Dye-Labeled Phosphoramidites

Thermo Fisher Scientific offers DyLight fluorescent–labeled phosphoramidites that feature absorption and emission spectra suitable for a broad range of applications, including microscopy and PCR. 

These phosphoramidites may be used on all automated DNA synthesizers using standard synthesis procedures

Our expertise includes the development of custom dye chemistries, linkers, and labeling strategies. Fluorescent tags can be incorporated at the 5′ end of an oligonucleotide using DyLight phosphoramidites with standard synthesis and deprotection procedures. In addition, these direct-labeled phosphoramidites can be used in research applications without the constraints of licensing and royalty fees.

Biotin-TEG can be placed throughout the oligo (3', 5', or internal) while also having a spacer arm, thereby minimizing steric hindrance between the biotin moiety and the oligo. 5'-Biotin amidite can only be synthesized to the 5′ end of the oligonucleotide.

DyLight-labeled Phosphoramidites

DyLight phosphoramidites have absorbance and emission spectra comparable to DyLight Cyanine dyes:

  • DyLight DY547 phosphoramidite is comparable to DyLight 3
  • DyLight DY647 phosphoramidite is comparable to DyLight 5
  • DyLight DY677 phosphoramidite is comparable to DyLight 5.5
 DyLight DY547 CEPDyLight DY647 CEPDyLight DY677 CEP
Cat. No.SY6332SY6334SY6336
Molecular weight756.74 g/mol827.07 g/mol927.18 g/mol
HPLC purity≥ 90% at 547 nm≥ 85% at 647 nm≥ 85% at 677 nm
IdentityUV-Vis spectrum conforms to that of the authentic sample
Shipping / Storage conditionDry ice / -20 °C
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DyLight 3, 3.5, and 5 (cyanine) Phosphoramidites

 DyLight 3 CEPDyLight 3.5 CEPDyLight 5 CEP
Cat. No.SY6333SY6380SY6335
Phosphoramidite Description1-[3-(4-monomethoxytrityloxy)propyl]-1′-[3-[(2-cyanoethyl)-(N,N-diisopropyl)-phosphoramidityl]propyl]-3,3,3′,3′-tetramethylindocarbocyanine chloride1-[3-(4-monomethoxytrityloxy)propyl]-1′-[3-[(2-cyanoethyl)-(N,N-diisopropyl)-phosphoramidityl]propyl]-3,3,3′,3′-tetramethyl-4,5-benzindocarbocyanine chloride1-[3-(4-monomethoxytrityloxy)propyl]-1′-[3-[(2-cyanoethyl)-(N,N-diisopropyl)-phosphoramidityl]propyl]-3,3,3′,3′-tetramethylindocarbocyanine chloride
Molecular weight953.64 g/mol1053.76 g/mol979.7 g/mol
HPLC purity≥ 90%≥ 85.0%≥ 85%
UV/VIS SpectrumRatio 280nm/lamda-max must be (less than/equal to) 0.1
UV/VIS Spectrumlamda-max must be 548 +/-2nm
Shipping / Storage  conditionDry ice / -20 °C
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DyLight Fluorescein-labeled Phosphoramidites

DyLight Fluorescein can be further purified to remove the 5-isomer and leaves ≥95% of the 6-isomer (FAM-6), making it ideal for applications requiring higher sensitivity.

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 DyLight FAM-6 CEPDyLight Fluorescein CEPDyLight HEX CEPDyLight TET CEP
Cat. No.27-160827-1606SY6342SY6341
Phosphoramidite DescriptionFluorescein dipivalate phosphoramidite, 6-isomer[(3′,6′-dipivaloylfluoresceinyl)-5,6-carboamidohexyl]-1-O-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite6-(4,7,2′,4′,5′,7′-Hexachloro-3′,6′-dipivaloylfluoresceinyl-6-carboxamido)-hexyl-1-O-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite5′-Tetrachloro-Fluorescein Phosphoramidite
FormulaC46H58N3O10P C46H58N3O10PC46H52N3O10Cl6PC46H54N3O10Cl4P
Molecular weight843.95g/mol843.94g/mol1050.63 g/mol981.73 g/mol
CAS / PubChem#204697-37-0 / 58114954N/A1360547-55-2877049-90-6
HPLC purity≥ 90%≥ 90%≥ 95%≥ 95%
31P NMR purity≥ 95% (6-isomer)85%N/AN/A
Shipping / Storage  conditionDry ice / -20 °C
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Biotin (Indirect-labeled) Phosphoramidites

 5′-Biotin CEPBiotin TEG CEP
Cat. No.27-179327-1773
Phosphoramidite Description[1-N-(4,4'-Dimethoxytrityl)-biotinyl-6-aminohexyl]-2-cyanoethyl-(N,N-diisopropyl)-phosphoramidite1-Dimethoxytrityloxy-3-O-(N-biotinyl-3-aminopropyl)-triethyleneglycol-glyceryl-2-O-(2-cyanoethyl)-(N,N-diisopropyl)-phosphoramidite
FormulaC46H64N5O6PS C52H76N6O11PS
Molecular weight846.08 g/mol1010.24 g/mol
AppearanceWhite solid
HPLC purity≥ 95.0%≥ 90%
31P NMR purity≥95.0%N/A
Solution Clarity0.1M solution in ACN is clear
Shipping / Storage conditionAmbient / -20 °C
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Process and supply chain control

  • A controlled raw material supply chain and established vendor partnerships ensure consistency and security of supply
  • All dye amidites are supplied with lot-specific quality control data including HPLC analysis
  • Processes are monitored from material procurement through final QC and product release, providing batch-to-batch reproducibility

Custom services

  • Custom manufacturing services are available to assist in the development or scale-up of phosphoramidite compounds
  • Specialty phosphoramidites can be manufactured with base or sugar (2′, 3′ or 5′ positions) modifications

Flexible packaging

  • Common oligo synthesizer pack sizes are available for immediate delivery
  • Custom and bulk packaging are also available. Contact us to learn more.


Not finding what you are looking for? We also offer DNA phosphoramiditesRNA phosphoramiditesspecialty phosphoramidites2′-modificationslinker and spacer phosphoramidites, and succinates and CPG support synthesis supportsContact us to learn more.