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  5. Quasar 570 C6 T Amidite

Quasar 570 C6 T Amidite

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Quasar® 570 C6 T 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 Quasar 570 moiety is coupled to a thymine for addition to synthetic oligonucleotides. Quasar 570 dye is an indocarbocyanine that fluoresces in the yellow-orange region of the visible spectrum and can be effectively quenched by BHQ®-2 dye. It is also a direct replacement for Cy™ 3 dye.

Properties:

  • Formula:

    C79H100F6N8O10P2

  • Molecular Weight:

    1496.62

  • Appearance:

    red solid

  • Absorption Maximum (Lambda Max):

    547

  • Extinction Coefficient at Lambda max:

    118000

  • Extinction Coefficient at 260 nm:

    20000

  • Fluorescence Maximum:

    570

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

Product Usage:

  • Synthesis Conditions:

    Due to the mild cleavage and deprotection conditions, we recommend using fast deprotecting amidites. Prior to dilution ensure that all product is at the bottom of the vial. Dilute to the recommended concentration and mix thoroughly in sealed vial to ensure that all contents are dissolved. For optimal coupling efficiency, we recommend treating the amidite solution with 3-4 Å activated molecular sieves (10% v/v).

  • Dilution:

    100 µmol/mL

  • Deprotection Conditions:

    The deprotecting conditions for this amidite will be depend on the types of amidites used for the synthesis of the oligo. If using fast deprotecting amidites deprotect in concentrated NH4OH for 1 hour at 60 °C. If using standard amidites deprotect in concentrated NH4OH for 5 hours at 60 °C. The use of methylamine should be avoided.

    • If all the solution is not used during the synthesis, it can be stored under argon and its functionality maintained up to 24 hours. Quasar 570 C6 T amidite is light sensitive material. Prolonged exposure to light may cause photo bleaching. This product is susceptible to oxidation when exposed to air or stored undessicated.
    Image of cleaved and deprotected structure:
    102323c.gif

  • The mass this product adds after conjugation and work-up (the additional mass seen by mass spectrometry) is:

    912.04

Storage and Handling:

  • Shipping Conditions:

    Cold

  • Storage Conditions:

    -15 to -30 °C

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