1
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Wu LF, Liu Z, Roberts SJ, Su M, Szostak JW, Sutherland JD. Template-Free Assembly of Functional RNAs by Loop-Closing Ligation. J Am Chem Soc 2022; 144:13920-13927. [PMID: 35880790 PMCID: PMC9354263 DOI: 10.1021/jacs.2c05601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The first ribozymes are thought to have emerged at a time when RNA replication proceeded via nonenzymatic template copying processes. However, functional RNAs have stable folded structures, and such structures are much more difficult to copy than short unstructured RNAs. How can these conflicting requirements be reconciled? Also, how can the inhibition of ribozyme function by complementary template strands be avoided or minimized? Here, we show that short RNA duplexes with single-stranded overhangs can be converted into RNA stem loops by nonenzymatic cross-strand ligation. We then show that loop-closing ligation reactions enable the assembly of full-length functional ribozymes without any external template. Thus, one can envisage a potential pathway whereby structurally complex functional RNAs could have formed at an early stage of evolution when protocell genomes might have consisted only of collections of short replicating oligonucleotides.
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Affiliation(s)
- Long-Fei Wu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom.,Department of Molecular Biology and Center for Computational and Integrative Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Ziwei Liu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Samuel J Roberts
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Meng Su
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Jack W Szostak
- Department of Molecular Biology and Center for Computational and Integrative Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - John D Sutherland
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
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2
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Leveau G, Pfeffer D, Altaner B, Kervio E, Welsch F, Gerland U, Richert C. Enzyme-Free Copying of 12 Bases of RNA with Dinucleotides. Angew Chem Int Ed Engl 2022; 61:e202203067. [PMID: 35445525 PMCID: PMC9401581 DOI: 10.1002/anie.202203067] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Indexed: 11/08/2022]
Abstract
The synthesis of complementary strands is the reaction underlying the replication of genetic information. It is likely that the earliest self-replicating systems used RNA as genetic material. How RNA was copied in the absence of enzymes and what sequences were most likely to have supported replication is not clear. Here we show that mixtures of dinucleotides with C and G as bases copy an RNA sequence of up to 12 nucleotides in dilute aqueous solution. Successful enzyme-free copying occurred with in situ activation at 4 °C and pH 6.0. Dimers were incorporated in favor of monomers when both competed as reactants, and little misincorporation was detectable in mass spectra. Simulations using experimental rate constants confirmed that mixed C/G sequences are good candidates for successful replication with dimers. Because dimers are intermediates in the synthesis of longer strands, our results support evolutionary scenarios encompassing formation and copying of RNA strands in enzyme-free fashion.
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Affiliation(s)
- Gabrielle Leveau
- Institute of Organic ChemistryUniversity of Stuttgart70569StuttgartGermany
| | - Daniel Pfeffer
- Institute of Organic ChemistryUniversity of Stuttgart70569StuttgartGermany
| | - Bernhard Altaner
- Physics of Complex BiosystemsTechnical University Munich85748GarchingGermany
| | - Eric Kervio
- Institute of Organic ChemistryUniversity of Stuttgart70569StuttgartGermany
| | - Franziska Welsch
- Institute of Organic ChemistryUniversity of Stuttgart70569StuttgartGermany
| | - Ulrich Gerland
- Physics of Complex BiosystemsTechnical University Munich85748GarchingGermany
| | - Clemens Richert
- Institute of Organic ChemistryUniversity of Stuttgart70569StuttgartGermany
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3
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Richert C, Leveau G, Pfeffer D, Altaner B, Kervio E, Gerland U, Welsch F. Enzyme‐Free Copying of 12 Bases of RNA with Dinucleotides. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Clemens Richert
- Universität Stuttgart Institut für Organische Chemie Pfaffenwaldring 55 70569 Stuttgart GERMANY
| | - Gabrielle Leveau
- University of Stuttgart: Universitat Stuttgart Chemistry GERMANY
| | - Daniel Pfeffer
- University of Stuttgart: Universitat Stuttgart Chemistry GERMANY
| | | | - Eric Kervio
- University of Stuttgart: Universitat Stuttgart Chemistry GERMANY
| | - Ulrich Gerland
- TU Munchen: Technische Universitat Munchen Physics GERMANY
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4
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Jia TZ, Nishikawa S, Fujishima K. Sequencing the Origins of Life. BBA ADVANCES 2022; 2:100049. [PMID: 37082609 PMCID: PMC10074849 DOI: 10.1016/j.bbadva.2022.100049] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/27/2022] [Accepted: 03/02/2022] [Indexed: 01/10/2023] Open
Abstract
One goal of origins of life research is to understand how primitive informational and catalytic biopolymers emerged and evolved. Recently, a number of sequencing techniques have been applied to analysis of replicating and evolving primitive biopolymer systems, providing a sequence-specific and high-resolution view of primitive chemical processes. Here, we review application of sequencing techniques to analysis of synthetic and primitive nucleic acids and polypeptides. This includes next-generation sequencing of primitive polymerization and evolution processes, followed by discussion of other novel biochemical techniques that could contribute to sequence analysis of primitive biopolymer driven chemical systems. Further application of sequencing to origins of life research, perhaps as a life detection technology, could provide insight into the origin and evolution of informational and catalytic biopolymers on early Earth or elsewhere.
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Affiliation(s)
- Tony Z. Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Blue Marble Space Institute of Science, 600 1st Ave, Floor 1, Seattle, WA 98104, USA
- Corresponding author
| | - Shota Nishikawa
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa-shi, Kanagawa 252-0882, Japan
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5
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Fried SD, Fujishima K, Makarov M, Cherepashuk I, Hlouchova K. Peptides before and during the nucleotide world: an origins story emphasizing cooperation between proteins and nucleic acids. J R Soc Interface 2022; 19:20210641. [PMID: 35135297 PMCID: PMC8833103 DOI: 10.1098/rsif.2021.0641] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 01/05/2022] [Indexed: 12/14/2022] Open
Abstract
Recent developments in Origins of Life research have focused on substantiating the narrative of an abiotic emergence of nucleic acids from organic molecules of low molecular weight, a paradigm that typically sidelines the roles of peptides. Nevertheless, the simple synthesis of amino acids, the facile nature of their activation and condensation, their ability to recognize metals and cofactors and their remarkable capacity to self-assemble make peptides (and their analogues) favourable candidates for one of the earliest functional polymers. In this mini-review, we explore the ramifications of this hypothesis. Diverse lines of research in molecular biology, bioinformatics, geochemistry, biophysics and astrobiology provide clues about the progression and early evolution of proteins, and lend credence to the idea that early peptides served many central prebiotic roles before they were encodable by a polynucleotide template, in a putative 'peptide-polynucleotide stage'. For example, early peptides and mini-proteins could have served as catalysts, compartments and structural hubs. In sum, we shed light on the role of early peptides and small proteins before and during the nucleotide world, in which nascent life fully grasped the potential of primordial proteins, and which has left an imprint on the idiosyncratic properties of extant proteins.
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Affiliation(s)
- Stephen D. Fried
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21212, USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21212, USA
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 1528550, Japan
- Graduate School of Media and Governance, Keio University, Fujisawa 2520882, Japan
| | - Mikhail Makarov
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12800, Czech Republic
| | - Ivan Cherepashuk
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12800, Czech Republic
| | - Klara Hlouchova
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12800, Czech Republic
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 16610, Czech Republic
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6
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Kim HJ, Benner SA. Abiotic Synthesis of Nucleoside 5'-Triphosphates with Nickel Borate and Cyclic Trimetaphosphate (CTMP). ASTROBIOLOGY 2021; 21:298-306. [PMID: 33533695 DOI: 10.1089/ast.2020.2264] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
While nucleoside 5'-triphosphates are precursors for RNA in modern biology, the presumed difficulty of making these triphosphates on Hadean Earth has caused many prebiotic researchers to consider other activated species for the prebiotic synthesis of RNA. We report here that nickel(II), in the presence of borate, gives substantial amounts (2-3%) of nucleoside 5'-triphosphates upon evaporative heating in the presence of urea, salts, and cyclic trimetaphosphate (CTMP). Also recovered are nucleoside 5'-diphosphates and nucleoside 5'-monophosphates, both likely arising from 5'-triphosphate intermediates. The total level of 5'-phosphorylation is typically 30%. Borate enhances the regiospecificity of phosphorylation, with increased amounts of other phosphorylated species seen in its absence. Experimentally supported paths are already available to make nucleosides in environments likely to have been present on Hadean Earth soon after a midsized 1021 to 1023 kg impactor, which would also have delivered nickel to the Hadean surface. Further, sources of prebiotic CTMP continue to be proposed. Thus, these results fill in one of the few remaining steps needed to demystify the prebiotic synthesis of RNA and support a continuous model from atmospheric components to oligomeric RNA that is lacking only a mechanism to obtain homochirality in the product RNA.
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Affiliation(s)
- Hyo-Joong Kim
- Foundation for Applied Molecular Evolution and Firebird Biomolecular Sciences LLC, Alachua, Florida, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution and Firebird Biomolecular Sciences LLC, Alachua, Florida, USA
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7
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Ertem G. The Role of Minerals in Events That Led to the Origin of Life. ASTROBIOLOGY 2021; 21:137-150. [PMID: 33544652 DOI: 10.1089/ast.2020.2245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The role of minerals in the events that led to the origin of life is discussed with regard to (1) their catalytic role for the formation of RNA-like oligomers from their monomers and (2) their protective role for organic molecules formed in space that were delivered to planetary surfaces. Results obtained in the laboratory demonstrate that minerals do catalyze the oligomerization of ribonucleic acid (RNA) monomers to produce short RNA chains. Furthermore, and more importantly, these synthetic RNA chains formed by mineral catalysis serve as a template for the formation of complementary RNA chains, which is a significant finding that demonstrates the role of minerals in the origin of life. Simulation experiments run under Mars-like conditions have also shown that Mars analog minerals can shield the precursors of RNA and proteins against the harmful effects of UV and gamma radiation at the martian surface and 5 cm below the surface.
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Affiliation(s)
- Gözen Ertem
- Carl Sagan Center, SETI Institute, Mountain View, California, USA
- University of Maryland, College Park, Maryland, USA
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8
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Walton T, DasGupta S, Duzdevich D, Oh SS, Szostak JW. In vitro selection of ribozyme ligases that use prebiotically plausible 2-aminoimidazole-activated substrates. Proc Natl Acad Sci U S A 2020; 117:5741-5748. [PMID: 32123094 PMCID: PMC7084097 DOI: 10.1073/pnas.1914367117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The hypothesized central role of RNA in the origin of life suggests that RNA propagation predated the advent of complex protein enzymes. A critical step of RNA replication is the template-directed synthesis of a complementary strand. Two experimental approaches have been extensively explored in the pursuit of demonstrating protein-free RNA synthesis: template-directed nonenzymatic RNA polymerization using intrinsically reactive monomers and ribozyme-catalyzed polymerization using more stable substrates such as biological 5'-triphosphates. Despite significant progress in both approaches in recent years, the assembly and copying of functional RNA sequences under prebiotic conditions remains a challenge. Here, we explore an alternative approach to RNA-templated RNA copying that combines ribozyme catalysis with RNA substrates activated with a prebiotically plausible leaving group, 2-aminoimidazole (2AI). We applied in vitro selection to identify ligase ribozymes that catalyze phosphodiester bond formation between a template-bound primer and a phosphor-imidazolide-activated oligomer. Sequencing revealed the progressive enrichment of 10 abundant sequences from a random sequence pool. Ligase activity was detected in all 10 RNA sequences; all required activation of the ligator with 2AI and generated a 3'-5' phosphodiester bond. We propose that ribozyme catalysis of phosphodiester bond formation using intrinsically reactive RNA substrates, such as imidazolides, could have been an evolutionary step connecting purely nonenzymatic to ribozyme-catalyzed RNA template copying during the origin of life.
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Affiliation(s)
- Travis Walton
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114
| | - Saurja DasGupta
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114
| | - Daniel Duzdevich
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114
| | - Seung Soo Oh
- Department of Materials Science and Engineering, Pohang University of Science and Technology, 37673 Pohang, Gyeongbuk, South Korea
| | - Jack W Szostak
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114;
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114
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9
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Oliver CG, Reinharz V, Waldispühl J. On the emergence of structural complexity in RNA replicators. RNA (NEW YORK, N.Y.) 2019; 25:1579-1591. [PMID: 31467146 PMCID: PMC6859851 DOI: 10.1261/rna.070391.119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 08/19/2019] [Indexed: 06/10/2023]
Abstract
The RNA world hypothesis relies on the ability of ribonucleic acids to spontaneously acquire complex structures capable of supporting essential biological functions. Multiple sophisticated evolutionary models have been proposed for their emergence, but they often assume specific conditions. In this work, we explore a simple and parsimonious scenario describing the emergence of complex molecular structures at the early stages of life. We show that at specific GC content regimes, an undirected replication model is sufficient to explain the apparition of multibranched RNA secondary structures-a structural signature of many essential ribozymes. We ran a large-scale computational study to map energetically stable structures on complete mutational networks of 50-nt-long RNA sequences. Our results reveal that the sequence landscape with stable structures is enriched with multibranched structures at a length scale coinciding with the appearance of complex structures in RNA databases. A random replication mechanism preserving a 50% GC content may suffice to explain a natural enrichment of stable complex structures in populations of functional RNAs. In contrast, an evolutionary mechanism eliciting the most stable folds at each generation appears to help reaching multibranched structures at highest GC content.
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Affiliation(s)
- Carlos G Oliver
- School of Computer Science, McGill University, Montreal, QC H3A 2B3, Canada
| | - Vladimir Reinharz
- Center for Soft and Living Matter, Institute for Basic Science, Ulsan 34126, South Korea
| | - Jérôme Waldispühl
- School of Computer Science, McGill University, Montreal, QC H3A 2B3, Canada
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10
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Flexible Nucleic Acids (FNAs) as Informational Molecules: Enzymatic Polymerization of fNTPs on DNA Templates and Nonenzymatic Oligomerization of RNA on FNA Templates. Methods Mol Biol 2019; 1973:213-236. [PMID: 31016705 DOI: 10.1007/978-1-4939-9216-4_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The methodology enabling enzymatic and nonenzymatic information transfer with FNAs is described. This methodology includes the chemical synthesis of fNTPs and fN phosphoramidites, in addition to protocols for the enzymatic and nonenzymatic transfer of information.
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11
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Walton T, Zhang W, Li L, Tam CP, Szostak JW. The Mechanism of Nonenzymatic Template Copying with Imidazole-Activated Nucleotides. Angew Chem Int Ed Engl 2019; 58:10812-10819. [PMID: 30908802 DOI: 10.1002/anie.201902050] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Indexed: 11/10/2022]
Abstract
The emergence of the replication of RNA oligonucleotides was a critical step in the origin of life. An important model for the study of nonenzymatic template copying, which would be a key part of any such pathway, involves the reaction of ribonucleoside-5'-phosphorimidazolides with an RNA primer/template complex. The mechanism by which the primer becomes extended by one nucleotide was assumed to be a classical in-line nucleophilic-substitution reaction in which the 3'-hydroxyl of the primer attacks the phosphate of the incoming activated monomer with displacement of the imidazole leaving group. Surprisingly, this simple model has turned out to be incorrect, and the dominant pathway has now been shown to involve the reaction of two activated nucleotides with each other to form a 5'-5'-imidazolium bridged dinucleotide intermediate. Here we review the discovery of this unexpected intermediate, and the chemical, kinetic, and structural evidence for its role in template copying chemistry.
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Affiliation(s)
- Travis Walton
- Howard Hughes Medical Institute and Dept. of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Wen Zhang
- Howard Hughes Medical Institute and Dept. of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Li Li
- Howard Hughes Medical Institute and Dept. of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Chun Pong Tam
- Howard Hughes Medical Institute and Dept. of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Dept. of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA.,Present address: Moderna Inc., Cambridge, MA, 02139, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute and Dept. of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Dept. of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
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12
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Walton T, Zhang W, Li L, Tam CP, Szostak JW. The Mechanism of Nonenzymatic Template Copying with Imidazole‐Activated Nucleotides. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201902050] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Travis Walton
- Howard Hughes Medical Institute and Dept. of Molecular Biology Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
| | - Wen Zhang
- Howard Hughes Medical Institute and Dept. of Molecular Biology Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
| | - Li Li
- Howard Hughes Medical Institute and Dept. of Molecular Biology Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
| | - Chun Pong Tam
- Howard Hughes Medical Institute and Dept. of Molecular Biology Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Dept. of Chemistry and Chemical Biology Harvard University Cambridge MA 02138 USA
- Present address: Moderna Inc. Cambridge MA 02139 USA
| | - Jack W. Szostak
- Howard Hughes Medical Institute and Dept. of Molecular Biology Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Dept. of Chemistry and Chemical Biology Harvard University Cambridge MA 02138 USA
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13
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Sosson M, Pfeffer D, Richert C. Enzyme-free ligation of dimers and trimers to RNA primers. Nucleic Acids Res 2019; 47:3836-3845. [PMID: 30869145 PMCID: PMC6486630 DOI: 10.1093/nar/gkz160] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 02/25/2019] [Accepted: 02/28/2019] [Indexed: 01/19/2023] Open
Abstract
The template-directed formation of phosphodiester bonds between two nucleic acid components is a pivotal process in biology. To induce such a reaction in the absence of enzymes is a challenge. This challenge has been met for the extension of a primer with mononucleotides, but the ligation of short oligonucleotides (dimers or trimers) has proven difficult. Here we report a method for ligating dimers and trimers of ribonucleotides using in situ activation in aqueous buffer. All 16 different dimers and two trimers were tested. Binding studies by NMR showed low millimolar dissociation constants for complexes between representative dimers and hairpins mimicking primer-template duplexes, confirming that a weak template effect is not the cause of the poor ligating properties of these short oligomers. Rather, cyclization was found to compete with ligation, with up to 90% of dimer being converted to the cyclic form during the course of an assay. This side reaction is strongly sequence dependent and more pronounced for dimers than for trimers. Under optimized reaction conditions, high yields were observed with strongly pairing purines at the 3'-terminus. These results show that short oligomers of ribonucleotides are competent reactants in enzyme-free copying.
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Affiliation(s)
- Marilyne Sosson
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Daniel Pfeffer
- 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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Kai L, Schwille P. Cell-Free Protein Synthesis and Its Perspectives for Assembling Cells from the Bottom-Up. ACTA ACUST UNITED AC 2019; 3:e1800322. [PMID: 32648712 DOI: 10.1002/adbi.201800322] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/14/2019] [Indexed: 12/20/2022]
Abstract
The underlying idea of synthetic biology is that biological reactions/modules/systems can be precisely engineered and controlled toward desired products. Numerous efforts in the past decades in deciphering the complexity of biological systems in vivo have led to a variety of tools for synthetic biology, especially based on recombinant DNA. However, one generic limitation of all living systems is that the vast majority of energy input is dedicated to maintain the system as a whole, rather than the small part of interest. Cell-free synthetic biology is aiming at exactly this fundamental limitation, providing the next level of flexibility for engineering and designing biological systems in vitro. New technology has continuously inspired cell-free biology and extended its applications, including gene circuits, spatiotemporally controlled pathways, coactivated catalysts systems, and rationally designed multienzyme pathways, in particular, minimal cell construction. In the context of this special issue, discussing work being carried out in the "MaxSynBio" consortium, the advances in characterizing stochasticity and dynamics of cell-free protein synthesis within cell-sized compartments, as well as the molecular crowding effect, are discussed. The organization of spatial heterogeneity is the key prerequisite for achieving hierarchy and stepwise assembly of minimal cells from the bottom-up.
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Affiliation(s)
- Lei Kai
- School of Life Sciences, Jiangsu Normal University, Shanghai Road 101, 221116, Xuzhou, P. R. China.,Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, D-82152, Martinsried, Germany
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, D-82152, Martinsried, Germany
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15
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Affiliation(s)
- Elena Hänle
- Institut für Organische Chemie; Universität Stuttgart; 70569 Stuttgart Germany
| | - Clemens Richert
- Institut für Organische Chemie; Universität Stuttgart; 70569 Stuttgart Germany
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16
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Hänle E, Richert C. Enzyme-Free Replication with Two or Four Bases. Angew Chem Int Ed Engl 2018; 57:8911-8915. [PMID: 29779237 DOI: 10.1002/anie.201803074] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 04/27/2018] [Indexed: 11/10/2022]
Abstract
All known forms of life encode their genetic information in a sequence of bases of a genetic polymer and produce copies through replication. How this process started before polymerase enzymes had evolved is unclear. Enzyme-free copying of short stretches of DNA or RNA has been demonstrated using activated nucleotides, but not replication. We have developed a method for enzyme-free replication. It involves extension with reversible termination, enzyme-free ligation, and strand capture. We monitored nucleotide incorporation for a full helical turn of DNA, during both a first and a second round of copying, by using mass spectrometry. With all four bases (A/C/G/T), an "error catastrophe" occurred, with the correct sequence being "overwhelmed" by incorrect ones. When only C and G were used, approximately half of the daughter strands had the mass of the correct sequence after 20 copying steps. We conclude that enzyme-free replication is more likely to be successful with just the two strongly pairing bases than with all four bases of the genetic alphabet.
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Affiliation(s)
- Elena Hänle
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Clemens Richert
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
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17
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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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18
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Costanzo G, Giorgi A, Scipioni A, Timperio AM, Mancone C, Tripodi M, Kapralov M, Krasavin E, Kruse H, Šponer J, Šponer JE, Ranc V, Otyepka M, Pino S, Di Mauro E. Nonenzymatic Oligomerization of 3',5'-Cyclic CMP Induced by Proton and UV Irradiation Hints at a Nonfastidious Origin of RNA. Chembiochem 2017; 18:1535-1543. [PMID: 28471098 DOI: 10.1002/cbic.201700122] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Indexed: 12/25/2022]
Abstract
We report that 3',5'-cyclic CMP undergoes nonenzymatic di- and trimerization at 20 °C under dry conditions upon proton or UV irradiation. The reaction involves stacking of the cyclic monomers and subsequent polymerization through serial transphosphorylations between the stacked monomers. Proton- and UV-induced oligomerization of 3',5'-cyclic CMP demonstrates that pyrimidines-similar to purines-might also have taken part in the spontaneous generation of RNA under plausible prebiotic conditions as well as in an extraterrestrial context. The observed polymerization of naturally occurring 3',5'-cyclic nucleotides supports the possibility that the extant genetic nucleic acids might have originated by way of a straight Occamian path, starting from simple reactions between plausibly preactivated monomers.
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Affiliation(s)
- Giovanna Costanzo
- Istituto di Biologia e Patologia Molecolari, CNR, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Alessandra Giorgi
- Dipartimento di Scienze Biochimiche, "Sapienza" Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Anita Scipioni
- Dipartimento di Chimica, "Sapienza" Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Anna Maria Timperio
- Department of Ecology and Biology, "La Tuscia" University, Viale dell'Università snc, 01100, Viterbo, Italy
| | - Carmine Mancone
- Department of Cellular Biotechnologies and Hematology, Sapienza University of Rome, Via Regina Elena 324, 00161, Roma, Italy.,National Institute for Infectious Diseases "L. Spallanzani", IRCCS, Via Portuense 292, 00149, Rome, Italy
| | - Marco Tripodi
- Department of Cellular Biotechnologies and Hematology, Sapienza University of Rome, Via Regina Elena 324, 00161, Roma, Italy.,National Institute for Infectious Diseases "L. Spallanzani", IRCCS, Via Portuense 292, 00149, Rome, Italy
| | - Michail Kapralov
- Joint Institute for Nuclear Research, Laboratory of Radiation Biology, 141980, Dubna, Russia
| | - Eugene Krasavin
- Joint Institute for Nuclear Research, Laboratory of Radiation Biology, 141980, Dubna, Russia
| | - Holger Kruse
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17. Listopadu, 771 46, Olomouc, Czech Republic
| | - Judit E Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic
| | - Václav Ranc
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17. Listopadu, 771 46, Olomouc, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17. Listopadu, 771 46, Olomouc, Czech Republic
| | - Samanta Pino
- Department of Biology and Biotechnology, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Ernesto Di Mauro
- Department of Biology and Biotechnology, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
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19
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Hodgson DR. Physicochemical Aspects of Aqueous and Nonaqueous Approaches to the Preparation of Nucleosides, Nucleotides and Phosphate Ester Mimics. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2017. [DOI: 10.1016/bs.apoc.2017.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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20
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Taming Prebiotic Chemistry: The Role of Heterogeneous and Interfacial Catalysis in the Emergence of a Prebiotic Catalytic/Information Polymer System. Life (Basel) 2016; 6:life6040040. [PMID: 27827919 PMCID: PMC5198075 DOI: 10.3390/life6040040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/31/2016] [Accepted: 11/01/2016] [Indexed: 01/10/2023] Open
Abstract
Cellular life is based on interacting polymer networks that serve as catalysts, genetic information and structural molecules. The complexity of the DNA, RNA and protein biochemistry suggests that it must have been preceded by simpler systems. The RNA world hypothesis proposes RNA as the prime candidate for such a primal system. Even though this proposition has gained currency, its investigations have highlighted several challenges with respect to bulk aqueous media: (1) the synthesis of RNA monomers is difficult; (2) efficient pathways for monomer polymerization into functional RNAs and their subsequent, sequence-specific replication remain elusive; and (3) the evolution of the RNA function towards cellular metabolism in isolation is questionable in view of the chemical mixtures expected on the early Earth. This review will address the question of the possible roles of heterogeneous media and catalysis as drivers for the emergence of RNA-based polymer networks. We will show that this approach to non-enzymatic polymerizations of RNA from monomers and RNA evolution cannot only solve some issues encountered during reactions in bulk aqueous solutions, but may also explain the co-emergence of the various polymers indispensable for life in complex mixtures and their organization into primitive networks.
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Kawamura K. A Hypothesis: Life Initiated from Two Genes, as Deduced from the RNA World Hypothesis and the Characteristics of Life-Like Systems. Life (Basel) 2016; 6:life6030029. [PMID: 27490571 PMCID: PMC5041005 DOI: 10.3390/life6030029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 07/22/2016] [Accepted: 07/25/2016] [Indexed: 11/18/2022] Open
Abstract
RNA played a central role in the emergence of the first life-like system on primitive Earth since RNA molecules contain both genetic information and catalytic activity. However, there are several drawbacks regarding the RNA world hypothesis. Here, I briefly discuss the feasibility of the RNA world hypothesis to deduce the RNA functions that are essential for forming a life-like system. At the same time, I have conducted a conceptual analysis of the characteristics of biosystems as a useful approach to deduce a realistic life-like system in relation to the definition of life. For instance, an RNA-based life-like system should possess enough stability to resist environmental perturbations, by developing a cell-like compartment, for instance. Here, a conceptual viewpoint is summarized to provide a realistic life-like system that is compatible with the primitive Earth environment and the capabilities of RNA molecules. According to the empirical and conceptual analysis, I propose the hypothesis that the first life-like system could have initiated from only two genes.
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Affiliation(s)
- Kunio Kawamura
- Department of Human Environmental Studies, Hiroshima Shudo University, 1-1-1, Ozuka-higashi, Asaminami-ku, Hiroshima 731-3195, Japan.
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Kervio E, Sosson M, Richert C. The effect of leaving groups on binding and reactivity in enzyme-free copying of DNA and RNA. Nucleic Acids Res 2016; 44:5504-14. [PMID: 27235418 PMCID: PMC4937335 DOI: 10.1093/nar/gkw476] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 05/06/2016] [Accepted: 05/09/2016] [Indexed: 01/29/2023] Open
Abstract
The template-directed incorporation of nucleotides at the terminus of a growing primer is the basis of the transmission of genetic information. Nature uses polymerases-catalyzed reactions, but enzyme-free versions exist that employ nucleotides with organic leaving groups. The leaving group affects yields, but it was not clear whether inefficient extensions are due to poor binding, low reactivity toward the primer, or rapid hydrolysis. We have measured the binding of a total of 15 different activated nucleotides to DNA or RNA sequences. Further, we determined rate constants for the chemical step of primer extension involving methylimidazolides or oxyazabenzotriazolides of deoxynucleotides or ribonucleotides. Binding constants range from 10 to >500 mM and rate constants from 0.1 to 370 M(-1) h(-1) For aminoterminal primers, a fast covalent step and slow hydrolysis are the main factors leading to high yields. For monomers with weakly pairing bases, the leaving group can improve binding significantly. A detailed mechanistic picture emerges that explains why some enzyme-free primer extensions occur in high yield, while others remain recalcitrant to copying without enzymatic catalysis. A combination of tight binding and rapid extension, coupled with slow hydrolysis induces efficient enzyme-free copying.
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Affiliation(s)
- Eric Kervio
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Marilyne Sosson
- 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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Jauker M, Griesser H, Richert C. Spontaneous Formation of RNA Strands, Peptidyl RNA, and Cofactors. Angew Chem Int Ed Engl 2015; 54:14564-9. [PMID: 26435376 PMCID: PMC4678511 DOI: 10.1002/anie.201506593] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 09/03/2015] [Indexed: 01/14/2023]
Abstract
How the biochemical machinery evolved from simple precursors is an open question. Here we show that ribonucleotides and amino acids condense to peptidyl RNAs in the absence of enzymes under conditions established for genetic copying. Untemplated formation of RNA strands that can encode genetic information, formation of peptidyl chains linked to RNA, and formation of the cofactors NAD(+), FAD, and ATP all occur under the same conditions. In the peptidyl RNAs, the peptide chains are phosphoramidate-linked to a ribonucleotide. Peptidyl RNAs with long peptide chains were selected from an initial pool when a lipophilic phase simulating the interior of membranes was offered, and free peptides were released upon acidification. Our results show that key molecules of genetics, catalysis, and metabolism can emerge under the same conditions, without a mineral surface, without an enzyme, and without the need for chemical pre-activation.
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Affiliation(s)
- Mario Jauker
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany)
| | - Helmut Griesser
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany)
| | - Clemens Richert
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany).
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Jauker M, Griesser H, Richert C. Copying of RNA Sequences without Pre-Activation. Angew Chem Int Ed Engl 2015; 54:14559-63. [PMID: 26435291 PMCID: PMC4678514 DOI: 10.1002/anie.201506592] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 09/03/2015] [Indexed: 11/23/2022]
Abstract
Template-directed incorporation of nucleotides at the terminus of a growing complementary strand is the basis of replication. For RNA, this process can occur in the absence of enzymes, if the ribonucleotides are first converted to an active species with a leaving group. Thus far, the activation required a separate chemical step, complicating prebiotically plausible scenarios. Here we show that a combination of a carbodiimide and an organocatalyst induces near-quantitative incorporation of any of the four ribonucleotides. Upon in situ activation, adenosine monophosphate was found to also form oligomers in aqueous solution. So, both de novo strand formation and sequence-specific copying can occur without an artificial synthetic step.
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Affiliation(s)
- Mario Jauker
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany)
| | - Helmut Griesser
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany)
| | - Clemens Richert
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany).
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25
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Four Ways to Oligonucleotides Without Phosphoimidazolides. J Mol Evol 2015; 82:5-10. [PMID: 26520151 DOI: 10.1007/s00239-015-9709-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 10/23/2015] [Indexed: 10/22/2022]
Abstract
Emergence of the very first RNA or RNA-like oligomers from simple nucleotide precursors is one of the most intriguing questions of the origin of life research. In the current paper, we analyse the mechanism of four non-enzymatic template-free scenarios suggested for the oligomerization of chemically non-modified cyclic and acyclic nucleotides in the literature. We show that amines may have a twofold role in these syntheses: due to their high affinity to bind protons they may activate the phosphorus of the phosphate group via proton transfer reactions, or indirectly they may serve as charge compensating species and influence the self-assembling of nucleotides to supramolecular architectures compatible with the oligomerization reactions. Effect of cations and pH on the reactions is also discussed.
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26
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Jauker M, Griesser H, Richert C. Kopieren von RNA-Sequenzen ohne Voraktivierung. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506592] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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27
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Jauker M, Griesser H, Richert C. Spontane Bildung von RNA-Strängen, Peptidyl-RNA und Cofaktoren. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506593] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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28
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Kawamura K, Da Silva L, Ogawa M, Konagaya N, Maurel MC. Verification of chemical evolution of RNA under hydrothermal environments on the primitive Earth. BIO WEB OF CONFERENCES 2015. [DOI: 10.1051/bioconf/20150400011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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29
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Cafferty BJ, Hud NV. Was a Pyrimidine-Pyrimidine Base Pair the Ancestor of Watson-Crick Base Pairs? Insights from a Systematic Approach to the Origin of RNA. Isr J Chem 2015. [DOI: 10.1002/ijch.201400206] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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30
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Heuberger BD, Pal A, Del Frate F, Topkar VV, Szostak JW. Replacing uridine with 2-thiouridine enhances the rate and fidelity of nonenzymatic RNA primer extension. J Am Chem Soc 2015; 137:2769-75. [PMID: 25654265 PMCID: PMC4985000 DOI: 10.1021/jacs.5b00445] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The
nonenzymatic replication of RNA oligonucleotides is thought
to have played a key role in the origin of life prior to the evolution
of ribozyme-catalyzed RNA replication. Although the copying of oligo-C
templates by 2-methylimidazole-activated G monomers can be quite efficient,
the copying of mixed sequence templates, especially those containing
A and U, is particularly slow and error-prone. The greater thermodynamic
stability of the 2-thio-U(s2U):A base pair, relative to
the canonical U:A base pair, suggests that replacing U with s2U might enhance the rate and fidelity of the nonenzymatic
copying of RNA templates. Here we report that this single atom substitution
in the activated monomer improves both the kinetics and the fidelity
of nonenzymatic primer extension on mixed-sequence RNA templates.
In addition, the mean lengths of primer extension products obtained
with s2U is greater than those obtained with U, augmenting
the potential for nonenzymatic replication of heritable function-rich
sequences. We suggest that noncanonical nucleotides such as s2U may have played a role during the infancy of the RNA world
by facilitating the nonenzymatic replication of genomic RNA oligonucleotides.
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Affiliation(s)
- Benjamin D Heuberger
- Howard Hughes Medical Institute, Center for Computational and Integrative Biology, and Department of Molecular Biology, Simches Research Center, Massachusetts General Hospital , Boston, Massachusetts 02114, United States
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Kervio E, Claasen B, Steiner UE, Richert C. The strength of the template effect attracting nucleotides to naked DNA. Nucleic Acids Res 2014; 42:7409-20. [PMID: 24875480 PMCID: PMC4066754 DOI: 10.1093/nar/gku314] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The transmission of genetic information relies on Watson–Crick base pairing between nucleoside phosphates and template bases in template–primer complexes. Enzyme-free primer extension is the purest form of the transmission process, without any chaperon-like effect of polymerases. This simple form of copying of sequences is intimately linked to the origin of life and provides new opportunities for reading genetic information. Here, we report the dissociation constants for complexes between (deoxy)nucleotides and template–primer complexes, as determined by nuclear magnetic resonance and the inhibitory effect of unactivated nucleotides on enzyme-free primer extension. Depending on the sequence context, Kd′s range from 280 mM for thymidine monophosphate binding to a terminal adenine of a hairpin to 2 mM for a deoxyguanosine monophosphate binding in the interior of a sequence with a neighboring strand. Combined with rate constants for the chemical step of extension and hydrolytic inactivation, our quantitative theory explains why some enzyme-free copying reactions are incomplete while others are not. For example, for GMP binding to ribonucleic acid, inhibition is a significant factor in low-yielding reactions, whereas for amino-terminal DNA hydrolysis of monomers is critical. Our results thus provide a quantitative basis for enzyme-free copying.
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Affiliation(s)
- Eric Kervio
- Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Birgit Claasen
- Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Ulrich E Steiner
- Fachbereich Chemie, Universität Konstanz, 78457 Konstanz, Germany
| | - Clemens Richert
- Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
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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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Kaiser A, Richert C. Nucleotide-based copying of nucleic acid sequences without enzymes. J Org Chem 2013; 78:793-9. [PMID: 23327991 DOI: 10.1021/jo3025779] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chemical primer extension is the enzyme-free incorporation of nucleotides at the end of an oligonucleotide, directed by a template. The reaction mimics the copying of sequences during replication but relies on recognition and reactivity of nucleic acids alone. Copying is low-yielding, particularly for long RNA. Hydrolysis of active esters and inhibition through hydrolysis products have been identified as factors that prevent high yields, and approaches to overcoming them have culminated in successful template-directed solid-phase syntheses for RNA and phosphoramidate DNA.
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Affiliation(s)
- Andreas Kaiser
- Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
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35
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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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36
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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: 131] [Impact Index Per Article: 10.1] [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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37
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Efficient enzyme-free copying of all four nucleobases templated by immobilized RNA. Nat Chem 2011; 3:603-8. [PMID: 21778979 DOI: 10.1038/nchem.1086] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Accepted: 06/06/2011] [Indexed: 11/08/2022]
Abstract
The transition from inanimate materials to the earliest forms of life must have involved multiplication of a catalytically active polymer that is able to replicate. The semiconservative replication that is characteristic of genetic information transfer requires strands that contain more than one type of nucleobase. Short strands of RNA can act as catalysts, but attempts to induce efficient self-copying of mixed sequences (containing four different nucleobases) have been unsuccessful with ribonucleotides. Here we show that inhibition by spent monomers, formed by the hydrolysis of the activated nucleotides, is the cause for incomplete extension of growing daughter strands on RNA templates. Immobilization of strands and periodic displacement of the solution containing the activated monomers overcome this inhibition. Any of the four nucleobases (A/C/G/U) is successfully copied in the absence of enzymes. We conclude therefore that in a prebiotic world, oligoribonucleotides may have formed and undergone self-copying on surfaces.
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Pino S, Biasiucci M, Scardamaglia M, Gigli G, Betti MG, Mariani C, Di Mauro E. Nonenzymatic ligation of an RNA oligonucleotide analyzed by atomic force microscopy. J Phys Chem B 2011; 115:6296-303. [PMID: 21500793 DOI: 10.1021/jp200832w] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The products of ligation reaction of a 24 nucleotides long PolyA RNA adsorbed on mica were observed by atomic force microscopy. The occurrence of oligonucleotides at different degrees of polymerization has been quantitatively studied before and after ligation reaction. The microscopy images at the nanoscale show that nonenzymatic ligation of pristine RNA monomers results in the formation of supramolecular aggregates, with prevalence of dimers and tetramers. Analytical conditions were defined allowing the identification, the quantitative evaluation, and their distribution after ligation reaction, also providing an estimate of the degree of hydration of the objects. Such investigation is of particular biological relevance and provides the simplest yet model system for direct investigation of RNA reactions by advanced microscopy.
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Affiliation(s)
- Samanta Pino
- Department of Physics, Sapienza University of Rome, P.le A. Moro 2, 00185 Rome, Italy
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Abstract
Template-directed synthesis of complementary strands is pivotal for life. Nature employs polymerases for this reaction, leaving the ability of DNA itself to direct the incorporation of individual nucleotides at the end of a growing primer difficult to assess. Using 64 sequences, we now find that any of the four nucleobases, in combination with any neighboring residue, support enzyme-free primer extension when primer and mononucleotide are sufficiently reactive, with >or=93% primer extension for all sequences. Between the 64 possible base triplets, the rate of extension for the poorest template, CAG, with A as templating base, and the most efficient template, TCT, with C as templating base, differs by less than two orders of magnitude. Further, primer extension with a balanced mixture of monomers shows >or=72% of the correct extension product in all cases, and >or=90% incorporation of the correct base for 46 out of 64 triplets in the presence of a downstream-binding strand. A mechanism is proposed with a binding equilibrium for the monomer, deprotonation of the primer, and two chemical steps, the first of which is most strongly modulated by the sequence. Overall, rates show a surprisingly smooth reactivity landscape, with similar incorporation on strongly and weakly templating sequences. These results help to clarify the substrate contribution to copying, as found in polymerase-catalyzed replication, and show an important feature of DNA as genetic material.
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Kim EK, Switzer C. Nonenzymatic oligomerization of activated nucleotides on hairpin templates. ACTA ACUST UNITED AC 2010; Chapter 3:Unit3.18. [PMID: 20013784 DOI: 10.1002/0471142700.nc0318s39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This unit describes a protocol for nonenzymatic oligomerization of activated ribonucleotides on DNA hairpins appended by templates containing threofuranosyl nucleic acid (TNA). TNA-cytidylate templates effectively promote oligomerization of 2-MeImpG, and give 3',5'-linked oligomerization products predominantly, with good base-pairing fidelity. Although the rates of oligomerization depend on TNA content, after 3 days of incubation, oligomerization products are apparent, and full-length products are present after 10 days. Characterization of product phosphodiester bond regiochemistry is accomplished by digestion with RNase T1. Additionally, exposure of oligomerization products to calf intestinal alkaline phosphatase enables detection of any endcapping due to pyrophosphate formation. Base-pairing fidelity is assessed by challenging the template to oligomerize 2-MeImpA. The protocols described for nonenzymatic, template-directed synthesis in this unit are applicable to oligomerization of activated monomers on templates of different compositions, with respect to both base identity and polymer backbone.
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Affiliation(s)
- Eun-Kyong Kim
- Department of Chemistry, University of California, Riverside, California, USA
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41
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Switzer C. A missing prebiotic link: discovery of a plausible synthesis of pyrimidine nucleotides. Chembiochem 2010; 10:2591-3. [PMID: 19746388 DOI: 10.1002/cbic.200900516] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Christopher Switzer
- Department of Chemistry, University of California, Riverside, CA 92521, USA.
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42
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Heuberger BD, Switzer C. An alternative nucleobase code: characterization of purine-purine DNA double helices bearing guanine-isoguanine and diaminopurine 7-deaza-xanthine base pairs. Chembiochem 2009; 9:2779-83. [PMID: 18985646 DOI: 10.1002/cbic.200800450] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Benjamin D Heuberger
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521, USA
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43
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Monnard PA, Ziock H. Eutectic Phase in Water-Ice: A Self-Assembled Environment Conducive to Metal-Catalyzed Non-Enzymatic RNA Polymerization. Chem Biodivers 2008; 5:1521-1539. [DOI: 10.1002/cbdv.200890141] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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44
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Monnard PA, Szostak JW. Metal-ion catalyzed polymerization in the eutectic phase in water-ice: a possible approach to template-directed RNA polymerization. J Inorg Biochem 2008; 102:1104-11. [PMID: 18329104 DOI: 10.1016/j.jinorgbio.2008.01.026] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2007] [Revised: 01/17/2008] [Accepted: 01/18/2008] [Indexed: 10/22/2022]
Abstract
The emergence of an RNA world requires among other processes the non-enzymatic, template-directed replication of genetic polymers such as RNA or related nucleic acids, possibly catalyzed by metal-ions. The absence of uridilate derivative polymerization on adenine containing templates has been the main issue preventing an efficient template-directed RNA polymerization. We report here the investigation of template-directed RNA polymerization in the eutectic phase in water-ice. In particular, it was found that activated uridilate monomers in the presence of metal-ion catalysts could efficiently elongate RNA hairpins whose 5'-overhangs served as the templating sequence. The same applies for every other pyrimidine and purine nucleobase. Moreover, the initial elongation rates were always higher in the presence of a template complementary to the nucleotide than in systems without proper base-pairing opportunities. These results suggest that a template-directed RNA polymerization catalyzed by metal-ions could be carried out under eutectic phase in water-ice conditions.
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Affiliation(s)
- Pierre-Alain Monnard
- Los Alamos National Laboratory, EES-6, PO Box 1663, MS-D462, Los Alamos, NM 87545, USA.
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45
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Schwartz AW. Leslie Orgel 1927-2007. ORIGINS LIFE EVOL B 2008; 38:1-3. [PMID: 18095184 DOI: 10.1007/s11084-007-9118-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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46
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Kauffman S. Question 1: origin of life and the living state. ORIGINS LIFE EVOL B 2007; 37:315-22. [PMID: 17674139 DOI: 10.1007/s11084-007-9093-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2007] [Accepted: 04/17/2007] [Indexed: 11/25/2022]
Abstract
The aim of this article is to discuss four topics: First, the origin of molecular reproduction. Second, the origin of agency - the capacity of a system to act on its own behalf. Agency is a stunning feature of human and some wider range of life. Third, to discuss a still poorly articulated feature of life noticed by the philosopher Immanuel Kant over 200 years ago: A self propagating organization of process. We have no theory for this aspect of life, yet it is central to life. Fourth, I will discuss constraints, as in Schroedinger's aperiodic crystal (Schroedinger E, What is life? The physical aspect of the living cell, 1944), as information, part of the total non-equilibrium union of matter, energy, work, work cycles, constraints, and information that appear to comprise the living state.
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Affiliation(s)
- Stuart Kauffman
- Institute for Biocomplexity and Informatics, University of Calgary, Calgary, Canada.
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47
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Vogel SR, Richert C. Adenosine residues in the template do not block spontaneous replication steps of RNA. Chem Commun (Camb) 2007:1896-8. [PMID: 17695221 DOI: 10.1039/b702768k] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sub-freezing temperatures, azabenzotriazolide activation, multiple monomer addition, and helper displacement help to overcome what seemed like an intrinsic block of adenine-templated RNA replication steps in the absence of enzymes.
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Affiliation(s)
- Stephanie R Vogel
- Institute for Organic Chemistry, University of Karlsruhe (TH), 76131 Karlsruhe, Germany
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48
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Costanzo G, Saladino R, Crestini C, Ciciriello F, Di Mauro E. Formamide as the main building block in the origin of nucleic acids. BMC Evol Biol 2007; 7 Suppl 2:S1. [PMID: 17767725 PMCID: PMC1963486 DOI: 10.1186/1471-2148-7-s2-s1] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The simplest molecules grouping the four most common elements of the universe H,C,O and N (with the exception of the biologically inert He) are isocyanate HNCO and formamide H2NCOH. Reasons for the availability of formamide on prebiotic Earth are presented. We review evidence showing that formamide in the presence of largely available catalysts and by moderate heating yields the complete set of nucleic bases necessary for the formation of nucleic acids. Formamide also favours the formation of acyclonucleosides and the phosphorylation and trans-phosphorylation of nucleosides, thus providing a plausible chemical frame for the passage from a simple one-carbon compound to nucleic polymers. Physico-chemical conditions exist in which formamide favours the stability of the phosphoester bonds in nucleic polymers relative to that of the same bonds in monomers. Starting from a formamide-laden environment subject only to the laws of chemistry, a hypothesis is outlined sketching the passage towards an aqueous world in which Darwinian rules apply.
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Affiliation(s)
- Giovanna Costanzo
- Istituto di Biologia e Patologia Molecolari, CNR, P.le Aldo Moro, 5, Rome 00185, Italy
| | - Raffaele Saladino
- Istituto di Biologia e Patologia Molecolari, CNR, P.le Aldo Moro, 5, Rome 00185, Italy
- Dipartimento A.B.A.C., Università della Tuscia, Via San Camillo De Lellis, Viterbo, Italy
| | - Claudia Crestini
- Marine Dipartimento di Scienze e Tecnologie Chimiche, Università "Tor Vergata", Rome 00133, Italy
| | - Fabiana Ciciriello
- Fondazione "Istituto Pasteur-Fondazione Cenci-Bolognetti" c/o Dipartimento di Genetica e Biologia Molecolare, Università "La Sapienza" di Roma, P.le Aldo Moro, 5, Rome 00185, Italy
| | - Ernesto Di Mauro
- Ernesto Di Mauro, Dipartimento di Genetica e Biologia Molecolare, Università "La Sapienza" di Roma, P.le Aldo Moro, 5, 00185 Rome, Italy
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49
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Saladino R, Crestini C, Ciciriello F, Costanzo G, Di Mauro E. Formamide chemistry and the origin of informational polymers. Chem Biodivers 2007; 4:694-720. [PMID: 17443884 DOI: 10.1002/cbdv.200790059] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Formamide (HCONH2) provides a chemical frame potentially affording all the monomeric components necessary for the formation of nucleic polymers. In the presence of the appropriate catalysts, and by moderate heating, formamide yields a complete set of nucleic bases, acyclonucleosides, and favors both phosphorylations and transphosphorylations. Physico-chemical conditions exist in which formamide favors the stability of the phosphoester bonds in nucleic polymers more than that of the same bonds in monomers. This property establishes 'thermodynamic niches' in which the polymeric forms are favored. The hypothesis that these specific attributes of formamide allowed the onset of prebiotic chemical equilibria capable of Darwinian evolution is discussed.
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Affiliation(s)
- Raffaele Saladino
- Dipartimento A. B. A. C., Università della Tuscia, Via San Camillo De Lellis, I-01100 Viterbo
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50
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Lutay AV, Zenkova MA, Vlassov VV. Nonenzymatic recombination of RNA: possible mechanism for the formation of novel sequences. Chem Biodivers 2007; 4:762-7. [PMID: 17443887 DOI: 10.1002/cbdv.200790062] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We report on the formation of novel RNA molecules in a recombination-like, nonenzymatic reaction proceeding in the complex of partially complementary RNA-oligonucleotides under very simple conditions. Analysis of the isolated products demonstrated that at least 5% of the formed linkages are of the (natural) 3',5'-phosphodiester type. We suggest that similar reactions could contribute to the development of the 'RNA world', but could also proceed in vivo within variously structured RNA or RNA complexes containing loops, bulges, or dangling ends, providing an emergence of novel RNA sequences.
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Affiliation(s)
- Alexei V Lutay
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrentiev Ave, 8, Novosibirsk, 630090, Russian Federation.
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