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RNAi — siRNA & miRNA Custom Oligo Modifications

Enhance stability, delivery, potency, and safety with backbone, sugar, terminal, and conjugation chemistries — including GalNAc, cholesterol, PEG, CPPs, and 2′-O-C16 Lipid-Modified siRNA (LMO). Both siRNA and miRNA solutions available.

ISO 9001 / 13485 RUO → GMP-like scale Texas Facilities Full QC & Analytics
Overview siRNA LMO miRNA FAQ Speak

Overview

Bio-Synthesis engineers siRNA, ASO, and anti-miR with fit-for-purpose chemistries—balancing nuclease resistance, target engagement, immune profile, and biodistribution. We combine backbone stabilization (PS), ribose analogs (2′-OMe, 2′-F, LNA), and delivery handles (GalNAc, cholesterol, CPPs) with PEG/TEG spacers and cleavable linkers to maximize in-system performance.

End-to-end services include scientist-to-scientist design help, custom synthesis, purification (HPLC/UPLC, PAGE), and analytics (LC-MS, OD260; optional endotoxin/residuals/stability). Supply scales from discovery µmol to bench-to-kilo, supported by ISO 9001/13485 quality and RUO→GMP-like documentation.

Explore related chemistries: Spacers & Linkers • Affinity Tags • Cell Delivery & Uptake • Fluorescent Probes

45+ Years ISO 9001 / 13485 RUO → GMP‑like Bench → Kilo

From Bench to Kilo-Scale

Seamless scale-up of RNAi oligos — from small research lots to up to 1000 g with ISO 9001/13485 quality controls and GMP-like workflows.

  • µmol discovery screens → mmol pilots → gram/kilogram batches
  • HPLC/UPLC, LC-MS, CE-PAGE, endotoxin & tailored release QC
  • Custom formulation, tubes/plates, barcoding & documentation
Speak to a Scientist Explore Modifications

1000 g

maximum target batch size
Texas facilities • RUO→GMP-like

siRNA Modifications

siRNA sections

Backbone Modified siRNA

Increase nuclease resistance and fine-tune pharmacology with backbone changes that preserve RNAi activity.

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Modification Description Application Code
Phosphorothioate (PS) Sulfur substitution End-capping, partial PS [PS]
Methylphosphonate (PM) Non-ionic methyl substitution Neutral backbone; may affect PK/uptake [PM]
Phosphoramidate (PN) P–N linkage variant Stability; altered RNase interactions [PN]
Boranophosphate (BPh) Boron substitution Metabolic stability; nuclease resistance [BPh]
  • PS: Use partial or terminal PS in duplex siRNA; uniform PS typical in ss-siRNA/anti-miRs.
  • PM: Neutralizes charge; evaluate potency vs uptake trade-offs.
  • PN: Tune stability/protein interactions; validate RISC loading.
  • BPh: Consider for added resistance; confirm by LC-MS and activity assays.

Sugar Modified siRNA

Balance affinity, activity, and immune profile with 2′-substitutions or locked/bridged sugars.

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Modification Description Application Code
2′-OMe 2′-O-Methyl ribose Resistance, immune reduction [2OMe]
2′-F 2′-Fluoro ribose Stability, potency [2F]
LNA/BNA Locked ribose Affinity, potency [LNA]
cEt Constrained ethyl bridge Affinity & safety [cEt]
MOE 2′-O-methoxyethyl Affinity, nuclease resistance [MOE]
2′-Amino Primary amine at 2′ Affinity↑; conjugation handle [2NH2]
2′-O-Propargyl Alkyne at 2′-O Click chemistry handle [2O-PRG]
2′-ONMA 2′-O-(N-methylacetamide) Affinity, nuclease resistance [2ONMA]
UNA Unlocked ribose Flexibility; structure–function [UNA]
Ara-FANA Arabinose 2′-fluoro-arabino Stability, antisense exploration [Ara-FANA]
ENA Ethylene-bridged nucleic acid Affinity↑; experimental [ENA]
TNA Threose nucleic acid Minimal backbone; orthogonal pairing [TNA]
GNA Glycol nucleic acid Simplified backbone; base-pairing [GNA]
SNA Serinol nucleic acid Biostability; synthetic research [SNA]
  • Patterning: Combine 2′-OMe/2′-F in antisense seed/termini; use LNA/cEt sparingly to preserve RISC loading.
  • Utility: MOE and 2′-handles support affinity/conjugation without over-stabilizing the guide seed.

Terminal End Blocker

Protect from exonucleases, enable conjugation, and control strand bias with selective end caps and handles.

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Modification Description Application Code
3′ End Caps 3′-InvdT, proprietary caps Exonuclease protection [3CAP]
5′ Handles Phosphate, thiol, amine Conjugation, labeling [5P],[5SH],[5NH2]
3′ dTdT / UU Two-base 3′ overhangs Stability; Dicer-style duplex [OVR-2NT]
5′-Phosphate (guide) 5′-P or pro-phosphate Ago2 loading [P5-GUIDE]

Lipid-Modified siRNA (LMO) and Conjugates

Lipid-modified siRNAs (LMOs) incorporate long-chain hydrophobic groups (cholesteryl, tocopherol, 2′-O-hexadecyl/C16) or GalNAc ligands. These enhance membrane association, serum stability, and cellular uptake—sometimes without LNPs.

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Modification Description Application Code
GalNAc ASGPR ligand Liver targeting [GalNAc]
Cholesterol Hydrophobic sterol Uptake [Chol]
PC-Cholesterol (PC-Chol) Cholesterol + phosphocholine Uptake, membrane stability, liver delivery [PC-Chol]
Tocopherol Vitamin E derivative Antioxidant stability; formulation robustness [Tocopherol]
PEG Hydrophilic polymer Circulation, solubility [PEG]
CPPs Cell-penetrating peptides Tissue delivery [CPP]
Docosahexaenoic Acid (DHA) Omega-3 fatty acid CNS-leaning biodistribution; uptake [DHA]
PC-DHA DHA + phosphocholine Delivery and membrane anchoring [PC-DHA]
Docosanoic Acid (DCA) Behenic acid (C22:0) Hydrophobic association; stability [DCA]
PC-DCA DCA + phosphocholine Anchoring; extended half-life [PC-DCA]
Eicosapentaenoic Acid (EPA) Omega-3 fatty acid Anti-inflammatory profile; uptake [EPA]
PC-EPA EPA + phosphocholine Targeted delivery; solubility [PC-EPA]
Lithocholic Acid (LA) Bile acid Uptake; receptor interactions [LA]
PC-LA LA + phosphocholine Targeted uptake via conjugation [PC-LA]
Retinoic Acid (RA) Vitamin A derivative Nuclear receptor targeting [RA]
PC-RA RA + phosphocholine Receptor-specific delivery [PC-RA]
2′-O-C16 A/C/G/U C16 lipidated nucleosides Membrane interaction; extrahepatic delivery [C16-A/C/G/U]
GalNAc (tri-antenna) ASGPR ligand with three GalNAc arms Optimized hepatocyte targeting [GalNAc3]
GalNAc (tetra-antenna) ASGPR ligand with four GalNAc arms Enhanced avidity for liver delivery [GalNAc4]
Mannose Sugar ligand Macrophage/DC targeting via mannose receptor [Man]
Lactose Disaccharide ligand Lectin-mediated uptake [Lac]
Stearic Acid (C18:0) Saturated fatty acid Improves hydrophobicity and uptake [SA]
Palmitic Acid (C16:0) Saturated fatty acid Enhances membrane anchoring [PA]
Myristic Acid (C14:0) Saturated fatty acid Classic lipid anchor [MA]
Oleic Acid (C18:1) Unsaturated fatty acid Improves delivery efficiency [OA]
Linoleic Acid (C18:2) Polyunsaturated fatty acid Membrane integration; biodistribution tuning [LinA]
Squalene Highly hydrophobic terpenoid Self-assembly into nanoparticles [SQL]
Diacylglycerol (DAG) Lipid conjugate Membrane anchoring and vesicle trafficking [DAG]
Phosphatidylethanolamine (PE) Lipid headgroup Anchoring and endosomal release [PE]
Ceramide Sphingolipid conjugate Trafficking via endolysosomal pathways [Cer]
Folate Vitamin B9 derivative Targeting folate receptor-positive tumors [FA]
Vitamin B12 (Cobalamin) Vitamin conjugate Receptor-mediated uptake [B12]
Biotin Vitamin H derivative Assay capture, purification, RUO applications [Biotin]
TAT Peptide Cell-penetrating peptide Facilitates membrane translocation [CPP-TAT]
Penetratin Cell-penetrating peptide Promotes endosomal uptake [CPP-PEN]
Poly-Arg (R9) Arginine-rich peptide High uptake CPP [CPP-R9]
RGD / iRGD Integrin-binding peptide Tumor homing and penetration [RGD]
Angiopep-2 LRP1-binding peptide Brain delivery across BBB [Ang2]
RVG29 Rabies virus glycoprotein peptide Neuron targeting [RVG29]
NLS Peptides Nuclear localization signal Directs oligos to nucleus [NLS]
2′-O-Stearyl (C18) Stearyl-modified nucleosides Membrane interaction; hydrophobic anchoring [C18-2-O-A/C/G/U]
2′-O-Oleyl (C18:1) Oleyl-modified nucleosides Extrahepatic delivery; flexible hydrophobic conjugation [C18:1-2-O-A/C/G/U]
Cleavable Disulfide Linker Redox-sensitive linkage Releases siRNA in cytosol [SS]
Val-Cit-PAB Linker Enzyme-cleavable peptide linker Release triggered by cathepsins [Val-Cit-PAB]
Hydrazone Linker pH-sensitive linkage Endosomal release [Hydrazone]
Photocleavable PC-Spacer Light-sensitive linkage Controlled release on irradiation [PC-Spacer]
Short PEG / TEG Spacer Flexible hydrophilic spacer Improves conjugate orientation, avoids steric hindrance [TEG]
  • Placement: Prefer passenger 3′ end; avoid over-lipidation to preserve RISC loading.
  • Combinations: Pair with 2′-OMe/2′-F and terminal PS; evaluate with/without uniform PS for ss-siRNA.
  • Formulation: LMO may reduce reliance on LNPs; pilot formulations tune biodistribution.

miRNA Modifications

Mimics & Inhibitors

Use miRNA mimics (synthetic duplexes) to restore or elevate miRNA function for gain-of-function studies, and miRNA inhibitors (LNA/PS anti-miRs or antagomirs) to silence endogenous miRNAs for loss-of-function. Typical patterns include terminal PS for stability, selective 2′-OMe/2′-F for immune tolerance, and LNA for potency in inhibitors; add 3′ cholesterol, GalNAc, or LMO for in vivo delivery.

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Product Description Application Code
LNA anti-miR LNA/PS inhibitor Knockdown [LNA-AMIR]
miRNA Mimic Duplex Duplex mirroring miRNA Gain-of-function [MIMIC-DX]
Antagomir 2′-OMe + PS + 3′ cholesterol In vivo delivery [ANTG-CHOL]

End-to-End Workflow

1
Design
pattern & placement
2
Synthesis
solid-phase / plates
3
Conjugation
GalNAc / Chol / CPP
4
Purification
HPLC / UPLC
5
QC
LC-MS, endotoxin
6
Packaging
labels & barcodes
7
Scale
µmol → kilo
🧬 Design & Conjugation
  • Sequence review & pattern selection (PS, 2′-OMe/2′-F, LNA/MOE)
  • Handle placement (GalNAc, Chol, CPPs) with PEG/TEG geometry
  • Lesion/seed management, 5′-P / Ago2 loading, duplex vs ss-formats
🧪 Purification & Analytics
  • HPLC/UPLC, LC-MS, CE/PAGE; OD260 & Tm as needed
  • Optional endotoxin/residuals; scheduled stability time-points
  • Method-matched release packages with detailed CoAs
🏭 Scale & Packaging
  • Discovery µmol → gram/kilo (RUO→GMP-like workflows)
  • Tubes, vials, plates/barcodes; concentration normalization
  • ISO 9001/13485 documentation for tech transfer

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

RNAi Technology & Design Suggestions

Guidelines for RNAi Oligo Design

Design effective RNAi oligos by balancing potency, stability, immune tolerance, and delivery.

Core Principles
  • Mechanism: 19–21 bp duplex + 2-nt overhangs; antisense guides Ago2 after RISC loading.
  • Guide 5′-phosphate: Improves Ago2 loading and potency.
  • Strand bias: Destabilize sense 5′ end; cap sense 3′ end.
  • Seed effects: Mitigate g2–g8 off-targets via selective 2′-OMe/2′-F.
  • Backbone: Add PS at termini or partial PS; avoid heavy uniform PS in duplex.
  • Analytics: Verify identity/duplex integrity (LC-MS, HPLC/UPLC, OD260, Tm).
Practical Design Suggestions
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Goal Recommendation Notes
Potency Ensure antisense 5′-P; light 2′-OMe/2′-F near seed Test 21-mer vs 19-mer
Nuclease resistance PS ends + 2′-OMe/2′-F on sense Avoid over-modifying antisense seed
Reduce immune activation 2′-OMe at immunogenic motifs Evaluate in PBMCs
Liver delivery Sense 3′ GalNAc ± PEG/TEG Subcutaneous hepatocyte targeting
Extrahepatic Sense 3′ Cholesterol/LMO CPPs + PEG spacers
Pattern recipes (starting points)
  • Balanced therapeutic: Sense heavier mods; antisense minimal near seed + 5′-P.
  • High-stability screen: Sense 2′-OMe/2′-F + 3′ cap + PS; antisense light mods.
  • LMO route: Sense 3′ LMO with short PEG/TEG; antisense 5′ unmodified.

Applications of RNAi Oligo Modifications

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Application Area Recommended Modifications Benefits
Liver-targeted therapeutics GalNAc, terminal PS, 2′-OMe/2′-F Efficient ASGPR uptake, nuclease resistance, improved safety
CNS delivery DHA, tocopherol, PEG BBB-leaning biodistribution, antioxidant stability
Oncology Cholesterol, CPPs, cEt/LNA Enhanced tumor uptake, potency, strand selectivity
Immunology & inflammation EPA, MOE, PS Anti-inflammatory profile, extended circulation
Research tools Fluorescent labels, biotin, spacers Imaging, pulldown, qPCR assay design

Need help choosing the right RNAi modifications?

We’ll optimize modification patterns, delivery conjugates, and QC to fit your target, route, and scale.

Speak to a Scientist Browse All Modifications

FAQ

Which modifications most improve nuclease resistance?

Phosphorothioate (PS) end caps, 2′-OMe/2′-F patterning on the sense strand, and selective LNA placements. For ss-siRNA/anti-miR, broader PS usage with MOE/LNA in non-seed regions is common.

How do I reduce innate immune activation?

Place 2′-OMe at immunogenic motifs and within/near the seed; avoid heavy LNA in the antisense seed. Validate in human PBMCs for translational programs.

Where should I place conjugates like GalNAc or cholesterol?

Prefer the passenger (sense) 3′ end via a short PEG/TEG spacer; keep the antisense 5′ end clear for Ago2 loading.

Can LMO (2′-O-C16) replace LNPs?

LMO can enhance uptake and sometimes reduce LNP dependence; pilot formulations can further tune biodistribution and tolerability.

What’s a good starting duplex design?

21-mer with 3′ dTdT/UU overhangs, selective 2′-OMe/2′-F, terminal PS, optional antisense 5′-P, and a conjugate on the sense 3′ end.

What length and overhangs work best for duplex siRNA?

Most programs start with a 21-mer duplex bearing 2-nt 3′ overhangs (dTdT/UU). Some targets prefer 19-mers or asymmetric designs; we can screen both.

Should the antisense strand be 5′-phosphorylated?

A 5′-phosphate (or pro-phosphate) on the antisense can improve Ago2 loading and potency. Compare with and without 5′-P in your first screen.

How do I minimize seed-mediated off-targets?

Use selective 2′-OMe/2′-F near g2–g8 on the antisense, keep excessive locking out of the seed, and verify activity against a mismatch control.

How much LNA is safe to use in siRNA?

Use sparingly in the antisense seed to preserve RISC loading. LNA works well in anti-miRs; for duplex siRNA keep LNA out of the most sensitive seed positions.

2′-OMe vs 2′-F—when should I choose each?

2′-OMe favors immune dampening and stability; 2′-F improves potency and stability. Mixed patterns in the wings are common; we’ll tailor to your readouts.

Where do I place GalNAc, cholesterol, or CPPs?

Usually on the sense 3′ end via a short PEG/TEG spacer. GalNAc targets hepatocytes; cholesterol/CPPs broaden tissue uptake. We can also test dual handles if needed.

What spacer length (PEG/TEG) should I use?

Short TEG/PEG lengths often balance geometry and solubility while minimizing steric hindrance. We’ll recommend a length based on your handle and assay format.

Uniform PS or partial PS—what’s better?

For duplex siRNA, partial or terminal PS typically preserves activity while adding stability. Uniform PS is more common in ss-siRNA/anti-miR.

What QC data do you provide with orders?

Release packages can include HPLC/UPLC traces, LC-MS, OD260, and optional endotoxin/residuals. Method-matched QC is available for regulated studies.

Can you plate, barcode, and normalize my oligos?

Yes. We can supply tubes/vials/plates with labels/barcodes and concentration normalization, aligned to your screening workflow.

How should I store and reconstitute my RNAi oligos?

Store dry at −20 °C (or lower) in desiccation. Reconstitute in RNase-free buffer, avoid repeated freeze-thaws (aliquot if needed), and follow the CoA guidance.

Do you support RUO, GMP-like, or GMP manufacturing?

We offer RUO and GMP-aligned (GMP-like) workflows with ISO 9001/13485 quality, and can scope full GMP via documentation and tech transfer.

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Greetings Researchers,

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