In-Line Probing Analysis of Riboswitches
Abstract
Riboswitches are intricate, metabolite-binding RNA structures found in the non-coding regions of mRNA. Allosteric changes in the riboswitch that are induced by metabolite binding are harnessed to control the genes of a variety of essential metabolic pathways in eubacteria and in some eukaryotes. In this chapter, we describe an RNA structure analysis technique called "in-line probing." This assay makes use of the natural instability of RNA to elucidate secondary structure characteristics and ligand-binding capabilities of riboswitches in an entirely protein-free manner. Although this method has most frequently been used to examine riboswitches, the structures of any RNAs can be examined using this technique.
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Sequences were filtered for low experimental noise and to ensure that the structure predicted in ViennaRNA matched the structure inferred through SHAPE mapping data collected at the same time; these filters resulted in 2165 sequences and corresponding secondary structures.
“For analysis of sequence and structure motifs, sequences were filtered for low experimental noise and to ensure that the structure predicted in ViennaRNA66 matched the structure inferred through SHAPE mapping data collected at the same time (see Methods); these filters resulted in 2165 sequences and corresponding secondary structures.”
From Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics (2022) · cites this paper as [66]
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Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics
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Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics
Leppek, K., Byeon, G. W., Kladwang, W., Wayment-Steele, H. K., Kerr, C. H., Xu, A. F., Kim, D. S., Topkar, V. V., Choe, C., Rothschild, D., et al. (2021) · doi:10.1101/2021.03.29.437587 · Cited by 399 · see citing works
Theoretical basis for stabilizing messenger RNA through secondary structure design
Wayment-Steele, H. K., Kim, D. S., Choe, C. A., Nicol, J. J., Wellington-Oguri, R., Watkins, A. M., Parra Sperberg, R. A., Huang, P.-S., Participants, E., & Das, R. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab764 · Cited by 197 · see citing works
- Authors
- Regulski, E. E., & Breaker, R. R.
- Affiliations
- Yale University (US)
- Howard Hughes Medical Institute (US)
- ORCID
- Breaker, Ronald R.
- Venue
- Methods In Molecular Biology™
- Publisher
- Humana Press
- Published
- 2008
- Volume
- 419
- Pages
- 53-67
- ISSN
- 1064-3745 (ISSN-L)
- 1940-6029
- OpenAlex
- W68267872
- Cited by
- 338
- References
- 0
- Citations by year
- 2026: 5 · 2025: 17 · 2024: 16 · 2023: 15 · 2022: 23 · 2021: 23 · 2020: 19 · 2019: 19 · 2018: 26 · 2017: 21 · 2016: 21 · 2015: 30 · 2014: 19 · 2013: 23 · 2012: 15
- FWCI
- 19.17
- Type
- book chapter
- Language
- en
- Open access
- closed
- Locations
- Methods in molecular biology (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Keywords
- riboswitches, RNA secondary structure, ligand binding, allosteric regulation, metabolite binding, RNA structure analysis
- MeSH terms
- Bacteria, Base Sequence, Binding Sites, Electrophoresis, Polyacrylamide Gel, Ligands, Molecular Sequence Data, Nucleic Acid Conformation, RNA, Bacterial, Transcription, Genetic, Molecular Probe Techniques, DNA Primers, RNA Stability, RNA, Untranslated
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