title: RNA mango aptamer-fluorophore: a bright, high-affinity complex for RNA labeling and tracking.
abstract: Because RNA lacks strong intrinsic fluorescence, it has proven challenging to track RNA molecules in real time. To address this problem and to allow the purification of fluorescently tagged RNA complexes, we have selected a high affinity RNA aptamer called RNA Mango. This aptamer binds a series of thiazole orange (fluorophore) derivatives with nanomolar affinity, while increasing fluorophore fluorescence by up to 1,100-fold. Visualization of RNA Mango by single-molecule fluorescence microscopy, together with injection and imaging of RNA Mango/fluorophore complex in C. elegans gonads demonstrates the potential for live-cell RNA imaging with this system. By inserting RNA Mango into a stem loop of the bacterial 6S RNA and biotinylating the fluorophore, we demonstrate that the aptamer can be used to simultaneously fluorescently label and purify biologically important RNAs. The high affinity and fluorescent properties of RNA Mango are therefore expected to simplify the study of RNA complexes.
authors.affiliation: Department of Molecular Biology and Biochemistry and ‡Department of Chemistry, Simon Fraser University , 8888 University Road, Burnaby, British Columbia V5A 1S6, Canada.
authors.forename: Elena V
authors.initials: EV
authors.lastname: Dolgosheina
authors.forename: Sunny C Y
authors.initials: SC
authors.lastname: Jeng
authors.forename: Shanker Shyam S
authors.initials: SS
authors.lastname: Panchapakesan
authors.forename: Razvan
authors.initials: R
authors.lastname: Cojocaru
authors.forename: Patrick S K
authors.initials: PS
authors.lastname: Chen
authors.forename: Peter D
authors.initials: PD
authors.lastname: Wilson
authors.forename: Nancy
authors.initials: N
authors.lastname: Hawkins
authors.forename: Paul A
authors.initials: PA
authors.lastname: Wiggins
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Unrau
mesh_terms: D000818:Animals; D052157:Aptamers, Nucleotide / Q000737:chemistry / Q000378:metabolism*; D052160:Benzothiazoles / Q000737:chemistry; D001710:Biotin / Q000378:metabolism; D017173:Caenorhabditis elegans / Q000235:genetics* / Q000378:metabolism; D005456:Fluorescent Dyes / Q000737:chemistry*; D006066:Gonads / Q000378:metabolism; D049452:Green Fluorescent Proteins / Q000737:chemistry / Q000378:metabolism; D031022:Mangifera / Q000737:chemistry; D008856:Microscopy, Fluorescence; D011804:Quinolines / Q000737:chemistry; D012313:RNA / Q000737:chemistry / Q000302:isolation & purification* / Q000378:metabolism*; D012329:RNA, Bacterial / Q000737:chemistry* / Q000378:metabolism; D022661:RNA, Untranslated / Q000737:chemistry* / Q000378:metabolism; D018724:Spinacia oleracea / Q000737:chemistry
chemical_list: C411065:6S RNA; D052157:Aptamers, Nucleotide; D052160:Benzothiazoles; D005456:Fluorescent Dyes; D011804:Quinolines; D012329:RNA, Bacterial; D022661:RNA, Untranslated; C584549:malachite green RNA aptamer; C051000:thiazole orange; D049452:Green Fluorescent Proteins; D012313:RNA; D001710:Biotin