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Brunderová M, Havlíček V, Matyašovský J, Pohl R, Poštová Slavětínská L, Krömer M, Hocek M. Expedient production of site specifically nucleobase-labelled or hypermodified RNA with engineered thermophilic DNA polymerases. Nat Commun 2024; 15:3054. [PMID: 38594306 PMCID: PMC11004144 DOI: 10.1038/s41467-024-47444-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 03/26/2024] [Indexed: 04/11/2024] Open
Abstract
Innovative approaches to controlled nucleobase-modified RNA synthesis are urgently needed to support RNA biology exploration and to synthesize potential RNA therapeutics. Here we present a strategy for enzymatic construction of nucleobase-modified RNA based on primer-dependent engineered thermophilic DNA polymerases - SFM4-3 and TGK. We demonstrate introduction of one or several different base-modified nucleotides in one strand including hypermodified RNA containing all four modified nucleotides bearing four different substituents, as well as strategy for primer segment removal. We also show facile site-specific or segmented introduction of fluorophores or other functional groups at defined positions in variety of RNA molecules, including structured or long mRNA. Intriguing translation efficacy of single-site modified mRNAs underscores the necessity to study isolated modifications placed at designer positions to disentangle their biological effects and enable development of improved mRNA therapeutics. Our toolbox paves the way for more precise dissecting RNA structures and functions, as well as for construction of diverse types of base-functionalized RNA for therapeutic applications and diagnostics.
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Affiliation(s)
- Mária Brunderová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843, Prague, 2, Czech Republic
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK
| | - Vojtěch Havlíček
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843, Prague, 2, Czech Republic
| | - Ján Matyašovský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic
| | - Lenka Poštová Slavětínská
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic
| | - Matouš Krömer
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic.
- The Rosalind Franklin Institute, Harwell Campus, Didcot, Oxfordshire, UK.
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic.
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843, Prague, 2, Czech Republic.
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2
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Bao L, Xiao Y. Exploring the Binding Process of Cognate Ligand to Add Adenine Riboswitch Aptamer by Using Explicit Solvent Molecular Dynamics (MD) Simulation. Methods Mol Biol 2023; 2568:103-122. [PMID: 36227564 DOI: 10.1007/978-1-0716-2687-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Riboswitches are RNA-structured elements that modulate gene expression by changing their conformation in response to specific metabolite ligand binding. Therefore, the biological functions of riboswitches mainly depend on the switching of secondary and three-dimensional structures in the presence and absence of the metabolite ligands. However, the binding mechanisms of cognate ligands to riboswitches are still not well understood. Here, we have introduced how to use explicit solvent molecular dynamics (MD) simulation to observe the binding process of cognate ligand to add adenine riboswitch aptamer at the atomic level. In addition, we have analyzed the driving factors of the binding process and calculated the binding free energy based on the Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) method.
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Affiliation(s)
- Lei Bao
- School of Public Health, Hubei University of Medicine, Shiyan, China.
| | - Yi Xiao
- Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, China
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3
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Chen J, Zeng Q, Wang W, Sun H, Hu G. Decoding the Identification Mechanism of an SAM-III Riboswitch on Ligands through Multiple Independent Gaussian-Accelerated Molecular Dynamics Simulations. J Chem Inf Model 2022; 62:6118-6132. [PMID: 36440874 DOI: 10.1021/acs.jcim.2c00961] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
S-Adenosyl-l-methionine (SAM)-responsive riboswitches play a central role in the regulation of bacterial gene expression at the level of transcription attenuation or translation inhibition. In this study, multiple independent Gaussian-accelerated molecular dynamics simulations were performed to decipher the identification mechanisms of SAM-III (SMK) on ligands SAM, SAH, and EEM. The results reveal that ligand binding highly affects the structural flexibility, internal dynamics, and conformational changes of SAM-III. The dynamic analysis shows that helices P3 and P4 as well as two junctions J23 and J24 of SAM-III are highly susceptible to ligand binding. Analyses of free energy landscapes suggest that ligand binding induces different free energy profiles of SAM-III, which leads to the difference in identification sites of SAM-III on ligands. The information on ligand-nucleotide interactions not only uncovers that the π-π, cation-π, and hydrogen bonding interactions drive identification of SAM-III on the three ligands but also reveals that different electrostatic properties of SAM, SAH, and EEM alter the active sites of SAM-III. Meanwhile, the results also verify that the adenine group of SAM, SAH, and EEM is well recognized by conserved nucleotides G7, A29, U37, A38, and G48. We expect that this study can provide useful information for understanding the applications of SAM-III in chemical, synthetic RNA biology, and biomedical fields.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan250357, China
| | - Qingkai Zeng
- School of Science, Shandong Jiaotong University, Jinan250357, China
| | - Wei Wang
- School of Science, Shandong Jiaotong University, Jinan250357, China
| | - Haibo Sun
- School of Science, Shandong Jiaotong University, Jinan250357, China
| | - Guodong Hu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou253023, China
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4
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Potential effects of metal ion induced two-state allostery on the regulatory mechanism of add adenine riboswitch. Commun Biol 2022; 5:1120. [PMID: 36273041 PMCID: PMC9588036 DOI: 10.1038/s42003-022-04096-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/11/2022] [Indexed: 11/09/2022] Open
Abstract
Riboswitches normally regulate gene expression through structural changes in response to the specific binding of cellular metabolites or metal ions. Taking add adenine riboswitch as an example, we explore the influences of metal ions (especially for K+ and Mg2+ ions) on the structure and dynamics of riboswitch aptamer (with and without ligand) by using molecular dynamic (MD) simulations. Our results show that a two-state transition marked by the structural deformation at the connection of J12 and P1 (CJ12-P1) is not only related to the binding of cognate ligands, but also strongly coupled with the change of metal ion environments. Moreover, the deformation of the structure at CJ12-P1 can be transmitted to P1 directly connected to the expression platform in multiple ways, which will affect the structure and stability of P1 to varying degrees, and finally change the regulation state of this riboswitch. Molecular dynamic simulations are employed to assess the influence of metal ions on riboswitch structure and dynamics, suggesting a conformational control of riboswitch aptamers by metal ions before ligand binding.
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5
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Dey SK, Filonov GS, Olarerin-George AO, Jackson BT, Finley LWS, Jaffrey SR. Repurposing an adenine riboswitch into a fluorogenic imaging and sensing tag. Nat Chem Biol 2022; 18:180-190. [PMID: 34937909 PMCID: PMC8967656 DOI: 10.1038/s41589-021-00925-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 10/18/2021] [Indexed: 02/02/2023]
Abstract
Fluorogenic RNA aptamers are used to genetically encode fluorescent RNA and to construct RNA-based metabolite sensors. Unlike naturally occurring aptamers that efficiently fold and undergo metabolite-induced conformational changes, fluorogenic aptamers can exhibit poor folding, which limits their cellular fluorescence. To overcome this, we evolved a naturally occurring well-folded adenine riboswitch into a fluorogenic aptamer. We generated a library of roughly 1015 adenine aptamer-like RNAs in which the adenine-binding pocket was randomized for both size and sequence, and selected Squash, which binds and activates the fluorescence of green fluorescent protein-like fluorophores. Squash exhibits markedly improved in-cell folding and highly efficient metabolite-dependent folding when fused to a S-adenosylmethionine (SAM)-binding aptamer. A Squash-based ratiometric sensor achieved quantitative SAM measurements, revealed cell-to-cell heterogeneity in SAM levels and revealed metabolic origins of SAM. These studies show that the efficient folding of naturally occurring aptamers can be exploited to engineer well-folded cell-compatible fluorogenic aptamers and devices.
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Affiliation(s)
- Sourav Kumar Dey
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY, USA
| | - Grigory S. Filonov
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY, USA.,Present address: Sartorius, Ann Arbor, Michigan, USA
| | | | - Benjamin T. Jackson
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lydia W. S. Finley
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samie R. Jaffrey
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY, USA.,
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6
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A transient conformation facilitates ligand binding to the adenine riboswitch. iScience 2021; 24:103512. [PMID: 34927032 PMCID: PMC8652005 DOI: 10.1016/j.isci.2021.103512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/14/2021] [Accepted: 11/22/2021] [Indexed: 11/29/2022] Open
Abstract
RNAs adopt various conformations to perform different functions in cells. Incapable of acquiring intermediates, the key initiations of ligand recognition in the adenine riboswitch have not been characterized. In this work, stopped-flow fluorescence was used to track structural switches in the full-length adenine riboswitch in real time. We used PLOR (position-selective labeling of RNA) to incorporate fluorophores into desired positions in the RNA. The switching sequence P1 responded to adenine more rapidly than helix P4 and the binding pocket, followed by stabilization of the binding pocket, P4, and annealing of P1. Moreover, a transient intermediate consisting of an unwound P1 was detected during adenine binding. These events were observed in both the WT riboswitch and a functional mutant. The findings provide insight into the conformational changes of the riboswitch RNA triggered by a ligand. Real-time tracking of the adenine riboswitch at nucleotide resolution A transient conformation with unwound P1 is identified in the adenine riboswitch Helix P1 responds to ligand quicker than the binding pocket or expression platform
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7
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Abstract
Transcription of DNA into RNA is crucial to life, and understanding RNA polymerase (RNAP) function has received considerable attention. In contrast, how the nascent RNA folds into structures that impact transcription itself and regulate gene expression remains poorly understood. Here, we combine single-molecule Förster resonance energy transfer and site-specific fluorescent labelling of transcripts within native complexes to enable real-time cotranscriptional folding studies of a metabolite-sensing riboswitch from Escherichia coli. By monitoring the folding of riboswitches stalled at RNAP pausing sites and during active elongation, we reveal a crucial role for RNAP, which directs RNA folding to allow thiamin pyrophosphate sensing within a precise, transcriptional hotspot. Our approach offers a unique opportunity to unveil cotranscriptional processes in eukaryotic and bacterial systems. Cotranscriptional RNA folding is crucial for the timely control of biological processes, but because of its transient nature, its study has remained challenging. While single-molecule Förster resonance energy transfer (smFRET) is unique to investigate transient RNA structures, its application to cotranscriptional studies has been limited to nonnative systems lacking RNA polymerase (RNAP)–dependent features, which are crucial for gene regulation. Here, we present an approach that enables site-specific labeling and smFRET studies of kilobase-length transcripts within native bacterial complexes. By monitoring Escherichia coli nascent riboswitches, we reveal an inverse relationship between elongation speed and metabolite-sensing efficiency and show that pause sites upstream of the translation start codon delimit a sequence hotspot for metabolite sensing during transcription. Furthermore, we demonstrate a crucial role of the bacterial RNAP actively delaying the formation, within the hotspot sequence, of competing structures precluding metabolite binding. Our approach allows the investigation of cotranscriptional regulatory mechanisms in bacterial and eukaryotic elongation complexes.
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8
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St-Pierre P, Shaw E, Jacques S, Dalgarno PA, Perez-Gonzalez C, Picard-Jean F, Penedo JC, Lafontaine DA. A structural intermediate pre-organizes the add adenine riboswitch for ligand recognition. Nucleic Acids Res 2021; 49:5891-5904. [PMID: 33963862 PMCID: PMC8191784 DOI: 10.1093/nar/gkab307] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 03/23/2021] [Accepted: 05/04/2021] [Indexed: 12/02/2022] Open
Abstract
Riboswitches are RNA sequences that regulate gene expression by undergoing structural changes upon the specific binding of cellular metabolites. Crystal structures of purine-sensing riboswitches have revealed an intricate network of interactions surrounding the ligand in the bound complex. The mechanistic details about how the aptamer folding pathway is involved in the formation of the metabolite binding site have been previously shown to be highly important for the riboswitch regulatory activity. Here, a combination of single-molecule FRET and SHAPE assays have been used to characterize the folding pathway of the adenine riboswitch from Vibrio vulnificus. Experimental evidences suggest a folding process characterized by the presence of a structural intermediate involved in ligand recognition. This intermediate state acts as an open conformation to ensure ligand accessibility to the aptamer and folds into a structure nearly identical to the ligand-bound complex through a series of structural changes. This study demonstrates that the add riboswitch relies on the folding of a structural intermediate that pre-organizes the aptamer global structure and the ligand binding site to allow efficient metabolite sensing and riboswitch genetic regulation.
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Affiliation(s)
- Patrick St-Pierre
- Department of Biology, Faculty of Science, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
| | - Euan Shaw
- Centre of Biophotonics, School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, KY16 9SS, UK
| | - Samuel Jacques
- Department of Biology, Faculty of Science, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
| | - Paul A Dalgarno
- Centre of Biophotonics, School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, KY16 9SS, UK
| | - Cibran Perez-Gonzalez
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife, KY16 9SS, UK
| | - Frédéric Picard-Jean
- Department of Biology, Faculty of Science, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
| | - J Carlos Penedo
- Centre of Biophotonics, School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, KY16 9SS, UK.,Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife, KY16 9SS, UK
| | - Daniel A Lafontaine
- Department of Biology, Faculty of Science, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
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9
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Wu L, Liu Z, Liu Y. Thermal adaptation of structural dynamics and regulatory function of adenine riboswitch. RNA Biol 2021; 18:2007-2015. [PMID: 33573442 DOI: 10.1080/15476286.2021.1886755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Ligand binding and temperature play important roles in riboswitch RNAs' structures and functions. However, most studies focused on studying structural dynamics or gene-regulation function of riboswitches from the aspect of ligand, instead of temperature. Here we combined NMR, ITC, stopped-flow and in vivo assays to investigate the ligand-triggered switch of adenine riboswitch from 10 to 45°C. Our results demonstrated that at single-nucleotide resolution, structural regions sensed ligand and temperature diversely. Temperature had opposite effects on ligand-binding and gene-regulation of adenine riboswitch. Compared with higher temperature, the RNA bound with its cognate ligand obviously stronger, while its regulatory capacity was weakened at lower temperature. In addition, application of specific-labelled RNAs to the stopped-flow experiments identified the real-time folding of the specific positions upon ligand addition at different temperatures. The kissing loop and internal loop at the riboswitch responded to ligand and temperature differently. The distinct thermo-dynamics of adenine riboswitch exposed here may contribute to the fields of RNA sensors and drug design.
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Affiliation(s)
- Lin Wu
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhijun Liu
- National Facility for Protein Science (Shanghai), Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai, China
| | - Yu Liu
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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10
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McCluskey K, Boudreault J, St-Pierre P, Perez-Gonzalez C, Chauvier A, Rizzi A, Beauregard PB, Lafontaine DA, Penedo JC. Unprecedented tunability of riboswitch structure and regulatory function by sub-millimolar variations in physiological Mg2. Nucleic Acids Res 2020; 47:6478-6487. [PMID: 31045204 PMCID: PMC6614840 DOI: 10.1093/nar/gkz316] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 04/16/2019] [Accepted: 04/18/2019] [Indexed: 02/06/2023] Open
Abstract
Riboswitches are cis-acting regulatory RNA biosensors that rival the efficiency of those found in proteins. At the heart of their regulatory function is the formation of a highly specific aptamer–ligand complex. Understanding how these RNAs recognize the ligand to regulate gene expression at physiological concentrations of Mg2+ ions and ligand is critical given their broad impact on bacterial gene expression and their potential as antibiotic targets. In this work, we used single-molecule FRET and biochemical techniques to demonstrate that Mg2+ ions act as fine-tuning elements of the amino acid-sensing lysC aptamer's ligand-free structure in the mesophile Bacillus subtilis. Mg2+ interactions with the aptamer produce encounter complexes with strikingly different sensitivities to the ligand in different, yet equally accessible, physiological ionic conditions. Our results demonstrate that the aptamer adapts its structure and folding landscape on a Mg2+-tunable scale to efficiently respond to changes in intracellular lysine of more than two orders of magnitude. The remarkable tunability of the lysC aptamer by sub-millimolar variations in the physiological concentration of Mg2+ ions suggests that some single-aptamer riboswitches have exploited the coupling of cellular levels of ligand and divalent metal ions to tightly control gene expression.
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Affiliation(s)
- Kaley McCluskey
- SUPA School of Physics and Astronomy, University of St. Andrews, Scotland KY16 9SS, UK
| | - Julien Boudreault
- Département de Biologie, Université de Sherbrooke, Québec, Canada J1K 2R1
| | - Patrick St-Pierre
- Département de Biologie, Université de Sherbrooke, Québec, Canada J1K 2R1
| | - Cibran Perez-Gonzalez
- SUPA School of Physics and Astronomy, University of St. Andrews, Scotland KY16 9SS, UK.,Centre SÈVE, Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Adrien Chauvier
- Département de Biologie, Université de Sherbrooke, Québec, Canada J1K 2R1
| | - Adrien Rizzi
- Département de Chimie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Pascale B Beauregard
- Centre SÈVE, Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | | | - J Carlos Penedo
- SUPA School of Physics and Astronomy, University of St. Andrews, Scotland KY16 9SS, UK.,Biomedical Sciences Research Complex, School of Biology, University of St. Andrews, Scotland KY16 9ST, UK
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11
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Bao L, Wang J, Xiao Y. Molecular dynamics simulation of the binding process of ligands to the add adenine riboswitch aptamer. Phys Rev E 2020; 100:022412. [PMID: 31574664 DOI: 10.1103/physreve.100.022412] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Indexed: 11/07/2022]
Abstract
Riboswitches are RNA-structured elements that modulate gene expression through changing their conformation in response to specific metabolite binding. However, the regulation mechanisms of riboswitches by ligand binding are still not well understood. At present two possible ligand-binding mechanisms have been proposed: conformational selection and induced fit. Based on explicit-solvent molecular dynamics (MD) simulations, we have studied the process of the binding of ligands (adenines) to add adenine riboswitch aptamer (AARA) in detail. Our results show that the relative high flexibility of the junction J23 of AARA allows the ligands to be captured by the binding pocket of AARA in a near-native state, which may be driven by hydrophobic and base-stacking interactions. In addition, the binding of a ligand makes the stem P1 and the junction J23 of AARA more stable than in the absence of the ligand. Generally, our analyses show that the ligand-binding process of the add adenine riboswitch may be partially embodied by a conformational selection mechanism.
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Affiliation(s)
- Lei Bao
- Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Jun Wang
- Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Yi Xiao
- Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
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12
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Liu J, Liu W, Zhang K, Shi J, Zhang Z. A Magnetic Drug Delivery System with "OFF-ON" State via Specific Molecular Recognition and Conformational Changes for Precise Tumor Therapy. Adv Healthc Mater 2020; 9:e1901316. [PMID: 31858730 DOI: 10.1002/adhm.201901316] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/22/2019] [Indexed: 11/07/2022]
Abstract
To enhance the tumor-targeting and tumor cell-specific drug-release capacity of nano drug delivery systems, a magnetic resonance imaging-traceable, magnetic-targeted nanoplatform is developed, and the nanoplatform is prepared by capping mesoporous silica (MSN)-coated iron oxide nanoparticles (IONPs) with programmable DNA hairpin sensor "gates." In normal cells (HL-7702, human liver cells), the nanoplatform is able to entrap the loaded drugs, showing an "OFF" state; the nanoplatform is activated by endogenous miRNA-21 overexpressed in tumor cells (HepG2, human liver tumor cells), which serve as an exclusive key to unlock the nanoplatform through hybridization with programmable DNA hairpin, leading to a rapid drug release, showing an "ON" state. The nanoplatform exhibits high antitumor efficacy and low toxicity in in vitro and in vivo studies owing to its magnetic targeting and tumor cell-activated properties, paving the way for targeted and personalized tumor treatment and showing potential for clinical applications.
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Affiliation(s)
- Junjie Liu
- School of Pharmaceutical SciencesZhengzhou University Zhengzhou 450001 P. R. China
- Collaborative Innovation Center of New Drug Research and Safety Evaluation Zhengzhou Henan Province 450001 P. R. China
- Key laboratory of Targeting Therapy and Diagnosis for Critical Diseases Zhengzhou Henan Province 450001 P. R. China
| | - Wei Liu
- School of Pharmaceutical SciencesZhengzhou University Zhengzhou 450001 P. R. China
- Collaborative Innovation Center of New Drug Research and Safety Evaluation Zhengzhou Henan Province 450001 P. R. China
- Key laboratory of Targeting Therapy and Diagnosis for Critical Diseases Zhengzhou Henan Province 450001 P. R. China
| | - Kaixiang Zhang
- School of Pharmaceutical SciencesZhengzhou University Zhengzhou 450001 P. R. China
- Collaborative Innovation Center of New Drug Research and Safety Evaluation Zhengzhou Henan Province 450001 P. R. China
- Key laboratory of Targeting Therapy and Diagnosis for Critical Diseases Zhengzhou Henan Province 450001 P. R. China
| | - Jinjin Shi
- School of Pharmaceutical SciencesZhengzhou University Zhengzhou 450001 P. R. China
- Collaborative Innovation Center of New Drug Research and Safety Evaluation Zhengzhou Henan Province 450001 P. R. China
- Key laboratory of Targeting Therapy and Diagnosis for Critical Diseases Zhengzhou Henan Province 450001 P. R. China
| | - Zhenzhong Zhang
- School of Pharmaceutical SciencesZhengzhou University Zhengzhou 450001 P. R. China
- Collaborative Innovation Center of New Drug Research and Safety Evaluation Zhengzhou Henan Province 450001 P. R. China
- Key laboratory of Targeting Therapy and Diagnosis for Critical Diseases Zhengzhou Henan Province 450001 P. R. China
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13
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Chen J, Wang X, Pang L, Zhang JZH, Zhu T. Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations. Nucleic Acids Res 2020; 47:6618-6631. [PMID: 31173143 PMCID: PMC6649850 DOI: 10.1093/nar/gkz499] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 05/22/2019] [Accepted: 05/29/2019] [Indexed: 12/14/2022] Open
Abstract
Riboswitches can regulate gene expression by direct and specific interactions with ligands and have recently attracted interest as potential drug targets for antibacterial. In this work, molecular dynamics (MD) simulations, free energy perturbation (FEP) and molecular mechanics generalized Born surface area (MM-GBSA) methods were integrated to probe the effect of mutations on the binding of ligands to guanine riboswitch (GR). The results not only show that binding free energies predicted by FEP and MM-GBSA obtain an excellent correlation, but also indicate that mutations involved in the current study can strengthen the binding affinity of ligands GR. Residue-based free energy decomposition was applied to compute ligand-nucleotide interactions and the results suggest that mutations highly affect interactions of ligands with key nucleotides U22, U51 and C74. Dynamics analyses based on MD trajectories indicate that mutations not only regulate the structural flexibility but also change the internal motion modes of GR, especially for the structures J12, J23 and J31, which implies that the aptamer domain activity of GR is extremely plastic and thus readily tunable by nucleotide mutations. This study is expected to provide useful molecular basis and dynamics information for the understanding of the function of GR and possibility as potential drug targets for antibacterial.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan 250357 China
| | - Xingyu Wang
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Laixue Pang
- School of Science, Shandong Jiaotong University, Jinan 250357 China
| | - John Z H Zhang
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China.,Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Tong Zhu
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China.,Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
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14
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McCluskey K, Carlos Penedo J. An integrated perspective on RNA aptamer ligand-recognition models: clearing muddy waters. Phys Chem Chem Phys 2018; 19:6921-6932. [PMID: 28225108 DOI: 10.1039/c6cp08798a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Riboswitches are short RNA motifs that sensitively and selectively bind cognate ligands to modulate gene expression. Like protein receptor-ligand pairs, their binding dynamics are traditionally categorized as following one of two paradigmatic mechanisms: conformational selection and induced fit. In conformational selection, ligand binding stabilizes a particular state already present in the receptor's dynamic ensemble. In induced fit, ligand-receptor interactions enable the system to overcome the energetic barrier into a previously inaccessible state. In this article, we question whether a polarized division of RNA binding mechanisms truly meets the conceptual needs of the field. We will review the history behind this classification of RNA-ligand interactions, and the way induced fit in particular has been rehabilitated by single-molecule studies of RNA aptamers. We will highlight several recent results from single-molecule experimental studies of riboswitches that reveal gaps or even contradictions between common definitions of the two terms, and we will conclude by proposing a more robust framework that considers the range of RNA behaviors unveiled in recent years as a reality to be described, rather than an increasingly unwieldy set of exceptions to the traditional models.
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Affiliation(s)
- K McCluskey
- Department of Physics and Astronomy, University of St. Andrews, St. Andrews, KY16 9SS, UK.
| | - J Carlos Penedo
- Department of Physics and Astronomy, University of St. Andrews, St. Andrews, KY16 9SS, UK. and Biomolecular Sciences Research Complex, University of St. Andrews, St. Andrews, KY16 9SS, UK.
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15
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Tenopala-Carmona F, Fronk S, Bazan GC, Samuel IDW, Penedo JC. Real-time observation of conformational switching in single conjugated polymer chains. SCIENCE ADVANCES 2018; 4:eaao5786. [PMID: 29487904 PMCID: PMC5817931 DOI: 10.1126/sciadv.aao5786] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 01/22/2018] [Indexed: 05/30/2023]
Abstract
Conjugated polymers (CPs) are an important class of organic semiconductors that combine novel optoelectronic properties with simple processing from organic solvents. It is important to study CP conformation in solution to understand the physics of these materials and because it affects the properties of solution-processed films. Single-molecule techniques are unique in their ability to extract information on a chain-to-chain basis; however, in the context of CPs, technical challenges have limited their general application to host matrices or semiliquid environments that constrain the conformational dynamics of the polymer. We introduce a conceptually different methodology that enables measurements in organic solvents using the single-end anchoring of polymer chains to avoid diffusion while preserving polymer flexibility. We explore the effect of organic solvents and show that, in addition to chain-to-chain conformational heterogeneity, collapsed and extended polymer segments can coexist within the same chain. The technique enables real-time solvent-exchange measurements, which show that anchored CP chains respond to sudden changes in solvent conditions on a subsecond time scale. Our results give an unprecedented glimpse into the mechanism of solvent-induced reorganization of CPs and can be expected to lead to a new range of techniques to investigate and conformationally manipulate CPs.
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Affiliation(s)
- Francisco Tenopala-Carmona
- Organic Semiconductor Centre, Scottish Universities Physics Alliance, School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9SS, UK
| | - Stephanie Fronk
- Department of Materials and Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Guillermo C. Bazan
- Department of Materials and Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Ifor D. W. Samuel
- Organic Semiconductor Centre, Scottish Universities Physics Alliance, School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9SS, UK
| | - J. Carlos Penedo
- Organic Semiconductor Centre, Scottish Universities Physics Alliance, School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9SS, UK
- Biomedical Sciences Research Complex, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9SS, UK
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16
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Warhaut S, Mertinkus KR, Höllthaler P, Fürtig B, Heilemann M, Hengesbach M, Schwalbe H. Ligand-modulated folding of the full-length adenine riboswitch probed by NMR and single-molecule FRET spectroscopy. Nucleic Acids Res 2017; 45:5512-5522. [PMID: 28204648 PMCID: PMC5605240 DOI: 10.1093/nar/gkx110] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 02/06/2017] [Indexed: 01/20/2023] Open
Abstract
The full-length translation-regulating add adenine riboswitch (Asw) from Vibrio vulnificus has a more complex conformational space than its isolated aptamer domain. In addition to the predicted apo (apoA) and holo conformation that feature the conserved three-way junctional purine riboswitch aptamer, it adopts a second apo (apoB) conformation with a fundamentally different secondary structure. Here, we characterized the ligand-dependent conformational dynamics of the full-length add Asw by NMR and by single-molecule FRET (smFRET) spectroscopy. Both methods revealed an adenine-induced secondary structure switch from the apoB-form to the apoA-form that involves no tertiary structural interactions between aptamer and expression platform. This strongly suggests that the add Asw triggers translation by capturing the apoA-form secondary structure in the holo state. Intriguingly, NMR indicated a homogenous, docked aptamer kissing loop fold for apoA and holo, while smFRET showed persistent aptamer kissing loop docking dynamics between comparably stable, undocked and docked substates of the apoA and the holo conformation. Unraveling the folding of large junctional riboswitches thus requires the integration of complementary solution structural techniques such as NMR and smFRET.
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Affiliation(s)
- Sven Warhaut
- Institute of Organic Chemistry and Chemical Biology, Centre for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, Frankfurt am Main, Hessen 60438, Germany
| | - Klara Rebecca Mertinkus
- Institute of Organic Chemistry and Chemical Biology, Centre for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, Frankfurt am Main, Hessen 60438, Germany
| | - Philipp Höllthaler
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-Universität, Frankfurt am Main, Hessen 60438, Germany
| | - Boris Fürtig
- Institute of Organic Chemistry and Chemical Biology, Centre for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, Frankfurt am Main, Hessen 60438, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-Universität, Frankfurt am Main, Hessen 60438, Germany
| | - Martin Hengesbach
- Institute of Organic Chemistry and Chemical Biology, Centre for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, Frankfurt am Main, Hessen 60438, Germany
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology, Centre for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, Frankfurt am Main, Hessen 60438, Germany
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17
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Smith-Peter E, Lamontagne AM, Lafontaine DA. Role of lysine binding residues in the global folding of the lysC riboswitch. RNA Biol 2016; 12:1372-82. [PMID: 26403229 DOI: 10.1080/15476286.2015.1094603] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Riboswitches regulate gene expression by rearranging their structure upon metabolite binding. The lysine-sensing lysC riboswitch is a rare example of an RNA aptamer organized around a 5-way helical junction in which ligand binding is performed exclusively through nucleotides located at the junction core. We have probed whether the nucleotides involved in ligand binding play any role in the global folding of the riboswitch. As predicted, our findings indicate that ligand-binding residues are critical for the lysine-dependent gene regulation mechanism. We also find that these residues are not important for the establishment of key magnesium-dependent tertiary interactions, suggesting that folding and ligand recognition are uncoupled in this riboswitch for the formation of specific interactions. However, FRET assays show that lysine binding results in an additional conformational change, indicating that lysine binding may also participate in a specific folding transition. Thus, in contrast to helical junctions being primary determinants in ribozymes and rRNA folding, we speculate that the helical junction of the lysine-sensing lysC riboswitch is not employed as structural a scaffold to direct global folding, but rather has a different role in establishing RNA-ligand interactions required for riboswitch regulation. Our work suggests that helical junctions may adopt different functions such as the coordination of global architecture or the formation of specific ligand binding site.
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Affiliation(s)
- Erich Smith-Peter
- a Department of Biology ; Faculty of Science, RNA Group, Université de Sherbrooke , Sherbrooke ; Quebec , Canada
| | - Anne-Marie Lamontagne
- a Department of Biology ; Faculty of Science, RNA Group, Université de Sherbrooke , Sherbrooke ; Quebec , Canada
| | - Daniel A Lafontaine
- a Department of Biology ; Faculty of Science, RNA Group, Université de Sherbrooke , Sherbrooke ; Quebec , Canada
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18
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Perez-Gonzalez C, Lafontaine DA, Penedo JC. Fluorescence-Based Strategies to Investigate the Structure and Dynamics of Aptamer-Ligand Complexes. Front Chem 2016; 4:33. [PMID: 27536656 PMCID: PMC4971091 DOI: 10.3389/fchem.2016.00033] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/11/2016] [Indexed: 12/11/2022] Open
Abstract
In addition to the helical nature of double-stranded DNA and RNA, single-stranded oligonucleotides can arrange themselves into tridimensional structures containing loops, bulges, internal hairpins and many other motifs. This ability has been used for more than two decades to generate oligonucleotide sequences, so-called aptamers, that can recognize certain metabolites with high affinity and specificity. More recently, this library of artificially-generated nucleic acid aptamers has been expanded by the discovery that naturally occurring RNA sequences control bacterial gene expression in response to cellular concentration of a given metabolite. The application of fluorescence methods has been pivotal to characterize in detail the structure and dynamics of these aptamer-ligand complexes in solution. This is mostly due to the intrinsic high sensitivity of fluorescence methods and also to significant improvements in solid-phase synthesis, post-synthetic labeling strategies and optical instrumentation that took place during the last decade. In this work, we provide an overview of the most widely employed fluorescence methods to investigate aptamer structure and function by describing the use of aptamers labeled with a single dye in fluorescence quenching and anisotropy assays. The use of 2-aminopurine as a fluorescent analog of adenine to monitor local changes in structure and fluorescence resonance energy transfer (FRET) to follow long-range conformational changes is also covered in detail. The last part of the review is dedicated to the application of fluorescence techniques based on single-molecule microscopy, a technique that has revolutionized our understanding of nucleic acid structure and dynamics. We finally describe the advantages of monitoring ligand-binding and conformational changes, one molecule at a time, to decipher the complexity of regulatory aptamers and summarize the emerging folding and ligand-binding models arising from the application of these single-molecule FRET microscopy techniques.
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Affiliation(s)
- Cibran Perez-Gonzalez
- Laboratory for Biophysics and Biomolecular Dynamics, SUPA School of Physics and Astronomy, University of St. AndrewsSt Andrews, UK
| | - Daniel A. Lafontaine
- RNA Group, Department of Biology, Faculty of Science, Université de SherbrookeSherbrooke, QC, Canada
| | - J. Carlos Penedo
- Laboratory for Biophysics and Biomolecular Dynamics, SUPA School of Physics and Astronomy, University of St. AndrewsSt Andrews, UK
- Laboratory for Biophysics and Biomolecular Dynamics, Biomedical Sciences Research Complex, School of Biology, University of St. AndrewsSt. Andrews, UK
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19
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Liu Y, Yu P, Dyba M, Sousa R, Stagno JR, Wang YX. Applications of PLOR in labeling large RNAs at specific sites. Methods 2016; 103:4-10. [PMID: 27033177 PMCID: PMC10802919 DOI: 10.1016/j.ymeth.2016.03.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/15/2016] [Accepted: 03/22/2016] [Indexed: 12/18/2022] Open
Abstract
Incorporation of modified or labeled nucleotides at specific sites in RNAs is critical for gaining insights into the structure and function of RNAs. Preparation of site-specifically labeled large RNAs in amounts suitable for structural or functional studies is extremely difficult using current methodologies. The position-selective labeling of RNA, PLOR, is a recently developed method that makes such syntheses possible. PLOR allows incorporation of various probes, including (2)D/(13)C/(15)N-isotopic labels, Cy3/Cy5/Alexa488/Alexa555 fluorescent dyes, biotin and other chemical groups, into specific positions in long RNAs. Here, we describe in detail the use of PLOR to label RNAs at specific segment(s) or discrete sites.
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Affiliation(s)
- Yu Liu
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
| | - Ping Yu
- Structural Biophysics Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Marzena Dyba
- Structural Biophysics Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Rui Sousa
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Jason R Stagno
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
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20
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Perez-Gonzalez C, Grondin JP, Lafontaine DA, Carlos Penedo J. Biophysical Approaches to Bacterial Gene Regulation by Riboswitches. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 915:157-91. [PMID: 27193543 DOI: 10.1007/978-3-319-32189-9_11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The last decade has witnessed the discovery of a variety of non-coding RNA sequences that perform a broad range of crucial biological functions. Among these, the ability of certain RNA sequences, so-called riboswitches, has attracted considerable interest. Riboswitches control gene expression in response to the concentration of particular metabolites to which they bind without the need for any protein. These RNA switches not only need to adopt a very specific tridimensional structure to perform their function, but also their sequence has been evolutionary optimized to recognize a particular metabolite with high affinity and selectivity. Thus, riboswitches offer a unique opportunity to get fundamental insights into RNA plasticity and how folding dynamics and ligand recognition mechanisms have been efficiently merged to control gene regulation. Because riboswitch sequences have been mostly found in bacterial organisms controlling the expression of genes associated to the synthesis, degradation or transport of crucial metabolites for bacterial survival, they offer exciting new routes for antibiotic development in an era where bacterial resistance is more than ever challenging conventional drug discovery strategies. Here, we give an overview of the architecture, diversity and regulatory mechanisms employed by riboswitches with particular emphasis on the biophysical methods currently available to characterise their structure and functional dynamics.
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Affiliation(s)
- Cibran Perez-Gonzalez
- SUPA School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, KY16 9SS, UK
| | - Jonathan P Grondin
- Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Daniel A Lafontaine
- Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada.
| | - J Carlos Penedo
- SUPA School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, KY16 9SS, UK. .,Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife, KY16 9ST, UK.
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21
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Lussier A, Bastet L, Chauvier A, Lafontaine DA. A kissing loop is important for btuB riboswitch ligand sensing and regulatory control. J Biol Chem 2015; 290:26739-51. [PMID: 26370077 DOI: 10.1074/jbc.m115.684134] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Indexed: 12/18/2022] Open
Abstract
RNA-based genetic regulation is exemplified by metabolite-binding riboswitches that modulate gene expression through conformational changes. Crystal structures show that the Escherichia coli btuB riboswitch contains a kissing loop interaction that is in close proximity to the bound ligand. To analyze the role of the kissing loop interaction in the riboswitch regulatory mechanism, we used RNase H cleavage assays to probe the structure of nascent riboswitch transcripts produced by the E. coli RNA polymerase. By monitoring the folding of the aptamer, kissing loop, and riboswitch expression platform, we established the conformation of each structural component in the absence or presence of bound adenosylcobalamin. We found that the kissing loop interaction is not essential for ligand binding. However, we showed that kissing loop formation improves ligand binding efficiency and is required to couple ligand binding to the riboswitch conformational changes involved in regulating gene expression. These results support a mechanism by which the btuB riboswitch modulates the formation of a tertiary structure to perform metabolite sensing and regulate gene expression.
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Affiliation(s)
- Antony Lussier
- From the Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada
| | - Laurène Bastet
- From the Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada
| | - Adrien Chauvier
- From the Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada
| | - Daniel A Lafontaine
- From the Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada
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22
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Shaw E, St-Pierre P, McCluskey K, Lafontaine DA, Penedo JC. Using sm-FRET and denaturants to reveal folding landscapes. Methods Enzymol 2015; 549:313-41. [PMID: 25432755 DOI: 10.1016/b978-0-12-801122-5.00014-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
RNA folding studies aim to clarify the relationship among sequence, tridimensional structure, and biological function. In the last decade, the application of single-molecule fluorescence resonance energy transfer (sm-FRET) techniques to investigate RNA structure and folding has revealed the details of conformational changes and timescale of the process leading to the formation of biologically active RNA structures with subnanometer resolution on millisecond timescales. In this review, we initially summarize the first wave of single-molecule FRET-based RNA techniques that focused on analyzing the influence of mono- and divalent metal ions on RNA function, and how these studies have provided very valuable information about folding pathways and the presence of intermediate and low-populated states. Next, we describe a second generation of single-molecule techniques that combine sm-FRET with the use of chemical denaturants as an emerging powerful approach to reveal information about the dynamics and energetics of RNA folding that remains hidden using conventional sm-FRET approaches. The main advantages of using the competing interplay between folding agents such as metal ions and denaturants to observe and manipulate the dynamics of RNA folding and RNA-ligand interactions is discussed in the context of the adenine riboswitch aptamer.
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Affiliation(s)
- Euan Shaw
- SUPA School of Physics and Astronomy, University of St. Andrews, St. Andrews, Fife, United Kingdom
| | - Patrick St-Pierre
- RNA Group, Department of Biology, Faculty of Science, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Kaley McCluskey
- SUPA School of Physics and Astronomy, University of St. Andrews, St. Andrews, Fife, United Kingdom
| | - Daniel A Lafontaine
- RNA Group, Department of Biology, Faculty of Science, Université de Sherbrooke, Sherbrooke, Québec, Canada.
| | - J Carlos Penedo
- SUPA School of Physics and Astronomy, University of St. Andrews, St. Andrews, Fife, United Kingdom; Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, Fife, United Kingdom.
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23
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Liu Y, Holmstrom E, Zhang J, Yu P, Wang J, Dyba MA, Chen D, Ying J, Lockett S, Nesbitt DJ, Ferré-D'Amaré AR, Sousa R, Stagno JR, Wang YX. Synthesis and applications of RNAs with position-selective labelling and mosaic composition. Nature 2015; 522:368-72. [PMID: 25938715 PMCID: PMC4800989 DOI: 10.1038/nature14352] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 02/25/2015] [Indexed: 12/13/2022]
Abstract
Knowledge of the structure and dynamics of RNA molecules is critical to understanding their many biological functions. Furthermore, synthetic RNAs have applications as therapeutics and molecular sensors. Both research and technological applications of RNA would be dramatically enhanced by methods that enable incorporation of modified or labelled nucleotides into specifically designated positions or regions of RNA. However, the synthesis of tens of milligrams of such RNAs using existing methods has been impossible. Here we develop a hybrid solid-liquid phase transcription method and automated robotic platform for the synthesis of RNAs with position-selective labelling. We demonstrate its use by successfully preparing various isotope- or fluorescently labelled versions of the 71-nucleotide aptamer domain of an adenine riboswitch for nuclear magnetic resonance spectroscopy or single-molecule Förster resonance energy transfer, respectively. Those RNAs include molecules that were selectively isotope-labelled in specific loops, linkers, a helix, several discrete positions, or a single internal position, as well as RNA molecules that were fluorescently labelled in and near kissing loops. These selectively labelled RNAs have the same fold as those transcribed using conventional methods, but they greatly simplify the interpretation of NMR spectra. The single-position isotope- and fluorescently labelled RNA samples reveal multiple conformational states of the adenine riboswitch. Lastly, we describe a robotic platform and the operation that automates this technology. Our selective labelling method may be useful for studying RNA structure and dynamics and for making RNA sensors for a variety of applications including cell-biological studies, substance detection, and disease diagnostics.
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Affiliation(s)
- Yu Liu
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
| | - Erik Holmstrom
- JILA, National Institute of Standards and Technology and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA
| | - Jinwei Zhang
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, Maryland 20892, USA
| | - Ping Yu
- Structural Biophysics Laboratory, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
| | - Jinbu Wang
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
| | - Marzena A Dyba
- Structural Biophysics Laboratory, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
| | - De Chen
- Optical Microscopy and Analysis Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
| | - Jinfa Ying
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Stephen Lockett
- Optical Microscopy and Analysis Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
| | - David J Nesbitt
- JILA, National Institute of Standards and Technology and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, Maryland 20892, USA
| | - Rui Sousa
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78229, USA
| | - Jason R Stagno
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
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24
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Holmstrom ED, Dupuis NF, Nesbitt DJ. Kinetic and thermodynamic origins of osmolyte-influenced nucleic acid folding. J Phys Chem B 2015; 119:3687-96. [PMID: 25621404 DOI: 10.1021/jp512491n] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The influential role of monovalent and divalent metal cations in facilitating conformational transitions in both RNA and DNA has been a target of intense biophysical research efforts. However, organic neutrally charged cosolutes can also significantly alter nucleic acid conformational transitions. For example, highly soluble small molecules such as trimethylamine N-oxide (TMAO) and urea are occasionally utilized by organisms to regulate cellular osmotic pressure. Ensemble studies have revealed that these so-called osmolytes can substantially influence the thermodynamics of nucleic acid conformational transitions. In the present work, we exploit single-molecule FRET (smFRET) techniques to measure, for first time, the kinetic origins of these osmolyte-induced changes to the folding free energy. In particular, we focus on smFRET RNA and DNA constructs designed as model systems for secondary and tertiary structure formation. These findings reveal that TMAO preferentially stabilizes both secondary and tertiary interactions by increasing kfold and decreasing kunfold, whereas urea destabilizes both conformational transitions, resulting in the exact opposite shift in kinetic rate constants (i.e., decreasing kfold and increasing kunfold). Complementary temperature-dependent smFRET experiments highlight a thermodynamic distinction between the two different mechanisms responsible for TMAO-facilitated conformational transitions, while only a single mechanism is seen for the destabilizing osmolyte urea. Finally, these results are interpreted in the context of preferential interactions between osmolytes, and the solvent accessible surface area (SASA) associated with the (i) nucleobase, (ii) sugar, and (iii) phosphate groups of nucleic acids in order to map out structural changes that occur during the conformational transitions.
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Affiliation(s)
- Erik D Holmstrom
- JILA, University of Colorado and National Institute of Standards and Technology, and Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0440, United States
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25
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Perez-Gonzalez DC, Penedo JC. Single-Molecule Strategies for DNA and RNA Diagnostics. RNA TECHNOLOGIES 2015. [DOI: 10.1007/978-3-319-17305-4_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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26
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Stephenson W, Wan G, Tenenbaum SA, Li PTX. Nanomanipulation of single RNA molecules by optical tweezers. J Vis Exp 2014. [PMID: 25177917 DOI: 10.3791/51542] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
A large portion of the human genome is transcribed but not translated. In this post genomic era, regulatory functions of RNA have been shown to be increasingly important. As RNA function often depends on its ability to adopt alternative structures, it is difficult to predict RNA three-dimensional structures directly from sequence. Single-molecule approaches show potentials to solve the problem of RNA structural polymorphism by monitoring molecular structures one molecule at a time. This work presents a method to precisely manipulate the folding and structure of single RNA molecules using optical tweezers. First, methods to synthesize molecules suitable for single-molecule mechanical work are described. Next, various calibration procedures to ensure the proper operations of the optical tweezers are discussed. Next, various experiments are explained. To demonstrate the utility of the technique, results of mechanically unfolding RNA hairpins and a single RNA kissing complex are used as evidence. In these examples, the nanomanipulation technique was used to study folding of each structural domain, including secondary and tertiary, independently. Lastly, the limitations and future applications of the method are discussed.
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Affiliation(s)
- William Stephenson
- Nanoscale Engineering Graduate Program, College of Nanoscale Science and Engineering, University at Albany, State University of New York
| | - Gorby Wan
- Nanoscale Science Undergraduate Program, College of Nanoscale Science and Engineering, University at Albany, State University of New York
| | - Scott A Tenenbaum
- Nanobioscience Constellation, College of Nanoscale Science and Engineering, University at Albany, State University of New York; The RNA Institute, University at Albany, State University of New York
| | - Pan T X Li
- The RNA Institute, University at Albany, State University of New York; Department of Biological Sciences, University at Albany, State University of New York;
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St-Pierre P, McCluskey K, Shaw E, Penedo JC, Lafontaine DA. Fluorescence tools to investigate riboswitch structural dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1005-1019. [PMID: 24863161 DOI: 10.1016/j.bbagrm.2014.05.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 05/14/2014] [Accepted: 05/15/2014] [Indexed: 11/15/2022]
Abstract
Riboswitches are novel regulatory elements that respond to cellular metabolites to control gene expression. They are constituted of highly conserved domains that have evolved to recognize specific metabolites. Such domains, so-called aptamers, are folded into intricate structures to enable metabolite recognition. Over the years, the development of ensemble and single-molecule fluorescence techniques has allowed to probe most of the mechanistic aspects of aptamer folding and ligand binding. In this review, we summarize the current fluorescence toolkit available to study riboswitch structural dynamics. We fist describe those methods based on fluorescent nucleotide analogues, mostly 2-aminopurine (2AP), to investigate short-range conformational changes, including some key steady-state and time-resolved examples that exemplify the versatility of fluorescent analogues as structural probes. The study of long-range structural changes by Förster resonance energy transfer (FRET) is mostly discussed in the context of single-molecule studies, including some recent developments based on the combination of single-molecule FRET techniques with controlled chemical denaturation methods. This article is part of a Special Issue entitled: Riboswitches.
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Affiliation(s)
- Patrick St-Pierre
- RNA Group, Department of Biology, Faculty of Science, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Kaley McCluskey
- SUPA, School of Physics and Astronomy University of St Andrews, St Andrews, Fife KY16 9SS, United Kingdom
| | - Euan Shaw
- SUPA, School of Physics and Astronomy University of St Andrews, St Andrews, Fife KY16 9SS, United Kingdom
| | - J C Penedo
- SUPA, School of Physics and Astronomy University of St Andrews, St Andrews, Fife KY16 9SS, United Kingdom; Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9SS, United Kingdom.
| | - D A Lafontaine
- RNA Group, Department of Biology, Faculty of Science, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada.
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Savinov A, Perez CF, Block SM. Single-molecule studies of riboswitch folding. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1030-1045. [PMID: 24727093 DOI: 10.1016/j.bbagrm.2014.04.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/27/2014] [Accepted: 04/03/2014] [Indexed: 10/25/2022]
Abstract
The folding dynamics of riboswitches are central to their ability to modulate gene expression in response to environmental cues. In most cases, a structural competition between the formation of a ligand-binding aptamer and an expression platform (or some other competing off-state) determines the regulatory outcome. Here, we review single-molecule studies of riboswitch folding and function, predominantly carried out using single-molecule FRET or optical trapping approaches. Recent results have supplied new insights into riboswitch folding energy landscapes, the mechanisms of ligand binding, the roles played by divalent ions, the applicability of hierarchical folding models, and kinetic vs. thermodynamic control schemes. We anticipate that future work, based on improved data sets and potentially combining multiple experimental techniques, will enable the development of more complete models for complex RNA folding processes. This article is part of a Special Issue entitled: Riboswitches.
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Affiliation(s)
- Andrew Savinov
- Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | | | - Steven M Block
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA.
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Esquiaqui JM, Sherman EM, Ye JD, Fanucci GE. Site-directed spin-labeling strategies and electron paramagnetic resonance spectroscopy for large riboswitches. Methods Enzymol 2014; 549:287-311. [PMID: 25432754 DOI: 10.1016/b978-0-12-801122-5.00013-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Genetic regulation effected by RNA riboswitches is governed by ligand-induced structural reorganization with modulation of RNA conformation and dynamics. Characterization of the conformational states of riboswitches in the presence or absence of salts and ligands is important for understanding how interconversion of riboswitch RNA folding states influences function. The methodology of site-directed spin labeling (SDSL) coupled with electron paramagnetic resonance (EPR) spectroscopy is suitable for such studies, wherein site-specific incorporation of a nitroxide radical spin probe allows for local dynamics and conformational changes to be investigated. This chapter reviews a strategy for SDSL-EPR studies of large riboswitches and uses the full length 232 nucleotide (nt) kink-turn motif-containing Vibrio cholerae (VC) glycine riboswitch as an example. Spin-labeling strategies and the challenges of incorporating spin labels into large riboswitches are reviewed and the approach to overcome these challenges is described. Results are subsequently presented illustrating changes in dynamics within the labeled region of the VC glycine riboswitch as observed using SDSL-EPR.
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Affiliation(s)
- Jackie M Esquiaqui
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Eileen M Sherman
- Department of Chemistry, University of Central Florida, Orlando, Florida, USA
| | - Jing-Dong Ye
- Department of Chemistry, University of Central Florida, Orlando, Florida, USA.
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, Gainesville, Florida, USA.
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