title: RNA complex purification using high-affinity fluorescent RNA aptamer tags.
abstract: RNA plays important roles in cellular processes, but RNA-protein complexes are notoriously hard to isolate and study. We compare and contrast existing RNA- and protein-purification strategies with the potential of new RNA-tagging systems such as RNA Spinach and RNA Mango. Each RNA aptamer binds a small fluorophore, resulting in a highly fluorescent complex that is thousands of times brighter than the unbound fluorophore. Provided that the aptamer binding affinity is high enough, derivatized dyes can be used in conjunction with these aptamers to purify RNA complexes while simultaneously using their intrinsic fluorescence to track the complex of interest. The known strengths and weakness of these RNA tagging systems are discussed.
authors.affiliation: Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada.
authors.forename: Shanker Shyam S
authors.initials: SS
authors.lastname: Panchapakesan
authors.forename: Sunny C Y
authors.initials: SC
authors.lastname: Jeng
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Unrau
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry / Q000378:metabolism*; D001483:Base Sequence; D001667:Binding, Competitive; D049452:Green Fluorescent Proteins / Q000737:chemistry / Q000378:metabolism*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D012313:RNA / Q000737:chemistry / Q000302:isolation & purification* / Q000378:metabolism*
chemical_list: D052157:Aptamers, Nucleotide; D049452:Green Fluorescent Proteins; D012313:RNA
keywords: RNA Mango; RNA aptamers; RNA purification tags; binding affinity; fluorescent enhancement; in vitro selection