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BHQ®-2 dT Linker 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-2 dT quencher was designed to have maximal absorption in the 560 to 670 nm range, which provides excellent quenching of fluorophores emitting in this range.

Properties:

  • Chemical Name:

    5'-Dimethoxytrityloxy-5-[(N-4''-carboxyethyl-4''-(N-ethyl)-4'-(4-Nitro-phenyldiazo)- 2'-methoxy-4'-methoxy-azobenzene)-aminohexyl-3-acrylimido]-2'-deoxyUridine- 3'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite

  • Formula:

    C73H87N12O15P

  • Molecular Weight:

    1403.52

  • Appearance:

    dark purple solid

  • Absorption Maximum (Lambda Max):

    592

  • Extinction Coefficient at Lambda max:

    44000

  • Extinction Coefficient at 260 nm:

    26100

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

Product usage:

  • Synthesis conditions:

    Prior to dilution ensure that all product is at the bottom of the vial. 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.

  • Dilution:

    100 µmol/mL

  • Coupling:

    10-minute coupling

  • Deprotection conditions:

    Deprotection conditions are dependent upon the type of amidites used for the synthesis of the oligo. If using standard amidites deprotect in concentrated NH4OH for 5 hours at 60 °C. If using fast deprotecting amidites deprotect in concentrated NH4OH for 1 hour at 60 °C. If you are using base sensitive fluorophores (ie. TAMRA or Rhodamine based dyes) we recommend deprotecting the dye labeled oligonucleotide in t-butylamine/H2O (1:3) for 12-16 hours at 60 °C.

  • If all the solution is not used during the synthesis, it can be stored under argon and its functionality maintained up to 48 hours. BHQ-2 dT 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:
    101265c.gif

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

    962.9

Storage and handling:

  • Shipping conditions:

    Cold

  • Storage conditions:

    -15 to -30 °C

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