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.
Coupling: This support should be used in a manner identical to normal protected nucleoside support since it contains the DMT group.
Deprotection: Cleavage of the oligonucleotide from this support requires 2 hours at room temperature with ammonium hydroxide. Complete the deprotection using the protocol required by the nucleobases.