Figure 1.

Structure and function of MB. (a) Stem-loop hairpin structure of a MB showing its four structural components: loop, stem, quencher, and reporter. The chemical structure of the linkers is drawn according to the manufacturer (Integrated DNA Technologies, Iowa, USA). (b) Mechanism of MB function. A MB in a solution containing both MB and target could be in three states: free in a stem-loop hairpin conformation, hybridized with it target, or unbound in a random-coil conformation. The random-coil conformation of the MB contributes to the background. (c) Fluorescence intensity. The blue line shows the fluorescence intensity for a MB in solution (50 nM) during 400 seconds (background), and the red line corresponds to the addition (100 seconds) of a target oligonucleotide (500 nM) that hybridize the MB at the loop region. An increase in fluorescent intensity of approximately thirteenfold is observed. The reporter is represented with a red circle and the quencher with a blue. UA means arbitrary units.