ArticleACS chemical biology2016
FRET Characterization of Complex Conformational Changes in a Large 16S Ribosomal RNA Fragment Site-Specifically Labeled Using Unnatural Base Pairs.
Article in ACS chemical biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 50 citations in OpenAlex.
- Engineered polymerase-mediated efficient synthesis of site-specifically functionalized RNA and 2'-modified RNA oligonucleotides via genetic alphabet expansion.Nature communications · 2026Article
- High-resolution melting analysis for rapid and cost-effective detection of unnatural base pairs.Biodesign research · 2026Article
- Heck-type C-glycosylations in the synthesis of artificial nucleotides and functional nucleic acids.RSC chemical biology · 2026Review
- Rapid and improved surface passivation method for Single-Molecule experiments.Methods (San Diego, Calif.) · 2026Article
- Omega Nucleic Acids (ΩNA), Ultimate Nucleic Acids for Future Technology.Molecules (Basel, Switzerland) · 2026Review
- Site-Specific Dual-Color Labeling of Long RNAs.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Phosphorothioate-Based Site-Specific Labeling of Large RNAs for Structural and Dynamic Studies.ACS chemical biology · 2022Article
- Analysis tools for single-monomer measurements of self-assembly processes.Scientific reports · 2022Article
- Total RNA Synthesis and its Covalent Labeling Innovation.Topics in current chemistry (Cham) · 2022Review
- Preparation of Site-Specifically Spin-Labeled RNA by in Vitro Transcription Using an Expanded Genetic Alphabet.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Pseudoknot length modulates the folding, conformational dynamics, and robustness of Xrn1 resistance of flaviviral xrRNAs.Nature communications · 2021Article
- Strategies for Covalent Labeling of Long RNAs.Chembiochem : a European journal of chemical biology · 2021Review
- Shape changes and cooperativity in the folding of the central domain of the 16S ribosomal RNA.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Application of Nucleic Acid Frameworks in the Construction of Nanostructures and Cascade Biocatalysts: Recent Progress and Perspective.Frontiers in bioengineering and biotechnology · 2021Review
- Optimization of N-hydroxysuccinimide ester coupling with aminoallyl-modified RNA for fluorescent labeling.Bioengineered · 2020Article
- Posttranscriptional site-directed spin labeling of large RNAs with an unnatural base pair system under non-denaturing conditions.Chemical science · 2020Article
- Site-specific covalent labeling of large RNAs with nanoparticles empowered by expanded genetic alphabet transcription.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- EPR Distance Measurements on Long Non-coding RNAs Empowered by Genetic Alphabet Expansion Transcription.Angewandte Chemie (International ed. in English) · 2020Article
- Simple alkanoyl acylating agents for reversible RNA functionalization and control.Chemical communications (Cambridge, England) · 2019Article
- Real-time assembly of ribonucleoprotein complexes on nascent RNA transcripts.Nature communications · 2018Article
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
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.
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