5′-Bispyrene molecular beacons for RNA detection

Abstract

New fluorescent excimer-forming 5′-bispyrene molecular beacons for the detection of RNA were designed. The probes are 2′-O-methyl RNAs containing 5′-bispyrenylmethylphosphorodiamidate group (bispyrene group) at the 5′-end and a fluorescence quencher (BHQ1) at the 3′-end. A comparative study of the fluorescent properties of the probes having different distance between 5′-bispyrene group and target RNA upon the formation of hybridization complex was performed. The probes with bispyrene group located in the close proximity to the duplex exhibit the greatest excimer fluorescence upon binding to a complementary the 43-nt target RNA, in contrast to the probes with 5′-bispyrene group at dangling end. The feasibility of the new probes for visualization of intracellular RNA was demonstrated using 28S rRNA as a target. The results obtained confirm that the probes proposed in the study can be used as selective tools for RNA detection.