CpG oligonucleotides and transcription-factor decoys
Unmethylated CpG motifs for innate immune adjuvancy in research settings, and double-stranded decoy oligos that compete for transcription factor binding. Sequences, backbone chemistry and endotoxin controls are aligned to the intended assay or model.
Class C/B
CpG motif families
15–30
nt decoy lengths
PS
typical CpG backbone
dsDNA
decoy structure
LAL
endotoxin tier when needed
CpG and decoy mechanisms
CpG oligonucleotides containing unmethylated CG dinucleotides in particular contexts can activate TLR9 in plasmacytoid dendritic cells and B cells in rodent and human systems, depending on motif class and backbone.
Decoy oligonucleotides present high-affinity consensus sites for transcription factors (e.g. NF-κB, STAT). When delivered into nuclei or cytosol in model systems, they titrate factor binding away from endogenous promoters.
Common CpG and decoy patterns
CpG classes (examples)
- Class B: robust B-cell activation motifs
- Class C: mixed pDC / B-cell activity
- Class A: high IFN-α with phosphodiester cores in some designs
- Control methylated CpG sequences
Decoy targets
- NF-κB consensus decoys
- STAT3 / STAT5 binding sites
- Custom motif from promoter literature
Controls
- Scrambled CpG
- GpC-inverted controls
- Mutated decoy with weakened binding
CpG vs decoy — practical differences
| Aspect | CpG oligo | TF decoy |
|---|---|---|
| Structure | Usually single-stranded PS | Double-stranded hairpin or duplex |
| Primary readout | Cytokine / immune activation | Reporter or target gene suppression |
| Delivery | Formulation-sensitive | Often requires transfection or local delivery |
| QC emphasis | Endotoxin, uniformity | Duplex Tm, strand stoichiometry |
Figures are indicative industry-typical values. Lot- and project-specific data appear on the quotation and certificate of analysis.
Indicative specifications
Identity
MS
CpG ss; decoy each strand
Purity
≥90% (typical research)
Higher on request
Endotoxin
<0.5–1 EU/mg (when tested)
Not assumed unless ordered
Bioburden
Per grade
GMP not default for adjuvant research
Salt
Na+ common
Specify for in vivo
Figures are indicative industry-typical values. Lot- and project-specific data appear on the quotation and certificate of analysis.
What you receive
- CpG or decoy material with COA
- Duplex annealing for decoys where ordered
- Endotoxin data when that tier is purchased
- Recommended reconstitution and storage
- Motif documentation as sequence file
- Quote with scale and control sequences if bundled
Frequently asked questions
Class B motifs are common for B-cell stimulation; Class C blends pDC and B-cell effects. Species-specific activity differs — pick motifs validated in your model.
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 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 detailsBackbone & 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 detailsClinical & 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.
View detailsReady to specify this for your program?
Share sequence, scale and documentation needs. We reply with indicative specs and a project-specific quotation.