Designing FRET (Taqman) probes for alternative splicing: considerations?

01 January 2013 1 10K Report

We would like to design FRET type of probes to detect the presence of alternatively spliced isoforms of certain genes. My question is regarding the optimal probe design. How long the probe should be? Would you use pure DNA probes or would you incorporate LNAs, and if yes which part of the probe (5', middle or 3')? Does it make sense to use a probe couple like FAM - Black Hole Quencher (BHQ) 1 and TAMRA - BHQ 2 for multiplexing?

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