Backbone and sugar modifications for therapeutic oligos
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.
PS
phosphorothioate backbone
2'-OMe
methyl at 2' position
2'-MOE
methoxyethyl sugar
LNA
locked ribose
cEt
constrained ethyl (ASO wings)
Why PS and 2' patterns matter
Phosphorothioate replaces a non-bridging oxygen on the phosphate with sulfur, creating a chiral P center and generally improving resistance to exonucleases and endonucleases. High PS content can increase TLR engagement and protein binding — patterns are often optimized rather than defaulted to full PS everywhere.
2'-O-methyl reduces charge-driven protein binding and TLR signaling relative to unmodified RNA while modestly increasing Tm. 2'-fluoro increases affinity and is common in siRNA guides. 2'-MOE and LNA substantially increase affinity; LNA is used sparingly to avoid overly stable off-target hybrids.
Modification selection guide
| Modification | Primary effect | Typical use |
|---|---|---|
| Phosphorothioate (PS) | Nuclease resistance; chiral P | ASO backbones; siRNA termini |
| 2'-OMe | Moderate affinity; lower innate immunity | siRNA passenger; ASO wings |
| 2'-F | Higher affinity | siRNA guide positions; aptamers |
| 2'-MOE | High affinity; ASO-tolerant | Gapmer wings; steric ASOs |
| LNA | Very high affinity | Discrete positions; short gapmers / miRNA tools |
Figures are indicative industry-typical values. Lot- and project-specific data appear on the quotation and certificate of analysis.
Synthesis and characterization
Chiral PS centers
Rp / Sp isomers
Reported as composite purity
Modification fidelity
>98% per position (indicative)
n–1 / n+1 monitored
Identity
HRMS
Confirms mass of full pattern
Purity
RP- or IE-HPLC
Method per backbone type
Hydration
Karl Fischer when required
GMP tiers
Figures are indicative industry-typical values. Lot- and project-specific data appear on the quotation and certificate of analysis.
Modification catalog
Backbone
- Phosphodiester (PO)
- Phosphorothioate (PS)
- Mixed PO/PS maps
- Methylphosphonate (project-specific)
2' sugars
- 2'-O-methyl
- 2'-fluoro
- 2'-O-methoxyethyl (2'-MOE)
- 2'-O-aminopropyl (limited positions)
- LNA (locked nucleic acid)
- cEt (constrained ethyl)
Termini
- Inverted dT cap
- 3' phosphoramidate
- 5' phosphate / thiophosphate
What you receive
- Oligo synthesized to your modification map (XLS or sequence notation)
- COA with identity, purity and noted isomer envelope
- Optional positional audit by enzymatic digest / MS fragment mapping
- Documentation of amidite lots for GMP programs
- Stability recommendation versus PO-rich designs
- Quote tied to modification density and length
Frequently asked questions
Standard shorthand (e.g. asterisk for PS) or position tables in the order sheet. We confirm maps before synthesis.
Related
Antisense (ASO)
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.
View detailssiRNA Duplexes
Chemically modified siRNA duplexes for RNAi: antisense (guide) and sense (passenger) strands annealed under controlled conditions. Strand-specific identity, duplex integrity and residual single strands are documented for screening through IND-enabling supply.
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 detailsLabels & Dyes
Oligonucleotides conjugated at the 5', 3' or internal positions with fluorophores, dark quenchers, biotin or other haptens for qPCR probes, FRET assays, imaging and pull-down. Compatibility with the underlying PS/2' map is validated during synthesis.
View detailsReady to specify this for your program?
Share sequence, scale and documentation needs. We reply with indicative specs and a project-specific quotation.