title: Site-specific fluorescent probing of RNA molecules by unnatural base-pair transcription for local structural conformation analysis.
abstract: Methods for fluorescent probing at a defined position of RNA provide powerful tools for analyzing the local structural conformation of functional RNA molecules by tracking fluorescence changes. In this article, we describe the site-specific fluorescent probing of RNA by transcription with an expanded genetic alphabet, using an extra, unnatural base pair between 2-amino-6-(2-thienyl)purine (s) and pyrrole-2-carbaldehyde (Pa). The protocol comprises template DNA preparation containing Pa, transcription involving fluorescent s incorporation and structural analysis of transcripts. The s base is strongly fluorescent, and its nucleoside 5'-triphosphate is site-specifically incorporated into RNA transcripts, opposite Pa in DNA templates, by conventional T7 transcription. The fluorescent intensity of s changes depending on its environment around the probe site, providing clues about the local structural features of RNA molecules. This is the first protocol for RNA transcript preparation with fluorescent labeling at a desired position. The procedure for s-containing RNA preparation takes about 2-3 d.
authors.affiliation: TagCyx Biotechnologies, Yokohama, Kanagawa, Japan.
authors.forename: Yasushi
authors.initials: Y
authors.lastname: Hikida
authors.forename: Michiko
authors.initials: M
authors.lastname: Kimoto
authors.forename: Shigeyuki
authors.initials: S
authors.lastname: Yokoyama
authors.forename: Ichiro
authors.initials: I
authors.lastname: Hirao
mesh_terms: D020029:Base Pairing / Q000235:genetics*; D012321:DNA-Directed RNA Polymerases; D005456:Fluorescent Dyes / Q000737:chemistry*; D011687:Purines / Q000737:chemistry*; D011758:Pyrroles; D012313:RNA / Q000737:chemistry* / Q000648:ultrastructure*; D014158:Transcription, Genetic; D014764:Viral Proteins
chemical_list: C435686:2-amino-6-(2-thienyl)purine; D005456:Fluorescent Dyes; D011687:Purines; D011758:Pyrroles; D014764:Viral Proteins; C051266:pyrrole-2-carboxaldehyde; D012313:RNA; C062210:bacteriophage T7 RNA polymerase; D012321:DNA-Directed RNA Polymerases