1
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Sangchai T, Al Shehimy S, Penocchio E, Ragazzon G. Artificial Molecular Ratchets: Tools Enabling Endergonic Processes. Angew Chem Int Ed Engl 2023; 62:e202309501. [PMID: 37545196 DOI: 10.1002/anie.202309501] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 08/08/2023]
Abstract
Non-equilibrium chemical systems underpin multiple domains of contemporary interest, including supramolecular chemistry, molecular machines, systems chemistry, prebiotic chemistry, and energy transduction. Experimental chemists are now pioneering the realization of artificial systems that can harvest energy away from equilibrium. In this tutorial Review, we provide an overview of artificial molecular ratchets: the chemical mechanisms enabling energy absorption from the environment. By focusing on the mechanism type-rather than the application domain or energy source-we offer a unifying picture of seemingly disparate phenomena, which we hope will foster progress in this fascinating domain of science.
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Affiliation(s)
- Thitiporn Sangchai
- University of Strasbourg, CNRS, Institut de Science et d'Ingénierie Supramoléculaires (ISIS) UMR 7006, 8 allée Gaspard Monge, 67000, Strasbourg, France
| | - Shaymaa Al Shehimy
- University of Strasbourg, CNRS, Institut de Science et d'Ingénierie Supramoléculaires (ISIS) UMR 7006, 8 allée Gaspard Monge, 67000, Strasbourg, France
| | - Emanuele Penocchio
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Giulio Ragazzon
- University of Strasbourg, CNRS, Institut de Science et d'Ingénierie Supramoléculaires (ISIS) UMR 7006, 8 allée Gaspard Monge, 67000, Strasbourg, France
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2
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Nogal N, Sanz-Sánchez M, Vela-Gallego S, Ruiz-Mirazo K, de la Escosura A. The protometabolic nature of prebiotic chemistry. Chem Soc Rev 2023; 52:7359-7388. [PMID: 37855729 PMCID: PMC10614573 DOI: 10.1039/d3cs00594a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Indexed: 10/20/2023]
Abstract
The field of prebiotic chemistry has been dedicated over decades to finding abiotic routes towards the molecular components of life. There is nowadays a handful of prebiotically plausible scenarios that enable the laboratory synthesis of most amino acids, fatty acids, simple sugars, nucleotides and core metabolites of extant living organisms. The major bottleneck then seems to be the self-organization of those building blocks into systems that can self-sustain. The purpose of this tutorial review is having a close look, guided by experimental research, into the main synthetic pathways of prebiotic chemistry, suggesting how they could be wired through common intermediates and catalytic cycles, as well as how recursively changing conditions could help them engage in self-organized and dissipative networks/assemblies (i.e., systems that consume chemical or physical energy from their environment to maintain their internal organization in a dynamic steady state out of equilibrium). In the article we also pay attention to the implications of this view for the emergence of homochirality. The revealed connectivity between those prebiotic routes should constitute the basis for a robust research program towards the bottom-up implementation of protometabolic systems, taken as a central part of the origins-of-life problem. In addition, this approach should foster further exploration of control mechanisms to tame the combinatorial explosion that typically occurs in mixtures of various reactive precursors, thus regulating the functional integration of their respective chemistries into self-sustaining protocellular assemblies.
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Affiliation(s)
- Noemí Nogal
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
| | - Marcos Sanz-Sánchez
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
| | - Sonia Vela-Gallego
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
| | - Kepa Ruiz-Mirazo
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, Leioa, Spain
- Department of Philosophy, University of the Basque Country, Leioa, Spain
| | - Andrés de la Escosura
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
- Institute for Advanced Research in Chemistry (IAdChem), Campus de Cantoblanco, 28049, Madrid, Spain
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3
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Okita H, Kondo S, Murayama K, Asanuma H. Rapid Chemical Ligation of DNA and Acyclic Threoninol Nucleic Acid ( aTNA) for Effective Nonenzymatic Primer Extension. J Am Chem Soc 2023; 145:17872-17880. [PMID: 37466125 PMCID: PMC10436273 DOI: 10.1021/jacs.3c04979] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Indexed: 07/20/2023]
Abstract
Previously, nonenzymatic primer extension reaction of acyclic l-threoninol nucleic acid (L-aTNA) was achieved in the presence of N-cyanoimidazole (CNIm) and Mn2+; however, the reaction conditions were not optimized and a mechanistic insight was not sufficient. Herein, we report investigation of the kinetics and reaction mechanism of the chemical ligation of L-aTNA to L-aTNA and of DNA to DNA. We found that Cd2+, Ni2+, and Co2+ accelerated ligation of both L-aTNA and DNA and that the rate-determining step was activation of the phosphate group. The activation was enhanced by duplex formation between a phosphorylated L-aTNA fragment and template, resulting in unexpectedly more effective L-aTNA ligation than DNA ligation. Under optimized conditions, an 8-mer L-aTNA primer could be elongated by ligation to L-aTNA trimers to produce a 29-mer full-length oligomer with 60% yield within 2 h at 4 °C. This highly effective chemical ligation system will allow construction of artificial genomes, robust DNA nanostructures, and xeno nucleic acids for use in selection methods. Our findings also shed light on the possible pre-RNA world.
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Affiliation(s)
- Hikari Okita
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Shuto Kondo
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Keiji Murayama
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
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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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Dirscherl CF, Ianeselli A, Tetiker D, Matreux T, Queener RM, Mast CB, Braun D. A heated rock crack captures and polymerizes primordial DNA and RNA. Phys Chem Chem Phys 2023; 25:3375-3386. [PMID: 36633199 DOI: 10.1039/d2cp04538a] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Life is based on informational polymers such as DNA or RNA. For their polymerization, high concentrations of complex monomer building blocks are required. Therefore, the dilution by diffusion poses a major problem before early life could establish a non-equilibrium of compartmentalization. Here, we explored a natural non-equilibrium habitat to polymerize RNA and DNA. A heat flux across thin rock cracks is shown to accumulate and maintain nucleotides. This boosts the polymerization to RNA and DNA inside the crack. Moreover, the polymers remain localized, aiding both the creation of longer polymers and fostering downstream evolutionary steps. In a closed system, we found single nucleotides concentrate 104-fold at the bottom of the crack compared to the top after 24 hours. We detected enhanced polymerization for 2 different activation chemistries: aminoimidazole-activated DNA nucleotides and 2',3'-cyclic RNA nucleotides. The copolymerization of 2',3'-cGMP and 2',3'-cCMP in the thermal pore showed an increased heterogeneity in sequence composition compared to isothermal drying. Finite element models unravelled the combined polymerization and accumulation kinetics and indicated that the escape of the nucleotides from such a crack is negligible over a time span of years. The thermal non-equilibrium habitat establishes a cell-like compartment that actively accumulates nucleotides for polymerization and traps the resulting oligomers. We argue that the setting creates a pre-cellular non-equilibrium steady state for the first steps of molecular evolution.
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Affiliation(s)
- Christina F Dirscherl
- Systems Biophysics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80799 Munich, Germany.
| | - Alan Ianeselli
- Systems Biophysics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80799 Munich, Germany.
| | - Damla Tetiker
- Systems Biophysics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80799 Munich, Germany.
| | - Thomas Matreux
- Systems Biophysics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80799 Munich, Germany.
| | - Robbin M Queener
- Systems Biophysics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80799 Munich, Germany.
| | - Christof B Mast
- Systems Biophysics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80799 Munich, Germany.
| | - Dieter Braun
- Systems Biophysics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80799 Munich, 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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Schaufelberger F, Ramström O. Activated Self-Resolution and Error-Correction in Catalytic Reaction Networks*. Chemistry 2021; 27:10335-10340. [PMID: 33780566 DOI: 10.1002/chem.202100208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Indexed: 01/02/2023]
Abstract
Understanding the emergence of function in complex reaction networks is a primary goal of systems chemistry and origin-of-life studies. Especially challenging is to create systems that simultaneously exhibit several emergent functions that can be independently tuned. In this work, a multifunctional complex reaction network of nucleophilic small molecule catalysts for the Morita-Baylis-Hillman (MBH) reaction is demonstrated. The dynamic system exhibited triggered self-resolution, preferentially amplifying a specific catalyst/product set out of a many potential alternatives. By utilizing selective reversibility of the products of the reaction set, systemic thermodynamically driven error-correction could also be introduced. To achieve this, a dynamic covalent MBH reaction based on adducts with internal H-transfer capabilities was developed. By careful tuning of the substituents, rate accelerations of retro-MBH reactions of up to four orders of magnitude could be obtained. This study thus demonstrates how efficient self-sorting of catalytic systems can be achieved through an interplay of several complex emergent functionalities.
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Affiliation(s)
- Fredrik Schaufelberger
- Department of Chemistry, KTH - Royal Institute of Technology Teknikringen 36, 10044 Stockholm (Sweden)
| | - Olof Ramström
- Department of Chemistry, KTH - Royal Institute of Technology Teknikringen 36, 10044 Stockholm (Sweden).,Department of Chemistry, University of Massachusetts Lowell, One University Ave., Lowell, MA, 01854, USA.,Department of Chemistry and Biomedical Sciences, Linnaeus University, 39182, Kalmar, Sweden
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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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Liu Z, Wu LF, Xu J, Bonfio C, Russell DA, Sutherland JD. Harnessing chemical energy for the activation and joining of prebiotic building blocks. Nat Chem 2020; 12:1023-1028. [PMID: 33093680 DOI: 10.1038/s41557-020-00564-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 09/21/2020] [Indexed: 11/09/2022]
Abstract
Life is an out-of-equilibrium system sustained by a continuous supply of energy. In extant biology, the generation of the primary energy currency, adenosine 5'-triphosphate and its use in the synthesis of biomolecules require enzymes. Before their emergence, alternative energy sources, perhaps assisted by simple catalysts, must have mediated the activation of carboxylates and phosphates for condensation reactions. Here, we show that the chemical energy inherent to isonitriles can be harnessed to activate nucleoside phosphates and carboxylic acids through catalysis by acid and 4,5-dicyanoimidazole under mild aqueous conditions. Simultaneous activation of carboxylates and phosphates provides multiple pathways for the generation of reactive intermediates, including mixed carboxylic acid-phosphoric acid anhydrides, for the synthesis of peptidyl-RNAs, peptides, RNA oligomers and primordial phospholipids. Our results indicate that unified prebiotic activation chemistry could have enabled the joining of building blocks in aqueous solution from a common pool and enabled the progression of a system towards higher complexity, foreshadowing today's encapsulated peptide-nucleic acid system.
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Affiliation(s)
- Ziwei Liu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Long-Fei Wu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Jianfeng Xu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Claudia Bonfio
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - David A Russell
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - John D Sutherland
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.
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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
![]()
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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11
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de la Escosura A. The Informational Substrate of Chemical Evolution: Implications for Abiogenesis. Life (Basel) 2019; 9:E66. [PMID: 31398942 PMCID: PMC6789672 DOI: 10.3390/life9030066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/26/2019] [Accepted: 08/05/2019] [Indexed: 12/11/2022] Open
Abstract
A key aspect of biological evolution is the capacity of living systems to process information, coded in deoxyribonucleic acid (DNA), and used to direct how the cell works. The overall picture that emerges today from fields such as developmental, synthetic, and systems biology indicates that information processing in cells occurs through a hierarchy of genes regulating the activity of other genes through complex metabolic networks. There is an implicit semiotic character in this way of dealing with information, based on functional molecules that act as signs to achieve self-regulation of the whole network. In contrast to cells, chemical systems are not thought of being able to process information, yet they must have preceded biological organisms, and evolved into them. Hence, there must have been prebiotic molecular assemblies that could somehow process information, in order to regulate their own constituent reactions and supramolecular organization processes. The purpose of this essay is then to reflect about the distinctive features of information in living and non-living matter, and on how the capacity of biological organisms for information processing was possibly rooted in a particular type of chemical systems (here referred to as autonomous chemical systems), which could self-sustain and reproduce through organizational closure of their molecular building blocks.
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Affiliation(s)
- Andrés de la Escosura
- Department of Organic Chemistry, Universidad Autónoma of Madrid, Cantoblanco Campus, 28049 Madrid, Spain.
- Department of Organic Chemistry, Institute for Advanced Research in Chemistry (IAdChem), Cantoblanco Campus, 28049 Madrid, Spain.
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12
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Abstract
IMPACT STATEMENT Advances in the understanding of the biophysics of membranes, the nonenzymatic and enzymatic polymerization of RNA, and in the design of complex chemical reaction networks have led to a new, integrated way of viewing the shared chemistry needed to sustain life. Although a protocell capable of Darwinian evolution has yet to be built, the seemingly disparate pieces are beginning to fit together. At the very least, better cellular mimics are on the horizon that will likely teach us much about the physicochemical underpinnings of cellular life.
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13
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Bonfio C, Caumes C, Duffy CD, Patel BH, Percivalle C, Tsanakopoulou M, Sutherland JD. Length-Selective Synthesis of Acylglycerol-Phosphates through Energy-Dissipative Cycling. J Am Chem Soc 2019; 141:3934-3939. [PMID: 30767518 PMCID: PMC6506141 DOI: 10.1021/jacs.8b12331] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
The main aim of origins
of life research is to find a plausible
sequence of transitions from prebiotic chemistry to nascent biology.
In this context, understanding how and when phospholipid membranes
appeared on early Earth is critical to elucidating the prebiotic pathways
that led to the emergence of primitive cells. Here we show that exposing
glycerol-2-phosphate to acylating agents leads to the formation of
a library of acylglycerol-phosphates. Medium-chain acylglycerol-phosphates
were found to self-assemble into vesicles stable across a wide range
of conditions and capable of retaining mono- and oligonucleotides.
Starting with a mixture of activated carboxylic acids of different
lengths, iterative cycling of acylation and hydrolysis steps allowed
for the selection of longer-chain acylglycerol-phosphates. Our results
suggest that a selection pathway based on energy-dissipative cycling
could have driven the selective synthesis of phospholipids on early
Earth.
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Affiliation(s)
- Claudia Bonfio
- Medical Research Council Laboratory of Molecular Biology , Cambridge Biomedical Campus, Francis Crick Avenue , Cambridge CB2 0QH , United Kingdom
| | - Cécile Caumes
- Medical Research Council Laboratory of Molecular Biology , Cambridge Biomedical Campus, Francis Crick Avenue , Cambridge CB2 0QH , United Kingdom
| | - Colm D Duffy
- Medical Research Council Laboratory of Molecular Biology , Cambridge Biomedical Campus, Francis Crick Avenue , Cambridge CB2 0QH , United Kingdom
| | - Bhavesh H Patel
- Medical Research Council Laboratory of Molecular Biology , Cambridge Biomedical Campus, Francis Crick Avenue , Cambridge CB2 0QH , United Kingdom
| | - Claudia Percivalle
- Medical Research Council Laboratory of Molecular Biology , Cambridge Biomedical Campus, Francis Crick Avenue , Cambridge CB2 0QH , United Kingdom
| | - Maria Tsanakopoulou
- Medical Research Council Laboratory of Molecular Biology , Cambridge Biomedical Campus, Francis Crick Avenue , Cambridge CB2 0QH , United Kingdom
| | - John D Sutherland
- Medical Research Council Laboratory of Molecular Biology , Cambridge Biomedical Campus, Francis Crick Avenue , Cambridge CB2 0QH , United Kingdom
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Mutschler H, Taylor AI, Porebski BT, Lightowlers A, Houlihan G, Abramov M, Herdewijn P, Holliger P. Random-sequence genetic oligomer pools display an innate potential for ligation and recombination. eLife 2018; 7:43022. [PMID: 30461419 PMCID: PMC6289569 DOI: 10.7554/elife.43022] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 11/16/2018] [Indexed: 02/06/2023] Open
Abstract
Recombination, the exchange of information between different genetic polymer strands, is of fundamental importance in biology for genome maintenance and genetic diversification and is mediated by dedicated recombinase enzymes. Here, we describe an innate capacity for non-enzymatic recombination (and ligation) in random-sequence genetic oligomer pools. Specifically, we examine random and semi-random eicosamer (N20) pools of RNA, DNA and the unnatural genetic polymers ANA (arabino-), HNA (hexitol-) and AtNA (altritol-nucleic acids). While DNA, ANA and HNA pools proved inert, RNA (and to a lesser extent AtNA) pools displayed diverse modes of spontaneous intermolecular recombination, connecting recombination mechanistically to the vicinal ring cis-diol configuration shared by RNA and AtNA. Thus, the chemical constitution that renders both susceptible to hydrolysis emerges as the fundamental determinant of an innate capacity for recombination, which is shown to promote a concomitant increase in compositional, informational and structural pool complexity and hence evolutionary potential.
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Affiliation(s)
| | | | | | | | | | - Mikhail Abramov
- REGA Institute, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Piet Herdewijn
- REGA Institute, Katholieke Universiteit Leuven, Leuven, Belgium
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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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Todisco M, Fraccia TP, Smith GP, Corno A, Bethge L, Klussmann S, Paraboschi EM, Asselta R, Colombo D, Zanchetta G, Clark NA, Bellini T. Nonenzymatic Polymerization into Long Linear RNA Templated by Liquid Crystal Self-Assembly. ACS NANO 2018; 12:9750-9762. [PMID: 30280566 DOI: 10.1021/acsnano.8b05821] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Self-synthesizing materials, in which supramolecular structuring enhances the formation of new molecules that participate to the process, represent an intriguing notion to account for the first appearance of biomolecules in an abiotic Earth. We present here a study of the abiotic formation of interchain phosphodiester bonds in solutions of short RNA oligomers in various states of supramolecular arrangement and their reaction kinetics. We found a spectrum of conditions in which RNA oligomers self-assemble and phase separate into highly concentrated ordered fluid liquid crystal (LC) microdomains. We show that such supramolecular state provides a template guiding their ligation into hundred-bases long chains. The quantitative analysis presented here demonstrates that nucleic acid LC boosts the rate of end-to-end ligation and suppresses the formation of the otherwise dominant cyclic oligomers. These results strengthen the concept of supramolecular ordering as an efficient pathway toward the emergence of the RNA World in the primordial Earth.
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Affiliation(s)
- Marco Todisco
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale , Università di Milano , via Vanvitelli 32 , 20129 Milano , Italy
| | - Tommaso P Fraccia
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale , Università di Milano , via Vanvitelli 32 , 20129 Milano , Italy
- Dipartimento di Scienze Umane e Promozione della Qualità della Vita , Università San Raffaele di Roma , via di Val Cannuta, 247 , I-00166 Roma , Italy
| | - Greg P Smith
- Department of Physics and Soft Materials Research Center , University of Colorado , Boulder , Colorado 80309-0390 , United States
| | - Andrea Corno
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale , Università di Milano , via Vanvitelli 32 , 20129 Milano , Italy
| | | | | | - Elvezia M Paraboschi
- Department of Biomedical Sciences , Humanitas University , via Rita Levi Montalcini 4 , Pieve Emanuele, Milano I-20090 , Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences , Humanitas University , via Rita Levi Montalcini 4 , Pieve Emanuele, Milano I-20090 , Italy
- Humanitas Clinical and Research Center , via Alessandro Manzoni 56 , Rozzano, Milano I-20089 , Italy
| | - Diego Colombo
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale , Università di Milano , via Vanvitelli 32 , 20129 Milano , Italy
| | - Giuliano Zanchetta
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale , Università di Milano , via Vanvitelli 32 , 20129 Milano , Italy
| | - Noel A Clark
- Department of Physics and Soft Materials Research Center , University of Colorado , Boulder , Colorado 80309-0390 , United States
| | - Tommaso Bellini
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale , Università di Milano , via Vanvitelli 32 , 20129 Milano , Italy
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17
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Abstract
The general notion of an "RNA world" is that, in the early development of life on the Earth, genetic continuity was assured by the replication of RNA, and RNA molecules were the chief agents of catalytic function. Assuming that all of the components of RNA were available in some prebiotic locale, these components could have assembled into activated nucleotides that condensed to form RNA polymers, setting the stage for the chemical replication of polynucleotides through RNA-templated RNA polymerization. If a sufficient diversity of RNAs could be copied with reasonable rate and fidelity, then Darwinian evolution would begin with RNAs that facilitated their own reproduction enjoying a selective advantage. The concept of a "protocell" refers to a compartment where replication of the primitive genetic material took place and where primitive catalysts gave rise to products that accumulated locally for the benefit of the replicating cellular entity. Replication of both the protocell and its encapsulated genetic material would have enabled natural selection to operate based on the differential fitness of competing cellular entities, ultimately giving rise to modern cellular life.
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Affiliation(s)
- Gerald F Joyce
- The Salk Institute for Biological Studies, La Jolla, California 92037
| | - Jack W Szostak
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114
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18
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Liu Z, Mariani A, Wu L, Ritson D, Folli A, Murphy D, Sutherland J. Tuning the reactivity of nitriles using Cu(ii) catalysis - potentially prebiotic activation of nucleotides. Chem Sci 2018; 9:7053-7057. [PMID: 30310625 PMCID: PMC6137443 DOI: 10.1039/c8sc02513d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 07/23/2018] [Indexed: 11/30/2022] Open
Abstract
A synergistic system was established involving activating nucleotides with nitriles using Cu(ii) and protecting RNA degradation by byproducts of alpha-aminonitriles.
During the transition from prebiotic chemistry to biology, a period of solution-phase, non-enzymatic activation of (oligo)nucleotides must have occurred, and accordingly, a mechanism for phosphate activation must have existed. Herein, we detail results of an investigation into prebiotic phosphate activation chemistry using simple, prebiotically available nitriles whose reactivity is increased by Cu2+ ions. Furthermore, although Cu2+ ions are known to catalyse the hydrolysis of phosphodiester bonds, we found this deleterious activity to be almost completely suppressed by inclusion of amino acids or dipeptides, which may suggest a productive relationship between protein and RNA from the outset.
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Affiliation(s)
- Ziwei Liu
- MRC Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge Biomedical Campus , CB2 0QH , UK .
| | - Angelica Mariani
- MRC Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge Biomedical Campus , CB2 0QH , UK .
| | - Longfei Wu
- MRC Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge Biomedical Campus , CB2 0QH , UK .
| | - Dougal Ritson
- MRC Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge Biomedical Campus , CB2 0QH , UK .
| | - Andrea Folli
- School of Chemistry , Cardiff University , Park Place , Cardiff CF10 3AT , UK
| | - Damien Murphy
- School of Chemistry , Cardiff University , Park Place , Cardiff CF10 3AT , UK
| | - John Sutherland
- MRC Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge Biomedical Campus , CB2 0QH , UK .
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19
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Fernández-García C, Grefenstette NM, Powner MW. Selective aqueous acetylation controls the photoanomerization of α-cytidine-5'-phosphate. Chem Commun (Camb) 2018; 54:4850-4853. [PMID: 29697101 DOI: 10.1039/c8cc01929k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids are central to information transfer and replication in living systems, providing the molecular foundations of Darwinian evolution. Here we report that prebiotic acetylation of the non-natural, but prebiotically plausible, ribonucleotide α-cytidine-5'-phosphate, selectively protects the vicinal diol moiety. Vicinal diol acetylation blocks oxazolidinone formation and prevents C2'-epimerization upon irradiation with UV-light. Consequently, acetylation enhances (4-fold) the photoanomerization of α-cytidine-5'-phosphate to produce the natural β-pyrimidine ribonucleotide-5'-phosphates required for RNA synthesis.
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20
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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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21
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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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22
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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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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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