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BHQ®-3 amidite is used for the 5' labeling of fluorogenic probes or to place the quencher internally. This amidite contains a DMT protecting group, which is removed under traditional conditions. The BHQ-3 dye was designed to have maximal absorption in the 620-730 nm range, which provides excellent quenching of fluorophores emitting in this range.


  • Chemical Name:

    BHQ-3 DMT Amidite

  • Formula:


  • Molecular Weight:


  • Appearance:

    purple solid

  • Absorption Maximum (Lambda Max):


  • Extinction Coefficient at Lambda max:


  • Extinction Coefficient at 260 nm:


Spectral properties measured in PCR buffer as 5'-labeled poly(T) oligo.

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

  • Coupling:

    10-minute coupling

  • Deprotection conditions:

    Oligonucleotides labeled with BHQ-3 amidite may be deprotected using concentrated NH4OH for 45 minutes at 60 °C.

  • BHQ-3 amidite is susceptible to oxidation when left out in the open or undessicated. For detailed information on BHQ fragmentation by MALDI-TOF MS, refer to your BHQ Licensee's Manual Appendix V.
    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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