title: Site-specific fluorescent labeling of large RNAs with pyrene.
abstract: Pyrene is a useful chromophore for monitoring the tertiary structure and folding of large RNAs. This unit describes the general preparation of a large RNA (>80 nucleotides in length) that has been site-specifically modified with pyrene at the 2'-position of an individual internal nucleotide. A protocol is provided for derivatizing a 2'-amino-RNA oligonucleotide with a suitably activated pyrene reagent. This pyrene-labeled oligonucleotide is then assembled with other RNA(s) either by covalent ligation or by noncovalent hybridization to form a full-length structured RNA, which may then be studied by equilibrium and stopped-flow fluorescence spectroscopy.
authors.affiliation: University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
authors.forename: Mary K
authors.initials: MK
authors.lastname: Smalley
authors.forename: Scott K
authors.initials: SK
authors.lastname: Silverman
mesh_terms: D005456:Fluorescent Dyes / Q000737:chemistry*; D009841:Oligonucleotides / Q000737:chemistry*; D011721:Pyrenes / Q000737:chemistry*; D012313:RNA / Q000737:chemistry*; D015347:RNA Probes / Q000737:chemistry*; D013050:Spectrometry, Fluorescence
chemical_list: D005456:Fluorescent Dyes; D009841:Oligonucleotides; D011721:Pyrenes; D015347:RNA Probes; D012313:RNA