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

We appended pyrene units covalently onto adenosine and uridine nucleosides (forming AP and UP 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 (APUP) and 3 (APAP) 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 UPUP system 2 exhibits quenching spectra. Systems 1 (APUP) and 3 (APAP) behave as effective molecular beacons (MBs) that change color from green to blue upon duplex formation, whereas 2 (UPUP) is an effective MB that changes the intensity of its fluorescence upon forming its perfectly matched duplex.