Abstract
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 P U P ) and 3 ( A P A 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 P U P system 2 exhibits quenching spectra. Systems 1 ( A P U P ) and 3 ( A P A P ) behave as effective molecular beacons (MBs) that change color from green to blue upon duplex formation, whereas 2 ( U P U P ) is an effective MB that changes the intensity of its fluorescence upon forming its perfectly matched duplex.
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