A new minor groove binding asymmetric cyanine reporter dye for real‐time PCR

The minor groove binding asymmetric cyanine dye 4‐[(3‐methyl‐6‐(benzothiazol‐2‐yl)‐2,3‐dihydro‐ (benzo‐1,3‐thiazole)‐2‐methylidene)]‐1‐methyl‐pyridin ium iodide (BEBO) is tested as sequence non‐ specific label in real‐time PCR. The fluorescence intensity of BEBO increases upon binding to double‐stranded DNA allowing emission to be measured at the end of the elongation phase in the PCR cycle. BEBO concentrations between 0.1 and 0.4 µM generated sufficient fluorescence signal without inhibiting the PCR. A comparison with the commonly used reporter dye SYBR Green I shows that the two dyes behave similarly in all important aspects.