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.

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

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  DyLight DY547 CEP DyLight DY647 CEP DyLight DY677 CEP
Cat. No. SY6332 SY6334 SY6336
Formula C38H54IN4O2P C47H63N4O5PS C55H67N4O5PS
Molecular weight 756.74 g/mol 827.07 g/mol 927.18 g/mol
HPLC purity ≥ 90% at 547 nm ≥ 85% at 647 nm ≥ 85% at 677 nm
Identity UV-Vis spectrum conforms to that of the authentic sample
Shipping / Storage condition Dry ice / –20 °C
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DyLight 3, 3.5, and 5 (cyanine) Phosphoramidites

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  DyLight 3 CEP DyLight 3.5 CEP DyLight 5 CEP
Cat. No. SY6333 SY6380 SY6335
Phosphoramidite Description 1-[3-(4-monomethoxytrityloxy)propyl]-1′-[3-[(2-cyanoethyl)-(N,N-diisopropyl)-phosphoramidityl]propyl]-3,3,3′,3′-tetramethylindocarbocyanine chloride 1-[3-(4-monomethoxytrityloxy)propyl]-1′-[3-[(2-cyanoethyl)-(N,N-diisopropyl)-phosphoramidityl]propyl]-3,3,3′,3′-tetramethyl-4,5-benzindocarbocyanine chloride 1-[3-(4-monomethoxytrityloxy)propyl]-1′-[3-[(2-cyanoethyl)-(N,N-diisopropyl)-phosphoramidityl]propyl]-3,3,3′,3′-tetramethylindocarbocyanine chloride
Formula C58H70N4O4PCl C66H74N4O4PCl C60H72N4O4PCl
Molecular weight 953.64 g/mol 1053.76 g/mol 979.7 g/mol
HPLC purity ≥ 90% ≥ 85.0% ≥ 85%
UV/VIS Spectrum Ratio 280nm/lamda-max must be (less than/equal to) 0.1
UV/VIS Spectrum lamda-max must be 548 +/-2nm
Shipping / Storage  condition Dry 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 CEP DyLight Fluorescein CEP DyLight HEX CEP DyLight TET CEP
Cat. No. 27-1608 27-1606 SY6342 SY6341
Phosphoramidite Description Fluorescein dipivalate phosphoramidite, 6-isomer [(3′,6′-dipivaloylfluoresceinyl)-5,6-carboamidohexyl]-1-O-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite 6-(4,7,2′,4′,5′,7′-Hexachloro-3′,6′-dipivaloylfluoresceinyl-6-carboxamido)-hexyl-1-O-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite 5′-Tetrachloro-Fluorescein Phosphoramidite
Formula C46H58N3O10P  C46H58N3O10P C46H52N3O10Cl6P C46H54N3O10Cl4P
Molecular weight 843.95g/mol 843.94g/mol 1050.63 g/mol 981.73 g/mol
CAS / PubChem# 204697-37-0 / 58114954 N/A 1360547-55-2 877049-90-6
HPLC purity ≥ 90% ≥ 90% ≥ 95% ≥ 95%
31P NMR purity ≥ 95% (6-isomer) 85% N/A N/A
Shipping / Storage  condition Dry ice / –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.