title: A stem-less probe using spontaneous pairing between Cy3 and quencher for RNA detection.
abstract: We herein report a stem-less probe for the detection of RNA that depends on pairing between Cy3 and nitro methyl red. In our design, two Cy3 residues and two nitro methyl red residues were introduced into an oligonucleotide. In the absence of the target, these dyes formed a complex, and emission of Cy3 was efficiently quenched. Hybridization with the target RNA disrupted this interaction and resulted in Cy3 emission. Under optimized conditions, the signal to background ratio was as high as 180. We demonstrated specific detection of target RNA in cells using a wash-free FISH protocol.
authors.affiliation: Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya464-8603, Japan; Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama332-0012, Japan.
authors.forename: Hiromu
authors.initials: H
authors.lastname: Kashida
authors.affiliation: Graduate School of Engineering, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8603 , Japan.
authors.forename: Kazuhiro
authors.initials: K
authors.lastname: Morimoto
authors.affiliation: Graduate School of Engineering, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8603 , Japan.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Asanuma
keywords: 101 Self-assembly/Self-organized materials; 208 Sensors and actuators; 30 Bio-inspired and biomedical materials; 301 Chemical syntheses/processing; 501 Chemical analyses; 505 Optical/Molecular spectroscopy; Cy3; DNA; Fluorescence in situ hybridization; RNA imaging