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Tamura T, Nakano S, Nakata E, Morii T. Construction of a library of structurally diverse ribonucleopeptides with catalytic groups. Bioorg Med Chem 2017; 25:1881-1888. [PMID: 28223024 DOI: 10.1016/j.bmc.2017.02.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 01/31/2017] [Accepted: 02/03/2017] [Indexed: 01/20/2023]
Abstract
Functional screening of structurally diverse libraries consisting of proteins or nucleic acids is an effective method to obtain receptors or aptamers with unique molecular recognition characteristics. However, further modification of these selected receptors to exert a newly desired function is still a challenging task. We have constructed a library of structurally diverse ribonucleopeptides (RNPs) that are modified with a catalytic group, in which the catalytic group aligns with various orientations against the ATP binding pocket of RNA subunit. As a proof-of-principle, the screening of the constructed RNP library for the catalytic reaction of ester hydrolysis was successfully carried out. The size of both the substrate-binding RNA library and the catalytic group modified peptide library are independently expandable, and thus, the size of RNPs library could be enlarged by a combination of these two subunits. We anticipate that the library of functionalized and structurally diverse RNPs would be expanded for various other catalytic reactions.
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Affiliation(s)
- Tomoki Tamura
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Shun Nakano
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
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2
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Kun Á, Szathmáry E. Fitness Landscapes of Functional RNAs. Life (Basel) 2015; 5:1497-517. [PMID: 26308059 PMCID: PMC4598650 DOI: 10.3390/life5031497] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 07/26/2015] [Accepted: 08/03/2015] [Indexed: 11/16/2022] Open
Abstract
The notion of fitness landscapes, a map between genotype and fitness, was proposed more than 80 years ago. For most of this time data was only available for a few alleles, and thus we had only a restricted view of the whole fitness landscape. Recently, advances in genetics and molecular biology allow a more detailed view of them. Here we review experimental and theoretical studies of fitness landscapes of functional RNAs, especially aptamers and ribozymes. We find that RNA structures can be divided into critical structures, connecting structures, neutral structures and forbidden structures. Such characterisation, coupled with theoretical sequence-to-structure predictions, allows us to construct the whole fitness landscape. Fitness landscapes then can be used to study evolution, and in our case the development of the RNA world.
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Affiliation(s)
- Ádám Kun
- Parmenides Center for the Conceptual Foundations of Science, Kirchplatz 1, 82049 Munich/Pullach, Germany.
- MTA-ELTE-MTMT Ecology Research Group, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary.
- Department of Plant Systematics, Ecology and Theoretical Biology, Institute of Biology, Eötvös University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary.
| | - Eörs Szathmáry
- Parmenides Center for the Conceptual Foundations of Science, Kirchplatz 1, 82049 Munich/Pullach, Germany.
- Department of Plant Systematics, Ecology and Theoretical Biology, Institute of Biology, Eötvös University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary.
- MTA-ELTE Theoretical Biology and Evolutionary Ecology Research Group, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary.
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3
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Ward WL, Plakos K, DeRose VJ. Nucleic acid catalysis: metals, nucleobases, and other cofactors. Chem Rev 2014; 114:4318-42. [PMID: 24730975 PMCID: PMC4002065 DOI: 10.1021/cr400476k] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Indexed: 12/17/2022]
Affiliation(s)
- W. Luke Ward
- Department of Chemistry and Biochemistry and Institute of
Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States
| | - Kory Plakos
- Department of Chemistry and Biochemistry and Institute of
Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States
| | - Victoria J. DeRose
- Department of Chemistry and Biochemistry and Institute of
Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States
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4
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Ameta S, Winz ML, Previti C, Jäschke A. Next-generation sequencing reveals how RNA catalysts evolve from random space. Nucleic Acids Res 2013; 42:1303-10. [PMID: 24157838 PMCID: PMC3902939 DOI: 10.1093/nar/gkt949] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Catalytic RNAs are attractive objects for studying molecular evolution. To understand how RNA libraries can evolve from randomness toward highly active catalysts, we analyze the original samples that led to the discovery of Diels-Alderase ribozymes by next-generation sequencing. Known structure-activity relationships are used to correlate abundance with catalytic performance. We find that efficient catalysts arose not just from selection for reactivity among the members of the starting library, but from improvement of less potent precursors by mutations. We observe changes in the ribozyme population in response to increasing selection pressure. Surprisingly, even after many rounds of enrichment, the libraries are highly diverse, suggesting that potential catalysts are more abundant in random space than generally thought. To highlight the use of next-generation sequencing as a tool for in vitro selections, we also apply this technique to a recent, less characterized ribozyme selection. Making use of the correlation between sequence evolution and catalytic activity, we predict mutations that improve ribozyme activity and validate them biochemically. Our study reveals principles underlying ribozyme in vitro selections and provides guidelines to render future selections more efficient, as well as to predict the conservation of key structural elements, allowing the rational improvement of catalysts.
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Affiliation(s)
- Sandeep Ameta
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, 69120-Heidelberg, Germany and High Throughput Sequencing Core Facility, German Cancer Research Center (DKFZ), 69120-Heidelberg, Germany
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5
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Schlatterer JC, Wieder MS, Jones CD, Pollack L, Brenowitz M. Pyrite footprinting of RNA. Biochem Biophys Res Commun 2012; 425:374-8. [PMID: 22842460 DOI: 10.1016/j.bbrc.2012.07.100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 07/19/2012] [Indexed: 10/28/2022]
Abstract
In RNA, function follows form. Mapping the surface of RNA molecules with chemical and enzymatic probes has revealed invaluable information about structure and folding. Hydroxyl radicals ((·)OH) map the surface of nucleic acids by cutting the backbone where it is accessible to solvent. Recent studies showed that a microfluidic chip containing pyrite (FeS(2)) can produce sufficient (·)OH to footprint DNA. The 49-nt Diels-Alder RNA enzyme catalyzes the C-C bond formation between a diene and a dienophile. A crystal structure, molecular dynamics simulation and atomic mutagenesis studies suggest that nucleotides of an asymmetric bulge participate in the dynamic architecture of the ribozyme's active center. Of note is that residue U42 directly interacts with the product in the crystallized RNA/product complex. Here, we use powdered pyrite held in a commercially available cartridge to footprint the Diels-Alderase ribozyme with single nucleotide resolution. Residues C39 to U42 are more reactive to (·)OH than predicted by the solvent accessibility calculated from the crystal structure suggesting that this loop is dynamic in solution. The loop's flexibility may contribute to substrate recruitment and product release. Our implementation of pyrite-mediated (·)OH footprinting is a readily accessible approach to gleaning information about the architecture of small RNA molecules.
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Affiliation(s)
- Jörg C Schlatterer
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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6
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Kraut S, Bebenroth D, Nierth A, Kobitski AY, Nienhaus GU, Jäschke A. Three critical hydrogen bonds determine the catalytic activity of the Diels-Alderase ribozyme. Nucleic Acids Res 2011; 40:1318-30. [PMID: 21976731 PMCID: PMC3273808 DOI: 10.1093/nar/gkr812] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Compared to protein enzymes, our knowledge about how RNA accelerates chemical reactions is rather limited. The crystal structures of a ribozyme that catalyzes Diels-Alder reactions suggest a rich tertiary architecture responsible for catalysis. In this study, we systematically probe the relevance of crystallographically observed ground-state interactions for catalytic function using atomic mutagenesis in combination with various analytical techniques. The largest energetic contribution apparently arises from the precise shape complementarity between transition state and catalytic pocket: A single point mutant that folds correctly into the tertiary structure but lacks one H-bond that normally stabilizes the pocket is completely inactive. In the rate-limiting chemical step, the dienophile is furthermore activated by two weak H-bonds that contribute ∼7-8 kJ/mol to transition state stabilization, as indicated by the 25-fold slower reaction rates of deletion mutants. These H-bonds are also responsible for the tight binding of the Diels-Alder product by the ribozyme that causes product inhibition. For high catalytic activity, the ribozyme requires a fine-tuned balance between rigidity and flexibility that is determined by the combined action of one inter-strand H-bond and one magnesium ion. A sharp 360° turn reminiscent of the T-loop motif observed in tRNA is found to be important for catalytic function.
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Affiliation(s)
- Stefanie Kraut
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
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7
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Strauss B, Nierth A, Singer M, Jäschke A. Direct structural analysis of modified RNA by fluorescent in-line probing. Nucleic Acids Res 2011; 40:861-70. [PMID: 21917852 PMCID: PMC3258135 DOI: 10.1093/nar/gkr733] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Chemical probing is a common method for the structural characterization of RNA. Typically, RNA is radioactively end-labelled, subjected to probing conditions, and the cleavage fragment pattern is analysed by gel electrophoresis. In recent years, many chemical modifications, like fluorophores, were introduced into RNA, but methods are lacking that detect the influence of the modification on the RNA structure with single-nucleotide resolution. Here, we first demonstrate that a 5′-terminal 32P label can be replaced by a dye label for in-line probing of riboswitch RNAs. Next, we show that small, highly structured FRET-labelled Diels–Alderase ribozymes can be directly probed, using the internal or terminal FRET dyes as reporters. The probing patterns indeed reveal whether or not the attachment of the dyes influences the structure. The existence of two dye labels in typical FRET constructs is found to be beneficial, as ‘duplexing’ allows observation of the complete RNA on a single gel. Structural information can be derived from the probing gels by deconvolution of the superimposed band patterns. Finally, we use fluorescent in-line probing to experimentally validate the structural consequences of photocaging, unambiguously demonstrating the intentional destruction of selected elements of secondary or tertiary structure.
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Affiliation(s)
- Benjamin Strauss
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
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8
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Silverman SK. DNA as a versatile chemical component for catalysis, encoding, and stereocontrol. Angew Chem Int Ed Engl 2011; 49:7180-201. [PMID: 20669202 DOI: 10.1002/anie.200906345] [Citation(s) in RCA: 201] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
DNA (deoxyribonucleic acid) is the genetic material common to all of Earth's organisms. Our biological understanding of DNA is extensive and well-exploited. In recent years, chemists have begun to develop DNA for nonbiological applications in catalysis, encoding, and stereochemical control. This Review summarizes key advances in these three exciting research areas, each of which takes advantage of a different subset of DNA's useful chemical properties.
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Affiliation(s)
- Scott K Silverman
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA.
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9
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Affiliation(s)
- Jose M. Palomo
- Departamento de Biocatálisis, Instituto de Catálisis (CSIC), c/ Marie Curie 2, Cantoblanco Campus UAM, 28049 Madrid, Spain, Fax: +34‐91‐585‐4760
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10
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Bereźniak T, Zahran M, Imhof P, Jäschke A, Smith JC. Magnesium-Dependent Active-Site Conformational Selection in the Diels−Alderase Ribozyme. J Am Chem Soc 2010; 132:12587-96. [DOI: 10.1021/ja101370e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tomasz Bereźniak
- Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany, Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany, and Oak Ridge National Laboratory, Post Office Box 2008 MS 6309, Oak Ridge, Tennessee 37831-6309
| | - Maï Zahran
- Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany, Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany, and Oak Ridge National Laboratory, Post Office Box 2008 MS 6309, Oak Ridge, Tennessee 37831-6309
| | - Petra Imhof
- Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany, Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany, and Oak Ridge National Laboratory, Post Office Box 2008 MS 6309, Oak Ridge, Tennessee 37831-6309
| | - Andres Jäschke
- Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany, Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany, and Oak Ridge National Laboratory, Post Office Box 2008 MS 6309, Oak Ridge, Tennessee 37831-6309
| | - Jeremy C. Smith
- Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany, Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany, and Oak Ridge National Laboratory, Post Office Box 2008 MS 6309, Oak Ridge, Tennessee 37831-6309
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11
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Silverman SK. DNA - eine vielseitige chemische Verbindung für die Katalyse, zur Kodierung und zur Stereokontrolle. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906345] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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12
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Masquida B, Beckert B, Jossinet F. Exploring RNA structure by integrative molecular modelling. N Biotechnol 2010; 27:170-83. [PMID: 20206310 DOI: 10.1016/j.nbt.2010.02.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
RNA molecular modelling is adequate to rapidly tackle the structure of RNA molecules. With new structured RNAs constituting a central class of cellular regulators discovered every year, the need for swift and reliable modelling methods is more crucial than ever. The pragmatic method based on interactive all-atom molecular modelling relies on the observation that specific structural motifs are recurrently found in RNA sequences. Once identified by a combination of comparative sequence analysis and biochemical data, the motifs composing the secondary structure of a given RNA can be extruded in three dimensions (3D) and used as building blocks assembled manually during a bioinformatic interactive process. Comparing the models to the corresponding crystal structures has validated the method as being powerful to predict the RNA topology and architecture while being less accurate regarding the prediction of base-base interactions. These aspects as well as the necessary steps towards automation will be discussed.
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Affiliation(s)
- Benoît Masquida
- Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC, CNRS, 15 rue René Descartes, Strasbourg, France.
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13
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Nierth A, Kobitski AY, Nienhaus GU, Jäschke A. Anthracene−BODIPY Dyads as Fluorescent Sensors for Biocatalytic Diels−Alder Reactions. J Am Chem Soc 2010; 132:2646-54. [DOI: 10.1021/ja9084397] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alexander Nierth
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany, Institute of Applied Physics and Center for Functional Nanostructures, Karlsruhe Institute of Technology, Wolfgang-Gaede-Strasse 1, 76131 Karlsruhe, Germany, and Department of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - Andrei Yu. Kobitski
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany, Institute of Applied Physics and Center for Functional Nanostructures, Karlsruhe Institute of Technology, Wolfgang-Gaede-Strasse 1, 76131 Karlsruhe, Germany, and Department of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - G. Ulrich Nienhaus
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany, Institute of Applied Physics and Center for Functional Nanostructures, Karlsruhe Institute of Technology, Wolfgang-Gaede-Strasse 1, 76131 Karlsruhe, Germany, and Department of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany, Institute of Applied Physics and Center for Functional Nanostructures, Karlsruhe Institute of Technology, Wolfgang-Gaede-Strasse 1, 76131 Karlsruhe, Germany, and Department of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
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14
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Manoharan V, Fürtig B, Jäschke A, Schwalbe H. Metal-Induced Folding of Diels−Alderase Ribozymes Studied by Static and Time-Resolved NMR Spectroscopy. J Am Chem Soc 2009; 131:6261-70. [DOI: 10.1021/ja900244x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Vijayalaxmi Manoharan
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Strasse 7, D-60438 Frankfurt/Main, Germany, and Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, D-69120 Heidelberg, Germany
| | - Boris Fürtig
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Strasse 7, D-60438 Frankfurt/Main, Germany, and Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, D-69120 Heidelberg, Germany
| | - Andres Jäschke
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Strasse 7, D-60438 Frankfurt/Main, Germany, and Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, D-69120 Heidelberg, Germany
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Strasse 7, D-60438 Frankfurt/Main, Germany, and Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, D-69120 Heidelberg, Germany
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15
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Gagnon KT, Ju SY, Goshe MB, Maxwell ES, Franzen S. A role for hydrophobicity in a Diels-Alder reaction catalyzed by pyridyl-modified RNA. Nucleic Acids Res 2009; 37:3074-82. [PMID: 19304744 PMCID: PMC2685102 DOI: 10.1093/nar/gkp177] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
New classes of RNA enzymes or ribozymes have been obtained by in vitro evolution and selection of RNA molecules. Incorporation of modified nucleotides into the RNA sequence has been proposed to enhance function. DA22 is a modified RNA containing 5-(4-pyridylmethyl) carboxamide uridines, which has been selected for its ability to promote a Diels–Alder cycloaddition reaction. Here, we show that DA_TR96, the most active member of the DA22 RNA sequence family, which was selected with pyridyl-modified nucleotides, accelerates a cycloaddition reaction between anthracene and maleimide derivatives with high turnover. These widely used reactants were not used in the original selection for DA22 and yet here they provide the first demonstration of DA_TR96 as a true multiple-turnover catalyst. In addition, the absence of a structural or essential kinetic role for Cu2+, as initially postulated, and nonsequence-specific hydrophobic interactions with the anthracene substrate have led to a reevaluation of the pyridine modification's role. These findings broaden the catalytic repertoire of the DA22 family of pyridyl-modified RNAs and suggest a key role for the hydrophobic effect in the catalytic mechanism.
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Affiliation(s)
- Keith T Gagnon
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
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16
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Petermeier M, Jäschke A. New theophylline-activated Diels–Alderase ribozymes by molecular engineering. Org Biomol Chem 2009; 7:288-92. [DOI: 10.1039/b816726e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Wombacher R, Jäschke A. Probing the active site of a diels-alderase ribozyme by photoaffinity cross-linking. J Am Chem Soc 2008; 130:8594-5. [PMID: 18543913 DOI: 10.1021/ja802931q] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The active site of a Diels-Alderase ribozyme is located in solution by photoaffinity cross-linking using a productlike azidobenzyl probe. Two key nucleotides are identified that contact the Diels-Alder product in a conformation-dependent fashion. The design of such probes does not require knowledge of the three-dimensional structure of the ribozyme, and the technique yields both static and dynamic structural information. This work establishes photoaffinity cross-linking as an empirical approach that is applied here for the first time to an artificial ribozyme.
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Affiliation(s)
- Richard Wombacher
- University of Heidelberg, Institute of Pharmacy and Molecular Biotechnology, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
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18
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Tijerina P, Mohr S, Russell R. DMS footprinting of structured RNAs and RNA-protein complexes. Nat Protoc 2008; 2:2608-23. [PMID: 17948004 DOI: 10.1038/nprot.2007.380] [Citation(s) in RCA: 189] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We describe a protocol in which dimethyl sulfate (DMS) modification of the base-pairing faces of unpaired adenosine and cytidine nucleotides is used for structural analysis of RNAs and RNA-protein complexes (RNPs). The protocol is optimized for RNAs of small to moderate size (< or = 500 nt). The RNA or RNP is first exposed to DMS under conditions that promote formation of the folded structure or complex, as well as 'control' conditions that do not allow folding or complex formation. The positions and extents of modification are then determined by primer extension, polyacrylamide gel electrophoresis and quantitative analysis. From changes in the extent of modification upon folding or protein binding (appearance of a 'footprint'), it is possible to detect local changes in the secondary and tertiary structure of RNA, as well as the formation of RNA-protein contacts. This protocol takes 1.5-3 d to complete, depending on the type of analysis used.
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Affiliation(s)
- Pilar Tijerina
- Department of Chemistry and Biochemistry and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
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19
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Famulok M, Hartig JS, Mayer G. Functional aptamers and aptazymes in biotechnology, diagnostics, and therapy. Chem Rev 2007; 107:3715-43. [PMID: 17715981 DOI: 10.1021/cr0306743] [Citation(s) in RCA: 666] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Michael Famulok
- LIMES Institute, Program Unit Chemical Biology and Medicinal Chemistry, c/o Kekulé-Institut für Organische Chemie und Biochemie, Gerhard Domagk-Strasse 1, 53121 Bonn, Germany.
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20
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Kisseleva N, Kraut S, Jäschke A, Schiemann O. Characterizing multiple metal ion binding sites within a ribozyme by cadmium-induced EPR silencing. HFSP JOURNAL 2007; 1:127-36. [PMID: 19404418 PMCID: PMC2639839 DOI: 10.2976/1.2756332] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2007] [Accepted: 06/18/2007] [Indexed: 11/19/2022]
Abstract
In ribozyme catalysis, metal ions are generally known to make structural andor mechanistic contributions. The catalytic activity of a previously described Diels-Alderase ribozyme was found to depend on the concentration of divalent metal ions, and crystallographic data revealed multiple binding sites. Here, we elucidate the interactions of this ribozyme with divalent metal ions in solution using electron paramagnetic resonance (EPR) spectroscopy. Manganese ion titrations revealed five high-affinity Mn(2+) binding sites with an upper K(d) of 0.6+/-0.2 muM. In order to characterize each binding site individually, EPR-silent Cd(2+) ions were used to saturate the other binding sites. This cadmium-induced EPR silencing showed that the Mn(2+) binding sites possess different affinities. In addition, these binding sites could be assigned to three different types, including innersphere, outersphere, and a Mn(2+) dimer. Based on simulations, the Mn(2+)-Mn(2+) distance within the dimer was found to be approximately 6 A, which is in good agreement with crystallographic data. The EPR-spectroscopic characterization reveals no structural changes upon addition of a Diels-Alder product, supporting the concept of a preorganized catalytic pocket in the Diels-Alder ribozyme and the structural role of these ions.
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Affiliation(s)
- Natalia Kisseleva
- Institute of Physical and Theoretical Chemistry, Center of
Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University,
Max-von-Laue Strasse 7, 60438 Frankfurt am Main, Germany
| | - Stefanie Kraut
- Institute of Pharmacy and Molecular Biotechnology, University
of Heidelberg, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology, University
of Heidelberg, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, Center of
Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University,
Max-von-Laue Strasse 7, 60438 Frankfurt am Main, Germany
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21
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Kobitski AY, Nierth A, Helm M, Jäschke A, Nienhaus GU. Mg2+-dependent folding of a Diels-Alderase ribozyme probed by single-molecule FRET analysis. Nucleic Acids Res 2007; 35:2047-59. [PMID: 17344321 PMCID: PMC1874616 DOI: 10.1093/nar/gkm072] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Here, we report a single-molecule fluorescence resonance energy transfer (FRET) study of a Diels-Alderase (DAse) ribozyme, a 49-mer RNA with true catalytic properties. The DAse ribozyme was labeled with Cy3 and Cy5 as a FRET pair of dyes to observe intramolecular folding, which is a prerequisite for its recognition and turnover of two organic substrate molecules. FRET efficiency histograms and kinetic data were taken on a large number of surface-immobilized ribozyme molecules as a function of the Mg(2+) concentration in the buffer solution. From these data, three separate states of the DAse ribozyme can be distinguished, the unfolded (U), intermediate (I) and folded (F) states. A thermodynamic model was developed to quantitatively analyze the dependence of these states on the Mg(2+) concentration. The FRET data also provide information on structural properties. The I state shows a strongly cooperative compaction with increasing Mg(2+) concentration that arises from association with several Mg(2+) ions. This transition is followed by a second Mg(2+)-dependent cooperative transition to the F state. The observation of conformational heterogeneity and continuous fluctuations between the I and F states on the approximately 100 ms timescale offers insight into the folding dynamics of this ribozyme.
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Affiliation(s)
- Andrei Yu. Kobitski
- Institute of Biophysics, University of Ulm, 89069 Ulm, Germany, Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, 69120 Heidelberg, Germany and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Alexander Nierth
- Institute of Biophysics, University of Ulm, 89069 Ulm, Germany, Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, 69120 Heidelberg, Germany and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Mark Helm
- Institute of Biophysics, University of Ulm, 89069 Ulm, Germany, Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, 69120 Heidelberg, Germany and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Andres Jäschke
- Institute of Biophysics, University of Ulm, 89069 Ulm, Germany, Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, 69120 Heidelberg, Germany and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - G. Ulrich Nienhaus
- Institute of Biophysics, University of Ulm, 89069 Ulm, Germany, Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, 69120 Heidelberg, Germany and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- *To whom correspondence should be addressed. +1-49-731-50-23050+1-49-731-50-23059
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22
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Chiorcea-Paquim AM, Piedade JAP, Wombacher R, Jäschke A, Oliveira-Brett AM. Atomic force microscopy and anodic voltammetry characterization of a 49-mer diels-alderase ribozyme. Anal Chem 2007; 78:8256-64. [PMID: 17165814 DOI: 10.1021/ac061040+] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Atomic force microscopy and differential pulse voltammetry were used to characterize the interaction of small highly structured ribozymes with two carbon electrode surfaces. The ribozymes spontaneously self-assemble in two-dimensional networks that cover the entire HOPG surface uniformly. The full-length ribozyme was adsorbed to a lesser extent than a truncated RNA sequence, presumably due to the formation of a more compact overall structure. All four nucleobases composing the ribozyme could be detected by anodic voltammetry on glassy carbon electrodes, and no signals corresponding to free nucleobases were found, indicating the integrity of the ribozyme molecules. Mg2+ cations significantly reduced the adsorption of ribozymes to the surfaces, in agreement with the stabilization of this ribozyme's compact, stable, and tightly folded tertiary structure by Mg2+ ions that could prevent the hydrophobic bases from interacting with the HOPG surface. Treatment with Pb2+ ions, on the other hand, resulted in an increased adsorption of the RNA due to well-known hydrolytic cleavage. The observed dependence of anodic peak currents on different folding states of RNA may provide an attractive method to electrochemically monitor structural changes associated with RNA folding, binding, and catalysis.
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Affiliation(s)
- A M Chiorcea-Paquim
- Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade de Coimbra, 3004-535 Coimbra, Portugal
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23
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Abstract
A computational comparison of the Diels-Alder reaction of a maleimide and an anthracene in water and the active site of the ribozyme Diels-Alderase is reported. During the course of the catalyzed reaction, the maleimide is held in the hydrophobic pocket while the anthracene approaches to the maleimide through the back passage of the active site. The active site is so narrow that the anthracene has to adopt a tilted approach angle toward maleimide. The conformation of the active site changes marginally at different states of the reaction. Active site dynamics contribution to catalysis has been ruled out. The active site stabilizes the product more than the transition state (TS). The reaction coordinates of the ribozyme reaction in TS, RC1-CD1 and RC4-CD2, are 2.35 and 2.33 A, respectively, compared to 2.37 and 2.36 A in water. The approach angle of anthracene toward maleimide is twisted by 18 degrees in the TS structure of ribozyme reaction while no twisted angle is found in TS of the reaction in water. The free energy barriers for reactions in both ribozyme and water were obtained by umbrella sampling combined with SCCDFTB/MM. The calculated free energy barriers for the ribozyme and water reactions are in good agreement with the experimental values. As expected, Mulliken charges of the atoms involved in the ribozyme reaction change in a similar manner as that of the reaction in water. The proficiency of the Diels-Alder ribozyme reaction originates from the active site holding the two reactants in reactive conformations, in which the reacting atoms are brought together in van der Waals distances and reactants approach to each other at an appropriate angle.
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Affiliation(s)
- Xiaohua Zhang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
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24
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Abstract
One of the hallmarks of DNA and RNA structures is their elegant chirality. Using these chiral structures to induce enantioselectivity in chemical synthesis is as enticing as it is challenging. In recent years, three general approaches have been developed to achieve this, including chirality transfer by nucleotide templated synthesis, enantioselective catalysis by RNA/DNAzymes and DNA-based asymmetric catalysis. In this article the concepts behind these strategies as well as the important achievements in this field will be discussed.
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Affiliation(s)
- Gerard Roelfes
- Department of Organic Chemistry, Stratingh Institute, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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25
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Cho B, Burke DH. Topological rearrangement yields structural stabilization and interhelical distance constraints in the Kin.46 self-phosphorylating ribozyme. RNA (NEW YORK, N.Y.) 2006; 12:2118-25. [PMID: 17068208 PMCID: PMC1664729 DOI: 10.1261/rna.173506] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The Kin.46 ribozyme catalyzes transfer of the gamma (thio)phosphoryl group of ATP (or ATPgammaS) to the ribozyme's 5' hydroxyl. Single-turnover catalytic activities of topologically rearranged versions of Kin.46 were studied to gain insight into its overall tertiary architecture. The distal ends of stems P3 and P4 were tethered through a single-stranded connection domain that altered the interhelical connectivity. The shortest linkers interfered with catalysis, while seven or more nucleotides (nt) in the linker allowed near-normal catalytic rates, suggesting that a distance of roughly 25-35 A optimally separates the termini of these helices. Activity was maximal when the tether contained 15 nt, at which point the k(cat) (0.016 min(-1)) and Km (1.2 mM) values were identical to those of a nontethered control. The presence of the tether alters Mg(2+) dependence, in that Mg2+ binding appears to be more cooperative in the tethered ribozyme (Hill coefficient 1.4-1.8 versus 0.8 for the nontethered ribozyme). Binding affinity for the ATPgammaS substrate increases at elevated concentrations of Mg2+, particularly for the tethered ribozyme. The tethered ribozyme displays significantly enhanced thermal stability, with a maximum initial velocity (0.126 min(-1)) at 60 degrees C, whereas the nontethered ribozyme has a lower maximum initial velocity (0.051 min(-1)) at 50 degrees C. The tether also significantly reduces the apparent entropy of activation. Both of these effects can be understood in terms of stabilization of the ribozyme in a conformation that is on-path with respect to catalysis, and in terms of facilitating formation of the allosteric activation helix P4.
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Affiliation(s)
- Bongrae Cho
- Department of Applied Chemistry, Division of Applied Science, Cheongju University, Cheongju 360-764, Korea
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26
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Abstract
All pairwise interactions occurring between bases which could be detected in three-dimensional structures of crystallized RNA molecules are annotated on new planar diagrams. The diagrams attempt to map the underlying complex networks of base–base interactions and, especially, they aim at conveying key relationships between helical domains: co-axial stacking, bending and all Watson–Crick as well as non-Watson–Crick base pairs. Although such wiring diagrams cannot replace full stereographic images for correct spatial understanding and representation, they reveal structural similarities as well as the conserved patterns and distances between motifs which are present within the interaction networks of folded RNAs of similar or unrelated functions. Finally, the diagrams could help devising methods for meaningfully transforming RNA structures into graphs amenable to network analysis.
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Affiliation(s)
| | - E. Westhof
- To whom correspondence should be addressed. Tel/Fax: +33 388 41 70 46; Email :
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27
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Amontov S, Jäschke A. Controlling the rate of organic reactions: rational design of allosteric Diels-Alderase ribozymes. Nucleic Acids Res 2006; 34:5032-8. [PMID: 16990253 PMCID: PMC1636424 DOI: 10.1093/nar/gkl613] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Allosteric mechanisms are widely used in nature to control the rates of enzymatic reactions, but little is known about RNA catalysts controlled by these principles. The only natural allosteric ribozyme reported to date catalyzes an RNA cleavage reaction, and so do almost all artificial systems. RNA has, however, been shown to accelerate a much wider range of chemical reactions. Here we report that RNA catalysts for organic reactions can be put under the stringent control of effector molecules by straight-forward rational design. This approach uses known RNA sequences with catalytic and ligand-binding properties, and exploits weakly conserved sequence elements and available structural information to induce the formation of alternative, catalytically inactive structures. The potential and general applicability is demonstrated by the design of three different systems in which the rate of a catalytic carbon–carbon bond forming reaction is positively regulated up to 2100-fold by theophylline, tobramycin and a specific mRNA sequence, respectively. Although smaller in size than a tRNA, all three ribozymes show typical features of allosteric metabolic enzymes, namely high rate acceleration and tight allosteric regulation. Not only do these findings demonstrate RNA's power as a catalyst, but also highlight on RNA's capabilities as signaling components in regulatory networks.
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Affiliation(s)
| | - Andres Jäschke
- To whom correspondence should be addressed. Tel: +49 6221 54 48 53; Fax: +49 6221 54 64 30;
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28
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Saran D, Held DM, Burke DH. Multiple-turnover thio-ATP hydrolase and phospho-enzyme intermediate formation activities catalyzed by an RNA enzyme. Nucleic Acids Res 2006; 34:3201-8. [PMID: 16790565 PMCID: PMC1484251 DOI: 10.1093/nar/gkl413] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Ribozymes that phosphorylate internal 2′-OH positions mimic the first mechanistic step of P-type ATPase enzymes by forming a phospho-enzyme intermediate. We previously described 2′-autophosphorylation and autothiophosphorylation by the 2PTmin3.2 ribozyme. In the present work we demonstrate that the thiophosphorylated form of this ribozyme can de-thiophosphorylate in the absence of ATPγS. Identical ionic conditions yield a thiophosphorylated strand when ATPγS is included, thus effecting a net ATPγS hydrolysis. The de-thiophosphorylation step is nearly independent of pH over the range of 6.3–8.5 and does not require a specifically folded RNA structure, but this step is greatly stimulated by transition metal ions. By monitoring thiophosphate release, we observe 29–46 ATPγS hydrolyzed per ribozyme strand in 24 h, corresponding to a turnover rate of 1.2–2.0 h−1. The existence of an ATP- (or thio-ATP-)powered catalytic cycle raises the possibility of using ribozymes to transduce chemical energy into mechanical work for nucleic acid nanodevices.
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Affiliation(s)
- Dayal Saran
- Department of Chemistry, Indiana UniversityBloomington, IN 47405, USA
- Department of Molecular Microbiology and Immunology, University of Missouri School of MedicineColumbia, MO 65211, USA
- Department of Biochemistry, University of Missouri School of MedicineColumbia, MO 65211, USA
| | - Daniel M. Held
- Department of Biology, Indiana UniversityBloomington, IN 47405, USA
- Department of Molecular Microbiology and Immunology, University of Missouri School of MedicineColumbia, MO 65211, USA
- Department of Biochemistry, University of Missouri School of MedicineColumbia, MO 65211, USA
| | - Donald H. Burke
- Department of Molecular Microbiology and Immunology, University of Missouri School of MedicineColumbia, MO 65211, USA
- Department of Biochemistry, University of Missouri School of MedicineColumbia, MO 65211, USA
- To whom correspondence should be address. Tel: +1 573 884 1316; Fax: +1 573 884 9676;
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29
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Schlatterer JC, Jäschke A. Universal initiator nucleotides for the enzymatic synthesis of 5'-amino- and 5'-thiol-modified RNA. Biochem Biophys Res Commun 2006; 344:887-92. [PMID: 16631608 DOI: 10.1016/j.bbrc.2006.03.218] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2006] [Accepted: 03/31/2006] [Indexed: 11/21/2022]
Abstract
We report the chemical synthesis of 5'-amino- and 5'-thiol-hexaethylene glycol guanosine nucleotides and their enzymatic incorporation into RNA, followed by chemical modifications at their nucleophilic ends. By using two similar routes, the conjugates of guanosine-5'-monophosphate and hexaethylene glycol with attached reactive groups (SH or NH(2)) were synthesized using phosphoramidite chemistry, and characterized by MALDI TOF mass spectrometry. These initiator molecules were efficiently incorporated into RNA at the 5'-end by run-off transcription using T7 RNA polymerase. The potential of these RNA conjugates for a broad reaction range with electrophiles is shown here, thereby enabling their use for diverse biochemical applications.
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Affiliation(s)
- Jörg C Schlatterer
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
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30
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Agresti JJ, Kelly BT, Jäschke A, Griffiths AD. Selection of ribozymes that catalyse multiple-turnover Diels-Alder cycloadditions by using in vitro compartmentalization. Proc Natl Acad Sci U S A 2005; 102:16170-5. [PMID: 16260754 PMCID: PMC1283419 DOI: 10.1073/pnas.0503733102] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In vitro compartmentalization (IVC) has previously been used to evolve protein enzymes. Here, we demonstrate how IVC can be applied to select RNA enzymes (ribozymes) for a property that has previously been unselectable: true intermolecular catalysis. Libraries containing 10(11) ribozyme genes are compartmentalized in the aqueous droplets of a water-in-oil emulsion, such that most droplets contain no more than one gene, and transcribed in situ. By coencapsulating the gene, RNA, and the substrates/products of the catalyzed reaction, ribozymes can be selected for all enzymatic properties: substrate recognition, product formation, rate acceleration, and turnover. Here we exploit the complementarity of IVC with systematic evolution of ligands by exponential enrichment (SELEX), which allows selection of larger libraries (>/=10(15)) and for very small rate accelerations (k(cat)/k(uncat)) but only selects for intramolecular single-turnover reactions. We selected approximately 10(14) random RNAs for Diels-Alderase activity with five rounds of SELEX, then six to nine rounds with IVC. All selected ribozymes catalyzed the Diels-Alder reaction in a truly bimolecular fashion and with multiple turnover. Nearly all ribozymes selected by using eleven rounds of SELEX alone contain a common catalytic motif. Selecting with SELEX then IVC gave ribozymes with significant sequence variations in this catalytic motif and ribozymes with completely novel motifs. Interestingly, the catalytic properties of all of the selected ribozymes were quite similar. The ribozymes are strongly product inhibited, consistent with the Diels-Alder transition state closely resembling the product. More efficient Diels-Alderases may need to catalyze a second reaction that transforms the product and prevents product inhibition.
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Affiliation(s)
- Jeremy J Agresti
- Laboratory of Molecular Biology, Medical Research Council, Hills Road, Cambridge CB2 2QH, United Kingdom
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31
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Fiammengo R, Musílek K, Jäschke A. Efficient preparation of organic substrate-RNA conjugates via in vitro transcription. J Am Chem Soc 2005; 127:9271-6. [PMID: 15969609 DOI: 10.1021/ja051179m] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A concise synthetic way has been developed for the preparation of guanosine monophosphate derivatives carrying a decaethylene glycol spacer at their 5'-oxygen to which are attached a range of organic substrates. The four different compounds, prepared via a convergent synthetic strategy, carry a tethered benzylallyl ether residue (1a), an anthracene (1b), a benzyl carbamate residue (1c), or a primary amino group (1d), respectively. All four compounds have been successfully incorporated at the 5'-end of a 25-mer long RNA transcript via T7 RNA polymerase, and no inhibition of chain elongation could be observed. Under proper conditions, 1a and 1b can be incorporated up to 90-95% and 1c up to 68%. The amino-terminated initiator 1d is incorporated less efficiently although still up to 49%. These results show that the more hydrophobic the guanosine monophosphate derivative is, the higher is its enzymatic incorporation.
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Affiliation(s)
- Roberto Fiammengo
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
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32
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Helm M, Petermeier M, Ge B, Fiammengo R, Jäschke A. Allosterically activated Diels-Alder catalysis by a ribozyme. J Am Chem Soc 2005; 127:10492-3. [PMID: 16045328 DOI: 10.1021/ja052886i] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe the allosteric control of Diels-Alder reactions by a small organic effector, theophylline. This is achieved by converting a Diels-Alder ribozyme into an allosterically regulated system. In contrast to other published systems, we have a bond-forming reaction with two small-molecule substrates and multiple turnover. This system could be very attractive for the development of assays for a variety of analytes and can be regarded as a prototype of fully synthetic signaling cascades.
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Affiliation(s)
- Mark Helm
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
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33
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Lilley DMJ. Structure, folding and mechanisms of ribozymes. Curr Opin Struct Biol 2005; 15:313-23. [PMID: 15919196 DOI: 10.1016/j.sbi.2005.05.002] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2005] [Revised: 02/08/2005] [Accepted: 05/04/2005] [Indexed: 01/20/2023]
Abstract
The past two years have seen exciting developments in RNA catalysis. A completely new ribozyme (possibly two) has come along and several new structures have been determined, including three different group I intron species. Although the origins of catalysis remain incompletely understood, a significant convergence of views has happened in the past year, together with the discovery of new super-fast ribozymes. There is persuasive evidence of general acid-base chemistry in nucleolytic ribozymes, whereas catalysis of peptidyl transfer in the ribosome seems to result largely from orientation and proximity effects. Lastly, important new folding-enhancing elements have been discovered.
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Affiliation(s)
- David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, University of Dundee, Dundee DD1 5EH, UK.
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34
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Lehman N, Unrau PJ. Recombination during in vitro evolution. J Mol Evol 2005; 61:245-52. [PMID: 16007485 DOI: 10.1007/s00239-004-0373-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2004] [Accepted: 03/16/2005] [Indexed: 10/25/2022]
Abstract
Recombination, the swapping of large portions of genetic information between and among parental genotypes, can be applied to in vitro evolution experiments on functional nucleic acids. Both homologous and heterologous recombination can be achieved using standard laboratory techniques. In many cases, recombination can allow for the discovery of a ribozyme or DNAzyme phenotype that would not likely be encountered by reliance on point mutations alone. In addition, recombination can often aid in the discovery of global optima in sequence space and/or lessen the number of generations it would take to reach optima. Recombination is most efficiently used in combination with point mutations and applied after the first couple of rounds of selection but before high-fitness genotypes dominate the selection. The "recombination zone" describes that region of sequence space-defined by the residues that will ultimately participate in the function of the winning nucleic acid(s)-where recombination is expected to be the most beneficial in the search for high-fitness genotypes.
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Affiliation(s)
- Niles Lehman
- Department of Chemistry, Portland State University, PO Box 751, Portland, OR 97207, USA.
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35
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36
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Serganov A, Keiper S, Malinina L, Tereshko V, Skripkin E, Höbartner C, Polonskaia A, Phan AT, Wombacher R, Micura R, Dauter Z, Jäschke A, Patel DJ. Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation. Nat Struct Mol Biol 2005; 12:218-24. [PMID: 15723077 PMCID: PMC4692364 DOI: 10.1038/nsmb906] [Citation(s) in RCA: 167] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2004] [Accepted: 01/24/2005] [Indexed: 11/08/2022]
Abstract
The majority of structural efforts addressing RNA's catalytic function have focused on natural ribozymes, which catalyze phosphodiester transfer reactions. By contrast, little is known about how RNA catalyzes other types of chemical reactions. We report here the crystal structures of a ribozyme that catalyzes enantioselective carbon-carbon bond formation by the Diels-Alder reaction in the unbound state and in complex with a reaction product. The RNA adopts a lambda-shaped nested pseudoknot architecture whose preformed hydrophobic pocket is precisely complementary in shape to the reaction product. RNA folding and product binding are dictated by extensive stacking and hydrogen bonding, whereas stereoselection is governed by the shape of the catalytic pocket. Catalysis is apparently achieved by a combination of proximity, complementarity and electronic effects. We observe structural parallels in the independently evolved catalytic pocket architectures for ribozyme- and antibody-catalyzed Diels-Alder carbon-carbon bond-forming reactions.
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Affiliation(s)
- Alexander Serganov
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA
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