Dabcyl Labeling

 A molecular beacon probe1 has its natural fluorescence quenched in solution unless it is hybridized to the target sequence.  Consequently, the design of a molecular beacon requires a fluorophore to be in one part of the sequence and the quencher molecule to be in another, with both molecules being separated from the oligonucleotide by a hydrocarbon spacer.  The Dabcyl group has been found to be a universal quencher.  3’-Dabsyl CPG and 3’-Dabcyl CPG are used to prepare probes with the quencher blocking the 3’-terminus.  5’-Dabcyl Phosphoramidite locates the quencher at the 5’-terminus and Dabcyl-dT places it within the sequence, leaving the 3’-terminus available for polymerase extension.

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