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CAL Fluor Orange 560 C6 dT Amidite

CAL Fluor Orange 560 C6 dT Amidite

A phosphoramidite used for CAL Fluor Orange 560-dT labelling of oligonucleotides.

Key features

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  • Used to add a yellow-orange fluorescent dye internally or to the 5' end of an oligonucleotide.
  • Maximal emission around 560 nm. Alternative to VIC, HEX and JOE.
  • Quenched by BHQ-1.
  • Has DMT functionality.
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Product information

Historically, there was a limited selection of dyes available for multiplex PCR: TET, JOE, VIC™, HEX, Texas Red®, Cy™ 3, and Cy™ 5. In recent years, the selection and quality of reporters and quenchers has dramatically improved. LGC, Biosearch Technologies has developed the CAL Fluor Dyes, a set of fluorescent dyes specifically designed for qPCR instruments. These novel xanthene fluorophores not only replicate the applicability of previous dyes, they have further unique patented features. These dyes can be efficiently manufactured and remain stable through oligo synthesis and work up. The attachment chemistry linking the CAL Fluor Dyes to biomolecules eliminates the problem of multiple isomers. This results in dye labels that are easier to manufacture, have a single RP-HPLC peak and have well-defined emission spectra. CAL Fluor Dyes are available as CPGs and as phosphoramidites for oligonucleotide synthesis, which results in more efficient label incorporation and fewer purification steps than post-synthesis labeling. The CAL Fluor Dyes have emission maxima from 544 nm to 637 nm and can be paired with BHQ-1 or BHQ-2 for efficient quenching in a variety of probe formats. Multiplex suggestions and PCR instrument compatibility of CAL Fluor Dyes can be found here. Carboxylic acids of the CAL Fluor Dyes 560, 590, and 610 are available to use for peptide labelling.


  • Formula: C78H95F6N9O13P2
  • Molecular Weight: 1542.58
  • Appearance: orange-red solid
  • Absorption Maximum (Lambda Max): 538
  • Extinction Coefficient at Lambda max: 85900
  • Extinction Coefficient at 260 nm: 36500
  • Fluorescence Maximum: 559

Spectral properties measured in PCR buffer as internal labeled poly(T) oligonucleotide.

Product usage:

  • Dilution: 100 µmol/mL
  • Coupling: 2-minute coupling
  • Deprotection conditions: Cleave and deprotect the CAL dye labeled oligo, in the presence of the CPG support, in 2-Methoxyethylamine (Ald# 241067-50) and MeOH (1:3) 3 hours at 60°C. Filter sample and evaporate supernatant. Re-dissolve the CAL dye labeled oligo in water.The use of strong bases, such as concentrated ammonia, causes degradation of the dye and should be avoided.
  • CAL Fluor Orange 560 is light sensitive. Prolonged exposure to light may cause photo bleaching.This product is susceptible to oxidation when left out in the open or undessicated. Unused amidite solution can be stored under argon and its functionality maintained for up to 24 hours.Image of cleaved and deprotected structure:
  • The mass this product adds after conjugation and work-up (the additional mass seen by mass spectrometry) is: 956

Storage and handling:

  • Shipping conditions: Cold
  • Storage conditions: -15 to -30 °C

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