Figure 1. Molecular beacon structure and control molecular beacons.

(a) A schematic of a molecular beacon in a stem-loop hairpin conformation. The stem brings the 5′ dye and 3′ quencher together to quench the fluorescence signal. The loop region with 15–30 base pairs is complementary to the target sequence of specific mRNA thus providing specificity. (b) A schematic depicting a molecular beacon in an open conformation after hybridizing to its complementary target mRNA sequence. Hybridization induces a conformational change that separates the fluorophore from the quencher, resulting in a >10-fold increase in fluorescence signal. (c) A schematic of a positive control molecular beacon with a fluorescent dye attached to both the 5′ and 3′ ends, thus is constitutively fluorescent. This probe is used to determine if MBs can be delivered into different cell types efficiently and uniformly. (d) A schematic depicting a specific negative control beacon. The four mutated bases should prohibit hybridization of the probe to the target region of specific mRNA. When delivered into 3T3 cells as negative control cells, this control beacon should yield very low background signal, confirming the MB specificity. (d) A predicted secondary structure of a cardiac specific gene, with a single stranded region highlighted and expanded.