore →

FAQ

What is the difference between a gapmer ASO and a steric-blocking SSO?

Gapmers recruit RNase H to cleave target RNA. Steric-blocking SSOs bind RNA to modulate splicing or block translation without RNase H cleavage.

Can Bio-Synthesis support bench-to-kilo ASO production?

Yes. Bio-Synthesis supports programs from µmol screening lots through pilot, gram and kilo-class production with scale-matched purification, analytical QC and documentation.

What is a common starting point for a gapmer?

Many gapmers use a central DNA gap flanked by modified wings such as LNA/BNA/cEt or 2′-MOE, often with PS backbone protection.

Which chemistries improve nuclease resistance?

Common choices include PS linkages, 2′-OMe, 2′-F, 2′-MOE, LNA/BNA/cEt, terminal caps and selected conjugation strategies.

What should I provide for a quote?

Provide sequence, format, modification pattern, conjugates, scale, purification, QC requirements, application, target information and documentation needs.

Which purification should I choose?

HPLC or UPLC is recommended for in vivo, translational and scale-up programs. Desalting may be suitable for some early screening applications.

More FAQ's All 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)

Scale-Up Focus

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

µmol mg gram kilo CoA

Production Package

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

HPLC/UPLC LC-MS OD260 Batch File QC

Why Choose Bio-Synthesis

Trusted by biotech leaders worldwide for over 45+ years of delivering high quality, fast and scalable synthetic biology solutions.

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Specialty Peptides

Catalog Peptide

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Educational Resources

Scientific Tools

Educational Resources

Scientific Tools

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Online Order

Printable Forms

MSDS / SDS Sheets

Additional Resources

ASO, SSO & Gapmer Oligonucleotide Manufacturing

Manufacturable Antisense Designs, Not Just Research Oligos

Bench-to-Kilo Manufacturing Pathway

Discovery Screens

Lead Confirmation

Pilot Production

Gram / Kilo-Class

Tech Transfer Ready

Choose the Right Antisense Platform

Gapmer ASO

Splice-Switching SSO

Steric-Blocking ASO

Modification Strategy for Potency, Stability and Scale

ASO / SSO / Gapmer Chemistry Selection

Design Guide by Function

ASO Chemistry Toolkit: What Bio-Synthesis Offers

Backbone Chemistry

Modified Sugars & Bases

Termini & Handles

Targeting & Delivery

Integrated Workflow for Scalable ASO Programs

Sequence & Target Review

Chemistry Pattern

Synthesis & Conjugation

Purification Route

Analytical QC

Formulation & Format

Documentation

Scale-Up Continuity

QC and Release Testing for Development-Ready Supply

Common QC Packages by Stage

Expanded QC & Release Menu

Related Oligonucleotide Services

Custom ASO Synthesis

Gapmer ASO Synthesis

Splice-Switching Oligos

Nuclease Resistance

Cellular Uptake & Delivery

Oligo Bioconjugation

Oligo Purification

Oligo Release QC

FAQ

Build Your ASO Scale-Up Plan

Need ASO, SSO or gapmer supply that can scale?

Need help before quoting?

Scale-Up Focus

Production Package

Recommended Reading & Literature References

Why Choose Bio-Synthesis

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