1
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Edri R, Fisher S, Menor-Salvan C, Williams LD, Frenkel-Pinter M. Assembly-driven protection from hydrolysis as key selective force during chemical evolution. FEBS Lett 2023; 597:2879-2896. [PMID: 37884438 DOI: 10.1002/1873-3468.14766] [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: 07/13/2023] [Revised: 09/07/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023]
Abstract
The origins of biopolymers pose fascinating questions in prebiotic chemistry. The marvelous assembly proficiencies of biopolymers suggest they are winners of a competitive evolutionary process. Sophisticated molecular assembly is ubiquitous in life where it is often emergent upon polymerization. We focus on the influence of molecular assembly on hydrolysis rates in aqueous media and suggest that assembly was crucial for biopolymer selection. In this model, incremental enrichment of some molecular species during chemical evolution was partially driven by the interplay of kinetics of synthesis and hydrolysis. We document a general attenuation of hydrolysis by assembly (i.e., recalcitrance) for all universal biopolymers and highlight the likely role of assembly in the survival of the 'fittest' molecules during chemical evolution.
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Affiliation(s)
- Rotem Edri
- Institute of Chemistry, The Hebrew University of Jerusalem, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Israel
| | - Sarah Fisher
- Institute of Chemistry, The Hebrew University of Jerusalem, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Israel
| | - Cesar Menor-Salvan
- Department of Biología de Sistemas, Universidad de Alcalá, Madrid, Spain
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
| | - Moran Frenkel-Pinter
- Institute of Chemistry, The Hebrew University of Jerusalem, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Israel
- Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
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2
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Moore DS. On the evolution of epigenetics via exaptation: A developmental systems perspective. Ann N Y Acad Sci 2023; 1529:21-32. [PMID: 37750405 DOI: 10.1111/nyas.15065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Evolution and development are interrelated processes influenced by genomic, epigenetic, and environmental factors. Epigenetic processes serve critical roles in development and operate as intermediaries that connect the genome to the rest of the world. Therefore, it is of interest to consider the evolution of epigenetic processes. The developmental systems perspective offers a distinctive, coherent, integrative way to understand the relationships between evolution, epigenetics, development, and the effects of experienced contexts. By adopting this perspective, this paper draws attention to the role of exaptation in the evolution of epigenetics in the RNA world and addresses the role of epigenetics in the later evolution of developmental processes such as cellular differentiation, learning, and memory. In so doing, the paper considers the appearance and functions of epigenetics in evolutionary history-sketching a pathway by which epigenetic processes might have evolved via exaptation and then contributed to the later development and evolution of phenotypes.
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Affiliation(s)
- David S Moore
- Psychology Field Group, Pitzer College, Claremont, California, USA
- Division of Behavioral & Organizational Sciences, Claremont Graduate University, Claremont, California, USA
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3
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Dagar S, Sarkar S, Rajamani S. Nonenzymatic Template-Directed Primer Extension Using 2'-3' Cyclic Nucleotides Under Wet-Dry Cycles. ORIGINS LIFE EVOL B 2023; 53:43-60. [PMID: 37243884 DOI: 10.1007/s11084-023-09636-z] [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: 12/10/2022] [Accepted: 04/15/2023] [Indexed: 05/29/2023]
Abstract
RNA World Hypothesis is centred around the idea of a period in the early history of life's origin, wherein nonenzymatic oligomerization and replication of RNA resulted in functional ribozymes. Previous studies in this endeavour have demonstrated template-directed primer extension using chemically modified nucleotides and primers. Nonetheless, similar studies that used non-activated nucleotides led to the formation of RNA only with abasic sites. In this study, we report template-directed primer extension with prebiotically relevant cyclic nucleotides, under dehydration-rehydration (DH-RH) cycles occurring at high temperature (90 °C) and alkaline conditions (pH 8). 2'-3' cyclic nucleoside monophosphates (cNMP) resulted in primer extension, while 3'-5' cNMP failed to do so. Intact extension of up to two nucleotide additions was observed with both canonical hydroxy-terminated (OH-primer) and activated amino-terminated (NH2-primer) primers. We demonstrate primer extension reactions using both purine and pyrimidine 2'-3' cNMPs, with higher product yield observed during cAMP additions. Further, the presence of lipid was observed to significantly enhance the extended product in cCMP reactions. In all, our study provides a proof-of-concept for nonenzymatic primer extension of RNA, using intrinsically activated prebiotically relevant cyclic nucleotides as monomers.
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Affiliation(s)
- Shikha Dagar
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Susovan Sarkar
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Sudha Rajamani
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India.
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4
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Benner SA. Rethinking nucleic acids from their origins to their applications. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220027. [PMID: 36633284 PMCID: PMC9835595 DOI: 10.1098/rstb.2022.0027] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/17/2022] [Indexed: 01/13/2023] Open
Abstract
Reviewed are three decades of synthetic biology research in our laboratory that has generated alternatives to standard DNA and RNA as possible informational systems to support Darwinian evolution, and therefore life, and to understand their natural history, on Earth and throughout the cosmos. From this, we have learned that: • the core structure of nucleic acids appears to be a natural outcome of non-biological chemical processes probably in constrained, intermittently irrigated, sub-aerial aquifers on the surfaces of rocky planets like Earth and/or Mars approximately 4.36 ± 0.05 billion years ago; • however, this core is not unique. Synthetic biology has generated many different molecular systems able to support the evolution of molecular information; • these alternatives to standard DNA and RNA support biotechnology, including DNA synthesis, human diagnostics, biomedical research and medicine; • in particular, they support laboratory in vitro evolution (LIVE) with performance to generate catalysts at least 104-105 fold better than standard DNA libraries, enhancing access to receptors and catalysts on demand. Coupling nanostructures to the products of LIVE with expanded DNA offers new approaches for disease therapy; and • nevertheless, a polyelectrolyte structure and size regular building blocks are required for any informational polymer to support Darwinian evolution. These features serve as universal and agnostic biosignatures, useful for seeking life throughout the Solar System. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.
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Affiliation(s)
- Steven A. Benner
- Foundation for Applied Molecular Evolution, 13709 Progress Boulevard no. 7, Alachua, FL 32615, USA
- Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard no. 17, Alachua, FL 32615, USA
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5
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Sydow C, Seiband C, Siegle AF, Trapp O. Phosphorylation in liquid sulfur dioxide under prebiotically plausible conditions. Commun Chem 2022; 5:143. [PMID: 36697619 PMCID: PMC9814524 DOI: 10.1038/s42004-022-00761-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022] Open
Abstract
In nature, organophosphates provide key functions such as information storage and transport, structural tasks, and energy transfer. Since condensations are unfavourable in water and nucleophilic attack at phosphate is kinetically inhibited, various abiogenesis hypotheses for the formation of organophosphate are discussed. Recently, the application of phosphites as phosphorylation agent showed promising results. However, elevated temperatures and additional reaction steps are required to obtain organophosphates. Here we show that in liquid sulfur dioxide, which acts as solvent and oxidant, efficient organophosphate formation is enabled. Phosphorous acid yields up to 32.6% 5' nucleoside monophosphate, 3.6% 5' nucleoside diphosphate, and the formation of nucleoside triphosphates and dinucleotides in a single reaction step at room temperature. In addition to the phosphorylation of organic compounds, we observed diserine formation. Thus, we suggest volcanic environments as reaction sites for biopolymer formation on Early Earth. Because of the simple recyclability of sulfur dioxide, the reaction is also interesting for synthesis chemistry.
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Affiliation(s)
- Constanze Sydow
- grid.5252.00000 0004 1936 973XDepartment of Chemistry and Pharmacy, Ludwig-Maximilians-University, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Christiane Seiband
- grid.5252.00000 0004 1936 973XDepartment of Chemistry and Pharmacy, Ludwig-Maximilians-University, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Alexander F. Siegle
- grid.5252.00000 0004 1936 973XDepartment of Chemistry and Pharmacy, Ludwig-Maximilians-University, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Oliver Trapp
- grid.5252.00000 0004 1936 973XDepartment of Chemistry and Pharmacy, Ludwig-Maximilians-University, Butenandtstr. 5-13, 81377 Munich, Germany ,grid.429508.20000 0004 0491 677XMax-Planck-Institute for Astronomy, Königstuhl 17, 69117 Heidelberg, Germany
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6
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Jerome CA, Kim HJ, Mojzsis SJ, Benner SA, Biondi E. Catalytic Synthesis of Polyribonucleic Acid on Prebiotic Rock Glasses. ASTROBIOLOGY 2022; 22:629-636. [PMID: 35588195 PMCID: PMC9233534 DOI: 10.1089/ast.2022.0027] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/12/2022] [Indexed: 05/21/2023]
Abstract
Reported here are experiments that show that ribonucleoside triphosphates are converted to polyribonucleic acid when incubated with rock glasses similar to those likely present 4.3-4.4 billion years ago on the Hadean Earth surface, where they were formed by impacts and volcanism. This polyribonucleic acid averages 100-300 nucleotides in length, with a substantial fraction of 3',-5'-dinucleotide linkages. Chemical analyses, including classical methods that were used to prove the structure of natural RNA, establish a polyribonucleic acid structure for these products. The polyribonucleic acid accumulated and was stable for months, with a synthesis rate of 2 × 10-3 pmoles of triphosphate polymerized each hour per gram of glass (25°C, pH 7.5). These results suggest that polyribonucleotides were available to Hadean environments if triphosphates were. As many proposals are emerging describing how triphosphates might have been made on the Hadean Earth, the process observed here offers an important missing step in models for the prebiotic synthesis of RNA.
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Affiliation(s)
- Craig A. Jerome
- Foundation for Applied Molecular Evolution, Alachua, Florida, USA
| | - Hyo-Joong Kim
- Firebird Biomolecular Sciences LLC, Alachua, Florida, USA
| | - Stephen J. Mojzsis
- Department of Geological Sciences, University of Colorado, Boulder, Colorado, USA
- Research Center of Astronomy and Earth Sciences, Budapest, Hungary
| | - Steven A. Benner
- Foundation for Applied Molecular Evolution, Alachua, Florida, USA
- Firebird Biomolecular Sciences LLC, Alachua, Florida, USA
| | - Elisa Biondi
- Foundation for Applied Molecular Evolution, Alachua, Florida, USA
- Firebird Biomolecular Sciences LLC, Alachua, Florida, USA
- Address correspondence to: Elisa Biondi, Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA
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7
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Steinberg J, Wadenpohl T, Jung S. The Endogenous RIG-I Ligand Is Generated in Influenza A-Virus Infected Cells. Viruses 2021; 13:1564. [PMID: 34452429 PMCID: PMC8402674 DOI: 10.3390/v13081564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/03/2021] [Accepted: 08/06/2021] [Indexed: 12/16/2022] Open
Abstract
As a result of a viral infection, viral genomes are not only recognized by RIG-I, but also lead to the activation of RNase L, which cleaves cellular RNA to generate the endogenous RIG-I ligand (eRL). The eRL was previously identified as a specific sequence derived from the internal transcribed spacer region 2, which bears a 2'3' cyclic phosphate instead of the common 5' triphosphate. By now, the generation of the eRL and its immunostimulatory effect were shown both in vitro and in reporter systems. In this work, we aimed to elucidate whether the eRL is also generated in Influenza A (IAV) and vesicular stomatitis virus (VSV) infected cells. RNA was extracted from virus-infected cells and used for immunostimulations as well as specific PCR-strategies to detect eRL cleavage. We show that the eRL is generated in IAV infected HEK293 cells, but we could not detect specific eRL fragments in VSV infected cells. Further, RIG-I mediated IFN-response depends not only on viral genomes but also on the eRL, as immunostimulatory properties remain present under 5'triphosphate degrading conditions. In summary, we prove the IAV infection induced eRL generation in HEK293 cells, amplifying the innate immune response.
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Affiliation(s)
| | | | - Stephanie Jung
- Institute of Cardiovascular Immunology, University Hospital Bonn, University of Bonn, 53127 Bonn, Germany; (J.S.); (T.W.)
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8
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Kim SC, O'Flaherty DK, Giurgiu C, Zhou L, Szostak JW. The Emergence of RNA from the Heterogeneous Products of Prebiotic Nucleotide Synthesis. J Am Chem Soc 2021; 143:3267-3279. [PMID: 33636080 DOI: 10.1021/jacs.0c12955] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent advances in prebiotic chemistry are beginning to outline plausible pathways for the synthesis of the canonical ribonucleotides and their assembly into oligoribonucleotides. However, these reaction pathways suggest that many noncanonical nucleotides are likely to have been generated alongside the standard ribonucleotides. Thus, the oligomerization of prebiotically synthesized nucleotides is likely to have led to a highly heterogeneous collection of oligonucleotides comprised of a wide range of types of nucleotides connected by a variety of backbone linkages. How then did relatively homogeneous RNA emerge from this primordial heterogeneity? Here we focus on nonenzymatic template-directed primer extension as a process that would have strongly enriched for homogeneous RNA over the course of multiple cycles of replication. We review the effects on copying the kinetics of nucleotides with altered nucleobase and sugar moieties, when they are present as activated monomers and when they are incorporated into primer and template oligonucleotides. We also discuss three variations in backbone connectivity, all of which are nonheritable and regenerate native RNA upon being copied. The kinetic superiority of RNA synthesis suggests that nonenzymatic copying served as a chemical selection mechanism that allowed relatively homogeneous RNA to emerge from a complex mixture of prebiotically synthesized nucleotides and oligonucleotides.
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Affiliation(s)
- Seohyun Chris Kim
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Derek K O'Flaherty
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Constantin Giurgiu
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Lijun Zhou
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
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9
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Jung S, von Thülen T, Yang I, Laukemper V, Rupf B, Janga H, Panagiotidis GD, Schoen A, Nicolai M, Schulte LN, Obermann HL, Weber F, Kaufmann A, Bauer S. A ribosomal RNA fragment with 2',3'-cyclic phosphate and GTP-binding activity acts as RIG-I ligand. Nucleic Acids Res 2020; 48:10397-10412. [PMID: 32946572 PMCID: PMC7544222 DOI: 10.1093/nar/gkaa739] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 08/19/2020] [Accepted: 08/26/2020] [Indexed: 12/13/2022] Open
Abstract
The RNA helicase RIG-I plays a key role in sensing pathogen-derived RNA. Double-stranded RNA structures bearing 5'-tri- or diphosphates are commonly referred to as activating RIG-I ligands. However, endogenous RNA fragments generated during viral infection via RNase L also activate RIG-I. Of note, RNase-digested RNA fragments bear a 5'-hydroxyl group and a 2',3'-cyclic phosphate. How endogenous RNA fragments activate RIG-I despite the lack of 5'-phosphorylation has not been elucidated. Here we describe an endogenous RIG-I ligand (eRL) that is derived from the internal transcribed spacer 2 region (ITS2) of the 45S ribosomal RNA after partial RNase A digestion in vitro, RNase A protein transfection or RNase L activation. The immunostimulatory property of the eRL is dependent on 2',3'-cyclic phosphate and its sequence is characterized by a G-quadruplex containing sequence motif mediating guanosine-5'-triphosphate (GTP) binding. In summary, RNase generated self-RNA fragments with 2',3'-cyclic phosphate function as nucleotide-5'-triphosphate binding aptamers activating RIG-I.
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Affiliation(s)
- Stephanie Jung
- Institut für Immunologie, Philipps-Universität Marburg, BMFZ, Hans-Meerwein-Straße 2, 35043 Marburg, Germany
| | - Tina von Thülen
- Institut für Immunologie, Philipps-Universität Marburg, BMFZ, Hans-Meerwein-Straße 2, 35043 Marburg, Germany
| | - Ines Yang
- Institut für Medizinische Mikrobiologie und Krankenhaushygiene, Medizinische Hochschule Hannover, Carl Neuberg Straße 1, 30625 Hannover, Germany
| | - Viktoria Laukemper
- Institut für Immunologie, Philipps-Universität Marburg, BMFZ, Hans-Meerwein-Straße 2, 35043 Marburg, Germany
| | - Benjamin Rupf
- Institut für Immunologie, Philipps-Universität Marburg, BMFZ, Hans-Meerwein-Straße 2, 35043 Marburg, Germany
| | - Harshavardhan Janga
- Institut für Lungenforschung/iLung, Philipps-Universität Marburg, BMFZ, Hans-Meerwein-Straße 2, 35043 Marburg, Germany
| | - Georgios-Dimitrios Panagiotidis
- Institut für Virologie, Fachbereich Veterinärmedizin (FB10), Justus-Liebig-Universität Gießen, Schubertstr. 81, 35392 Gießen, Germany
| | - Andreas Schoen
- Institut für Virologie, Fachbereich Veterinärmedizin (FB10), Justus-Liebig-Universität Gießen, Schubertstr. 81, 35392 Gießen, Germany
| | - Marina Nicolai
- Institut für Immunologie, Philipps-Universität Marburg, BMFZ, Hans-Meerwein-Straße 2, 35043 Marburg, Germany
| | - Leon N Schulte
- Institut für Lungenforschung/iLung, Philipps-Universität Marburg, BMFZ, Hans-Meerwein-Straße 2, 35043 Marburg, Germany
- Deutsches Zentrum für Lungenforschung (DZL), 35392 Gießen, Germany
| | - Hannah-Lena Obermann
- Institut für Immunologie, Philipps-Universität Marburg, BMFZ, Hans-Meerwein-Straße 2, 35043 Marburg, Germany
| | - Friedemann Weber
- Institut für Virologie, Fachbereich Veterinärmedizin (FB10), Justus-Liebig-Universität Gießen, Schubertstr. 81, 35392 Gießen, Germany
| | - Andreas Kaufmann
- Institut für Immunologie, Philipps-Universität Marburg, BMFZ, Hans-Meerwein-Straße 2, 35043 Marburg, Germany
| | - Stefan Bauer
- Institut für Immunologie, Philipps-Universität Marburg, BMFZ, Hans-Meerwein-Straße 2, 35043 Marburg, Germany
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10
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Habibian M, Harikrishna S, Fakhoury J, Barton M, Ageely EA, Cencic R, Fakih HH, Katolik A, Takahashi M, Rossi J, Pelletier J, Gagnon KT, Pradeepkumar PI, Damha MJ. Effect of 2'-5'/3'-5' phosphodiester linkage heterogeneity on RNA interference. Nucleic Acids Res 2020; 48:4643-4657. [PMID: 32282904 PMCID: PMC7229817 DOI: 10.1093/nar/gkaa222] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/19/2020] [Accepted: 03/25/2020] [Indexed: 12/12/2022] Open
Abstract
We report on the synthesis of siRNAs containing both 2′-5′- and 3′-5′-internucleotide linkages and their effects on siRNA structure, function, and interaction with RNAi proteins. Screening of these siRNAs against their corresponding mRNA targets showed that 2′-5′ linkages were well tolerated in the sense strand, but only at a few positions in the antisense strand. Extensive modification of the antisense strand minimally affected 5′-phosphorylation of the siRNA by kinases, however, it negatively affected siRNA loading into human AGO2. Modelling and molecular dynamics simulations were fully consistent with these findings. Furthermore, our studies indicated that the presence of a single 5′p-rN1-(2′-5′)-N2 unit in the antisense strand does not alter the ‘clover leaf’ bend and sugar puckers that are critical for anchoring the 5′-phosphate to Ago 2 MID domain. Importantly, 2′-5′-linkages had the added benefit of abrogating immune-stimulatory activity of siRNAs. Together, these results demonstrate that 2′-5′/3′-5′-modified siRNAs, when properly designed, can offer an efficient new class of siRNAs with diminished immune-stimulatory responses.
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Affiliation(s)
- Maryam Habibian
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
| | - S Harikrishna
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Johans Fakhoury
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
| | - Maria Barton
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL, USA
| | - Eman A Ageely
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, IL, USA
| | - Regina Cencic
- Department of Biochemistry and Goodman Cancer Center, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Hassan H Fakih
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
| | - Adam Katolik
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
| | - Mayumi Takahashi
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - John Rossi
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Jerry Pelletier
- Department of Biochemistry and Goodman Cancer Center, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Keith T Gagnon
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL, USA.,Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, IL, USA
| | - P I Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Masad J Damha
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
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11
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Dagar S, Sarkar S, Rajamani S. Geochemical influences on nonenzymatic oligomerization of prebiotically relevant cyclic nucleotides. RNA (NEW YORK, N.Y.) 2020; 26:756-769. [PMID: 32205323 PMCID: PMC7266160 DOI: 10.1261/rna.074302.119] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/19/2020] [Indexed: 06/01/2023]
Abstract
The spontaneous emergence of long RNA molecules on the early Earth, a phenomenon central to the RNA World hypothesis, continues to remain an enigma in the field of origins of life. Few studies have looked at the nonenzymatic oligomerization of cyclic mononucleotides under neutral to alkaline conditions, albeit in fully dehydrated state. In this study, we systematically investigated the oligomerization of cyclic nucleotides under prebiotically relevant conditions, wherein starting reactants were subjected to repeated dehydration-rehydration (DH-RH) regimes. DH-RH conditions, a recurring geological theme that was prevalent on prebiotic Earth, are driven by naturally occurring processes including diurnal cycles and tidal pool activity. These conditions have been shown to facilitate uphill oligomerization reactions. The polymerization of 2'-3' and 3'-5' cyclic nucleotides of a purine (adenosine) and a pyrimidine (cytidine) was investigated. Additionally, the effect of amphiphiles was also evaluated. Furthermore, to discern the effect of "realistic" conditions on this process, the reactions were also performed using a hot spring water sample from a candidate early Earth environment. Our study showed that the oligomerization of cyclic nucleotides under DH-RH conditions resulted in intact informational oligomers. Amphiphiles increased the stability of both the starting monomers and the resultant oligomers in selected reactions. In the hot spring reactions, both the oligomerization of nucleotides and the back hydrolysis of the resultant oligomers were pronounced. Altogether, this study demonstrates how nonenzymatic oligomerization of cyclic nucleotides, under both laboratory-simulated prebiotic conditions and in a candidate early Earth environment, could have resulted in RNA oligomers of a putative RNA World.
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Affiliation(s)
- Shikha Dagar
- Department of Biology, Indian Institute of Science Education and Research, Pune 411008, India
| | - Susovan Sarkar
- Department of Biology, Indian Institute of Science Education and Research, Pune 411008, India
| | - Sudha Rajamani
- Department of Biology, Indian Institute of Science Education and Research, Pune 411008, India
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12
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Motsch S, Pfeffer D, Richert C. 2'/3' Regioselectivity of Enzyme-Free Copying of RNA Detected by NMR. Chembiochem 2020; 21:2013-2018. [PMID: 32017335 PMCID: PMC7497262 DOI: 10.1002/cbic.202000014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Indexed: 11/06/2022]
Abstract
The RNA-templated extension of oligoribonucleotides by nucleotides produces either a 3',5' or a 2',5'-phosphodiester. Nature controls the regioselectivity during RNA chain growth with polymerases, but enzyme-free versions of genetic copying have modest specificity. Thus far, enzymatic degradation of products, combined with chromatography or electrophoresis, has been the preferred mode of detecting 2',5'-diesters produced in enzyme-free reactions. This approach hinges on the substrate specificity of nucleases, and is not suitable for in situ monitoring. Here we report how 1 H NMR spectroscopy can be used to detect the extension of self-templating RNA hairpins and that this reveals the regioisomeric nature of the newly formed phosphodiesters. We studied several modes of activating nucleotides, including imidazolides, a pyridinium phosphate, an active ester, and in situ activation with carbodiimide and organocatalyst. Conversion into the desired extension product ranged from 20 to 90 %, depending on the leaving group. Integration of the resonances of H1' protons of riboses and H5 protons of pyrimidines gave regioselectivities ranging from 40:60 to 85:15 (3',5' to 2',5' diester), but no simple correlation between 3',5' selectivity and yield. Our results show how monitoring with a high-resolution technique sheds a new light on a process that may have played an important role during the emergence of life.
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Affiliation(s)
- Sebastian Motsch
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Daniel Pfeffer
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
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13
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Motsch S, Tremmel P, Richert C. Regioselective formation of RNA strands in the absence of magnesium ions. Nucleic Acids Res 2020; 48:1097-1107. [PMID: 31819977 PMCID: PMC7026634 DOI: 10.1093/nar/gkz1125] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/08/2019] [Accepted: 11/18/2019] [Indexed: 11/28/2022] Open
Abstract
The oligomerization of ribonucleotides can produce short RNA strands in the absence of enzymes. This reaction gives one of two regioisomeric phosphodiester linkages, a 2',5'- or a 3',5'-diester. The former, non-natural linkage is detrimental for duplex stability, and is known to form preferentially in oligomerizations occurring in homogeneous solution with preactivated nucleotides in the presence of magnesium cations. We have studied ribonucleotide oligomerization with in situ activation, using NMR as monitoring technique. Unexpectedly, the known preference for 2',5'-linkages in the oligomerization of AMP was reversed in the absence of magnesium ions at slightly basic pH. Further, oligomerization was surprisingly efficient in the absence of Mg2+ salts, producing oligomers long enough for duplex formation. A quantitative systems chemistry analysis then revealed that the absence of magnesium ions favors the activation of nucleotides, and that the high concentration of active species can compensate for slower coupling. Further, organocatalytic intermediates can help to overcome the unfavorable regioselectivity of the magnesium-catalyzed reactions. Our findings allay concerns that RNA may have been difficult to form in the absence of enzymes. They also show that there is an efficient path to genetic material that does not require mineral surfaces or cations known to catalyze RNA hydrolysis.
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Affiliation(s)
- Sebastian Motsch
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Peter Tremmel
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
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14
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Wright TH, Giurgiu C, Zhang W, Radakovic A, O'Flaherty DK, Zhou L, Szostak JW. Prebiotically Plausible "Patching" of RNA Backbone Cleavage through a 3'-5' Pyrophosphate Linkage. J Am Chem Soc 2019; 141:18104-18112. [PMID: 31651170 PMCID: PMC7577263 DOI: 10.1021/jacs.9b08237] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
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Achieving multiple cycles of RNA
replication within a model protocell
would be a critical step toward demonstrating a path from prebiotic
chemistry to cellular biology. Any model for early life based on an
“RNA world” must account for RNA strand cleavage and
hydrolysis, which would degrade primitive genetic information and
lead to an accumulation of truncated, phosphate-terminated strands.
We show here that cleavage of the phosphodiester backbone is not an
end point for RNA replication. Instead, 3′-phosphate-terminated
RNA strands can participate in template-directed copying reactions
with activated ribonucleotide monomers. These reactions form a pyrophosphate
linkage, the stability of which we have characterized in the context
of RNA copying chemistry. The presence of free magnesium cations results
in cleavage of the pyrophosphate bond within minutes. However, we
found that the pyrophosphate bond is relatively stable within an RNA
duplex and in the presence of chelated magnesium. We show that, under
these conditions, pyrophosphate-linked RNA can act as a template for
the polymerization of ribonucleotides into canonical 3′–5′
phosphodiester-linked RNA. We suggest that primer extension of 3′-phosphate-terminated
RNA followed by template-directed copying represents a plausible nonenzymatic
pathway for the salvage and recovery of genetic information following
strand cleavage.
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Affiliation(s)
- Tom H Wright
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology , Massachusetts General Hospital , 185 Cambridge Street , Boston , Massachusetts 02114 , United States
| | - Constantin Giurgiu
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology , Massachusetts General Hospital , 185 Cambridge Street , Boston , Massachusetts 02114 , United States
| | - Wen Zhang
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology , Massachusetts General Hospital , 185 Cambridge Street , Boston , Massachusetts 02114 , United States
| | - Aleksandar Radakovic
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology , Massachusetts General Hospital , 185 Cambridge Street , Boston , Massachusetts 02114 , United States
| | - Derek K O'Flaherty
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology , Massachusetts General Hospital , 185 Cambridge Street , Boston , Massachusetts 02114 , United States
| | - Lijun Zhou
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology , Massachusetts General Hospital , 185 Cambridge Street , Boston , Massachusetts 02114 , United States
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology , Massachusetts General Hospital , 185 Cambridge Street , Boston , Massachusetts 02114 , United States
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15
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Mariani A, Bonfio C, Johnson CM, Sutherland JD. pH-Driven RNA Strand Separation under Prebiotically Plausible Conditions. Biochemistry 2018; 57:6382-6386. [PMID: 30383375 PMCID: PMC6340128 DOI: 10.1021/acs.biochem.8b01080] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Replication of nucleic acids in the absence of genetically encoded enzymes represents a critical process for the emergence of cellular life. Repeated separation of complementary RNA strands is required to achieve multiple cycles of chemical replication, yet thermal denaturation under plausible prebiotic conditions is impaired by the high temperatures required to separate long RNA strands and by concurrent degradation pathways, the latter accelerated by divalent metal ions. Here we show how the melting temperature of oligoribonucleotide duplexes can be tuned by changes in pH, enabling the separation of RNA strands at moderate temperatures. At the same time, the risk of phosphodiester bond cleavage is reduced under the acid denaturation conditions herein described, both in the presence and in the absence of divalent metal ions. Through a combination of ultraviolet and circular dichroism thermal studies and gel electrophoresis, we demonstrate the relevance of geological pH oscillations in the context of the RNA strand separation problem. Our results reveal new insights in the field of prebiotic chemistry, supporting plausible geochemical scenarios in which non-enzymatic RNA replication might have taken place.
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Affiliation(s)
- Angelica Mariani
- MRC Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge Biomedical Campus , Cambridge CB2 0QH , U.K
| | - Claudia Bonfio
- MRC Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge Biomedical Campus , Cambridge CB2 0QH , U.K
| | - Christopher M Johnson
- MRC Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge Biomedical Campus , Cambridge CB2 0QH , U.K
| | - John D Sutherland
- MRC Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge Biomedical Campus , Cambridge CB2 0QH , U.K
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16
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Chemomimesis and Molecular Darwinism in Action: From Abiotic Generation of Nucleobases to Nucleosides and RNA. Life (Basel) 2018; 8:life8020024. [PMID: 29925796 PMCID: PMC6027154 DOI: 10.3390/life8020024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 06/14/2018] [Accepted: 06/19/2018] [Indexed: 01/26/2023] Open
Abstract
Molecular Darwinian evolution is an intrinsic property of reacting pools of molecules resulting in the adaptation of the system to changing conditions. It has no a priori aim. From the point of view of the origin of life, Darwinian selection behavior, when spontaneously emerging in the ensembles of molecules composing prebiotic pools, initiates subsequent evolution of increasingly complex and innovative chemical information. On the conservation side, it is a posteriori observed that numerous biological processes are based on prebiotically promptly made compounds, as proposed by the concept of Chemomimesis. Molecular Darwinian evolution and Chemomimesis are principles acting in balanced cooperation in the frame of Systems Chemistry. The one-pot synthesis of nucleosides in radical chemistry conditions is possibly a telling example of the operation of these principles. Other indications of similar cases of molecular evolution can be found among biogenic processes.
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17
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Self-selection of dissipative assemblies driven by primitive chemical reaction networks. Nat Commun 2018; 9:2044. [PMID: 29795292 PMCID: PMC5966463 DOI: 10.1038/s41467-018-04488-y] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 04/10/2018] [Indexed: 11/23/2022] Open
Abstract
Life is a dissipative nonequilibrium structure that requires constant consumption of energy to sustain itself. How such an unstable state could have selected from an abiotic pool of molecules remains a mystery. Here we show that liquid phase-separation offers a mechanism for the selection of dissipative products from a library of reacting molecules. We bring a set of primitive carboxylic acids out-of-equilibrium by addition of high-energy condensing agents. The resulting anhydrides are transiently present before deactivation via hydrolysis. We find the anhydrides that phase-separate into droplets to protect themselves from hydrolysis and to be more persistent than non-assembling ones. Thus, after several starvation-refueling cycles, the library self-selects the phase-separating anhydrides. We observe that the self-selection mechanism is more effective when the library is brought out-of-equilibrium by periodic addition of batches as opposed to feeding it continuously. Our results suggest that phase-separation offers a selection mechanism for energy dissipating assemblies. Selection and persistence of chemical non-equilibrium species is crucial for the emergence of life and the exact mechanisms remain elusive. Here the authors show that phase separation is an efficient way to control selection of chemical species when primitive carboxylic acids are brought out-of-equilibrium by high-energy condensing agents.
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18
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Kumar VA. Evolution of specific 3'-5'-linkages in RNA in pre-biotic soup: a new hypothesis. Org Biomol Chem 2018; 14:10123-10133. [PMID: 27714238 DOI: 10.1039/c6ob01796g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
This article reviews the different possibilities towards progression of the formation of DNA/RNA in the chemical world, before life, in enzyme-free conditions. The advent of deoxyribo- and ribopentose-sugars, nucleosides, nucleotides and oligonucleotides in the prebiotic soup is briefly discussed. Further, the formation of early single stranded oligomers, base-pairing possibilities and information transfer based on the stability parameters of the derived duplexes is reviewed. Each theory has its own merits and demerits which we have elaborated upon. Lastly, using clues from this literature, a possible explanation for the specific 3'-5'-linkages in RNA is proposed.
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Affiliation(s)
- Vaijayanti A Kumar
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Dr Homi Bhabha Road, Pune, 411008, India.
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19
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Saladino R, Šponer JE, Šponer J, Di Mauro E. Rewarming the Primordial Soup: Revisitations and Rediscoveries in Prebiotic Chemistry. Chembiochem 2018; 19:22-25. [PMID: 29164768 PMCID: PMC5768021 DOI: 10.1002/cbic.201700534] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Indexed: 01/11/2023]
Abstract
A short history of Campbell's primordial soup: In this essay we try to disclose some of the historical connections between the studies that have contributed to our current understanding of the emergence of catalytic RNA molecules and their components from an inanimate matter.
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Affiliation(s)
- Raffaele Saladino
- Dipartimento di Scienze Ecologiche e BiologicheUniversità della TusciaVia San Camillo De Lellis01100ViterboItaly
| | - Judit E. Šponer
- Institute of Biophysics of the Czech Academy of SciencesKrálovopolská 13561265BrnoCzech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of SciencesKrálovopolská 13561265BrnoCzech Republic
| | - Ernesto Di Mauro
- Dipartimento di Scienze Ecologiche e BiologicheUniversità della TusciaVia San Camillo De Lellis01100ViterboItaly
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20
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Giurgiu C, Li L, O’Flaherty DK, Tam CP, Szostak JW. A Mechanistic Explanation for the Regioselectivity of Nonenzymatic RNA Primer Extension. J Am Chem Soc 2017; 139:16741-16747. [PMID: 29112424 PMCID: PMC6326530 DOI: 10.1021/jacs.7b08784] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Indexed: 11/28/2022]
Abstract
A working model of nonenzymatic RNA primer extension could illuminate how prebiotic chemistry transitioned to biology. All currently known experimental reconstructions of nonenzymatic RNA primer extension yield a mixture of 2'-5' and 3'-5' internucleotide linkages. Although long seen as a major problem, the causes of the poor regioselectivity of the reaction are unknown. We used a combination of different leaving groups, nucleobases, and templating sequences to uncover the factors that yield selective formation of 3'-5' internucleotide linkages. We found that fast and high yielding reactions selectively form 3'-5' linkages. Additionally, in all cases with high 3'-5' regioselectivity, Watson-Crick base pairing between the RNA monomers and the template is observed at the extension site and at the adjacent downstream position. Mismatched base-pairs and other factors that would perturb the geometry of the imidazolium bridged intermediate lower both the rate and regioselectivity of the reaction.
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Affiliation(s)
- Constantin Giurgiu
- Howard Hughes Medical Institute, Department
of Molecular Biology, and Center for Computational and Integrative
Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Li Li
- Howard Hughes Medical Institute, Department
of Molecular Biology, and Center for Computational and Integrative
Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Derek K. O’Flaherty
- Howard Hughes Medical Institute, Department
of Molecular Biology, and Center for Computational and Integrative
Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Chun Pong Tam
- Howard Hughes Medical Institute, Department
of Molecular Biology, and Center for Computational and Integrative
Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Jack W. Szostak
- Howard Hughes Medical Institute, Department
of Molecular Biology, and Center for Computational and Integrative
Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
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21
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Tupper AS, Shi K, Higgs PG. The Role of Templating in the Emergence of RNA from the Prebiotic Chemical Mixture. Life (Basel) 2017; 7:life7040041. [PMID: 29088116 PMCID: PMC5745554 DOI: 10.3390/life7040041] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/25/2017] [Accepted: 10/26/2017] [Indexed: 01/11/2023] Open
Abstract
Biological RNA is a uniform polymer in three senses: it uses nucleotides of a single chirality; it uses only ribose sugars and four nucleobases rather than a mixture of other sugars and bases; and it uses only 3'-5' bonds rather than a mixture of different bond types. We suppose that prebiotic chemistry would generate a diverse mixture of potential monomers, and that random polymerization would generate non-uniform strands of mixed chirality, monomer composition, and bond type. We ask what factors lead to the emergence of RNA from this mixture. We show that template-directed replication can lead to the emergence of all the uniform properties of RNA by the same mechanism. We study a computational model in which nucleotides react via polymerization, hydrolysis, and template-directed ligation. Uniform strands act as templates for ligation of shorter oligomers of the same type, whereas mixed strands do not act as templates. The three uniform properties emerge naturally when the ligation rate is high. If there is an exact symmetry, as with the chase of chirality, the uniform property arises via a symmetry-breaking phase transition. If there is no exact symmetry, as with monomer selection and backbone regioselectivity, the uniform property emerges gradually as the rate of template-directed ligation is increased.
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Affiliation(s)
- Andrew S Tupper
- Origins Institute and Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, ON L8S 4L8, Canada.
| | - Kevin Shi
- Origins Institute and Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4K1, Canada.
| | - Paul G Higgs
- Origins Institute and Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4K1, Canada.
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22
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Shen F, Luo Z, Liu H, Wang R, Zhang S, Gan J, Sheng J. Structural insights into RNA duplexes with multiple 2΄-5΄-linkages. Nucleic Acids Res 2017; 45:3537-3546. [PMID: 28034958 PMCID: PMC5389462 DOI: 10.1093/nar/gkw1307] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 12/20/2016] [Indexed: 01/15/2023] Open
Abstract
2΄-5΄-linked RNAs play important roles in many biological systems. In addition, the mixture of 2΄-5΄ and 3΄-5΄ phosphodiester bonds have emerged as a plausible structural element in prebiotic RNAs. Toward our mechanistic studies of RNA folding and structures with heterogeneous backbones, we recently reported two crystal structures of a decamer RNA duplex containing two and six 2΄-5΄-linkages, showing how RNA duplexes adjust the structures to accommodate these non-canonical linkages (Proc. Natl. Acad. Sci. USA, 2014, 111, 3050-3055). Herein, we present two additional high-resolution crystal structures of the same RNA duplex containing four and eight 2΄-5΄-linkages at different positions, providing new insights into the effects of these modifications and a dynamic view of RNA structure changes with increased numbers of 2΄-5΄-linkages in the same duplex. Our results show that the local structural perturbations caused by 2΄-5΄ linkages can be distributed to nearly all the nucleotides with big ranges of changes in different geometry parameters. In addition, hydration pattern and solvation energy analysis indicate less favorable solvent interactions of 2΄-5΄-linkages comparing to the native 3΄-5΄-linkages. This study not only promotes our understanding of RNA backbone flexibility, but also provides a knowledge base for studying the biochemical and prebiotic significance of RNA 2΄-5΄-linkages.
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Affiliation(s)
- Fusheng Shen
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.,The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Zhipu Luo
- Synchrotron Radiation Research Section, MCL National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Hehua Liu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Rui Wang
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.,The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Shenglong Zhang
- Department of Life Sciences, New York Institute of Technology, New York, NY 10023, USA
| | - Jianhua Gan
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jia Sheng
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.,The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
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23
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Mariani A, Sutherland JD. Non-Enzymatic RNA Backbone Proofreading through Energy-Dissipative Recycling. Angew Chem Int Ed Engl 2017; 56:6563-6566. [PMID: 28467695 PMCID: PMC5488188 DOI: 10.1002/anie.201703169] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Indexed: 11/12/2022]
Abstract
Non-enzymatic oligomerization of activated ribonucleotides leads to ribonucleic acids that contain a mixture of 2',5'- and 3',5'-linkages, and overcoming this backbone heterogeneity has long been considered a major limitation to the prebiotic emergence of RNA. Herein, we demonstrate non-enzymatic chemistry that progressively converts 2',5'-linkages into 3',5'-linkages through iterative degradation and repair. The energetic costs of this proofreading are met by the hydrolytic turnover of a phosphate activating agent and an acylating agent. With multiple rounds of this energy-dissipative recycling, we show that all-3',5'-linked duplex RNA can emerge from a backbone heterogeneous mixture, thereby delineating a route that could have driven RNA evolution on the early earth.
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Affiliation(s)
- Angelica Mariani
- PNACMRC Laboratory of Molecular BiologyFrancis Crick Avenue, Cambridge Biomedical CampusCambridgeCB2 0QHUK
| | - John D. Sutherland
- PNACMRC Laboratory of Molecular BiologyFrancis Crick Avenue, Cambridge Biomedical CampusCambridgeCB2 0QHUK
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24
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Mariani A, Sutherland JD. Non-Enzymatic RNA Backbone Proofreading through Energy-Dissipative Recycling. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Angelica Mariani
- PNAC; MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge Biomedical Campus Cambridge CB2 0QH UK
| | - John D. Sutherland
- PNAC; MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge Biomedical Campus Cambridge CB2 0QH UK
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25
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26
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Rana AK, Ankri S. Reviving the RNA World: An Insight into the Appearance of RNA Methyltransferases. Front Genet 2016; 7:99. [PMID: 27375676 PMCID: PMC4893491 DOI: 10.3389/fgene.2016.00099] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/23/2016] [Indexed: 12/13/2022] Open
Abstract
RNA, the earliest genetic and catalytic molecule, has a relatively delicate and labile chemical structure, when compared to DNA. It is prone to be damaged by alkali, heat, nucleases, or stress conditions. One mechanism to protect RNA or DNA from damage is through site-specific methylation. Here, we propose that RNA methylation began prior to DNA methylation in the early forms of life evolving on Earth. In this article, the biochemical properties of some RNA methyltransferases (MTases), such as 2′-O-MTases (Rlml/RlmN), spOUT MTases and the NSun2 MTases are dissected for the insight they provide on the transition from an RNA world to our present RNA/DNA/protein world.
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Affiliation(s)
- Ajay K Rana
- Division of Biology, State Forensic Science Laboratory, Ministry of Home Affairs, Government of Jharkhand Ranchi, India
| | - Serge Ankri
- Department of Molecular Microbiology, The Ruth and Bruce Rappaport Faculty of Medicine, Technion Israel Institute of Technology Haifa, Israel
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27
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Dogandzhiyski P, Ghidini A, Danneberg F, Strömberg R, Göbel MW. Studies on Tris(2-aminobenzimidazole)-PNA Based Artificial Nucleases: A Comparison of Two Analytical Techniques. Bioconjug Chem 2015; 26:2514-9. [PMID: 26544527 DOI: 10.1021/acs.bioconjchem.5b00534] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A new peptide nucleic acid (PNA) construct carrying a tris(2-aminobenzimidazole) phosphodiester cleaver is presented. This non-metal-based artificial nuclease hydrolyzes RNA substrates that form a bulge upon binding to the PNA. Reaction rates depend on the bulge sequence. For conjugates of tris(2-aminobenzimidazole), substrate turnover is shown for the first time. Two methods of analysis for the kinetics are compared: IE-HPLC separation of oligonucleotide fragments and analysis of Cy5-labeled oligonucleotide fragments by denaturating PAGE on a DNA sequencer, respectively. The different methods give rates that are in the same range where, in general, the substrates for the sequencer method give slightly lower rates.
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Affiliation(s)
- Plamena Dogandzhiyski
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt , Max-von-Laue-Str. 7, D-60439 Frankfurt am Main, Germany
| | - Alice Ghidini
- Department of Biosciences and Nutrition, Karolinska Institutet , Novum, S-14157, Huddinge, Sweden
| | - Friederike Danneberg
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt , Max-von-Laue-Str. 7, D-60439 Frankfurt am Main, Germany
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet , Novum, S-14157, Huddinge, Sweden
| | - Michael W Göbel
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt , Max-von-Laue-Str. 7, D-60439 Frankfurt am Main, Germany
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28
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Li S, Lünse CE, Harris KA, Breaker RR. Biochemical analysis of hatchet self-cleaving ribozymes. RNA (NEW YORK, N.Y.) 2015; 21:1845-1851. [PMID: 26385510 PMCID: PMC4604424 DOI: 10.1261/rna.052522.115] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 06/22/2015] [Indexed: 06/01/2023]
Abstract
Hatchet RNAs are members of a novel self-cleaving ribozyme class that was recently discovered by using a bioinformatics search strategy. The consensus sequence and secondary structure of this class includes 13 highly conserved and numerous other modestly conserved nucleotides interspersed among bulges linking four base-paired substructures. A representative hatchet ribozyme from a metagenomic source requires divalent ions such as Mg(2+) to promote RNA strand scission with a maximum rate constant of ∼4 min(-1). As with all other small self-cleaving ribozymes discovered to date, hatchet ribozymes employ a general mechanism for catalysis involving the nucleophilic attack of a ribose 2'-oxygen atom on an adjacent phosphorus center. Kinetic characteristics of the reaction demonstrate that members of this ribozyme class have an essential requirement for divalent metal ions and that they might have a complex active site that employs multiple catalytic strategies to accelerate RNA cleavage by internal phosphoester transfer.
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Affiliation(s)
- Sanshu Li
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Christina E Lünse
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Kimberly A Harris
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Ronald R Breaker
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103, USA
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Xu L, Wang W, Chong J, Shin JH, Xu J, Wang D. RNA polymerase II transcriptional fidelity control and its functional interplay with DNA modifications. Crit Rev Biochem Mol Biol 2015; 50:503-19. [PMID: 26392149 DOI: 10.3109/10409238.2015.1087960] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Accurate genetic information transfer is essential for life. As a key enzyme involved in the first step of gene expression, RNA polymerase II (Pol II) must maintain high transcriptional fidelity while it reads along DNA template and synthesizes RNA transcript in a stepwise manner during transcription elongation. DNA lesions or modifications may lead to significant changes in transcriptional fidelity or transcription elongation dynamics. In this review, we will summarize recent progress toward understanding the molecular basis of RNA Pol II transcriptional fidelity control and impacts of DNA lesions and modifications on Pol II transcription elongation.
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Affiliation(s)
- Liang Xu
- a Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego , La Jolla , CA , USA
| | - Wei Wang
- a Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego , La Jolla , CA , USA
| | - Jenny Chong
- a Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego , La Jolla , CA , USA
| | - Ji Hyun Shin
- a Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego , La Jolla , CA , USA
| | - Jun Xu
- a Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego , La Jolla , CA , USA
| | - Dong Wang
- a Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego , La Jolla , CA , USA
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Cleaves HJ, Meringer M, Goodwin J. 227 Views of RNA: Is RNA Unique in Its Chemical Isomer Space? ASTROBIOLOGY 2015; 15. [PMID: 26200431 PMCID: PMC4523004 DOI: 10.1089/ast.2014.1213] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Ribonucleic acid (RNA) is one of the two nucleic acids used by extant biochemistry and plays a central role as the intermediary carrier of genetic information in transcription and translation. If RNA was involved in the origin of life, it should have a facile prebiotic synthesis. A wide variety of such syntheses have been explored. However, to date no one-pot reaction has been shown capable of yielding RNA monomers from likely prebiotically abundant starting materials, though this does not rule out the possibility that simpler, more easily prebiotically accessible nucleic acids may have preceded RNA. Given structural constraints, such as the ability to form complementary base pairs and a linear covalent polymer, a variety of structural isomers of RNA could potentially function as genetic platforms. By using structure-generation software, all the potential structural isomers of the ribosides (BC5H9O4, where B is nucleobase), as well as a set of simpler minimal analogues derived from them, that can potentially serve as monomeric building blocks of nucleic acid-like molecules are enumerated. Molecules are selected based on their likely stability under biochemically relevant conditions (e.g., moderate pH and temperature) and the presence of at least two functional groups allowing the monomers to be incorporated into linear polymers. The resulting structures are then evaluated by using molecular descriptors typically applied in quantitative structure-property relationship (QSPR) studies and predicted physicochemical properties. Several databases have been queried to determine whether any of the computed isomers had been synthesized previously. Very few of the molecules that emerge from this structure set have been previously described. We conclude that ribonucleosides may have competed with a multitude of alternative structures whose potential proto-biochemical roles and abiotic syntheses remain to be explored.
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Affiliation(s)
- H. James Cleaves
- Earth-Life Science Institute (ELSI), Tokyo Institute of Technology, Tokyo, Japan
- Institute for Advanced Study, Princeton, New Jersey, USA
- Blue Marble Space Institute of Science, Washington, DC, USA
- Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Markus Meringer
- German Aerospace Center (DLR), Earth Observation Center (EOC), Oberpfaffenhofen-Wessling, Germany
| | - Jay Goodwin
- Department of Chemistry, Emory University, Atlanta, Georgia, USA
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Xu L, Wang W, Zhang L, Chong J, Huang X, Wang D. Impact of template backbone heterogeneity on RNA polymerase II transcription. Nucleic Acids Res 2015; 43:2232-41. [PMID: 25662224 PMCID: PMC4344504 DOI: 10.1093/nar/gkv059] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 01/15/2015] [Accepted: 01/16/2015] [Indexed: 02/03/2023] Open
Abstract
Variations in the sugar component (ribose or deoxyribose) and the nature of the phosphodiester linkage (3'-5' or 2'-5' orientation) have been a challenge for genetic information transfer from the very beginning of evolution. RNA polymerase II (pol II) governs the transcription of DNA into precursor mRNA in all eukaryotic cells. How pol II recognizes DNA template backbone (phosphodiester linkage and sugar) and whether it tolerates the backbone heterogeneity remain elusive. Such knowledge is not only important for elucidating the chemical basis of transcriptional fidelity but also provides new insights into molecular evolution. In this study, we systematically and quantitatively investigated pol II transcriptional behaviors through different template backbone variants. We revealed that pol II can well tolerate and bypass sugar heterogeneity sites at the template but stalls at phosphodiester linkage heterogeneity sites. The distinct impacts of these two backbone components on pol II transcription reveal the molecular basis of template recognition during pol II transcription and provide the evolutionary insight from the RNA world to the contemporary 'imperfect' DNA world. In addition, our results also reveal the transcriptional consequences from ribose-containing genomic DNA.
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Affiliation(s)
- Liang Xu
- Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego, La Jolla, CA 92093-0625, USA
| | - Wei Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego, La Jolla, CA 92093-0625, USA
| | - Lu Zhang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Jenny Chong
- Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego, La Jolla, CA 92093-0625, USA
| | - Xuhui Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Dong Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego, La Jolla, CA 92093-0625, USA
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Strand-specific (asymmetric) contribution of phosphodiester linkages on RNA polymerase II transcriptional efficiency and fidelity. Proc Natl Acad Sci U S A 2014; 111:E3269-76. [PMID: 25074911 DOI: 10.1073/pnas.1406234111] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Nonenzymatic RNA polymerization in early life is likely to introduce backbone heterogeneity with a mixture of 2'-5' and 3'-5' linkages. On the other hand, modern nucleic acids are dominantly composed of 3'-5' linkages. RNA polymerase II (pol II) is a key modern enzyme responsible for synthesizing 3'-5'-linked RNA with high fidelity. It is not clear how modern enzymes, such as pol II, selectively recognize 3'-5' linkages over 2'-5' linkages of nucleic acids. In this work, we systematically investigated how phosphodiester linkages of nucleic acids govern pol II transcriptional efficiency and fidelity. Through dissecting the impacts of 2'-5' linkage mutants in the pol II catalytic site, we revealed that the presence of 2'-5' linkage in RNA primer only modestly reduces pol II transcriptional efficiency without affecting pol II transcriptional fidelity. In sharp contrast, the presence of 2'-5' linkage in DNA template leads to dramatic decreases in both transcriptional efficiency and fidelity. These distinct effects reveal that pol II has an asymmetric (strand-specific) recognition of phosphodiester linkage. Our results provided important insights into pol II transcriptional fidelity, suggesting essential contributions of phosphodiester linkage to pol II transcription. Finally, our results also provided important understanding on the molecular basis of nucleic acid recognition and genetic information transfer during molecular evolution. We suggest that the asymmetric recognition of phosphodiester linkage by modern nucleic acid enzymes likely stems from the distinct evolutionary pressures of template and primer strand in genetic information transfer during molecular evolution.
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Xu J, Duffy CD, Chan CKW, Sutherland JD. Solid-phase synthesis and hybrization behavior of partially 2'/3'-O-acetylated RNA oligonucleotides. J Org Chem 2014; 79:3311-26. [PMID: 24666354 PMCID: PMC4323357 DOI: 10.1021/jo5002824] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Indexed: 11/30/2022]
Abstract
Synthesis of partially 2'/3'-O-acetylated oligoribonucleotides has been accomplished by using a 2'/3'-O-acetyl orthogonal protecting group strategy in which non-nucleophilic strong-base (DBU) labile nucleobase protecting groups and a UV-light cleavable linker were used. Strong-base stability of the photolabile linker allowed on-column nucleobase and phosphate deprotection, followed by a mild cleavage of the acetylated oligonucleotides from the solid support with UV light. Two 17nt oligonucleotides, which were synthesized possessing one specific internal 2'- or 3'-acetyl group, were used as synthetic standards in a recent report from this laboratory detailing the prebiotically plausible ligation of RNA oligonucleotides. In order to further investigate the effect of 2'/3'-O-acetyl groups on the stability of RNA duplex structure, two complementary bis-acetylated RNA oligonucleotides were also expediently obtained with the newly developed protocols. UV melting curves of 2'-O-acetylated RNA duplexes showed a consistent ~3.1 °C decrease in Tm per 2'-O-acetyl group.
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Affiliation(s)
- Jianfeng Xu
- Medical Research Council
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K.
| | - Colm D. Duffy
- Medical Research Council
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K.
| | - Christopher K. W. Chan
- Medical Research Council
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K.
| | - John D. Sutherland
- Medical Research Council
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K.
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Structural insights into the effects of 2'-5' linkages on the RNA duplex. Proc Natl Acad Sci U S A 2014; 111:3050-5. [PMID: 24516151 DOI: 10.1073/pnas.1317799111] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The mixture of 2'-5' and 3'-5' linkages generated during the nonenzymatic replication of RNA has long been regarded as a central problem for the origin of the RNA world. However, we recently observed that both a ribozyme and an RNA aptamer retain considerable functionality in the presence of prebiotically plausible levels of linkage heterogeneity. To better understand the RNA structure and function in the presence of backbone linkage heterogeneity, we obtained high-resolution X-ray crystal structures of a native 10-mer RNA duplex (1.32 Å) and two variants: one containing one 2'-5' linkage per strand (1.55 Å) and one containing three such linkages per strand (1.20 Å). We found that RNA duplexes adjust their local structures to accommodate the perturbation caused by 2'-5' linkages, with the flanking nucleotides buffering the disruptive effects of the isomeric linkage and resulting in a minimally altered global structure. Although most 2'-linked sugars were in the expected 2'-endo conformation, some were partially or fully in the 3'-endo conformation, suggesting that the energy difference between these conformations was relatively small. Our structural and molecular dynamic studies also provide insight into the diminished thermal and chemical stability of the duplex state associated with the presence of 2'-5' linkages. Our results contribute to the view that a low level of 2'-5' substitution would not have been fatal in an early RNA world and may in contrast have been helpful for both the emergence of nonenzymatic RNA replication and the early evolution of functional RNAs.
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35
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Functional RNAs exhibit tolerance for non-heritable 2'-5' versus 3'-5' backbone heterogeneity. Nat Chem 2013; 5:390-4. [PMID: 23609089 PMCID: PMC4088963 DOI: 10.1038/nchem.1623] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 03/12/2013] [Indexed: 11/08/2022]
Abstract
A plausible process for non-enzymatic RNA replication would greatly simplify models of the transition from prebiotic chemistry to simple biology. However, all known conditions for the chemical copying of an RNA template result in the synthesis of a complementary strand that contains a mixture of 2'-5' and 3'-5' linkages, rather than the selective synthesis of only 3'-5' linkages as found in contemporary RNA. Here we show that such backbone heterogeneity is compatible with RNA folding into defined three-dimensional structures that retain molecular recognition and catalytic properties and, therefore, would not prevent the evolution of functional RNAs such as ribozymes. Moreover, the same backbone heterogeneity lowers the melting temperature of RNA duplexes that would otherwise be too stable for thermal strand separation. By allowing copied strands to dissociate, this heterogeneity may have been one of the essential features that allowed RNA to emerge as the first biopolymer.
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36
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Di Mauro E, Saladino R, Trifonov EN. The path to life's origins. Remaining hurdles. J Biomol Struct Dyn 2013; 32:512-22. [PMID: 23582097 DOI: 10.1080/07391102.2013.783509] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Recent progress in abiotic syntheses, especially self-catalytic syntheses, as well as theoretical breakthroughs such as reconstruction of events of early molecular evolution and tracing repeat expansions in contemporary genomes, converge to a rather simple possible scenario of origin of life, notwithstanding the enormity of the problem. The scenario includes self-replicating RNA duplexes, supplemented by monomers and high-energy compounds that, as demonstrated or assumed, can all be synthesized abiotically. The self-replication would proceed with occasional mutational changes, propagated in later cycles. This audacious, as it may seem, walk toward the life origin already involves many laboratories, each exploring its own scenario. The one suggested in this outline seems to the authors well justified to engage in, while bypassing few steps to deal with later.
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Affiliation(s)
- Ernesto Di Mauro
- a Dipartimento di, Biologia e Biotecnologie "Charles Darwin" , Istituto Pasteur "Fondazione Cenci-Bolognetti", "Sapienza" Universita' , di Roma, P.leAldo Moro, 5, Rome , 00185 , Italy
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37
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Bowler FR, Chan CKW, Duffy CD, Gerland B, Islam S, Powner MW, Sutherland JD, Xu J. Prebiotically plausible oligoribonucleotide ligation facilitated by chemoselective acetylation. Nat Chem 2013; 5:383-9. [PMID: 23609088 DOI: 10.1038/nchem.1626] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 03/14/2013] [Indexed: 11/09/2022]
Abstract
The recent synthesis of pyrimidine ribonucleoside-2',3'-cyclic phosphates under prebiotically plausible conditions has strengthened the case for the involvement of ribonucleic acid (RNA) at an early stage in the origin of life. However, a prebiotic conversion of these weakly activated monomers, and their purine counterparts, to the 3',5'-linked RNA polymers of extant biochemistry has been lacking (previous attempts led only to short oligomers with mixed linkages). Here we show that the 2'-hydroxyl group of oligoribonucleotide-3'-phosphates can be chemoselectively acetylated in water under prebiotically credible conditions, which allows rapid and efficient template-directed ligation. The 2'-O-acetyl group at the ligation junction of the product RNA strand can be removed under conditions that leave the internucleotide bonds intact. Remarkably, acetylation of mixed oligomers that possess either 2'- or 3'-terminal phosphates is selective for the 2'-hydroxyl group of the latter. This newly discovered chemistry thus suggests a prebiotic route from ribonucleoside-2',3'-cyclic phosphates to predominantly 3',5'-linked RNA via partially 2'-O-acetylated RNA.
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Affiliation(s)
- Frank R Bowler
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
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38
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Lönnberg TA. Can phosphate-branched RNA persist under physiological conditions? Chembiochem 2012; 13:2690-700. [PMID: 23255258 DOI: 10.1002/cbic.201200629] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Indexed: 11/10/2022]
Abstract
A 2'-O-methyl-RNA oligonucleotide containing a single free 2'-OH group flanking a branching phosphotriester linkage was prepared as a model for phosphate-branched RNA by using an orthogonally protected dimeric phosphoramidite building block in solid-phase synthesis. The strategy allows the synthesis of phosphate-branched oligonucleotides, the three branches of which may be of any desired sequence. Hydrolytic reactions of the phosphotriester linkages in such oligonucleotides were studied at physiological pH in the presence (and absence) of various complementary oligonucleotides. The fully hybridized oligonucleotide model is an order of magnitude more stable than its single-stranded counterpart, which, in turn, is an order of magnitude more stable than its trinucleoside phosphotriester core lacking any oligonucleotide arms. Furthermore, kinked structures obtained by hybridizing the phosphate-branched oligonucleotide with partially complementary oligonucleotides are three to five times more stable than fully double-stranded ones and only approximately three times less stable than the so-called RNA X structure, which has been postulated to incorporate an RNA phosphotriester linkage. The results indicate that when the intrinsically unstable RNA phosphotriester linkage is embedded in an oligonucleotide of appropriate tertiary structure, its half-life can be at least several hours.
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39
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Saladino R, Botta G, Pino S, Costanzo G, Di Mauro E. Genetics first or metabolism first? The formamide clue. Chem Soc Rev 2012; 41:5526-65. [PMID: 22684046 DOI: 10.1039/c2cs35066a] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Life is made of the intimate interaction of metabolism and genetics, both built around the chemistry of the most common elements of the Universe (hydrogen, oxygen, nitrogen, and carbon). The transmissible interaction of metabolic and genetic cycles results in the hypercycles of organization and de-organization of chemical information, of living and non-living. The origin-of-life quest has long been split into several attitudes exemplified by the aphorisms "genetics-first" or "metabolism-first". Recently, the opposition between these approaches has been solved by more unitary theoretical and experimental frames taking into account energetic, evolutionary, proto-metabolic and environmental aspects. Nevertheless, a unitary and simple chemical frame is still needed that could afford both the precursors of the synthetic pathways eventually leading to RNA and to the key components of the central metabolic cycles, possibly connected with the synthesis of fatty acids. In order to approach the problem of the origin of life it is therefore reasonable to start from the assumption that both metabolism and genetics had a common origin, shared a common chemical frame, and were embedded under physical-chemical conditions favourable for the onset of both. The singleness of such a prebiotically productive chemical process would partake of Darwinian advantages over more complex fragmentary chemical systems. The prebiotic chemistry of formamide affords in a single and simple physical-chemical frame nucleic bases, acyclonucleosides, nucleotides, biogenic carboxylic acids, sugars, amino sugars, amino acids and condensing agents. Thus, we suggest the possibility that formamide could have jointly provided the main components for the onset of both (pre)genetic and (pre)metabolic processes. As a note of caution, we discuss the fact that these observations only indicate possible solutions at the level of organic substrates, not at the systemic chemical level.
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Affiliation(s)
- Raffaele Saladino
- Dipartimento di Agrobiologia ed Agrochimica, Università della Tuscia, Via San Camillo De Lellis, 01100 Viterbo, Italy.
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40
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Saladino R, Crestini C, Pino S, Costanzo G, Di Mauro E. Formamide and the origin of life. Phys Life Rev 2012; 9:84-104. [DOI: 10.1016/j.plrev.2011.12.002] [Citation(s) in RCA: 194] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Accepted: 12/06/2011] [Indexed: 11/16/2022]
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41
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Saladino R, Crestini C, Pino S, Costanzo G, Di Mauro E. Formamide in non-life/life transition. Phys Life Rev 2012. [DOI: 10.1016/j.plrev.2012.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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42
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Saladino R, Botta G, Pino S, Costanzo G, Di Mauro E. From the one-carbon amide formamide to RNA all the steps are prebiotically possible. Biochimie 2012; 94:1451-6. [PMID: 22738728 DOI: 10.1016/j.biochi.2012.02.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 02/16/2012] [Indexed: 01/07/2023]
Abstract
Formamide provides the raw material and the reaction leads connecting hydrogen cyanide HCN chemistry with higher complexity molecular structures. Formamide is liquid between 4 and 210 °C and, upon heating in the presence of one of several catalysts, affords nucleic bases, acyclonucleosides, carboxylic acids and aminoacids. In formamide in the presence of a source of phosphate, nucleosides are non-fastidiously phosphorylated in every position of the sugar residue, also yielding cyclic nucleotides. Guanine 3',5' cyclic nucleotide monophosphates polymerize to oligonucleotides, up to 30 nucleotides long. Adenine 3',5' cyclic nucleotide monophosphate reacts similarly but less efficiently. Preformed oligonucleotides may undergo terminal ligation in the absence of enzymes, thus allowing the formation of abiotically obtained long RNA chains.
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Affiliation(s)
- Raffaele Saladino
- Dipartimento di Agrobiologia ed Agrochimica, Università della Tuscia, Via San Camillo De Lellis, 01100 Viterbo, Italy
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43
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44
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Lönnberg TA, Helkearo M, Jancsó A, Gajda T. Mimics of small ribozymes utilizing a supramolecular scaffold. Dalton Trans 2012; 41:3328-38. [DOI: 10.1039/c2dt10193a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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45
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Eschenmoser A. Ätiologie potentiell primordialer Biomolekül-Strukturen: Vom Vitamin B12 zu den Nukleinsäuren und der Frage nach der Chemie der Entstehung des Lebens - ein Rückblick. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103672] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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46
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Eschenmoser A. Etiology of potentially primordial biomolecular structures: from vitamin B12 to the nucleic acids and an inquiry into the chemistry of life's origin: a retrospective. Angew Chem Int Ed Engl 2011; 50:12412-72. [PMID: 22162284 DOI: 10.1002/anie.201103672] [Citation(s) in RCA: 135] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Indexed: 11/10/2022]
Abstract
"We'll never be able to know" is a truism that leads to resignation with respect to any experimental effort to search for the chemistry of life's origin. But such resignation runs radically counter to the challenge imposed upon chemistry as a natural science. Notwithstanding the prognosis according to which the shortest path to understanding the metamorphosis of the chemical into the biological is by way of experimental modeling of "artificial chemical life", the scientific search for the route nature adopted in creating the life we know will arguably never truly end. It is, after all, part of the search for our own origin.
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Affiliation(s)
- Albert Eschenmoser
- Organisch-chemisches Laboratorium der ETH Zürich, Hönggerberg, Wolfgang-Pauli-Str. 10, CHI H309, CH-8093 Zürich, Switzerland
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47
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Lönnberg T, Kero KM. Impact of steric constraints on the product distribution of phosphate-branched oligonucleotide models of the large ribozymes. Org Biomol Chem 2011; 10:569-74. [PMID: 22113401 DOI: 10.1039/c1ob06399e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To assess the extent to which steric constraints may influence the product distribution of the reactions of the large ribozymes, phosphate-branched oligonucleotides of varying length and sequence have been synthesized and their alkaline hydrolysis studied over a wide temperature range. At low temperatures, the branching trinucleoside-3',3',5'-monophosphate moiety is hydrolyzed almost exclusively by P-O3' fission. At higher temperatures, P-O5' fission competes, accounting at most for 22% of the overall reaction. The results suggest that steric constraints imposed by the secondary structure of the reaction site may significantly contribute to the observed regioselectivity of the transesterification reactions catalyzed by the large ribozymes.
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Affiliation(s)
- Tuomas Lönnberg
- Department of Chemistry, University of Turku, FIN-20014, Turku, Finland.
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48
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Saleh AD, Miller PS. Hydrolysis of bulged nucleotides in hybrids formed by RNA and imidazole-derivatized oligo-2'-O-methylribonucleotides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2011; 30:235-55. [PMID: 21491332 DOI: 10.1080/15257770.2011.569810] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In order to enhance the efficacy of small antisense molecules, we examined a series of antisense oligonucleotides derivatized with functional groups designed to enable them to hydrolyze their RNA target. Solid phase synthetic methods were used to prepare imidazole-derivatized antisense oligo-2'-O-methylribonucleotides. Upon binding, these oligonucleotides create internal bulged bases in the target RNA that serve as sites for hydrolysis. We observed that an oligonucleotide derivatized with a side chain containing two imidazole groups was capable of hydrolyzing 58% of its RNA target when incubated with the target for 48 hours at 37°C and physiological pH.
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Affiliation(s)
- Anthony D Saleh
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA
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49
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Obermayer B, Krammer H, Braun D, Gerland U. Emergence of information transmission in a prebiotic RNA reactor. PHYSICAL REVIEW LETTERS 2011; 107:018101. [PMID: 21797574 DOI: 10.1103/physrevlett.107.018101] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Indexed: 05/31/2023]
Abstract
A poorly understood step in the transition from a chemical to a biological world is the emergence of self-replicating molecular systems. We study how a precursor for such a replicator might arise in a hydrothermal RNA reactor, which accumulates longer sequences from unbiased monomer influx and random ligation. In the reactor, intra- and intermolecular base pairing locally protects from random cleavage. By analyzing stochastic simulations, we find temporal sequence correlations that constitute a signature of information transmission, weaker but of the same form as in a true replicator.
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Affiliation(s)
- Benedikt Obermayer
- Arnold-Sommerfeld-Center für Theoretische Physik and Center for NanoScience, Ludwig-Maximilians-Universität München, Germany
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50
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Abstract
Since the structure of DNA was elucidated more than 50 years ago, Watson-Crick base pairing has been widely speculated to be the likely mode of both information storage and transfer in the earliest genetic polymers. The discovery of catalytic RNA molecules subsequently provided support for the hypothesis that RNA was perhaps even the first polymer of life. However, the de novo synthesis of RNA using only plausible prebiotic chemistry has proven difficult, to say the least. Experimental investigations, made possible by the application of synthetic and physical organic chemistry, have now provided evidence that the nucleobases (A, G, C, and T/U), the trifunctional moiety ([deoxy]ribose), and the linkage chemistry (phosphate esters) of contemporary nucleic acids may be optimally suited for their present roles-a situation that suggests refinement by evolution. Here, we consider studies of variations in these three distinct components of nucleic acids with regard to the question: Is RNA, as is generally acknowledged of DNA, the product of evolution? If so, what chemical and structural features might have been more likely and advantageous for a proto-RNA?
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Affiliation(s)
- Aaron E Engelhart
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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