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Du C, Wang Y, Gong S. Regulation of the ThiM riboswitch is facilitated by the trapped structure formed during transcription of the wild-type sequence. FEBS Lett 2021; 595:2816-2828. [PMID: 34644399 DOI: 10.1002/1873-3468.14202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 09/17/2021] [Accepted: 09/20/2021] [Indexed: 11/09/2022]
Abstract
The ThiM riboswitch from Escherichia coli is a typical mRNA device that modulates downstream gene expression by sensing TPP. The helix-based RNA folding theory is used to investigate its detailed regulatory behaviors in cells. This RNA molecule is transcriptionally trapped in a state with the unstructured SD sequence in the absence of TPP, which induces downstream gene expression. As a key step to turn on gene expression, formation of this trapped state (the genetic ON state) highly depends on the co-transcriptional folding of its wild-type sequence. Instead of stabilities of the genetic ON and OFF states, the transcription rate, pause, and ligand levels are combined to affect the ThiM riboswitch-mediated gene regulation, which is consistent with a kinetic control model.
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Affiliation(s)
- Chengyi Du
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, China
| | - Yujie Wang
- Department of Physics and Telecommunication Engineering, Zhoukou Normal University, China
| | - Sha Gong
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, China
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2
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Velema WA, Park HS, Kadina A, Orbai L, Kool ET. Trapping Transient RNA Complexes by Chemically Reversible Acylation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202010861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Willem A. Velema
- Institute for Molecules and Materials Radboud University Nijmegen 6525 AJ The Netherlands
| | - Hyun Shin Park
- Department of Chemistry Stanford University Stanford CA 94305 USA
| | - Anastasia Kadina
- Department of Chemistry Stanford University Stanford CA 94305 USA
| | - Lucian Orbai
- Cell Data Sciences 46127 Landing Pkwy Fremont CA 94538 USA
| | - Eric T. Kool
- Department of Chemistry Stanford University Stanford CA 94305 USA
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3
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Velema WA, Park HS, Kadina A, Orbai L, Kool ET. Trapping Transient RNA Complexes by Chemically Reversible Acylation. Angew Chem Int Ed Engl 2020; 59:22017-22022. [PMID: 32845055 DOI: 10.1002/anie.202010861] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Indexed: 01/01/2023]
Abstract
RNA-RNA interactions are essential for biology, but they can be difficult to study due to their transient nature. While crosslinking strategies can in principle be used to trap such interactions, virtually all existing strategies for crosslinking are poorly reversible, chemically modifying the RNA and hindering molecular analysis. We describe a soluble crosslinker design (BINARI) that reacts with RNA through acylation. We show that it efficiently crosslinks noncovalent RNA complexes with mimimal sequence bias and establish that the crosslink can be reversed by phosphine reduction of azide trigger groups, thereby liberating the individual RNA components for further analysis. The utility of the new approach is demonstrated by reversible protection against nuclease degradation and trapping transient RNA complexes of E. coli DsrA-rpoS derived bulge-loop interactions, which underlines the potential of BINARI crosslinkers to probe RNA regulatory networks.
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Affiliation(s)
- Willem A Velema
- Institute for Molecules and Materials, Radboud University, Nijmegen, 6525, AJ, The Netherlands
| | - Hyun Shin Park
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Anastasia Kadina
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Lucian Orbai
- Cell Data Sciences, 46127 Landing Pkwy, Fremont, CA, 94538, USA
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
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Kabza AM, Sczepanski JT. An l-RNA Aptamer with Expanded Chemical Functionality that Inhibits MicroRNA Biogenesis. Chembiochem 2017; 18:1824-1827. [PMID: 28696509 DOI: 10.1002/cbic.201700362] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Indexed: 01/07/2023]
Abstract
To facilitate isolation of l-aptamers with novel RNA-binding properties, we employed a cationic nucleotide, 5-aminoallyluridine, during the mirror image in vitro selection process. Through this effort, we identified a modified l-RNA aptamer (MlRA) capable of binding oncogenic precursor microRNA 19a (pre-miR-19a) with exceptional affinity, and we showed that cationic modification is absolutely critical for binding. Furthermore, formation of the MlRA-pre-miR-19a complex inhibited Dicer-mediated cleavage of the pre-miR, thus blocking formation of the mature functional microRNA. The MlRA reported here not only represents the first l-aptamer to be evolved by using modified nucleotides but also the first modified aptamer (of any type) to be selected against a structured RNA target. Our results demonstrate that functionalized l-aptamers, which are intrinsically nuclease-resistant, provide an attractive approach for developing robust RNA-binding reagents.
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Affiliation(s)
- Adam M Kabza
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
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Hong C, Hagihara M, Nakatani K. Ligand-Assisted Complex Formation of Two DNA Hairpin Loops. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201100075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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6
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Hong C, Hagihara M, Nakatani K. Ligand-Assisted Complex Formation of Two DNA Hairpin Loops. Angew Chem Int Ed Engl 2011; 50:4390-3. [DOI: 10.1002/anie.201100075] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Indexed: 11/11/2022]
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Lau PS, Coombes BK, Li Y. A general approach to the construction of structure-switching reporters from RNA aptamers. Angew Chem Int Ed Engl 2011; 49:7938-42. [PMID: 20845339 DOI: 10.1002/anie.201002621] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Pui Sai Lau
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main St. W., Hamilton, ON L8N 3Z5, Canada
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Lau PS, Coombes BK, Li Y. A General Approach to the Construction of Structure-Switching Reporters from RNA Aptamers. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201002621] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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9
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Lünse CE, Michlewski G, Hopp CS, Rentmeister A, Cáceres JF, Famulok M, Mayer G. An aptamer targeting the apical-loop domain modulates pri-miRNA processing. Angew Chem Int Ed Engl 2010; 49:4674-7. [PMID: 20533473 DOI: 10.1002/anie.200906919] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Christina E Lünse
- Life and Medical Sciences (LIMES), University of Bonn, Gerhard-Domagk-Strasse 1, Bonn, Germany
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Lünse C, Michlewski G, Hopp C, Rentmeister A, Cáceres J, Famulok M, Mayer G. Modulation der pri-miRNA-Reifung durch ein die apikale Schleife bindendes Aptamer. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906919] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Chen L, Cressina E, Leeper FJ, Smith AG, Abell C. A fragment-based approach to identifying ligands for riboswitches. ACS Chem Biol 2010; 5:355-8. [PMID: 20158266 DOI: 10.1021/cb9003139] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Riboswitches are regions of mRNA that directly bind metabolites, leading to alteration of gene expression. We have developed fragment-based methods to screen for compounds that bind the Escherichia coli thiM riboswitch. Using complementary biophysical techniques we have identified several ligands with K(D) <100 microM. From these there is the potential to develop potent and selective modulators of riboswitch function.
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Affiliation(s)
- Liuhong Chen
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Elena Cressina
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | - Finian J. Leeper
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Alison G. Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
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Abstract
Aptamers are small single-stranded nucleic acids that fold into a well-defined three-dimensional structure. They show a high affinity and specificity for their target molecules and inhibit their biological functions. Aptamers belong to the nucleic acids family and can be synthesized by chemical or enzymatic procedures, or a combination of the two. They can, therefore, be considered as both chemical and biological substances. This Review summarizes the most convenient approaches to their preparation and new developments in the field of aptamers. The application of aptamers in chemical biology is also discussed.
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Affiliation(s)
- Günter Mayer
- Life and Medical Sciences, Prog. Unit Chemical Biology and Medicinal Chemistry, University of Bonn c/o Kekulé-Institute for Organic Chemistry and Biochemistry, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany.
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Raddatz MSL, Dolf A, Endl E, Knolle P, Famulok M, Mayer G. Enrichment of cell-targeting and population-specific aptamers by fluorescence-activated cell sorting. Angew Chem Int Ed Engl 2008; 47:5190-3. [PMID: 18512861 DOI: 10.1002/anie.200800216] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Marie-Sophie L Raddatz
- Life and Medical Science, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
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Liu Q, Olman V, Liu H, Ye X, Qiu S, Xu Y. RNACluster: An integrated tool for RNA secondary structure comparison and clustering. J Comput Chem 2008; 29:1517-26. [PMID: 18271070 DOI: 10.1002/jcc.20911] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
RNA structure comparison is a fundamental problem in structural biology, structural chemistry, and bioinformatics. It can be used for analysis of RNA energy landscapes, conformational switches, and facilitating RNA structure prediction. The purpose of our integrated tool RNACluster is twofold: to provide a platform for computing and comparison of different distances between RNA secondary structures, and to perform cluster identification to derive useful information of RNA structure ensembles, using a minimum spanning tree (MST) based clustering algorithm. RNACluster employs a cluster identification approach based on a MST representation of the RNA ensemble data and currently supports six distance measures between RNA secondary structures. RNACluster provides a user-friendly graphical interface to allow a user to compare different structural distances, analyze the structure ensembles, and visualize predicted structural clusters.
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Affiliation(s)
- Qi Liu
- James D. Watson Institute of Genomic Science, Zhejiang University, Hangzhou 310008, China
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Raddatz M, Dolf A, Endl E, Knolle P, Famulok M, Mayer G. Enrichment of Cell‐Targeting and Population‐Specific Aptamers by Fluorescence‐Activated Cell Sorting. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200800216] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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17
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Mayer G, Ackermann D, Kuhn N, Famulok M. Construction of DNA architectures with RNA hairpins. Angew Chem Int Ed Engl 2008; 47:971-3. [PMID: 18176928 DOI: 10.1002/anie.200704709] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Günter Mayer
- Universität Bonn, LIMES-Life and Medical Science Institut, Programmeinheit Chemische Biologie und Medizinische Chemie, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
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Mayer G, Ackermann D, Kuhn N, Famulok M. Aufbau von DNA-Architekturen mit RNA-Haarnadelschleifen. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200704709] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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