Molecular beacons closed" conformation

Figure 2.8a. Schematic representation of excimer-monomer switching molecular beacons (EMS MBs). EMS-MBs were dually labeled with pyrene at both 3 and S ends of single-stranded oligonucleotides with a stem-and-loop structure. In tlie absence of target DNAs. the slem-close-shaped EMS MBs predominantly emit the exclmer fluorescence (yellow-green). Upon hybridization with target DNAs, the EMS-MBs undergo the ilynamic conformational change to emit the monoincr fluorescence (pale Uue).

Figure 5.1 Sketch of the DNA molecular beacon. The five bases at the two ends of the beacon are complementary to each other. The size of the loop and its content are varied. The beacon flips between open and closed states with the characteristic rates and k+.Thefluorophore(F)and the quencher (Q) are covalently linked to the two arms of the beacon. In the open state the beacon fluoresces, in the closed state the fluorescence is quenched. Reprinted with permission from Bonnet etal., Kinetics of conformational fluctuations in DNA hairpin-loops. Proceedings of the National Academy of Sciences of the United States of America 95 (1998) 8602-8606. Copyright 1998 NationalAcademy of Sciences, USA.

Enzyme activation. In addition to DNA/RNA chains, peptides can also be used to construct molecular beacons, termed peptide-based photodynamic molecular beacons (PPMBs), where the PS and quencher, initially held close together by the peptide conformation, separate by the action of specific enzymes that cleave the linking sequence. The most-used peptide is caspase-3 ° (GDEVDGSGC) which is cleaved at the underlined sequence by caspase-3 protease. Similar peptides containing the DEVD sequence have been used as well. Another example is FAPMB, a molecular beacon for the fibroblast activation protein, cell-surface... 

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