Optimization of bimolecular Mango II Beacons by modulating the position of the DNA oligo suppressor. (A, B) Aligned with respect to C, which shows the positioning and sequence of suppressor 6, which produced the highest contrast between “ON” and “OFF” states. (A) Maximum fluorescence of bimolecular Mango Beacon constructs following the addition of a trigger sequence. Numbers along the x-axis represent the 3′ position of a complementary DNA suppressor. The standard deviation of three replicates is shown (error bars). (M) Mango II control, (C) MIIB in the absence of a DNA suppressor oligo. (B) Contrast ratios of bimolecular Mango Beacon constructs, defined as the ratio of fluorescence before and after the addition of a trigger strand. The contrast and fluorescence values for the construct with the highest contrast (inhibited with DNA suppressor 6) are highlighted in red. (C) Sequence of Mango Beacon (MIIB) inhibited by suppressor 6. The Mango core is underlined, to highlight the two noncore linker A's. G-stacks for a given column of G residues in the G-quadruplex structures are highlighted in gray. The Mango Beacon arms are highlighted in blue, and are complementary to the trigger sequence used (shown in orange).
