Fluorescent labels, quenchers and biotin on oligos
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.
FAM / Cy5
common fluorophores
BHQ / TAMRA
quencher pairs
5' / 3'
terminal labeling
Dual
FRET probe format
Biotin
capture tag
Labels without compromising drug substance
Research probes and drug substance are synthesized on the same chemistries where possible, but dye choice affects purification and stability. Large hydrophobic dyes can shift HPLC retention and require dedicated methods.
Quencher placement for qPCR and RNase H–independent assays follows spacing rules (typically 10–30 nt between fluorophore and quencher for TaqMan-style probes). Internal labels require protected amidites compatible with deprotection conditions.
Fluorophores, quenchers and tags
Fluorophores (examples)
- FAM (fluorescein)
- HEX, TET
- Cy3, Cy5, Cy5.5
- AF488, AF647 (where amidite available)
- Texas Red / ROX class dyes
Quenchers (examples)
- BHQ-1, BHQ-2, BHQ-3
- TAMRA
- DABCYL
- Iowa Black FQ / RQ
- MGB (minor groove binder) — probe format specific
Non-fluorescent tags
- Biotin (5' or 3')
- Digoxigenin
- Amino linker (C6 / C12) for post-labeling
- Azide / alkyne for click conjugation
Probe format selection
| Assay | Format | Label pattern |
|---|---|---|
| qPCR (hydrolysis) | TaqMan | 5' fluorophore + 3' quencher; PS backbone common |
| qPCR (hybridization) | Molecular beacon | Stem-loop with fluor + quencher |
| FRET melting | Dual-labeled duplex | Donor on one strand, acceptor on complement |
| Pull-down | Biotinylated capture | Biotin terminus; minimal dye if elution is MS |
Figures are indicative industry-typical values. Lot- and project-specific data appear on the quotation and certificate of analysis.
Indicative labeled oligo specs
Identity
LC-MS
Mass includes label
Label incorporation
≥90% (typical)
UV ratio where applicable
Purity
≥85%
Hydrophobic dyes may need alternate column
Quencher bleed
Assay-specific
Background checked in buffer
Storage
Dark, cold
Protect high-energy fluorophores from photobleaching
Figures are indicative industry-typical values. Lot- and project-specific data appear on the quotation and certificate of analysis.
What you receive
- Labeled oligo with dye / quencher identity on COA
- Absorbance and fluorescence QC where methods exist
- Recommended TE or buffer for reconstitution
- Spectral pairing note for FRET sets
- MS confirmation of label mass adduct
- Quote per label type and oligo length
Frequently asked questions
Yes, with adapted purification. Highly modified backbones may shift retention; methods are qualified per order.
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View detailsReady to specify this for your program?
Share sequence, scale and documentation needs. We reply with indicative specs and a project-specific quotation.