Quencher-free molecular beacon systems with two pyrene units in the stem region

We appended pyrene units covalently onto adenosine and uridine nucleosides (forming A^P and U^P units, respectively) and then incorporated them into oligonucleotides such that they were positioned in complementary locations in opposite strands in the middle positions of hairpin stems. Systems 1 (A^PU^P) and 3 (A^PA^P) individually exhibit aromatic stacking between the opposing pyrene units in the stems of their hairpins and display in their spectra the photophysical properties of strongly red-shifted bands; in contrast, the U^PU^P system 2 exhibits quenching spectra. Systems 1 (A^PU^P) and 3 (A^PA^P) behave as effective molecular beacons (MBs) that change color from green to blue upon duplex formation, whereas 2 (U^PU^P) is an effective MB that changes the intensity of its fluorescence upon forming its perfectly matched duplex.