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DABCYL Amidite (N-DABCYL-6-Aminohexyl Amidite)

DABCYL Amidite (N-DABCYL-6-Aminohexyl Amidite)

Phosphoramidite used to 5'-label an oligonucleotide with the dabcyl quencher moiety.

Key features

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  • Used to add a yellow-green fluorescent quencher to the 5' end of an oligonucleotide.
  • Emission range at 400-550 nm (absorption maximum, 471 nm). Alternative to BHQ-1 in certain applications.
  • Does not have DMT functionality.
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Product information

Dabcyl is a non-fluorescent molecule, (so-called dark quencher) efficiently quenching various fluorescent dyes. It has been widely used as a quencher in diagnostic probes such as Molecular Beacons.(1) A Molecular Beacon is a hybridisation probe consisting of a fluorophore, a quencher and a defined section of the oligonucleotide sequence complementary to that of the target nucleic acid. In the inactive state, when the probe is not hybridised to its target sequence, the fluorescence energy of the fluorophore is transferred to the quencher by a process of collisional quenching. For light energy transfer to take place efficiently, both fluorophore and quencher have to be in close proximity. This requirement is accounted for in the design of Molecular Beacons in that the two parts of the stem hybridise to hold the F/Q pair in close proximity. Hybridisation of the Molecular Beacon probe to its target sequence results in the separation of the stem and hence the F/Q pair, resulting in fluorescence. We offer a variety of CPG and phosphoramidite Dabcyl products for myriad applications. Since Dabcyl is stable to oligo synthesis it can be incorporated at any point in the sequence. 5’ modification is used in TwistAmp fpg probes; 3’ modification in Taqman probes, duplex Scorpions and Molecular Beacons; and internal modification has been utilised in Scorpion Primers. Deprotection of the oligo is dependent on the F/Q pair but in general is as per unmodified oligos. Dabcyl’s absorption properties limit the range of dyes it can quench to those emitting at 400-550 nm such fluorescein and JOE (absorption maximum, 471 nm), but tends to overlap poorly with fluorophores emitting above 480 nm. However, when used in Molecular Beacons, the fluorophore and Dabcyl are brought close enough to allow a slightly broader spectrum of dyes to be quenched, thereby increasing the versatility of the Dabcyl molecule. Although Dabcyl was originally the quencher of choice, for the most part this has been superceded by Black Hole Quenchers (BHQs) for newer applications.


  1. Molecular beacons: probes that fluoresce upon hybridisation, S. Tyagi and F.R. Kramer, Nature Biotechnology, 14, 303-308, 1996.


  • Chemical Name: 6-(N-4'-carboxy-4-(dimethylamino)azobenzene)- amidohexyl-1-O-(2-cyanoethyl)-(N,N-diisopropyl)-phosphoramidite
  • Formula: C30H45N6O3P
  • Molecular Weight: 568.69
  • Appearance: orange solid
  • Absorption Maximum (Lambda Max): 482
  • Extinction Coefficient at Lambda max: 25500
  • Extinction Coefficient at 260 nm: 20000

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

Product usage:

  • 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. With fast deprotecting amidites (ie. C-Ac, G-DMF, G-PAC) use concentrated NH4OH for 1 hour at 60 °C. With standard amidites (ie. C-Bz, G-iBu) use concentrated NH4OH for 5 hours at 60 °C. With base-sensitive fluorophores (eg. TAMRA) we recommend using t-butylamine/water (1:3) for 6 hours at 65 °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.Image of cleaved and deprotected structure:
  • The mass this product adds after conjugation and work-up (the additional mass seen by mass spectrometry) is: 430.43

Storage and handling:

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

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