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Do you recommend a specific combination of reporters and quenchers to do multiplexed (two-color) allele discrimination QPCR using molecular beacons?

For instance if one probe is 5 6-FAM/ 3 Dabcyl what reporter and quencher do you recommend for the other probe?

Many researchers will use HEX as their second reporter in a multiplex reaction.  You will want to check the filter sets on your machine to make sure you can detect these dyes before making a final choice.  I would recommend using Dabcyl as the quencher for this beacon.

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