The use of molecular beacons to detect and quantify microRNA

Molecular beacons are oligonucleotide (DNA or RNA) probes that have become increasingly important tools for RNA sensitive detection both in vitro and in living cells. From their inception, molecular beacons have been used to determine the expression levels of RNA transcripts, but they also have the specificity to identify splice variants and single-nucleotide polymorphisms. Our group has performed extensive studies on molecular beacon design, molecular beacon hybridization assays, and cellular imaging of mRNA molecules. Compared to other methods for assessing RNA transcript expression, such as qRT-PCR, the beacon-based approach is potentially simpler, faster, more cost effective, and more specific. Recently, our group demonstrated that molecular beacons can readily distinguish mature- and precursor microRNAs, and reliably quantify microRNA expression. MicroRNAs (miRNAs) are a class of short (19-25 nt), single-stranded, noncoding RNAs that regulate an array of cellular functions through the degradation and translational repression of mRNA targets. Importantly, tissue levels of specific miRNAs have been shown to correlate with pathological development of diseases. Thus, a rapid and efficient method of assessing miRNA expression is useful for diagnosing diseases and identifying novel therapeutic targets. Here, we describe the methods for designing and using molecular beacons to detect and quantify miRNA.