title: FRET Characterization of Complex Conformational Changes in a Large 16S Ribosomal RNA Fragment Site-Specifically Labeled Using Unnatural Base Pairs.
abstract: Ribosome assembly has been studied intensively using Förster resonance energy transfer (FRET) with fluorophore-labeled fragments of RNA produced by chemical synthesis. However, these studies are limited by the size of the accessible RNA fragments. We have developed a replicable unnatural base pair (UBP) formed between (d)5SICS and (d)MMO2 or (d)NaM, which efficiently directs the transcription of RNA containing unnatural nucleotides. We now report the synthesis and evaluation of several of the corresponding ribotriphosphates bearing linkers that enable the chemoselective attachment of different functionalities. We found that the RNA polymerase from T7 bacteriophage does not incorporate NaM derivatives but does efficiently incorporate 5SICS(CO), whose linker enables functional group conjugation via Click chemistry, and when combined with the previously identified MMO2(A), whose amine side chains permits conjugation via NHS coupling chemistry, enables site-specific double labeling of transcribed RNA. To study ribosome assembly, we transcribed RNA corresponding to a 243-nt fragment of the central domain of Thermus thermophilus 16S rRNA containing 5SICS(CO) and MMO2(A) at defined locations and then site-specifically attached the fluorophores Cy3 and Cy5. FRET was characterized using single-molecule total internal reflection fluorescence (smTIRF) microscopy in the presence of various combinations of added ribosomal proteins. We demonstrate that each of the fragment's two three-helix junctions exist in open and closed states, with the latter favored by sequential protein binding. These results elucidate early and previously uncharacterized folding events underlying ribosome assembly and demonstrate the applicability of UBPs for biochemical, structural, and functional studies of RNAs.
authors.affiliation: Department of Chemistry and ‡Department of Integrative Structural and Computational Biology, The Scripps Research Institute , 10550 N. Torrey Pines Road, La Jolla, California 92037, United States.
authors.forename: Thomas
authors.initials: T
authors.lastname: Lavergne
authors.affiliation: Department of Chemistry and ‡Department of Integrative Structural and Computational Biology, The Scripps Research Institute , 10550 N. Torrey Pines Road, La Jolla, California 92037, United States.
authors.forename: Rajan
authors.initials: R
authors.lastname: Lamichhane
authors.affiliation: Department of Chemistry and ‡Department of Integrative Structural and Computational Biology, The Scripps Research Institute , 10550 N. Torrey Pines Road, La Jolla, California 92037, United States.
authors.forename: Denis A
authors.initials: DA
authors.lastname: Malyshev
authors.affiliation: Department of Chemistry and ‡Department of Integrative Structural and Computational Biology, The Scripps Research Institute , 10550 N. Torrey Pines Road, La Jolla, California 92037, United States.
authors.forename: Zhengtao
authors.initials: Z
authors.lastname: Li
authors.affiliation: Department of Chemistry and ‡Department of Integrative Structural and Computational Biology, The Scripps Research Institute , 10550 N. Torrey Pines Road, La Jolla, California 92037, United States.
authors.forename: Lingjun
authors.initials: L
authors.lastname: Li
authors.affiliation: Department of Chemistry and ‡Department of Integrative Structural and Computational Biology, The Scripps Research Institute , 10550 N. Torrey Pines Road, La Jolla, California 92037, United States.
authors.forename: Edit
authors.initials: E
authors.lastname: Sperling
authors.affiliation: Department of Chemistry and ‡Department of Integrative Structural and Computational Biology, The Scripps Research Institute , 10550 N. Torrey Pines Road, La Jolla, California 92037, United States.
authors.forename: James R
authors.initials: JR
authors.lastname: Williamson
authors.affiliation: Department of Chemistry and ‡Department of Integrative Structural and Computational Biology, The Scripps Research Institute , 10550 N. Torrey Pines Road, La Jolla, California 92037, United States.
authors.forename: David P
authors.initials: DP
authors.lastname: Millar
authors.affiliation: Department of Chemistry and ‡Department of Integrative Structural and Computational Biology, The Scripps Research Institute , 10550 N. Torrey Pines Road, La Jolla, California 92037, United States.
authors.forename: Floyd E
authors.initials: FE
authors.lastname: Romesberg
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D002232:Carbocyanines / Q000737:chemistry; D031541:Fluorescence Resonance Energy Transfer; D005456:Fluorescent Dyes / Q000737:chemistry; D012329:RNA, Bacterial / Q000737:chemistry*; D012336:RNA, Ribosomal, 16S / Q000737:chemistry*; D016963:Thermus thermophilus / Q000737:chemistry*
chemical_list: D002232:Carbocyanines; D005456:Fluorescent Dyes; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; C089187:cyanine dye 3; C085321:cyanine dye 5