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Duplex RNA

siRNA duplexes with sense and antisense QC

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.

All oligonucleotides

19–23

bp duplex (typical)

2

strands QC'd separately

≥90%

duplex purity bands (indicative)

PS

terminal linkage option

GalNAc / LNP

common delivery pairings

Why sense and antisense are tested separately

Each strand is synthesized and characterized before annealing. Mass spectrometry on the antisense strand confirms guide sequence and modification placement; sense strand identity is equally important because mis-loaded duplexes create silent off-target risk.

After annealing, duplex purity, melting temperature and residual single-stranded material are reported. Thermal ramps and non-denaturing methods help confirm strand pairing without over-interpreting heterogeneity from partial modification isomers.

Indicative siRNA QC matrix

Antisense identity

LC-MS / HRMS

Guide strand before annealing

Sense identity

LC-MS / HRMS

Passenger strand before annealing

Duplex purity

IE-HPLC / AEX

Project method

Residual ssRNA

Reported %

Acceptance limit program-specific

Tm (duplex)

UV thermal shift

Validates annealing stoichiometry

Endotoxin

LAL (when required)

In vivo / GMP tiers

Bioburden

Per grade

GMP supply chain

Figures are indicative industry-typical values. Lot- and project-specific data appear on the quotation and certificate of analysis.

Sense vs antisense design choices

ElementAntisense (guide)Sense (passenger)Notes
Core roleRISC loadingDenatured / discarded5' phosphate chemistry on guide as required by design
Modification patternOften more heavily modifiedComplementary patternAsymmetric 2'-F / 2'-OMe common
Terminal PS3' and/or 5'Mirror or asymmetricImproves serum stability
Overhangs2 nt 3' overhang typicalComplementMismatch controls for specificity studies

Figures are indicative industry-typical values. Lot- and project-specific data appear on the quotation and certificate of analysis.

Frequent siRNA modification patterns

Sugar / base

  • 2'-O-methyl on passenger at selected positions
  • 2'-fluoro on guide for affinity
  • 2'-OMe at blunt ends to reduce TLR activation
  • Universal methyl or inverted abasic at 3' termini

Backbone

  • Phosphorothioate at terminal 1–3 linkages
  • Fully phosphodiester core in some research designs

Duplex formats

  • Standard 19–21 mer duplex
  • Dicer-substrate style (longer precursor)
  • Bifunctional or mismatch controls

Indicative annealing outline

Annealing conditions are optimized to your buffer, concentration and modification pattern.

  1. 01

    Combine equimolar antisense and sense in annealing buffer at defined ionic strength.

  2. 02

    Heat to ~85–95 °C briefly, then slow cool to room temperature or use programmed thermal ramp.

  3. 03

    Verify duplex formation by Tm shift and non-denaturing chromatography.

  4. 04

    Aliquot, store at recommended temperature, and ship with chain-specific and duplex COA data.

What you receive

  • Annealed siRNA duplex at stated concentration
  • Separate COA data package for antisense and sense strands pre-annealing
  • Duplex COA: purity, identity, Tm, residual ssRNA where applicable
  • Chromatograms and mass spectra on request
  • Recommended storage (often –20 °C or –80 °C for long hold)
  • Quote referencing modification map and duplex scale

Frequently asked questions

Yes. Many teams purchase antisense and sense separately and anneal in-house; we can also supply pre-annealed duplex with full QC.

Related

Backbone & Sugar Modifications

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.

View details

GalNAc 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.

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Peptide & Lipid Conjugates

Oligos linked to cell-penetrating peptides (CPP), peptide-PMO (PPMO) constructs, cholesterol and other lipid anchors, and miscellaneous delivery ligands. Conjugation chemistry preserves oligo integrity while enabling uptake in muscle, CNS and other tissues beyond GalNAc-liver programs.

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Labels & 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.

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Clinical & Commercial GMP

GMP manufacturing of oligonucleotide drug substance for clinical trials and commercial supply: batch records, validated release and stability methods, change control, and documentation packages suitable for regulatory filing — described at capability level without inventing facility certifications.

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Next step

Ready to specify this for your program?

Share sequence, scale and documentation needs. We reply with indicative specs and a project-specific quotation.