A series of Molecular beacons with different structure carried JOE was tested in qPCR.
JOE proved to be brighter than FAM with probes with the same sequence.
The length of MB's stem was varied from 4 to 8 bp to optimize MBs design.
A rigid linker for JOE attaching is preferable for increasing light-up of fluorescence.
The second BHQ1 in probe significantly decrease background of fluorescence.