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CAL Fluor® Orange 560 C6 dT amidite is used for the 5' or internal labeling of synthetic oligonucleotides for a wide array of applications including dual labeled fluorogenic probes for real time PCR. The CAL Fluor Orange 560 moiety is coupled to a thymine for addition to synthetic oligonucleotides. CAL Fluor Orange 560 dye fluoresces in the yellow-orange region of the visible spectrum and can be effectively quenched by BHQ®-1 dye. CAL Fluor Orange 560 dye is an alternative for VIC and HEX.


  • Formula:


  • Molecular Weight:


  • Appearance:

    orange-red solid

  • Absorption Maximum (Lambda Max):


  • Extinction Coefficient at Lambda max:


  • Extinction Coefficient at 260 nm:


  • Fluorescence Maximum:


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

Product usage:

  • Synthesis conditions:

    Due to the mild deprotection conditions we recommend using fast deprotecting amidites. Dissolve product in DCM dried over molecular sieves. DCM should not contain EtOH stablizers. Following dilution, mix thoroughly in sealed vial to ensure that all contents are dissolved. We recommend using Ethyl thiol tetrazole for the activator reagent with this product.

  • 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:


Storage and handling:

  • Shipping conditions:


  • Storage conditions:

    -15 to -30 °C


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