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Bush JA, Williams CC, Meyer SM, Tong Y, Haniff HS, Childs-Disney JL, Disney MD. Systematically Studying the Effect of Small Molecules Interacting with RNA in Cellular and Preclinical Models. ACS Chem Biol 2021; 16:1111-1127. [PMID: 34166593 PMCID: PMC8867596 DOI: 10.1021/acschembio.1c00014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The interrogation and manipulation of biological systems by small molecules is a powerful approach in chemical biology. Ideal compounds selectively engage a target and mediate a downstream phenotypic response. Although historically small molecule drug discovery has focused on proteins and enzymes, targeting RNA is an attractive therapeutic alternative, as many disease-causing or -associated RNAs have been identified through genome-wide association studies. As the field of RNA chemical biology emerges, the systematic evaluation of target validation and modulation of target-associated pathways is of paramount importance. In this Review, through an examination of case studies, we outline the experimental characterization, including methods and tools, to evaluate comprehensively the impact of small molecules that target RNA on cellular phenotype.
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Affiliation(s)
- Jessica A Bush
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Christopher C Williams
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Samantha M Meyer
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Yuquan Tong
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Hafeez S Haniff
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jessica L Childs-Disney
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Matthew D Disney
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
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2
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Zhan H, Li A, Cai Z, Huang W, Liu Y. Improving transgene expression and CRISPR-Cas9 efficiency with molecular engineering-based molecules. Clin Transl Med 2020; 10:e194. [PMID: 33135339 PMCID: PMC7533053 DOI: 10.1002/ctm2.194] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/08/2020] [Accepted: 09/18/2020] [Indexed: 01/04/2023] Open
Abstract
As a novel and robust gene‐editing tool, the Clustered Regularly Interspaced Short Palindromic Repeats CRISPR‐associated protein 9 (CRISPR‐Cas9) system has revolutionized gene therapy. Plasmid vector delivery is the most commonly used method for integrating the CRISPR‐Cas9 system into cells. However, such foreign cytosolic DNAs trigger an innate immune response (IIR) within cells, which can hinder gene editing by inhibiting transgene expression. Although some small molecules have been shown to avoid the action of IIR on plasmids, they only work on a single target and may also affect cell viability. A genetic approach that works at a comprehensive level for manipulating IIR is still lacking. Here, we designed and constructed several artificial nucleic acid molecules (ANAMs), which are combinations of aptamers binding to two key players of IIR (β‐catenin and NF‐κB). ANAMs strongly inhibited the IIR in cells, thus improving transgene expression. We also used ANAMs to improve the gene‐editing efficiency of the CRISPR‐Cas9 system and its derivatives, thus enhancing the apoptosis of cancer cells induced by CRISPR‐Cas9. ANAMs can be valuable tools for improving transgene expression and gene editing in mammalian cells.
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Affiliation(s)
- Hengji Zhan
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.,Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen, China
| | - Aolin Li
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.,Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen, China
| | - Zhiming Cai
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.,Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen, China
| | - Weiren Huang
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.,Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen, China
| | - Yuchen Liu
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.,Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen, China
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3
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Kasprzak WK, Ahmed NA, Shapiro BA. Modeling ligand docking to RNA in the design of RNA-based nanostructures. Curr Opin Biotechnol 2020; 63:16-25. [DOI: 10.1016/j.copbio.2019.10.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 10/30/2019] [Indexed: 12/30/2022]
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Shaver ZM, Bent SS, Bilby SR, Brown M, Buser A, Cuellar IG, Davis AJ, Doolan L, Enriquez FC, Estrada A, Herner S, Herron JC, Hunn AM, Hunter M, Johnston H, Koucky O, Mackley CC, Maghini D, Mattoon D, McDonald HT, Sinks H, Sprague AJ, Sullivan D, Tutar A, Umphreys A, Watson C, Zweerink D, Heyer LJ, Poet JL, Eckdahl TT, Campbell AM. Attempted use of PACE for riboswitch discovery generates three new translational theophylline riboswitch side products. BMC Res Notes 2018; 11:861. [PMID: 30518404 PMCID: PMC6280357 DOI: 10.1186/s13104-018-3965-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 11/29/2018] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE The purpose of this project was to use an in vivo method to discover riboswitches that are activated by new ligands. We employed phage-assisted continuous evolution (PACE) to evolve new riboswitches in vivo. We started with one translational riboswitch and one transcriptional riboswitch, both of which were activated by theophylline. We used xanthine as the new target ligand during positive selection followed by negative selection using theophylline. The goal was to generate very large M13 phage populations that contained unknown mutations, some of which would result in new aptamer specificity. We discovered side products of three new theophylline translational riboswitches with different levels of protein production. RESULTS We used next generation sequencing to identify M13 phage that carried riboswitch mutations. We cloned and characterized the most abundant riboswitch mutants and discovered three variants that produce different levels of translational output while retaining their theophylline specificity. Although we were unable to demonstrate evolution of new riboswitch ligand specificity using PACE, we recommend careful design of recombinant M13 phage to avoid evolution of "cheaters" that short circuit the intended selection pressure.
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Affiliation(s)
| | | | - Steven R Bilby
- Department of Biology, Missouri Western State University, Saint Joseph, USA
| | - Michael Brown
- Department of Computer Science, Math, and Physics, Missouri Western State University, Saint Joseph, USA
| | - Anna Buser
- Department of Biology, Davidson College, Davidson, USA
| | | | - Athena J Davis
- Department of Biology, Missouri Western State University, Saint Joseph, USA
| | - Lindsay Doolan
- Department of Biology, Missouri Western State University, Saint Joseph, USA
| | | | - Autumn Estrada
- Department of Computer Science, Math, and Physics, Missouri Western State University, Saint Joseph, USA
| | - Shelby Herner
- Department of Biology, Missouri Western State University, Saint Joseph, USA
| | - J Cody Herron
- Department of Biology, Davidson College, Davidson, USA
| | - Andrew M Hunn
- Department of Biology, Missouri Western State University, Saint Joseph, USA
| | | | | | - Owen Koucky
- Department of Biology, Davidson College, Davidson, USA
| | | | - Dylan Maghini
- Department of Biology, Davidson College, Davidson, USA.,Department of Math and Computer Science, Davidson College, Davidson, USA
| | - Devin Mattoon
- Department of Computer Science, Math, and Physics, Missouri Western State University, Saint Joseph, USA
| | - Haden T McDonald
- Department of Computer Science, Math, and Physics, Missouri Western State University, Saint Joseph, USA
| | - Hannah Sinks
- Department of Biology, Davidson College, Davidson, USA.,Department of Math and Computer Science, Davidson College, Davidson, USA
| | - Austin J Sprague
- Department of Computer Science, Math, and Physics, Missouri Western State University, Saint Joseph, USA
| | - David Sullivan
- Department of Computer Science, Math, and Physics, Missouri Western State University, Saint Joseph, USA
| | - Altan Tutar
- Department of Math and Computer Science, Davidson College, Davidson, USA
| | - Avery Umphreys
- Department of Biology, Missouri Western State University, Saint Joseph, USA
| | - Chris Watson
- Department of Biology, Missouri Western State University, Saint Joseph, USA
| | - Daniel Zweerink
- Department of Computer Science, Math, and Physics, Missouri Western State University, Saint Joseph, USA
| | - Laurie J Heyer
- Department of Math and Computer Science, Davidson College, Davidson, USA
| | - Jeffrey L Poet
- Department of Computer Science, Math, and Physics, Missouri Western State University, Saint Joseph, USA
| | - Todd T Eckdahl
- Department of Biology, Missouri Western State University, Saint Joseph, USA
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Affiliation(s)
- Amanda L. Garner
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan USA
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Abstract
Biological RNA architectures are composed of autonomously folding modules which can be tailored as building blocks for the construction of RNA nanostructures. Designed base pair interactions allow complex nano-objects to self-assemble from simple RNA motifs. X-ray crystallography plays an important role in both the design and analysis of such RNA nanostructures. Here, we describe methods for the design and X-ray crystallographic structure analysis of an RNA square and two different triangles, which self-assemble from short oligonucleotides and serve as a platform for building functional nano-sized nucleic acid architectures.
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Affiliation(s)
- Mark A Boerneke
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Thomas Hermann
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
- Center for Drug Discovery Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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7
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Liu Y, Zhan Y, Chen Z, He A, Li J, Wu H, Liu L, Zhuang C, Lin J, Guo X, Zhang Q, Huang W, Cai Z. Directing cellular information flow via CRISPR signal conductors. Nat Methods 2016; 13:938-944. [PMID: 27595406 DOI: 10.1038/nmeth.3994] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 08/08/2016] [Indexed: 12/20/2022]
Abstract
The complex phenotypes of eukaryotic cells are controlled by decision-making circuits and signaling pathways. A key obstacle to implementing artificial connections in signaling networks has been the lack of synthetic devices for efficient sensing, processing and control of biological signals. By extending sgRNAs to include modified riboswitches that recognize specific signals, we can create CRISPR-Cas9-based 'signal conductors' that regulate transcription of endogenous genes in response to external or internal signals of interest. These devices can be used to construct all the basic types of Boolean logic gates that perform logical signal operations in mammalian cells without needing the layering of multiple genetic circuits. They can also be used to rewire cellular signaling events by constructing synthetic links that couple different signaling pathways. Moreover, this approach can be applied to redirect oncogenic signal transduction by controlling simultaneous bidirectional (ON-OFF) gene transcriptions, thus enabling reprogramming of the fate of cancer cells.
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Affiliation(s)
- Yuchen Liu
- State Engineering Laboratory of Medical Key Technologies Application of Synthetic Biology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Yonghao Zhan
- State Engineering Laboratory of Medical Key Technologies Application of Synthetic Biology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Zhicong Chen
- State Engineering Laboratory of Medical Key Technologies Application of Synthetic Biology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Anbang He
- State Engineering Laboratory of Medical Key Technologies Application of Synthetic Biology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Jianfa Li
- State Engineering Laboratory of Medical Key Technologies Application of Synthetic Biology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen, China
- State Engineering Laboratory of Medical Key Technologies Application of Synthetic Biology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Hanwei Wu
- State Engineering Laboratory of Medical Key Technologies Application of Synthetic Biology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Li Liu
- State Engineering Laboratory of Medical Key Technologies Application of Synthetic Biology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Chengle Zhuang
- State Engineering Laboratory of Medical Key Technologies Application of Synthetic Biology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Junhao Lin
- State Engineering Laboratory of Medical Key Technologies Application of Synthetic Biology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Xiaoqiang Guo
- State Engineering Laboratory of Medical Key Technologies Application of Synthetic Biology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Qiaoxia Zhang
- State Engineering Laboratory of Medical Key Technologies Application of Synthetic Biology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Weiren Huang
- State Engineering Laboratory of Medical Key Technologies Application of Synthetic Biology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Zhiming Cai
- State Engineering Laboratory of Medical Key Technologies Application of Synthetic Biology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen, China
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Hermann T. Small molecules targeting viral RNA. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:726-743. [PMID: 27307213 PMCID: PMC7169885 DOI: 10.1002/wrna.1373] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 04/29/2016] [Accepted: 05/23/2016] [Indexed: 02/06/2023]
Abstract
Highly conserved noncoding RNA (ncRNA) elements in viral genomes and transcripts offer new opportunities to expand the repertoire of drug targets for the development of antiinfective therapy. Ligands binding to ncRNA architectures are able to affect interactions, structural stability or conformational changes and thereby block processes essential for viral replication. Proof of concept for targeting functional RNA by small molecule inhibitors has been demonstrated for multiple viruses with RNA genomes. Strategies to identify antiviral compounds as inhibitors of ncRNA are increasingly emphasizing consideration of drug‐like properties of candidate molecules emerging from screening and ligand design. Recent efforts of antiviral lead discovery for RNA targets have provided drug‐like small molecules that inhibit viral replication and include inhibitors of human immunodeficiency virus (HIV), hepatitis C virus (HCV), severe respiratory syndrome coronavirus (SARS CoV), and influenza A virus. While target selectivity remains a challenge for the discovery of useful RNA‐binding compounds, a better understanding is emerging of properties that define RNA targets amenable for inhibition by small molecule ligands. Insight from successful approaches of targeting viral ncRNA in HIV, HCV, SARS CoV, and influenza A will provide a basis for the future exploration of RNA targets for therapeutic intervention in other viral pathogens which create urgent, unmet medical needs. Viruses for which targeting ncRNA components in the genome or transcripts may be promising include insect‐borne flaviviruses (Dengue, Zika, and West Nile) and filoviruses (Ebola and Marburg). WIREs RNA 2016, 7:726–743. doi: 10.1002/wrna.1373 This article is categorized under:
RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Interactions with Proteins and Other Molecules > Small Molecule–RNA Interactions Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs
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Affiliation(s)
- Thomas Hermann
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA. .,Center for Drug Discovery Innovation, University of California, San Diego, La Jolla, CA, USA.
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Boerneke MA, Dibrov SM, Hermann T. Kristallstruktur-geleitetes Design selbstorganisierender RNA-Nanodreiecke. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201600233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Mark A. Boerneke
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093 USA
| | - Sergey M. Dibrov
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093 USA
| | - Thomas Hermann
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093 USA
- Center for Drug Discovery Innovation; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093 USA
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Boerneke MA, Dibrov SM, Hermann T. Crystal-Structure-Guided Design of Self-Assembling RNA Nanotriangles. Angew Chem Int Ed Engl 2016; 55:4097-100. [PMID: 26914842 DOI: 10.1002/anie.201600233] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 01/25/2016] [Indexed: 12/11/2022]
Abstract
RNA nanotechnology uses RNA structural motifs to build nanosized architectures that assemble through selective base-pair interactions. Herein, we report the crystal-structure-guided design of highly stable RNA nanotriangles that self-assemble cooperatively from short oligonucleotides. The crystal structure of an 81 nucleotide nanotriangle determined at 2.6 Å resolution reveals the so-far smallest circularly closed nanoobject made entirely of double-stranded RNA. The assembly of the nanotriangle architecture involved RNA corner motifs that were derived from ligand-responsive RNA switches, which offer the opportunity to control self-assembly and dissociation.
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Affiliation(s)
- Mark A Boerneke
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Sergey M Dibrov
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Thomas Hermann
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA. .,Center for Drug Discovery Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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11
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Conformational flexibility of viral RNA switches studied by FRET. Methods 2015; 91:35-39. [PMID: 26381686 DOI: 10.1016/j.ymeth.2015.09.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 09/10/2015] [Accepted: 09/14/2015] [Indexed: 12/19/2022] Open
Abstract
The function of RNA switches involved in the regulation of transcription and translation relies on their ability to adopt different, structurally well-defined states. A new class of ligand-responsive RNA switches, which we recently discovered in positive strand RNA viruses, are distinct from conventional riboswitches. The viral switches undergo large conformational changes in response to ligand binding while retaining the same secondary structure in their free and ligand-bound forms. Here, we describe FRET experiments to study folding and ligand binding of the viral RNA switches. In addition to reviewing previous approaches involving RNA model constructs which were directly conjugated with fluorescent dyes, we outline the design and application of new modular constructs for FRET experiments, in which dye labeling is achieved by hybridization of a core RNA switch module with universal DNA fluorescent probes. As an example, folding and ligand binding of the RNA switch from the internal ribosome entry site of hepatitis C virus is studied comparatively with conventional and modular FRET constructs.
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