Stemless self-quenching reporter molecules identify target sequences in mRNA

Abstract The design of oligonucleotides for gene silencing requires a rational method for identifying hybridization-accessible sequences within the target RNA. To this end, we have developed stem–loop self-quenching reporter molecules (SQRMs) as probes for such sequence. SQRMs have a 5′ fluorophore, a quenching moiety on the 3′ end, an intervening sequence that forms an ∼5-basepaired stem, and a loop sequence of ∼20–30 bases. We have previously described a mapping strategy employing SQRMs to locate stem–loop structures in the target mRNA molecule. We now show that the original design constraint of a basepaired stem is not needed, either in vitro or in vivo. We propose that stemless probes possess sufficient signal-to-noise for use in vivo and that this ratio is an indication of hybridization of the probe to its target. Data showing that these SQRMs can specifically target and reduce c-Myb protein synthesis and can be used for real-time in vivo assays are presented.