ArticleMethods in molecular biology (Clifton, N.J.)2012
Crystallographic analysis of small ribozymes and riboswitches.
Article in Methods in molecular biology (Clifton, N.J.), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 22 citations in OpenAlex.
- Two riboswitch classes that share a common ligand-binding fold show major differences in the ability to accommodate mutations.Nucleic acids research · 2024Article
- Full-Length NADBiochemistry · 2023Article
- Structure and function analysis of a type III preQThe Journal of biological chemistry · 2023Article
- A riboswitch separated from its ribosome-binding site still regulates translation.Nucleic acids research · 2023Article
- Synthetic biology tools to promote the folding and function of RNA aptamers in mammalian cells.RNA biology · 2023Article
- A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control.Nature communications · 2022Article
- Engineering Crystal Packing in RNA Structures I: Past and Future Strategies for Engineering RNA Packing in Crystals.Crystals · 2021Article
- Affinity and Structural Analysis of the U1A RNA Recognition Motif with Engineered Methionines to Improve Experimental Phasing.Crystals · 2021Article
- Co-crystal structures of HIV TAR RNA bound to lab-evolved proteins show key roles for arginine relevant to the design of cyclic peptide TAR inhibitors.The Journal of biological chemistry · 2020Article
- Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation.Nucleic acids research · 2020Article
- Nucleobase mutants of a bacterial preQThe Journal of biological chemistry · 2020Article
- Observation of preQRNA biology · 2019Article
- Coupling Green Fluorescent Protein Expression with Chemical Modification to Probe Functionally Relevant Riboswitch Conformations in Live Bacteria.Biochemistry · 2018Article
- Structure of HIV TAR in complex with a Lab-Evolved RRM provides insight into duplex RNA recognition and synthesis of a constrained peptide that impairs transcription.Nucleic acids research · 2018Article
- Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- ITC analysis of ligand binding to preQ₁ riboswitches.Methods in enzymology · 2014Article
- Structure of a class II preQ1 riboswitch reveals ligand recognition by a new fold.Nature chemical biology · 2013Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Ribozymes and riboswitches are RNA motifs that accelerate biological reactions and regulate gene expression in response to metabolite recognition, respectively. These RNA molecules gain functionality via complex folding that cannot be predicted a priori, and thus requires high-resolution three-dimensional structure determination to locate key functional attributes. Herein, we present an overview of the methods used to determine small RNA structures with an emphasis on RNA preparation, crystallization, and structure refinement. We draw upon examples from our own research in the analysis of the leadzyme ribozyme, the hairpin ribozyme, a class I preQ(1) riboswitch, and variants of a larger class II preQ(1) riboswitch. The methods presented provide a guide for comparable investigations of noncoding RNA molecules including a 48-solution, "first choice" RNA crystal screen compiled from our prior successes with commercially available screens.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.