Molecular Beacons: Powerful Tools for Imaging RNA in Living Cells
Figure 2
Different positions for MB-target hybridization. The loop region is illustrated in green and the stem in purple for all panels, target is brown and the bonds MB target are black ((b), (c), (d) y (e)). (a) MB with a stem of five nucleotides in the stem-loop hairpin conformation. (b) MB with a stem of five nucleotides and twenty two nucleotides in the loop, target hybridization occurs only at loop region. (c) MB with a stem of five nucleotides and a stem of seventeen nucleotides, using the loop and all the 3′ arm to hybridize the target (3′ shared stem MB). (d) MB with a stem of five nucleotides and a loop of seventeen nucleotides, using the loop and completely the 5′ arm to hybridize its target (5′ shared stem MB). (e) MB with a stem of five nucleotides and loop of eighteen nucleotides using partially both arms to hybridize its target (two nucleotides of every arm). Notice that a target that makes possible the design of a MB that hybridizes it using completely both arms could have a strong secondary structure that makes impossible the MB-target hybridization.
