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.
Details
Usage
Coupling: 6 minute coupling time recommended
Deprotection: No changes needed from standard method recommended by synthesizer manufacturer.
Specifications
Diluent
Anhydrous Acetonitrile
Storage
Freezer storage, -10 to -30°C, dry
Stability
2-3 days
Dilution/Coupling Data
The table below show pack size data and, for solutions, dilution and approximate coupling based on normal priming procedures.
