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Examples of the design constraint of shared-stem molecular beacons with certain stem/probe combinations. (A) The design of a molecular beacon with a probe length of 19 bases and a stem length of 6 bases inadvertently resulted in additional bases participating in stem formation (red circles). (B) The design of a molecular beacon with a probe length of 18 bases and a stem length of 4 bases inadvertently resulted in an additional base participating in target hybridization (red circle).
