Terminal dual-labeling of a transcribed RNA

We report here a site-specific terminal dual-labeling strategy for a transcribed RNA. The combination of 5'-thiophosphoryl and 3'-amino functionalities enables efficient RNA dual labeling with different fluorophores at both 5'- and 3'-terminal positions specifically. This dual-labeling strategy is applied to pre-miRNA for construction of molecular beacons. The RNA beacons in their native hairpin formation bring the fluorophore and quencher groups into close proximity, leading to fluorescence quenching by FRET effect. Ribonuclease (dicer enzyme or micrococcal nuclease) can efficiently cleave RNA beacons leading to concentration- and time-dependent fluorescence increase. The dual-labeling strategy for transcribed RNAs involves only commercially available reagents, enzymes and native RNA, making it more accessible for general applications.