1
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Olenginski LT, Spradlin SF, Batey RT. Flipping the script: Understanding riboswitches from an alternative perspective. J Biol Chem 2024; 300:105730. [PMID: 38336293 PMCID: PMC10907184 DOI: 10.1016/j.jbc.2024.105730] [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: 09/30/2023] [Revised: 01/14/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024] Open
Abstract
Riboswitches are broadly distributed regulatory elements most frequently found in the 5'-leader sequence of bacterial mRNAs that regulate gene expression in response to the binding of a small molecule effector. The occupancy status of the ligand-binding aptamer domain manipulates downstream information in the message that instructs the expression machinery. Currently, there are over 55 validated riboswitch classes, where each class is defined based on the identity of the ligand it binds and/or sequence and structure conservation patterns within the aptamer domain. This classification reflects an "aptamer-centric" perspective that dominates our understanding of riboswitches. In this review, we propose a conceptual framework that groups riboswitches based on the mechanism by which RNA manipulates information directly instructing the expression machinery. This scheme does not replace the established aptamer domain-based classification of riboswitches but rather serves to facilitate hypothesis-driven investigation of riboswitch regulatory mechanisms. Based on current bioinformatic, structural, and biochemical studies of a broad spectrum of riboswitches, we propose three major mechanistic groups: (1) "direct occlusion", (2) "interdomain docking", and (3) "strand exchange". We discuss the defining features of each group, present representative examples of riboswitches from each group, and illustrate how these RNAs couple small molecule binding to gene regulation. While mechanistic studies of the occlusion and docking groups have yielded compelling models for how these riboswitches function, much less is known about strand exchange processes. To conclude, we outline the limitations of our mechanism-based conceptual framework and discuss how critical information within riboswitch expression platforms can inform gene regulation.
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Affiliation(s)
| | | | - Robert T Batey
- Department of Biochemistry, University of Colorado, Boulder, Colorado, USA.
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2
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Parmar S, Bume DD, Conelly C, Boer R, Prestwood PR, Wang Z, Labuhn H, Sinnadurai K, Feri A, Ouellet J, Homan P, Numata T, Schneekloth JS. Mechanistic Analysis of Riboswitch Ligand Interactions Provides Insights into Pharmacological Control over Gene Expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.23.581746. [PMID: 38903087 PMCID: PMC11188086 DOI: 10.1101/2024.02.23.581746] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Riboswitches are structured RNA elements that regulate gene expression upon binding to small molecule ligands. Understanding the mechanisms by which small molecules impact riboswitch activity is key to developing potent, selective ligands for these and other RNA targets. We report the structure-informed design of chemically diverse synthetic ligands for PreQ1 riboswitches. Multiple X-ray co-crystal structures of synthetic ligands with the Thermoanaerobacter tengcongensis (Tte)-PreQ1 riboswitch confirm a common binding site with the cognate ligand, despite considerable chemical differences among the ligands. Structure probing assays demonstrate that one ligand causes conformational changes similar to PreQ1 in six structurally and mechanistically diverse PreQ1 riboswitch aptamers. Single-molecule force spectroscopy is used to demonstrate differential modes of riboswitch stabilization by the ligands. Binding of the natural ligand brings about the formation of a persistent, folded pseudoknot structure, whereas a synthetic ligand decreases the rate of unfolding through a kinetic mechanism. Single round transcription termination assays show the biochemical activity of the ligands, while a GFP reporter system reveals compound activity in regulating gene expression in live cells without toxicity. Taken together, this study reveals that diverse small molecules can impact gene expression in live cells by altering conformational changes in RNA structures through distinct mechanisms.
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Affiliation(s)
- Shaifaly Parmar
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Desta Doro Bume
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Colleen Conelly
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Robert Boer
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Peri R. Prestwood
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Zhen Wang
- Depixus SAS, 3-5 Impasse Reille, 75014 Paris, France
| | | | | | - Adeline Feri
- Depixus SAS, 3-5 Impasse Reille, 75014 Paris, France
| | - Jimmy Ouellet
- Depixus SAS, 3-5 Impasse Reille, 75014 Paris, France
| | - Philip Homan
- Center for Cancer Research Collaborative Bioinformatics Resource, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Tomoyuki Numata
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - John S. Schneekloth
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
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3
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Eichler C, Himmelstoß M, Plangger R, Weber LI, Hartl M, Kreutz C, Micura R. Advances in RNA Labeling with Trifluoromethyl Groups. Chemistry 2023; 29:e202302220. [PMID: 37534701 PMCID: PMC10947337 DOI: 10.1002/chem.202302220] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 08/04/2023]
Abstract
Fluorine labeling of ribonucleic acids (RNA) in conjunction with 19 F NMR spectroscopy has emerged as a powerful strategy for spectroscopic analysis of RNA structure and dynamics, and RNA-ligand interactions. This study presents the first syntheses of 2'-OCF3 guanosine and uridine phosphoramidites, their incorporation into oligoribonucleotides by solid-phase synthesis and a comprehensive study of their properties. NMR spectroscopic analysis showed that the 2'-OCF3 modification is associated with preferential C2'-endo conformation of the U and G ribose in single-stranded RNA. When paired to the complementary strand, slight destabilization of the duplex caused by the modification was revealed by UV melting curve analysis. Moreover, the power of the 2'-OCF3 label for NMR spectroscopy is demonstrated by dissecting RNA pseudoknot folding and its binding to a small molecule. Furthermore, the 2'-OCF3 modification has potential for applications in therapeutic oligonucleotides. To this end, three 2'-OCF3 modified siRNAs were tested in silencing of the BASP1 gene which indicated enhanced performance for one of them. Importantly, together with earlier work, the present study completes the set of 2'-OCF3 nucleoside phosphoramidites to all four standard nucleobases (A, U, C, G) and hence enables applications that utilize the favorable properties of the 2'-OCF3 group without any restrictions in placing the modification into the RNA target sequence.
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Affiliation(s)
- Clemens Eichler
- Institute of Organic ChemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Maximilian Himmelstoß
- Institute of Organic ChemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Raphael Plangger
- Institute of Organic ChemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Leonie I. Weber
- Institute of BiochemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Markus Hartl
- Institute of BiochemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Christoph Kreutz
- Institute of Organic ChemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Ronald Micura
- Institute of Organic ChemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
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4
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Roy R, Geng A, Shi H, Merriman DK, Dethoff EA, Salmon L, Al-Hashimi HM. Kinetic Resolution of the Atomic 3D Structures Formed by Ground and Excited Conformational States in an RNA Dynamic Ensemble. J Am Chem Soc 2023; 145:22964-22978. [PMID: 37831584 DOI: 10.1021/jacs.3c04614] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
Knowing the 3D structures formed by the various conformations populating the RNA free-energy landscape, their relative abundance, and kinetic interconversion rates is required to obtain a quantitative and predictive understanding of how RNAs fold and function at the atomic level. While methods integrating ensemble-averaged experimental data with computational modeling are helping define the most abundant conformations in RNA ensembles, elucidating their kinetic rates of interconversion and determining the 3D structures of sparsely populated short-lived RNA excited conformational states (ESs) remains challenging. Here, we developed an approach integrating Rosetta-FARFAR RNA structure prediction with NMR residual dipolar couplings and relaxation dispersion that simultaneously determines the 3D structures formed by the ground-state (GS) and ES subensembles, their relative abundance, and kinetic rates of interconversion. The approach is demonstrated on HIV-1 TAR, whose six-nucleotide apical loop was previously shown to form a sparsely populated (∼13%) short-lived (lifetime ∼ 45 μs) ES. In the GS, the apical loop forms a broad distribution of open conformations interconverting on the pico-to-nanosecond time scale. Most residues are unpaired and preorganized to bind the Tat-superelongation protein complex. The apical loop zips up in the ES, forming a narrow distribution of closed conformations, which sequester critical residues required for protein recognition. Our work introduces an approach for determining the 3D ensemble models formed by sparsely populated RNA conformational states, provides a rare atomic view of an RNA ES, and kinetically resolves the atomic 3D structures of RNA conformational substates, interchanging on time scales spanning 6 orders of magnitude, from picoseconds to microseconds.
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Affiliation(s)
- Rohit Roy
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Ainan Geng
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Dawn K Merriman
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Elizabeth A Dethoff
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Loïc Salmon
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hashim M Al-Hashimi
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States
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5
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Dayie TK, Olenginski LT, Taiwo KM. Isotope Labels Combined with Solution NMR Spectroscopy Make Visible the Invisible Conformations of Small-to-Large RNAs. Chem Rev 2022; 122:9357-9394. [PMID: 35442658 PMCID: PMC9136934 DOI: 10.1021/acs.chemrev.1c00845] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Indexed: 02/07/2023]
Abstract
RNA is central to the proper function of cellular processes important for life on earth and implicated in various medical dysfunctions. Yet, RNA structural biology lags significantly behind that of proteins, limiting mechanistic understanding of RNA chemical biology. Fortunately, solution NMR spectroscopy can probe the structural dynamics of RNA in solution at atomic resolution, opening the door to their functional understanding. However, NMR analysis of RNA, with only four unique ribonucleotide building blocks, suffers from spectral crowding and broad linewidths, especially as RNAs grow in size. One effective strategy to overcome these challenges is to introduce NMR-active stable isotopes into RNA. However, traditional uniform labeling methods introduce scalar and dipolar couplings that complicate the implementation and analysis of NMR measurements. This challenge can be circumvented with selective isotope labeling. In this review, we outline the development of labeling technologies and their application to study biologically relevant RNAs and their complexes ranging in size from 5 to 300 kDa by NMR spectroscopy.
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Affiliation(s)
- Theodore K. Dayie
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Lukasz T. Olenginski
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Kehinde M. Taiwo
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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6
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Zhou Y, Jiang Y, Chen SJ. RNA-ligand molecular docking: advances and challenges. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2022; 12:e1571. [PMID: 37293430 PMCID: PMC10250017 DOI: 10.1002/wcms.1571] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/20/2021] [Indexed: 12/16/2022]
Abstract
With rapid advances in computer algorithms and hardware, fast and accurate virtual screening has led to a drastic acceleration in selecting potent small molecules as drug candidates. Computational modeling of RNA-small molecule interactions has become an indispensable tool for RNA-targeted drug discovery. The current models for RNA-ligand binding have mainly focused on the docking-and-scoring method. Accurate docking and scoring should tackle four crucial problems: (1) conformational flexibility of ligand, (2) conformational flexibility of RNA, (3) efficient sampling of binding sites and binding poses, and (4) accurate scoring of different binding modes. Moreover, compared with the problem of protein-ligand docking, predicting ligand binding to RNA, a negatively charged polymer, is further complicated by additional effects such as metal ion effects. Thermodynamic models based on physics-based and knowledge-based scoring functions have shown highly encouraging success in predicting ligand binding poses and binding affinities. Recently, kinetic models for ligand binding have further suggested that including dissociation kinetics (residence time) in ligand docking would result in improved performance in estimating in vivo drug efficacy. More recently, the rise of deep-learning approaches has led to new tools for predicting RNA-small molecule binding. In this review, we present an overview of the recently developed computational methods for RNA-ligand docking and their advantages and disadvantages.
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Affiliation(s)
- Yuanzhe Zhou
- Department of Physics and Astronomy, Department of Biochemistry, Institute of Data Sciences and Informatics, University of Missouri, Columbia, MO 65211-7010, USA
| | - Yangwei Jiang
- Department of Physics and Astronomy, Department of Biochemistry, Institute of Data Sciences and Informatics, University of Missouri, Columbia, MO 65211-7010, USA
| | - Shi-Jie Chen
- Department of Physics and Astronomy, Department of Biochemistry, Institute of Data Sciences and Informatics, University of Missouri, Columbia, MO 65211-7010, USA
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7
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Balaratnam S, Rhodes C, Bume DD, Connelly C, Lai CC, Kelley JA, Yazdani K, Homan PJ, Incarnato D, Numata T, Schneekloth Jr JS. A chemical probe based on the PreQ 1 metabolite enables transcriptome-wide mapping of binding sites. Nat Commun 2021; 12:5856. [PMID: 34615874 PMCID: PMC8494917 DOI: 10.1038/s41467-021-25973-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 08/26/2021] [Indexed: 02/08/2023] Open
Abstract
The role of metabolite-responsive riboswitches in regulating gene expression in bacteria is well known and makes them useful systems for the study of RNA-small molecule interactions. Here, we study the PreQ1 riboswitch system, assessing sixteen diverse PreQ1-derived probes for their ability to selectively modify the class-I PreQ1 riboswitch aptamer covalently. For the most active probe (11), a diazirine-based photocrosslinking analog of PreQ1, X-ray crystallography and gel-based competition assays demonstrated the mode of binding of the ligand to the aptamer, and functional assays demonstrated that the probe retains activity against the full riboswitch. Transcriptome-wide mapping using Chem-CLIP revealed a highly selective interaction between the bacterial aptamer and the probe. In addition, a small number of RNA targets in endogenous human transcripts were found to bind specifically to 11, providing evidence for candidate PreQ1 aptamers in human RNA. This work demonstrates a stark influence of linker chemistry and structure on the ability of molecules to crosslink RNA, reveals that the PreQ1 aptamer/ligand pair are broadly useful for chemical biology applications, and provides insights into how PreQ1, which is similar in structure to guanine, interacts with human RNAs.
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Affiliation(s)
- Sumirtha Balaratnam
- grid.48336.3a0000 0004 1936 8075Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702 USA
| | - Curran Rhodes
- grid.48336.3a0000 0004 1936 8075Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702 USA
| | - Desta Doro Bume
- grid.48336.3a0000 0004 1936 8075Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702 USA
| | - Colleen Connelly
- grid.48336.3a0000 0004 1936 8075Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702 USA
| | - Christopher C. Lai
- grid.48336.3a0000 0004 1936 8075Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702 USA
| | - James A. Kelley
- grid.48336.3a0000 0004 1936 8075Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702 USA
| | - Kamyar Yazdani
- grid.48336.3a0000 0004 1936 8075Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702 USA
| | - Philip J. Homan
- grid.48336.3a0000 0004 1936 8075Center for Cancer Research Collaborative Bioinformatics Resource, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA ,grid.418021.e0000 0004 0535 8394Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21702 USA
| | - Danny Incarnato
- grid.4830.f0000 0004 0407 1981Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands
| | - Tomoyuki Numata
- grid.177174.30000 0001 2242 4849Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka-shi Fukuoka, 812-8582 Japan ,grid.208504.b0000 0001 2230 7538Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba-shi, Ibaraki, 305-8566 Japan
| | - John S. Schneekloth Jr
- grid.48336.3a0000 0004 1936 8075Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702 USA
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8
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Sarkar B, Ishii K, Tahara T. Microsecond Folding of preQ 1 Riboswitch and Its Biological Significance Revealed by Two-Dimensional Fluorescence Lifetime Correlation Spectroscopy. J Am Chem Soc 2021; 143:7968-7978. [PMID: 34013733 DOI: 10.1021/jacs.1c01077] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Riboswitches are regulatory elements of bacterial mRNA which function with conformational switching upon binding of specific cellular metabolites. In particular, transcriptional riboswitches regulate gene expression kinetically through the conformational change of the aptamer domain. In this study, we investigate the conformational dynamics and ligand binding mechanisms of the aptamer domain of a transcriptional prequeuosine (preQ1) riboswitch from Bacillus subtilis using two-dimensional fluorescence lifetime correlation spectroscopy (2D FLCS) with microsecond time resolution. The obtained time-resolved single-molecule data indicate that the aptamer domain undergoes folding/unfolding including three forms, which are attributed to hairpin (O), pseudoknot-like (pF), and H-type pseudoknot (fF) structures. It is found that a cofactor, Mg2+, binds only to the fF form with the conformational selection mechanism. In contrast, it is indicated that the ligand, preQ1, binds to the O form with the induced-fit mechanism and significantly accelerates the microsecond O → pF folding process. It is also shown that the binding with preQ1 substantially stabilizes the fF form that is generated from the pF form with a long time constant (>10 ms). Combining these results with the results of a former smFRET study on the slower time scale, we obtain an overall picture of the folding/unfolding dynamics of the aptamer domain as well as its energy landscape. On the basis of the picture obtained, we discuss the significance of the microsecond folding/unfolding of the aptamer domain for biological function of the riboswitch and propose the molecular mechanism of the gene expression controlled by the structural dynamics of the aptamer domain.
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Affiliation(s)
- Bidyut Sarkar
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Kunihiko Ishii
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan.,Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan.,Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
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9
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Himmelstoß M, Erharter K, Renard E, Ennifar E, Kreutz C, Micura R. 2'- O-Trifluoromethylated RNA - a powerful modification for RNA chemistry and NMR spectroscopy. Chem Sci 2020; 11:11322-11330. [PMID: 34094374 PMCID: PMC8162808 DOI: 10.1039/d0sc04520a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 09/18/2020] [Indexed: 11/21/2022] Open
Abstract
New RNA modifications are needed to advance our toolbox for targeted manipulation of RNA. In particular, the development of high-performance reporter groups facilitating spectroscopic analysis of RNA structure and dynamics, and of RNA-ligand interactions has attracted considerable interest. To this end, fluorine labeling in conjunction with 19F-NMR spectroscopy has emerged as a powerful strategy. Appropriate probes for RNA previously focused on single fluorine atoms attached to the 5-position of pyrimidine nucleobases or at the ribose 2'-position. To increase NMR sensitivity, trifluoromethyl labeling approaches have been developed, with the ribose 2'-SCF3 modification being the most prominent one. A major drawback of the 2'-SCF3 group, however, is its strong impact on RNA base pairing stability. Interestingly, RNA containing the structurally related 2'-OCF3 modification has not yet been reported. Therefore, we set out to overcome the synthetic challenges toward 2'-OCF3 labeled RNA and to investigate the impact of this modification. We present the syntheses of 2'-OCF3 adenosine and cytidine phosphoramidites and their incorporation into oligoribonucleotides by solid-phase synthesis. Importantly, it turns out that the 2'-OCF3 group has only a slight destabilizing effect when located in double helical regions which is consistent with the preferential C3'-endo conformation of the 2'-OCF3 ribose as reflected in the 3 J (H1'-H2') coupling constants. Furthermore, we demonstrate the exceptionally high sensitivity of the new label in 19F-NMR analysis of RNA structure equilibria and of RNA-small molecule interactions. The study is complemented by a crystal structure at 0.9 Å resolution of a 27 nt hairpin RNA containing a single 2'-OCF3 group that well integrates into the minor groove. The new label carries high potential to outcompete currently applied fluorine labels for nucleic acid NMR spectroscopy because of its significantly advanced performance.
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Affiliation(s)
- Maximilian Himmelstoß
- University of Innsbruck, Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI) Innrain 80-82 6020 Innsbruck Austria
| | - Kevin Erharter
- University of Innsbruck, Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI) Innrain 80-82 6020 Innsbruck Austria
| | - Eva Renard
- Université de Strasbourg, Architecture et Réactivité de l'ARN-CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire 67000 Strasbourg France
| | - Eric Ennifar
- Université de Strasbourg, Architecture et Réactivité de l'ARN-CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire 67000 Strasbourg France
| | - Christoph Kreutz
- University of Innsbruck, Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI) Innrain 80-82 6020 Innsbruck Austria
| | - Ronald Micura
- University of Innsbruck, Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI) Innrain 80-82 6020 Innsbruck Austria
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10
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Gong Z, Yang S, Dong X, Yang QF, Zhu YL, Xiao Y, Tang C. Hierarchical Conformational Dynamics Confers Thermal Adaptability to preQ 1 RNA Riboswitches. J Mol Biol 2020; 432:4523-4543. [PMID: 32522558 DOI: 10.1016/j.jmb.2020.06.002] [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: 03/14/2020] [Revised: 06/03/2020] [Accepted: 06/03/2020] [Indexed: 11/26/2022]
Abstract
Single-stranded noncoding regulatory RNAs, as exemplified by bacterial riboswitches, are highly dynamic. The conformational dynamics allow the riboswitch to reach maximum switching efficiency under appropriate conditions. Here we characterize the conformational dynamics of preQ1 riboswitches from mesophilic and thermophilic bacterial species at various temperatures. With the integrative use of small-angle X-ray scattering, NMR, and molecular dynamics simulations, we model the ensemble-structures of the preQ1 riboswitch aptamers without or with a ligand bound. We show that the preQ1 riboswitch is sufficiently dynamic and fluctuating among multiple folding intermediates only near the physiological temperature of the microorganism. The hierarchical folding dynamics of the RNA involves the docking of 3'-tail to form a second RNA helix and the helical stacking to form an H-type pseudoknot structure. Further, we show that RNA secondary and tertiary dynamics can be modulated by temperature and by the length of an internal loop. The coupled equilibria between RNA folding intermediates are essential for preQ1 binding, and a four-state exchange model can account for the change of ligand-triggered switching efficiency with temperature. Together, we have established a relationship between the hierarchical dynamics and riboswitch function, and illustrated how the RNA adapts to high temperature.
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Affiliation(s)
- Zhou Gong
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China.
| | - Shuai Yang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xu Dong
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China
| | - Qing-Fen Yang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China
| | - Yue-Ling Zhu
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China
| | - Yi Xiao
- Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei Province 430074, China
| | - Chun Tang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China; Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei Province 430074, China.
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11
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Suddala KC, Zhang J. High-affinity recognition of specific tRNAs by an mRNA anticodon-binding groove. Nat Struct Mol Biol 2019; 26:1114-1122. [PMID: 31792448 PMCID: PMC6903423 DOI: 10.1038/s41594-019-0335-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 10/21/2019] [Indexed: 11/10/2022]
Abstract
T-box riboswitches are modular bacterial noncoding RNAs that sense and regulate amino acid availability through direct interactions with tRNAs. Between the 5' anticodon-binding stem I domain and the 3' amino acid sensing domains of most T-boxes lies the stem II domain of unknown structure and function. Here, we report a 2.8-Å cocrystal structure of the Nocardia farcinica ileS T-box in complex with its cognate tRNAIle. The structure reveals a perpendicularly arranged ultrashort stem I containing a K-turn and an elongated stem II bearing an S-turn. Both stems rest against a compact pseudoknot, dock via an extended ribose zipper and jointly create a binding groove specific to the anticodon of its cognate tRNA. Contrary to proposed distal contacts to the tRNA elbow region, stem II locally reinforces the codon-anticodon interactions between stem I and tRNA, achieving low-nanomolar affinity. This study illustrates how mRNA junctions can create specific binding sites for interacting RNAs of prescribed sequence and structure.
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Affiliation(s)
- Krishna C Suddala
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA.
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12
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Murata A, Nakamori M, Nakatani K. Modulating RNA secondary and tertiary structures by mismatch binding ligands. Methods 2019; 167:78-91. [DOI: 10.1016/j.ymeth.2019.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 05/05/2019] [Accepted: 05/07/2019] [Indexed: 12/21/2022] Open
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13
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Widom JR, Nedialkov YA, Rai V, Hayes RL, Brooks CL, Artsimovitch I, Walter NG. Ligand Modulates Cross-Coupling between Riboswitch Folding and Transcriptional Pausing. Mol Cell 2019; 72:541-552.e6. [PMID: 30388413 PMCID: PMC6565381 DOI: 10.1016/j.molcel.2018.08.046] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 06/11/2018] [Accepted: 08/30/2018] [Indexed: 12/31/2022]
Abstract
Numerous classes of riboswitches have been found to regulate bacterial gene expression in response to physiological cues, offering new paths to antibacterial drugs. As common studies of isolated riboswitches lack the functional context of the transcription machinery, we here combine single-molecule, biochemical, and simulation approaches to investigate the coupling between co-transcriptional folding of the pseudoknot-structured preQ1 riboswitch and RNA polymerase (RNAP) pausing. We show that pausing at a site immediately downstream of the riboswitch requires a ligand-free pseudoknot in the nascent RNA, a precisely spaced sequence resembling the pause consensus, and electrostatic and steric interactions with the RNAP exit channel. While interactions with RNAP stabilize the native fold of the riboswitch, binding of the ligand signals RNAP release from the pause. Our results demonstrate that the nascent riboswitch and its ligand actively modulate the function of RNAP and vice versa, a paradigm likely to apply to other cellular RNA transcripts.
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Affiliation(s)
- Julia R Widom
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yuri A Nedialkov
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Victoria Rai
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA; Biophysics Program and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ryan L Hayes
- Biophysics Program and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Charles L Brooks
- Biophysics Program and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Irina Artsimovitch
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA.
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14
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Combined smFRET and NMR analysis of riboswitch structural dynamics. Methods 2019; 153:22-34. [DOI: 10.1016/j.ymeth.2018.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 10/08/2018] [Accepted: 10/09/2018] [Indexed: 12/13/2022] Open
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15
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Kerzhner M, Matsuoka H, Wuebben C, Famulok M, Schiemann O. High-Yield Spin Labeling of Long RNAs for Electron Paramagnetic Resonance Spectroscopy. Biochemistry 2018; 57:2923-2931. [PMID: 29715006 DOI: 10.1021/acs.biochem.8b00040] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Site-directed spin labeling is a powerful tool for investigating the conformation and dynamics of biomacromolecules such as RNA. Here we introduce a spin labeling strategy based on click chemistry in solution that, in combination with enzymatic ligation, allows highly efficient labeling of complex and long RNAs with short reaction times and suppressed RNA degradation. With this approach, a 34-nucleotide aptamer domain of the preQ1 riboswitch and an 81-nucleotide TPP riboswitch aptamer could be labeled with two labels in several positions. We then show that conformations of the preQ1 aptamer and its dynamics can be monitored in the absence and presence of Mg2+ and a preQ1 ligand by continuous wave electron paramagnetic resonance spectroscopy at room temperature and pulsed electron-electron double resonance spectroscopy (PELDOR or DEER) in the frozen state.
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Affiliation(s)
- Mark Kerzhner
- Life & Medical Sciences Institute Chemical Biology & Medicinal Chemistry Unit c/o Kekulé-Institut für Organische Chemie und Biochemie University of Bonn , Gerhard-Domagk-Strasse 1 , 53121 Bonn , Germany
| | - Hideto Matsuoka
- Institute of Physical and Theoretical Chemistry , University of Bonn , Wegelerstrasse 12 , 53115 Bonn , Germany
| | - Christine Wuebben
- Institute of Physical and Theoretical Chemistry , University of Bonn , Wegelerstrasse 12 , 53115 Bonn , Germany
| | - Michael Famulok
- Life & Medical Sciences Institute Chemical Biology & Medicinal Chemistry Unit c/o Kekulé-Institut für Organische Chemie und Biochemie University of Bonn , Gerhard-Domagk-Strasse 1 , 53121 Bonn , Germany.,Max Planck Fellowship Chemical Biology Group , Stiftung caesar , Ludwig-Erhard-Allee 2 , 53175 Bonn , Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry , University of Bonn , Wegelerstrasse 12 , 53115 Bonn , Germany
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16
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Reiling-Steffensmeier C, Marky LA. Structural Insight into the Unbound State of the DNA Analogue of the PreQ 1 Riboswitch: A Thermodynamic Approach. Biochemistry 2017; 56:6231-6239. [PMID: 29076719 DOI: 10.1021/acs.biochem.7b00596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The preQ1 riboswitch aptamer domain is very dynamic in its unbound state with the ability to form multiple structures: a hairpin, kissing hairpins, and pseudoknot-like structure. The aim of this study is to determine whether the DNA analogue (PreQ1) is able to form structures similar to that of the reported RNA aptamer. Using a thermodynamic approach, we report on structural determination using differential scanning calorimetry under different salt conditions. Further analysis of the primary sequence allowed us to design modified molecules to determine what potential structures are forming in this single-stranded DNA analogue. We found, in a 16 mM Na+ solution, PreQ1 has three transitions with TM values of 14.8, 19.4, and 26.2 °C and a total ΔH of -44.7 kcal/mol. With the increase in salt concentration to 116 mM, there are TM values of 22.3, 28.7, and 38.9 °C and a ΔH of -69.1 kcal/mol, while at 216 mM, the three transitions have TM values of 24.4, 31.6, and 42.9 °C with a total ΔH of -71.5 kcal/mol. Therefore, the increase in enthalpy is due to the formation of additional base-pair stacks. The modified molecules, which would inhibit pseudoknot formation, kissing hairpins, and internal loop interactions, were fully characterized and compared to the native DNA analogue. The analysis of the enthalpy and differential binding of counterions allows us to conclude this single-stranded DNA analogue under physiological conditions is not forming a pseudoknot-like structure. Instead, two potential structures, Compact-Hairpin and Kissing-Complex, are more likely and could be in equilibrium.
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Affiliation(s)
- Calliste Reiling-Steffensmeier
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center , 986025 Nebraska Medical Center, Omaha, Nebraska 68198-6025, United States
| | - Luis A Marky
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center , 986025 Nebraska Medical Center, Omaha, Nebraska 68198-6025, United States
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17
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Choi YJ, Gibala KS, Ayele T, Deventer KV, Resendiz MJE. Biophysical properties, thermal stability and functional impact of 8-oxo-7,8-dihydroguanine on oligonucleotides of RNA-a study of duplex, hairpins and the aptamer for preQ1 as models. Nucleic Acids Res 2017; 45:2099-2111. [PMID: 28426093 PMCID: PMC5389535 DOI: 10.1093/nar/gkw885] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 09/22/2016] [Indexed: 01/12/2023] Open
Abstract
A better understanding of the effects that oxidative lesions have on RNA is of importance to understand their role in the development/progression of disease. 8-oxo-7,8-dihydroguanine was incorporated into RNA to understand its structural and functional impact on RNA:RNA and RNA:DNA duplexes, hairpins and pseudoknots. One to three modifications were incorporated into dodecamers of RNA [AAGAGGGAUGAC] resulting in thermal destabilization (ΔTm – 10°C per lesion). Hairpins with tetraloops c-UUCG*-g* (8-10), a-ACCG-g* (11-12), c-UUG*G*-g* (13-16) and c-ACG*G*-g* (17-20) were modified and used to determine thermal stabilities, concluding that: (i) modifying the stem leads to destabilization unless adenosine is the opposing basepair of 8-oxoGua; (ii) modification at the loop is position- and sequence-dependent and varies from slight stabilization to large destabilization, in some cases leading to formation of other secondary structures (hairpin→duplex). Functional effects were established using the aptamer for preQ1 as model. Modification at G5 disrupted the stem P1 and inhibited recognition of the target molecule 7-methylamino-7-deazaguanine (preQ1). Modifying G11 results in increased thermal stability, albeit with a Kd 4-fold larger than its canonical analog. These studies show the capability of 8-oxoG to affect structure and function of RNA, resulting in distinct outcomes as a function of number and position of the lesion.
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Affiliation(s)
- Yu J Choi
- Department of Chemistry, University of Colorado Denver, Science Building 1151 Arapahoe St, Denver, CO 80204, USA
| | - Krzysztof S Gibala
- Department of Chemistry, University of Colorado Denver, Science Building 1151 Arapahoe St, Denver, CO 80204, USA
| | - Tewoderos Ayele
- Department of Chemistry, University of Colorado Denver, Science Building 1151 Arapahoe St, Denver, CO 80204, USA
| | - Katherine V Deventer
- Department of Chemistry, University of Colorado Denver, Science Building 1151 Arapahoe St, Denver, CO 80204, USA
| | - Marino J E Resendiz
- Department of Chemistry, University of Colorado Denver, Science Building 1151 Arapahoe St, Denver, CO 80204, USA
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18
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Zhang JM, Jiang C, Ye W, Luo R, Chen HF. Allosteric pathways in tetrahydrofolate sensing riboswitch with dynamics correlation network. MOLECULAR BIOSYSTEMS 2017; 13:156-164. [PMID: 27841427 DOI: 10.1039/c6mb00630b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Riboswitches are cis-acting genetic control elements. Due to their fundamental importance in bacteria gene regulation, they have been proposed as antibacterial drug targets. Tetrahydrofolate (THF) is an essential cofactor of one-carbon transfer reactions and downregulates the expression of downstream genes. However, information on how to transfer from the binding site of THF to the expression platform is still unavailable. Herein, a nucleotide/nucleotide dynamics correlation network based on an all-atom molecular dynamic simulation was used to reveal the regulation mechanism of a THF-sensing riboswitch. Shortest pathway analysis based on the network illustrates that there is an allosteric pathway through the P2 helix to the pseudoknot, then to the P1 helix in the THF-riboswitch. Thus the hypothesis of "THF-binding induced allosteric switching" was proposed and evaluated using THF and pseudoknot weakened experiments. Furthermore, a possible allosteric pathway of C30-C31-G33-A34-G35-G36-G37-A38-G48-G47-U46-A90-U91-C92-G93-C94-G95-C96 was identified and confirmed through the perturbation of the network. The proposed allosteric mechanism and the underlying allosteric pathway provide fundamental insights for the regulation of THF sensing riboswitches.
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Affiliation(s)
- Jin-Mai Zhang
- State Key Laboratory of Microbial metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China.
| | - Cheng Jiang
- State Key Laboratory of Microbial metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China.
| | - Wei Ye
- State Key Laboratory of Microbial metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China.
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry and Biomedical Engineering, University of California, Irvine, CA 92697-3900, USA.
| | - Hai-Feng Chen
- State Key Laboratory of Microbial metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China. and Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Shanghai, 200235, China
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19
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Neuner S, Kreutz C, Micura R. The synthesis of 15N(7)-Hoogsteen face-labeled adenosine phosphoramidite for solid-phase RNA synthesis. MONATSHEFTE FUR CHEMIE 2016; 148:149-155. [PMID: 28127100 PMCID: PMC5225212 DOI: 10.1007/s00706-016-1882-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 11/21/2016] [Indexed: 01/08/2023]
Abstract
ABSTRACT We have developed an efficient route for the synthesis of 15N(7)-labeled adenosine as phosphoramidite building block for site- and atom-specific incorporation into RNA by automated solid-phase synthesis. Such labeled RNA is required for the evaluation of selected non-canonical base pair interactions in folded RNA using NMR spectroscopic methods. GRAPHICAL ABSTRACT
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Affiliation(s)
- Sandro Neuner
- Institute of Organic Chemistry, Leopold-Franzens University, Innrain 80-82, Innsbruck, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry, Leopold-Franzens University, Innrain 80-82, Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry, Leopold-Franzens University, Innrain 80-82, Innsbruck, Austria
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20
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McPhie P, Brown P, Chen B, Dayie TK, Minton AP. Modulation of Conformational Equilibria in the S-Adenosylmethionine (SAM) II Riboswitch by SAM, Mg(2+), and Trimethylamine N-Oxide. Biochemistry 2016; 55:5010-20. [PMID: 27552169 DOI: 10.1021/acs.biochem.6b00283] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The dependence of the conformation of the S-adenosylmethionine (SAM) II riboswitch on the concentration of added Mg(2+) ions and SAM, individually and in mixtures, was monitored by circular dichroism (CD) spectroscopy and by measurement of the diffusion coefficient. The results are analyzed in the context of two complementary quantitative models, both of which are consistent with a single underlying physical model. Magnesium binding sites in the open state have an affinity on average higher than the affinity of those in the compact state, but formation of the compact state is accompanied by an increase in the number of binding sites. Consequently, at low Mg(2+) concentrations, Mg(2+) binds preferentially to the open state, favoring its formation, but at high concentrations, Mg(2+) binds preferentially to the compact state. The affinity of the riboswitch for SAM increases drastically with an increased level of binding of Mg(2+) to the compact pseudoknot conformation. The effect of increasing concentrations of trimethylamine N-oxide (TMAO), a well-studied molecular crowding agent, on the conformation of the riboswitch and its affinity for SAM were also monitored by CD spectroscopy and measurement of diffusion. In the absence of added Mg(2+), high concentrations of TMAO were found to induce a conformational change compatible with the formation of the pseudoknot form but have only a small effect on the affinity of the RNA for SAM.
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Affiliation(s)
- Peter McPhie
- Section on Physical Biochemistry, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Patrick Brown
- Section on Dynamics of Macromolecular of Assembly, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Bin Chen
- Department of Chemistry and Biochemistry, University of Maryland , College Park, Maryland 20742, United States
| | - Theodore K Dayie
- Department of Chemistry and Biochemistry, University of Maryland , College Park, Maryland 20742, United States
| | - Allen P Minton
- Section on Physical Biochemistry, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
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21
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Mn(2+)-sensing mechanisms of yybP-ykoY orphan riboswitches. Mol Cell 2016; 57:1110-1123. [PMID: 25794619 DOI: 10.1016/j.molcel.2015.02.016] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 01/30/2015] [Accepted: 02/09/2015] [Indexed: 02/05/2023]
Abstract
Gene regulation in cis by riboswitches is prevalent in bacteria. The yybP-ykoY riboswitch family is quite widespread, yet its ligand and function remained unknown. Here, we characterize the Lactococcus lactis yybP-ykoY orphan riboswitch as a Mn(2+)-dependent transcription-ON riboswitch, with a ∼30-40 μM affinity for Mn(2+). We further determined its crystal structure at 2.7 Å to elucidate the metal sensing mechanism. The riboswitch resembles a hairpin, with two coaxially stacked helices tethered by a four-way junction and a tertiary docking interface. The Mn(2+)-sensing region, strategically located at the highly conserved docking interface, has two metal binding sites. Whereas one site tolerates the binding of either Mg(2+) or Mn(2+), the other site strongly prefers Mn(2+) due to a direct contact from the N7 of an invariable adenosine. Mutagenesis and a Mn(2+)-free E. coli yybP-ykoY structure further reveal that Mn(2+) binding is coupled with stabilization of the Mn(2+)-sensing region and the aptamer domain.
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22
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Frener M, Micura R. Conformational Rearrangements of Individual Nucleotides during RNA-Ligand Binding Are Rate-Differentiated. J Am Chem Soc 2016; 138:3627-30. [PMID: 26974261 PMCID: PMC4959565 DOI: 10.1021/jacs.5b11876] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A pronounced rate differentiation has been found for conformational rearrangements of individual nucleobases that occur during ligand recognition of the preQ1 class-I riboswitch aptamer from Thermoanaerobacter tengcongensis. Rate measurements rely on the 2ApFold approach by analyzing the fluorescence response of riboswitch variants, each with a single, strategically positioned 2-aminopurine nucleobase substitution. Observed rate discrimination between the fastest and the slowest conformational adaption is 22-fold, with the largest rate observed for the rearrangement of a nucleoside directly at the binding site and the smallest rate observed for the 3'-unpaired nucleoside that stacks onto the pseudo-knot-closing Watson-Crick base pair. Our findings provide novel insights into how compact, prefolded RNAs that follow the induced-fit recognition mechanism adapt local structural elements in response to ligand binding on a rather broad time scale and how this process culminates in a structural signal that is responsible for efficient downregulation of ribosomal translation.
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Affiliation(s)
- Marina Frener
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, 6020 Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, 6020 Innsbruck, Austria
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23
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Suddala KC, Wang J, Hou Q, Walter NG. Mg(2+) shifts ligand-mediated folding of a riboswitch from induced-fit to conformational selection. J Am Chem Soc 2015; 137:14075-83. [PMID: 26471732 DOI: 10.1021/jacs.5b09740] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacterial riboswitches couple small-molecule ligand binding to RNA conformational changes that widely regulate gene expression, rendering them potential targets for antibiotic intervention. Despite structural insights, the ligand-mediated folding mechanisms of riboswitches are still poorly understood. Using single-molecule fluorescence resonance energy transfer (smFRET), we have investigated the folding mechanism of an H-type pseudoknotted preQ1 riboswitch in dependence of Mg(2+) and three ligands of distinct affinities. We show that, in the absence of Mg(2+), both weakly and strongly bound ligands promote pseudoknot docking through an induced-fit mechanism. By contrast, addition of as low as 10 μM Mg(2+) generally shifts docking toward conformational selection by stabilizing a folded-like conformation prior to ligand binding. Supporting evidence from transition-state analysis further highlights the particular importance of stacking interactions during induced-fit and of specific hydrogen bonds during conformational selection. Our mechanistic dissection provides unprecedented insights into the intricate synergy between ligand- and Mg(2+)-mediated RNA folding.
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Affiliation(s)
- Krishna C Suddala
- Biophysics, ‡Single Molecule Analysis Group, Department of Chemistry, University of Michigan , 930 N. University, Ann Arbor, Michigan 48109, United States
| | - Jiarui Wang
- Biophysics, ‡Single Molecule Analysis Group, Department of Chemistry, University of Michigan , 930 N. University, Ann Arbor, Michigan 48109, United States
| | - Qian Hou
- Biophysics, ‡Single Molecule Analysis Group, Department of Chemistry, University of Michigan , 930 N. University, Ann Arbor, Michigan 48109, United States
| | - Nils G Walter
- Biophysics, ‡Single Molecule Analysis Group, Department of Chemistry, University of Michigan , 930 N. University, Ann Arbor, Michigan 48109, United States
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24
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Neuner S, Santner T, Kreutz C, Micura R. The "Speedy" Synthesis of Atom-Specific (15)N Imino/Amido-Labeled RNA. Chemistry 2015; 21:11634-11643. [PMID: 26237536 PMCID: PMC4946632 DOI: 10.1002/chem.201501275] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Although numerous reports on the synthesis of atom-specific (15)N-labeled nucleosides exist, fast and facile access to the corresponding phosphoramidites for RNA solid-phase synthesis is still lacking. This situation represents a severe bottleneck for NMR spectroscopic investigations on functional RNAs. Here, we present optimized procedures to speed up the synthesis of (15)N(1) adenosine and (15)N(1) guanosine amidites, which are the much needed counterparts of the more straightforward-to-achieve (15)N(3) uridine and (15)N(3) cytidine amidites in order to tap full potential of (1)H/(15)N/(15)N-COSY experiments for directly monitoring individual Watson-Crick base pairs in RNA. Demonstrated for two preQ1 riboswitch systems, we exemplify a versatile concept for individual base-pair labeling in the analysis of conformationally flexible RNAs when competing structures and conformational dynamics are encountered.
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Affiliation(s)
- Sandro Neuner
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck (Austria)
| | - Tobias Santner
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck (Austria)
| | - Christoph Kreutz
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck (Austria)
| | - Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck (Austria)
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25
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Rinaldi AJ, Suddala KC, Walter NG. Native purification and labeling of RNA for single molecule fluorescence studies. Methods Mol Biol 2015; 1240:63-95. [PMID: 25352138 DOI: 10.1007/978-1-4939-1896-6_6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The recent discovery that non-coding RNAs are considerably more abundant and serve a much wider range of critical cellular functions than recognized over previous decades of research into molecular biology has sparked a renewed interest in the study of structure-function relationships of RNA. To perform their functions in the cell, RNAs must dominantly adopt their native conformations, avoiding deep, non-productive kinetic traps that may exist along a frustrated (rugged) folding free energy landscape. Intracellularly, RNAs are synthesized by RNA polymerase and fold co-transcriptionally starting from the 5' end, sometimes with the aid of protein chaperones. By contrast, in the laboratory RNAs are commonly generated by in vitro transcription or chemical synthesis, followed by purification in a manner that includes the use of high concentrations of urea, heat and UV light (for detection), resulting in the denaturation and subsequent refolding of the entire RNA. Recent studies into the nature of heterogeneous RNA populations resulting from this process have underscored the need for non-denaturing (native) purification methods that maintain the co-transcriptional fold of an RNA. Here, we present protocols for the native purification of an RNA after its in vitro transcription and for fluorophore and biotin labeling methods designed to preserve its native conformation for use in single molecule fluorescence resonance energy transfer (smFRET) inquiries into its structure and function. Finally, we present methods for taking smFRET data and for analyzing them, as well as a description of plausible overall preparation schemes for the plethora of non-coding RNAs.
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Affiliation(s)
- Arlie J Rinaldi
- W. M. Keck Science Center, The Claremont Colleges, Claremont, CA, 91711, USA
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26
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Jud L, Košutić M, Schwarz V, Hartl M, Kreutz C, Bister K, Micura R. Expanding the Scope of 2'-SCF3 Modified RNA. Chemistry 2015; 21:10400-7. [PMID: 26074479 PMCID: PMC4515092 DOI: 10.1002/chem.201500415] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Indexed: 11/14/2022]
Abstract
The 2′-trifluoromethylthio (2′-SCF3) modification endows ribonucleic acids with exceptional properties and has attracted considerable interest as a reporter group for NMR spectroscopic applications. However, only modified pyrimidine nucleosides have been generated so far. Here, the syntheses of 2′-SCF3 adenosine and guanosine phosphoramidites of which the latter was obtained in highly efficient manner by an unconventional Boc-protecting group strategy, are reported. RNA solid-phase synthesis provided site-specifically 2′-SCF3-modified oligoribonucleotides that were investigated intensively. Their excellent behavior in 19F NMR spectroscopic probing of RNA ligand binding was exemplified for a noncovalent small molecule–RNA interaction. Moreover, comparably to the 2′-SCF3 pyrimidine nucleosides, the purine counterparts were also found to cause a significant thermodynamic destabilization when located in double helical regions. This property was considered beneficial for siRNA design under the aspect to minimize off-target effects and their performance in silencing of the BASP1 gene was demonstrated.
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Affiliation(s)
- Lukas Jud
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck (Austria)
| | - Marija Košutić
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck (Austria)
| | - Veronika Schwarz
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck (Austria)
| | - Markus Hartl
- Institute of Biochemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck (Austria)
| | - Christoph Kreutz
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck (Austria)
| | - Klaus Bister
- Institute of Biochemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck (Austria)
| | - Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck (Austria).
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27
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Bian Y, Zhang J, Wang J, Wang J, Wang W. Free energy landscape and multiple folding pathways of an H-type RNA pseudoknot. PLoS One 2015; 10:e0129089. [PMID: 26030098 PMCID: PMC4451515 DOI: 10.1371/journal.pone.0129089] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 04/24/2015] [Indexed: 11/19/2022] Open
Abstract
How RNA sequences fold to specific tertiary structures is one of the key problems for understanding their dynamics and functions. Here, we study the folding process of an H-type RNA pseudoknot by performing a large-scale all-atom MD simulation and bias-exchange metadynamics. The folding free energy landscapes are obtained and several folding intermediates are identified. It is suggested that the folding occurs via multiple mechanisms, including a step-wise mechanism starting either from the first helix or the second, and a cooperative mechanism with both helices forming simultaneously. Despite of the multiple mechanism nature, the ensemble folding kinetics estimated from a Markov state model is single-exponential. It is also found that the correlation between folding and binding of metal ions is significant, and the bound ions mediate long-range interactions in the intermediate structures. Non-native interactions are found to be dominant in the unfolded state and also present in some intermediates, possibly hinder the folding process of the RNA.
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Affiliation(s)
- Yunqiang Bian
- Collaborative Innovation Center of Advanced Microstructures and Department of Physics, Nanjing University, Nanjing 210093, China
- Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Jian Zhang
- Collaborative Innovation Center of Advanced Microstructures and Department of Physics, Nanjing University, Nanjing 210093, China
- * E-mail: (JZ); (WW)
| | - Jun Wang
- Collaborative Innovation Center of Advanced Microstructures and Department of Physics, Nanjing University, Nanjing 210093, China
| | - Jihua Wang
- Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Wei Wang
- Collaborative Innovation Center of Advanced Microstructures and Department of Physics, Nanjing University, Nanjing 210093, China
- * E-mail: (JZ); (WW)
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28
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Zhao B, Zhang Q. Characterizing excited conformational states of RNA by NMR spectroscopy. Curr Opin Struct Biol 2015; 30:134-146. [PMID: 25765780 DOI: 10.1016/j.sbi.2015.02.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 02/14/2015] [Accepted: 02/18/2015] [Indexed: 11/25/2022]
Abstract
Conformational dynamics is a hallmark of diverse non-coding RNA functions. During these functional processes, RNA molecules almost ubiquitously undergo conformational transitions that are tuned to meet distinct structural and kinetic requirements for proper function. A complete mechanistic understanding of RNA function requires comprehensive structural and dynamic knowledge of these complex transitions, which often involve alternative higher-energy conformational states that pose a major challenge for high-resolution structural study by conventional methods. In this review, we describe recent progress in RNA NMR that has started to unveil detailed structural, thermodynamic and kinetic insights into some of these excited conformational states of RNA and their functional roles in biology.
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Affiliation(s)
- Bo Zhao
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States; Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Qi Zhang
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States.
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29
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Abstract
Introduction of novel and diverse functional groups in drug discovery is always seen with hesitancy until good activity and low toxicity characteristics are proven. The introduction of fluorine in drug-like compounds is now a well-accepted strategy in medicinal chemistry. However, polyfluoroalkyl groups, with the exception of trifluoromethyl substituents, are not well explored yet. Our aim is to show to the readers how polyfluorinated groups can be beneficial to the properties of pharmaceutically active compounds by highlighting the structure–activity relationship (SAR) studies that led to the selection of polyfluorinated moieties as key structural features. Despite the fact that the use of higher polyfluoroalkyl/aryl moieties is still in its infancy, we believe that they will soon acquire the same importance of their lower parents.
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30
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Matzner D, Mayer G. (Dis)similar Analogues of Riboswitch Metabolites as Antibacterial Lead Compounds. J Med Chem 2015; 58:3275-86. [PMID: 25603286 DOI: 10.1021/jm500868e] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The rise of antimicrobial resistance in human pathogenic bacteria has increased the necessity for the discovery of novel, yet unexplored antibacterial drug targets. Riboswitches, which are embedded in untranslated regions of bacterial messenger RNA (mRNA), represent such an interesting target structure. These RNA elements regulate gene expression upon binding to natural metabolites, second messengers, and inorganic ions, such as fluoride with high affinity and in a highly discriminative manner. Recently, efforts have been directed toward the identification of artificial riboswitch activators by establishing high-throughput screening assays, fragment-based screening, and structure-guided ligand design approaches. Emphasis in this review is placed on the special requirements and synthesis of new potential antibiotic drugs that target riboswitches in which dissimilarity is an important aspect in the design of potential lead compounds.
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Affiliation(s)
- Daniel Matzner
- Life and Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| | - Günter Mayer
- Life and Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
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31
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Moschen T, Wunderlich CH, Spitzer R, Levic J, Micura R, Tollinger M, Kreutz C. Ligand-detected relaxation dispersion NMR spectroscopy: dynamics of preQ1-RNA binding. Angew Chem Int Ed Engl 2015; 54:560-3. [PMID: 25403518 PMCID: PMC4353840 DOI: 10.1002/anie.201409779] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Indexed: 12/21/2022]
Abstract
An NMR-based approach to characterizing the binding kinetics of ligand molecules to biomolecules, like RNA or proteins, by ligand-detected Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments is described. A (15)N-modified preQ1 ligand is used to acquire relaxation dispersion experiments in the presence of low amounts of the Fsu class I preQ1 aptamer RNA, and increasing ligand concentrations to probe the RNA small molecule interaction. Our experimental data strongly support the conformational selection mechanism postulated. The approach gives direct access to two parameters of a ligand-receptor interaction: the off rate and the population of the small molecule-receptor complex. A detailed description of the kinetics underlying the ligand binding process is of crucial importance to fully understanding a riboswitch's function and to evaluate potential new antibiotics candidates targeting the noncoding RNA species. Ligand-detected NMR relaxation dispersion experiments represent a valuable diagnostic tool for the characterization of binding mechanisms.
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Affiliation(s)
- Thomas Moschen
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck (Austria)
| | - Christoph Hermann Wunderlich
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck (Austria)
| | - Romana Spitzer
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck (Austria)
| | - Jasmin Levic
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck (Austria)
| | - Ronald Micura
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck (Austria)
| | - Martin Tollinger
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck (Austria)
| | - Christoph Kreutz
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck (Austria)
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32
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Moschen T, Wunderlich CH, Spitzer R, Levic J, Micura R, Tollinger M, Kreutz C. Ligand-Detected Relaxation Dispersion NMR Spectroscopy: Dynamics of preQ1-RNA Binding. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409779] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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33
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Levic J, Micura R. Syntheses of (15)N-labeled pre-queuosine nucleobase derivatives. Beilstein J Org Chem 2014; 10:1914-8. [PMID: 25246950 PMCID: PMC4168690 DOI: 10.3762/bjoc.10.199] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Accepted: 07/14/2014] [Indexed: 01/21/2023] Open
Abstract
Pre-queuosine or queuine (preQ1) is a guanine derivative that is involved in the biosynthetic pathway of the hypermodified tRNA nucleoside queuosine (Que). The core structure of preQ1 is represented by 7-(aminomethyl)-7-deazaguanine (preQ1 base). Here, we report the synthesis of three preQ1 base derivatives with complementary (15)N-labeling patterns, utilizing [(15)N]-KCN, [(15)N]-phthalimide, and [(15)N3]-guanidine as cost-affordable (15)N sources. Such derivatives are required to explore the binding process of the preQ1 base to RNA targets using advanced NMR spectroscopic methods. PreQ1 base specifically binds to bacterial mRNA domains and thereby regulates genes that are required for queuosine biosynthesis.
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Affiliation(s)
- Jasmin Levic
- Institute of Organic Chemistry, University of Innsbruck and Center for Molecular Biosciences Innsbruck, Innrain 80–82, 6020 Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry, University of Innsbruck and Center for Molecular Biosciences Innsbruck, Innrain 80–82, 6020 Innsbruck, Austria
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34
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Jiang T, Kennedy SD, Moss WN, Kierzek E, Turner DH. Secondary structure of a conserved domain in an intron of influenza A M1 mRNA. Biochemistry 2014; 53:5236-48. [PMID: 25026548 PMCID: PMC4139153 DOI: 10.1021/bi500611j] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Influenza A virus utilizes RNA throughout infection. Little is known, however, about the roles of RNA structures. A previous bioinformatics survey predicted multiple regions of influenza A virus that are likely to generate evolutionarily conserved and stable RNA structures. One predicted conserved structure is in the pre-mRNA coding for essential proteins, M1 and M2. This structure starts 79 nucleotides downstream of the M2 mRNA 5' splice site. Here, a combination of biochemical structural mapping, mutagenesis, and NMR confirms the predicted three-way multibranch structure of this RNA. Imino proton NMR spectra reveal no change in secondary structure when 80 mM KCl is supplemented with 4 mM MgCl2. Optical melting curves in 1 M NaCl and in 100 mM KCl with 10 mM MgCl2 are very similar, with melting temperatures ∼14 °C higher than that for 100 mM KCl alone. These results provide a firm basis for designing experiments and potential therapeutics to test for function in cell culture.
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Affiliation(s)
- Tian Jiang
- Department of Chemistry and Center for RNA Biology, University of Rochester , Rochester, New York 14627, United States
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35
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Peselis A, Serganov A. Structure and function of pseudoknots involved in gene expression control. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:803-22. [PMID: 25044223 DOI: 10.1002/wrna.1247] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 05/09/2014] [Accepted: 05/21/2014] [Indexed: 11/08/2022]
Abstract
Natural RNA molecules can have a high degree of structural complexity but even the most complexly folded RNAs are assembled from simple structural building blocks. Among the simplest RNA elements are double-stranded helices that participate in the formation of different folding topologies and constitute the major fraction of RNA structures. One common folding motif of RNA is a pseudoknot, defined as a bipartite helical structure formed by base-pairing of the apical loop in the stem-loop structure with an outside sequence. Pseudoknots constitute integral parts of the RNA structures essential for various cellular activities. Among many functions of pseudoknotted RNAs is feedback regulation of gene expression, carried out through specific recognition of various molecules. Pseudoknotted RNAs autoregulate ribosomal and phage protein genes in response to downstream encoded proteins, while many metabolic and transport genes are controlled by cellular metabolites interacting with pseudoknotted RNA elements from the riboswitch family. Modulation of some genes also depends on metabolite-induced messenger RNA (mRNA) cleavage performed by pseudoknotted ribozymes. Several regulatory pseudoknots have been characterized biochemically and structurally in great detail. These studies have demonstrated a plethora of pseudoknot-based folds and have begun uncovering diverse molecular principles of the ligand-dependent gene expression control. The pseudoknot-mediated mechanisms of gene control and many unexpected and interesting features of the regulatory pseudoknots have significantly advanced our understanding of the genetic circuits and laid the foundation for modulation of their outcomes.
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Affiliation(s)
- Alla Peselis
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
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36
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Wilson SC, Cohen DT, Wang XC, Hammond MC. A neutral pH thermal hydrolysis method for quantification of structured RNAs. RNA (NEW YORK, N.Y.) 2014; 20:1153-60. [PMID: 24860014 PMCID: PMC4114692 DOI: 10.1261/rna.045856.114] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Accepted: 04/16/2014] [Indexed: 05/05/2023]
Abstract
Riboswitch aptamers adopt diverse and complex tertiary structural folds that contain both single-stranded and double-stranded regions. We observe that this high degree of secondary structure leads to an appreciable hypochromicity that is not accounted for in the standard method to calculate extinction coefficients using nearest-neighbor effects, which results in a systematic underestimation of RNA concentrations. Here we present a practical method for quantifying riboswitch RNAs using thermal hydrolysis to generate the corresponding pool of mononucleotides, for which precise extinction coefficients have been measured. Thermal hydrolysis can be performed at neutral pH without reaction quenching, avoids the use of nucleases or expensive fluorescent dyes, and does not require generation of calibration curves. The accuracy of this method for determining RNA concentrations has been validated using quantitative (31)P-NMR calibrated to an external standard. We expect that this simple procedure will be generally useful for the accurate quantification of any sequence-defined RNA sample, which is often a critical parameter for in vitro binding and kinetic assays.
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Affiliation(s)
- Stephen C. Wilson
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Daniel T. Cohen
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Xin C. Wang
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Ming C. Hammond
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
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37
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Eichhorn CD, Kang M, Feigon J. Structure and function of preQ 1 riboswitches. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:939-950. [PMID: 24798077 DOI: 10.1016/j.bbagrm.2014.04.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 04/22/2014] [Accepted: 04/25/2014] [Indexed: 12/17/2022]
Abstract
PreQ1 riboswitches help regulate the biosynthesis and transport of preQ1 (7-aminomethyl-7-deazaguanine), a precursor of the hypermodified guanine nucleotide queuosine (Q), in a number of Firmicutes, Proteobacteria, and Fusobacteria. Queuosine is almost universally found at the wobble position of the anticodon in asparaginyl, tyrosyl, histidyl and aspartyl tRNAs, where it contributes to translational fidelity. Two classes of preQ1 riboswitches have been identified (preQ1-I and preQ1-II), and structures of examples from both classes have been determined. Both classes form H-type pseudoknots upon preQ1 binding, each of which has distinct unusual features and modes of preQ1 recognition. These features include an unusually long loop 2 in preQ1-I pseudoknots and an embedded hairpin in loop 3 in preQ1-II pseudoknots. PreQ1-I riboswitches are also notable for their unusually small aptamer domain, which has been extensively investigated by NMR, X-ray crystallography, FRET, and other biophysical methods. Here we review the discovery, structural biology, ligand specificity, cation interactions, folding, dynamics, and applications to biotechnology of preQ1 riboswitches. This article is part of a Special Issue entitled: Riboswitches.
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Affiliation(s)
- Catherine D Eichhorn
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Mijeong Kang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA; UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
| | - Juli Feigon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA; UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
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38
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Global analysis of riboswitches by small-angle X-ray scattering and calorimetry. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1020-1029. [PMID: 24769285 DOI: 10.1016/j.bbagrm.2014.04.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 04/10/2014] [Accepted: 04/13/2014] [Indexed: 11/22/2022]
Abstract
Riboswitches are phylogenetically widespread non-coding mRNA domains that directly bind cellular metabolites and regulate transcription, translation, RNA stability or splicing via alternative RNA structures modulated by ligand binding. The details of ligand recognition by many riboswitches have been elucidated using X-ray crystallography and NMR. However, the global dynamics of riboswitch-ligand interactions and their thermodynamic driving forces are less understood. By compiling the work of many laboratories investigating riboswitches using small-angle X-ray scattering (SAXS) and isothermal titration calorimetry (ITC), we uncover general trends and common themes. There is a pressing need for community-wide consensus experimental conditions to allow results of riboswitch studies to be compared rigorously. Nonetheless, our meta-analysis reveals considerable diversity in the extent to which ligand binding reorganizes global riboswitch structures. It also demonstrates a wide spectrum of enthalpy-entropy compensation regimes across riboswitches that bind a diverse set of ligands, giving rise to a relatively narrow range of physiologically relevant free energies and ligand affinities. From the strongly entropy-driven binding of glycine to the predominantly enthalpy-driven binding of c-di-GMP to their respective riboswitches, these distinct thermodynamic signatures reflect the versatile strategies employed by RNA to adapt to the chemical natures of diverse ligands. Riboswitches have evolved to use a combination of long-range tertiary interactions, conformational selection, and induced fit to work with distinct ligand structure, charge, and solvation properties. This article is part of a Special Issue entitled: Riboswitches.
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39
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Gong Z, Zhao Y, Chen C, Duan Y, Xiao Y. Insights into ligand binding to PreQ1 Riboswitch Aptamer from molecular dynamics simulations. PLoS One 2014; 9:e92247. [PMID: 24663240 PMCID: PMC3963873 DOI: 10.1371/journal.pone.0092247] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 02/19/2014] [Indexed: 11/19/2022] Open
Abstract
Riboswitches play roles in transcriptional or translational regulation through specific ligand binding of their aptamer domains. Although a number of ligand-bound aptamer complex structures have been solved, it is important to know ligand-free conformations of the aptamers in order to understand the mechanism of specific binding by ligands. In this paper, preQ1 riboswitch aptamer domain from Bacillus subtilis is studied by overall 1.5 μs all-atom molecular dynamics simulations We found that the ligand-free aptamer has a stable state with a folded P1-L3 and open binding pocket. The latter forms a cytosine-rich pool in which the nucleotide C19 oscillates between close and open positions, making it a potential conformation for preQ1 entrance. The dynamic picture further suggests that the specific recognition of preQ1 by the aptamer domain is not only facilitated by the key nucleotide C19 but also aided and enhanced by other cytosines around the binding pocket. These results should help to understand the details of preQ1 binding.
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Affiliation(s)
- Zhou Gong
- Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yunjie Zhao
- Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Changjun Chen
- Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yong Duan
- Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Genome Center and Department of Biomedical Engineering, University of California Davis, Davis, California, United States of America
| | - Yi Xiao
- Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
- * E-mail:
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40
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Abstract
Riboswitches are structured noncoding RNA elements that control the expression of their embedding messenger RNAs by sensing the intracellular concentration of diverse metabolites. As the name suggests, riboswitches are dynamic in nature so that studying their inherent conformational dynamics and ligand-mediated folding is important for understanding their mechanism of action. Single-molecule fluorescence energy transfer (smFRET) microscopy is a powerful and versatile technique for studying the folding pathways and intra- and intermolecular dynamics of biological macromolecules, especially RNA. The ability of smFRET to monitor intramolecular distances and their temporal evolution make it a particularly insightful tool for probing the structure and dynamics of riboswitches. Here, we detail the general steps for using prism-based total internal reflection fluorescence microscopy for smFRET studies of the structure, dynamics, and ligand-binding mechanisms of riboswitches.
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41
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Wunderlich C, Huber RG, Spitzer R, Liedl KR, Kloiber K, Kreutz C. A novel paramagnetic relaxation enhancement tag for nucleic acids: a tool to study structure and dynamics of RNA. ACS Chem Biol 2013; 8:2697-706. [PMID: 24053726 PMCID: PMC3870906 DOI: 10.1021/cb400589q] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 09/20/2013] [Indexed: 01/10/2023]
Abstract
In this work, we present a novel 2,2,6,6-tetramethylpiperidine 1-oxyl (TEMPO) radical phosphoramidite building block, which can be attached to the 5'-terminus of nucleic acids. To investigate the paramagnetic relaxation enhancement (PRE) emanating from this radical center, we incorporated the TEMPO label into various types of RNAs. We measured proton PREs for selectively (13)C-isotope labeled nucleotides to derive long-range distance restraints in a short 15 nucleotide stem-loop model system, underscoring the potential of the 5'-TEMPO tag to determine long-range distance restraints for solution structure determination. We subsequently applied the distance-dependent relaxation enhancement induced by the nitroxide radical to discern two folding states in a bistable RNA. Finally, we investigated the fast conformational sampling of the HIV-1 TAR RNA, a paradigm for structural flexibility in nucleic acids. With PRE NMR in combination with molecular dynamics simulations, the structural plasticity of this RNA was analyzed in the absence and presence of the ligand L-argininamide.
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Affiliation(s)
- Christoph
H. Wunderlich
- Institute
of Organic Chemistry and Center for Molecular Biosciences Innsbruck
(CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Roland G. Huber
- Institute
of General, Inorganic and Theoretical Chemistry and Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, Innrain
80/82, 6020 Innsbruck, Austria
| | - Romana Spitzer
- Institute
of Organic Chemistry and Center for Molecular Biosciences Innsbruck
(CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Klaus R. Liedl
- Institute
of General, Inorganic and Theoretical Chemistry and Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, Innrain
80/82, 6020 Innsbruck, Austria
| | - Karin Kloiber
- Institute
of Organic Chemistry and Center for Molecular Biosciences Innsbruck
(CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Christoph Kreutz
- Institute
of Organic Chemistry and Center for Molecular Biosciences Innsbruck
(CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
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Micura R, Kreutz C, Breuker K. A personal perspective on chemistry-driven RNA research. Biopolymers 2013; 99:1114-23. [PMID: 23754524 PMCID: PMC4477180 DOI: 10.1002/bip.22299] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 05/27/2013] [Indexed: 12/14/2022]
Abstract
In this mini review, we discuss how our understanding of ribonucleic acid (RNA) properties becomes significantly deepened when a broad range of modern chemical and biophysical methods is applied. We span our perspective from RNA solid-phase synthesis and site-specific labeling to single-molecule fluorescence-resonance-energy-transfer imaging and NMR spectroscopy approaches to explore the dynamics of RNA over a broad timescale. We then move on to Fourier-transform-ion-cyclotron-resonance mass spectrometry (FT-ICR-MS) as a powerful technique for RNA sequencing and modification analysis. The novel methodological developments are discussed for selected biological systems that include the thiamine-pyrophosphate riboswitch, HIV and ribosomal A-site RNA, and transfer RNA.
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Affiliation(s)
- Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI), Center for Chemistry and Biomedicine (CCB), University of Innsbruck, Innrain 80-82, Innsbruck, 6020, Austria
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Suddala KC, Rinaldi AJ, Feng J, Mustoe AM, Eichhorn CD, Liberman JA, Wedekind JE, Al-Hashimi HM, Brooks CL, Walter NG. Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure. Nucleic Acids Res 2013; 41:10462-75. [PMID: 24003028 PMCID: PMC3905878 DOI: 10.1093/nar/gkt798] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Riboswitches are structural elements in the 5′ untranslated regions of many bacterial messenger RNAs that regulate gene expression in response to changing metabolite concentrations by inhibition of either transcription or translation initiation. The preQ1 (7-aminomethyl-7-deazaguanine) riboswitch family comprises some of the smallest metabolite sensing RNAs found in nature. Once ligand-bound, the transcriptional Bacillus subtilis and translational Thermoanaerobacter tengcongensis preQ1 riboswitch aptamers are structurally similar RNA pseudoknots; yet, prior structural studies have characterized their ligand-free conformations as largely unfolded and folded, respectively. In contrast, through single molecule observation, we now show that, at near-physiological Mg2+ concentration and pH, both ligand-free aptamers adopt similar pre-folded state ensembles that differ in their ligand-mediated folding. Structure-based Gō-model simulations of the two aptamers suggest that the ligand binds late (Bacillus subtilis) and early (Thermoanaerobacter tengcongensis) relative to pseudoknot folding, leading to the proposal that the principal distinction between the two riboswitches lies in their relative tendencies to fold via mechanisms of conformational selection and induced fit, respectively. These mechanistic insights are put to the test by rationally designing a single nucleotide swap distal from the ligand binding pocket that we find to predictably control the aptamers′ pre-folded states and their ligand binding affinities.
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Affiliation(s)
- Krishna C Suddala
- Biophysics, University of Michigan, Ann Arbor, MI 48109, USA, Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA, Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA, Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA and Center for Theoretical Biological Physics, University of California San Diego, San Diego, CA 92037, USA
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44
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Tuning a riboswitch response through structural extension of a pseudoknot. Proc Natl Acad Sci U S A 2013; 110:E3256-64. [PMID: 23940363 DOI: 10.1073/pnas.1304585110] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Structural and dynamic features of RNA folding landscapes represent critical aspects of RNA function in the cell and are particularly central to riboswitch-mediated control of gene expression. Here, using single-molecule fluorescence energy transfer imaging, we explore the folding dynamics of the preQ1 class II riboswitch, an upstream mRNA element that regulates downstream encoded modification enzymes of queuosine biosynthesis. For reasons that are not presently understood, the classical pseudoknot fold of this system harbors an extra stem-loop structure within its 3'-terminal region immediately upstream of the Shine-Dalgarno sequence that contributes to formation of the ligand-bound state. By imaging ligand-dependent preQ1 riboswitch folding from multiple structural perspectives, we reveal that the extra stem-loop strongly influences pseudoknot dynamics in a manner that decreases its propensity to spontaneously fold and increases its responsiveness to ligand binding. We conclude that the extra stem-loop sensitizes this RNA to broaden the dynamic range of the ON/OFF regulatory switch.
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Ligand-inducible formation of RNA pseudoknot. Bioorg Med Chem Lett 2013; 23:3539-41. [DOI: 10.1016/j.bmcl.2013.04.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 04/12/2013] [Accepted: 04/15/2013] [Indexed: 11/23/2022]
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46
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Soulière MF, Haller A, Santner T, Micura R. Neue Erkenntnisse zur Genregulation - hochaufgelöste Strukturen von Cobalamin-Riboschaltern. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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47
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Soulière MF, Haller A, Santner T, Micura R. New insights into gene regulation--high-resolution structures of cobalamin riboswitches. Angew Chem Int Ed Engl 2013; 52:1874-7. [PMID: 23296745 DOI: 10.1002/anie.201208167] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Indexed: 01/05/2023]
Affiliation(s)
- Marie F Soulière
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Center for Chemistry and Biomedicine, 6020 Innsbruck, Austria
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48
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Socher E, Grossmann TN. Chemical biology 2012: from drug targets to biological systems and back. Chembiochem 2013. [PMID: 23184865 DOI: 10.1002/cbic.201200697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Multiple sites sharing a common target: This year's EMBO conference on chemical biology encouraged over 340 researchers to come to Heidelberg, Germany, and discuss the use of diverse chemical strategies and tools to investigate biological questions and better understand cellular processes.
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Affiliation(s)
- Elke Socher
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
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49
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Fauster K, Kreutz C, Micura R. 2'-SCF3 uridine-a powerful label for probing structure and function of RNA by 19F NMR spectroscopy. Angew Chem Int Ed Engl 2012; 51:13080-4. [PMID: 23161779 PMCID: PMC3555429 DOI: 10.1002/anie.201207128] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Indexed: 12/20/2022]
Abstract
Fluorishing: the Togni reagent allows efficient synthetic access to fluorine-labeled RNA molecules. These are in turn highly useful for NMR spectroscopic analyses of secondary and tertiary structures, RNA-protein interactions, and functionality of riboswitch modules.
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Affiliation(s)
- Katja Fauster
- Institute of Organic Chemistry (IOC) and Center for Molecular Biosciences (CMBI), University of Innsbruck, Center for Chemistry and Biomedicine (CCB)020 Innsbruck (Austria)
| | - Christoph Kreutz
- Institute of Organic Chemistry (IOC) and Center for Molecular Biosciences (CMBI), University of Innsbruck, Center for Chemistry and Biomedicine (CCB)020 Innsbruck (Austria)
| | - Ronald Micura
- Institute of Organic Chemistry (IOC) and Center for Molecular Biosciences (CMBI), University of Innsbruck, Center for Chemistry and Biomedicine (CCB)020 Innsbruck (Austria)
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50
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Fauster K, Kreutz C, Micura R. 2′-SCF3Uridine-A Powerful Label for Probing Structure and Function of RNA by19F NMR Spectroscopy. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201207128] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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