Pseudo-Dumbbell-Type Molecular Beacon Probes Bearing Modified Deoxyuridine Derivatives and a Silylated Pyrene as a Fluorophore

Abstract We have recently reported a novel pseudo-dumbbell-type molecular beacon probe (Probe 1) possessing polyamine-connected deoxyuridine (U) and silylated pyrene. The probe showed weak fluorescence signal while it stayed alone. Fluorescence signal of the probe was increased in the presence of the complementary DNA. In this study, we prepared new molecular beacons, Probe 2 and Probe 3, possessing the elongated stem portion of Probe 1. In addition, one U in Probe 2 is substituted by anthraquinone-bearing deoxyuridine residue (Y) in Probe 3. Probe 4 is essentially the same as Probe 1 but one deoxyguanosine in the loop portion of Probe 1 is substituted by deoxyinosine in Probe 4. In Probe 5, 3′-terminal deoxycytidine of Probe 3 is substituted by deoxyadenosine. The fluorescence signal of these probes is effectively quenched in the absence of target DNA. Among all, Probe 3 shows the most effective quenching. On the other hand, the signal is substantially increased in the presence of complementary DNA. The ratio of signal to background in case of Probe 3 is the highest. All these probes also recognize single nucleotide alternation in the target DNA to a different extent. The sequence recognition ability of Probe 3 is also the highest among all the probes.