1
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Mittal S, Nisler C, Szostak JW. Simulations predict preferred Mg 2+ coordination in a nonenzymatic primer-extension reaction center. Biophys J 2024; 123:1579-1591. [PMID: 38702884 PMCID: PMC11214020 DOI: 10.1016/j.bpj.2024.04.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 04/24/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024] Open
Abstract
The mechanism by which genetic information was copied prior to the evolution of ribozymes is of great interest because of its importance to the origin of life. The most effective known process for the nonenzymatic copying of an RNA template is primer extension by a two-step pathway in which 2-aminoimidazole-activated nucleotides first react with each other to form an imidazolium-bridged intermediate that subsequently reacts with the primer. Reaction kinetics, structure-activity relationships, and X-ray crystallography have provided insight into the overall reaction mechanism, but many puzzles remain. In particular, high concentrations of Mg2+ are required for efficient primer extension, but the mechanism by which Mg2+ accelerates primer extension remains unknown. By analogy with the mechanism of DNA and RNA polymerases, a role for Mg2+ in facilitating the deprotonation of the primer 3'-hydroxyl is often assumed, but no catalytic metal ion is seen in crystal structures of the primer-extension complex. To explore the potential effects of Mg2+ binding in the reaction center, we performed atomistic molecular dynamics simulations of a series of modeled complexes in which a Mg2+ ion was placed in the reaction center with inner-sphere coordination with different sets of functional groups. Our simulations suggest that coordination of a Mg2+ ion with both O3' of the terminal primer nucleotide and the pro-Sp nonbridging oxygen of the reactive phosphate of an imidazolium-bridged dinucleotide would help to pre-organize the structure of the primer/template substrate complex to favor the primer-extension reaction. Our results suggest that the catalytic metal ion may play an important role in overcoming electrostatic repulsion between a deprotonated O3' and the reactive phosphate of the bridged dinucleotide and lead to testable predictions of the mode of Mg2+ binding that is most relevant to catalysis of primer extension.
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Affiliation(s)
- Shriyaa Mittal
- Howard Hughes Medical Institute, Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts; Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Collin Nisler
- Howard Hughes Medical Institute, Department of Chemistry, University of Chicago, Chicago, Illinois
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts; Department of Genetics, Harvard Medical School, Boston, Massachusetts; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts; Howard Hughes Medical Institute, Department of Chemistry, University of Chicago, Chicago, Illinois.
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2
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Calaça Serrão A, Wunnava S, Dass AV, Ufer L, Schwintek P, Mast CB, Braun D. High-Fidelity RNA Copying via 2',3'-Cyclic Phosphate Ligation. J Am Chem Soc 2024; 146:8887-8894. [PMID: 38503430 PMCID: PMC10995993 DOI: 10.1021/jacs.3c10813] [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: 10/02/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 03/21/2024]
Abstract
Templated ligation offers an efficient approach to replicate long strands in an RNA world. The 2',3'-cyclic phosphate (>P) is a prebiotically available activation that also forms during RNA hydrolysis. Using gel electrophoresis and high-performance liquid chromatography, we found that the templated ligation of RNA with >P proceeds in simple low-salt aqueous solutions with 1 mM MgCl2 under alkaline pH ranging from 9 to 11 and temperatures from -20 to 25 °C. No additional catalysts were required. In contrast to previous reports, we found an increase in the number of canonical linkages to 50%. The reaction proceeds in a sequence-specific manner, with an experimentally determined ligation fidelity of 82% at the 3' end and 91% at the 5' end of the ligation site. With splinted oligomers, five ligations created a 96-mer strand, demonstrating a pathway for the ribozyme assembly. Due to the low salt requirements, the ligation conditions will be compatible with strand separation. Templated ligation mediated by 2',3'-cyclic phosphate in alkaline conditions therefore offers a performant replication and elongation reaction for RNA on early Earth.
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Affiliation(s)
- Adriana Calaça Serrão
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
| | - Sreekar Wunnava
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
| | - Avinash V. Dass
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
- Department
of Physics and Astronomy, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S4M1, Canada
| | - Lennard Ufer
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
| | - Philipp Schwintek
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
| | - Christof B. Mast
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
| | - Dieter Braun
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
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3
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Callaghan KL, Sherrell PC, Ellis AV. The Impact of Activating Agents on Non-Enzymatic Nucleic Acid Extension Reactions. Chembiochem 2024; 25:e202300859. [PMID: 38282207 DOI: 10.1002/cbic.202300859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/21/2024] [Accepted: 01/28/2024] [Indexed: 01/30/2024]
Abstract
Non-enzymatic template-directed primer extension is increasingly being studied for the production of RNA and DNA. These reactions benefit from producing RNA or DNA in an aqueous, protecting group free system, without the need for expensive enzymes. However, these primer extension reactions suffer from a lack of fidelity, low reaction rates, low overall yields, and short primer extension lengths. This review outlines a detailed mechanistic pathway for non-enzymatic template-directed primer extension and presents a review of the thermodynamic driving forces involved in entropic templating. Through the lens of entropic templating, the rate and fidelity of a reaction are shown to be intrinsically linked to the reactivity of the activating agent used. Thus, a strategy is discussed for the optimization of non-enzymatic template-directed primer extension, providing a path towards cost-effective in vitro synthesis of RNA and DNA.
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Affiliation(s)
- Kimberley L Callaghan
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Peter C Sherrell
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria, 3010, Australia
- School of Science, RMIT University, Melbourne, Victoria, 3000, Australia
| | - Amanda V Ellis
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria, 3010, Australia
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4
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Patki GM, Rajamani S. Nonenzymatic RNA replication in a mixture of 'spent' nucleotides. FEBS Lett 2023; 597:3125-3134. [PMID: 38058189 DOI: 10.1002/1873-3468.14785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/23/2023] [Accepted: 11/19/2023] [Indexed: 12/08/2023]
Abstract
Nonenzymatic template-directed replication would have been affected by co-solutes in a heterogeneous prebiotic soup due to lack of enzymatic machinery. Unlike in contemporary biology, these reactions use chemically activated nucleotides, which undergo rapid hydrolysis forming nucleoside monophosphates ('spent' monomers). These co-solutes cannot extend the primer but continue to base pair with the template, thereby interfering with replication. We, therefore, aimed to understand how a mixture of 'spent' ribonucleotides would affect nonenzymatic replication. We observed the inhibition of replication in the mixture, wherein the predominant contribution came from the cognate Watson-Crick monomer, showing potential sequence dependence. Our study highlights how nonenzymatic RNA replication would have been directly affected by co-solutes, with ramifications for the emergence of functional polymers in an RNA World.
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Affiliation(s)
- Gauri M Patki
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, India
| | - Sudha Rajamani
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, India
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5
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Welsch F, Kervio E, Tremmel P, Richert C. Prolinyl Nucleotides Drive Enzyme-Free Genetic Copying of RNA. Angew Chem Int Ed Engl 2023; 62:e202307591. [PMID: 37382466 DOI: 10.1002/anie.202307591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 06/30/2023]
Abstract
Proline is one of the proteinogenic amino acids. It is found in all kingdoms of life. It also has remarkable activity as an organocatalyst and is of structural importance in many folded polypeptides. Here, we show that prolinyl nucleotides with a phosphoramidate linkage are active building blocks in enzyme- and ribozyme-free copying of RNA in the presence of monosubstituted imidazoles as organocatalysts. Both dinucleotides and mononucleotides are incorporated at the terminus of RNA primers in aqueous buffer, as instructed by the template sequence, in up to eight consecutive extension steps. Our results show that condensation products of amino acids and ribonucleotides can act like nucleoside triphosphates in media devoid of enzymes or ribozymes. Prolinyl nucleotides are metastable building blocks, readily activated by catalysts, helping to explain why the combination of α-amino acids and nucleic acids was selected in molecular evolution.
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Affiliation(s)
- Franziska Welsch
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
| | - Eric Kervio
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
| | - Peter Tremmel
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
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6
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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 Chemistry University of Stuttgart 70569 Stuttgart Germany
| | - Daniel Pfeffer
- Institute of Organic Chemistry University of Stuttgart 70569 Stuttgart Germany
| | - Bernhard Altaner
- Physics of Complex Biosystems Technical University Munich 85748 Garching Germany
| | - Eric Kervio
- Institute of Organic Chemistry University of Stuttgart 70569 Stuttgart Germany
| | - Franziska Welsch
- Institute of Organic Chemistry University of Stuttgart 70569 Stuttgart Germany
| | - Ulrich Gerland
- Physics of Complex Biosystems Technical University Munich 85748 Garching Germany
| | - Clemens Richert
- Institute of Organic Chemistry University of Stuttgart 70569 Stuttgart Germany
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7
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Freeze-thaw cycles enable a prebiotically plausible and continuous pathway from nucleotide activation to nonenzymatic RNA copying. Proc Natl Acad Sci U S A 2022; 119:e2116429119. [PMID: 35446612 PMCID: PMC9169909 DOI: 10.1073/pnas.2116429119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The replication of RNA without the aid of evolved enzymes may have enabled the inheritance of useful molecular functions during the origin of life. Template-directed RNA copying is a posited step in RNA replication. Key steps on the path to copying of RNA templates have been studied in isolation, including chemical nucleotide activation, generation of a key reactive intermediate, and template-directed polymerization. Here we report a prebiotically plausible scenario under which these reactions can happen together under mutually compatible conditions. Thus, this pathway could potentially have operated in nature without the complicating requirement for exchange of materials between distinct environments. Nonenzymatic template-directed RNA copying using chemically activated nucleotides is thought to have played a key role in the emergence of genetic information on the early Earth. A longstanding question concerns the number and nature of different environments that might have been necessary to enable all of the steps from nucleotide synthesis to RNA copying. Here we explore three sequential steps from this overall pathway: nucleotide activation, synthesis of imidazolium-bridged dinucleotides, and template-directed RNA copying. We find that all three steps can take place in one reaction mixture undergoing multiple freeze-thaw cycles. Recent experiments have demonstrated a potentially prebiotic methyl isocyanide-based nucleotide activation chemistry. However, the original version of this approach is incompatible with nonenzymatic RNA copying because the high required concentration of the imidazole activating group prevents the accumulation of the essential imidazolium-bridged dinucleotide. Here we report that ice eutectic phase conditions facilitate not only the methyl isocyanide-based activation of ribonucleotide 5′-monophosphates with stoichiometric 2-aminoimidazole, but also the subsequent conversion of these activated mononucleotides into imidazolium-bridged dinucleotides. Furthermore, this one-pot approach is compatible with template-directed RNA copying in the same reaction mixture. Our results suggest that the simple and common environmental fluctuation of freeze-thaw cycles could have played an important role in prebiotic nucleotide activation and nonenzymatic RNA copying.
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8
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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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9
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Rodrigues F, Georgelin T, Rigaud B, Zhuang G, Fonseca MG, Valtchev V, Jaber M. Deadlocks of adenine ribonucleotide synthesis: evaluation of adsorption and condensation reactions in a zeolite micropore space. Inorg Chem Front 2022. [DOI: 10.1039/d2qi00837h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, we report on adenine, d-ribose, and monophosphate adsorption/co-adsorption into the synthetic analog of the zeolite mineral mordenite followed by drying at 50 °C and thermal activation at 150 °C under an argon atmosphere.
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Affiliation(s)
- Francisco Rodrigues
- Sorbonne University, CNRS UMR 8220, Laboratoire d'Archéologie Moléculaire et Structurale, 4 place Jussieu, F-75005 Paris, France
- State University of Paraíba, UEPB, Department of Chemistry, Campina Grande, Paraíba, Brazil
| | - Thomas Georgelin
- Centre de Biophysique Moléculaire, CNRS, Rue Charles Sadron, 45000 Orléans, France
| | - Baptiste Rigaud
- CNRS Institut des Matériaux de Paris Centre (FR2482), 4 place jussieu, 75005 Paris, France
| | - Guanzheng Zhuang
- Sorbonne University, CNRS UMR 8220, Laboratoire d'Archéologie Moléculaire et Structurale, 4 place Jussieu, F-75005 Paris, France
| | | | - Valentin Valtchev
- Normandy University, Laboratoire Catalyse & Spectrochimie, ENSICAEN, 6 bl Maréchal Juin, 14050 Caen, France
| | - Maguy Jaber
- Sorbonne University, CNRS UMR 8220, Laboratoire d'Archéologie Moléculaire et Structurale, 4 place Jussieu, F-75005 Paris, France
- Institut Universitaire de France, France
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10
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Han J, Kervio E, Richert C. High Fidelity Enzyme-Free Primer Extension with an Ethynylpyridone Thymidine Analog. Chemistry 2021; 27:15918-15921. [PMID: 34559417 PMCID: PMC9293356 DOI: 10.1002/chem.202102996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Indexed: 11/07/2022]
Abstract
High fidelity base pairing is important for the transmission of genetic information. Weak base pairs can lower fidelity, complicating sequencing, amplification and replication of DNA. Thymidine 5′‐monophosphate (TMP) is the most weakly pairing nucleotide among the canonical deoxynucleotides, causing high errors rates in enzyme‐free primer extension. Here we report the synthesis of an ethynylpyridone C‐nucleoside analog of 3′‐amino‐2′,3′‐dideoxythymidine monophosphate and its incorporation in a growing strand by enzyme‐free primer extension. The ethynylpyridone C‐nucleotide accelerates extension more than five‐fold, reduces misincorporation and readily displaces TMP in competition experiments. The results bode well for the use of the C‐nucleoside as replacements for thymidine in practical applications.
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Affiliation(s)
- Jianyang Han
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Eric Kervio
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Clemens Richert
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
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11
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Murayama K, Okita H, Kuriki T, Asanuma H. Nonenzymatic polymerase-like template-directed synthesis of acyclic L-threoninol nucleic acid. Nat Commun 2021; 12:804. [PMID: 33547322 PMCID: PMC7864931 DOI: 10.1038/s41467-021-21128-0] [Citation(s) in RCA: 6] [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: 08/24/2020] [Accepted: 01/04/2021] [Indexed: 02/08/2023] Open
Abstract
Evolution of xeno nucleic acid (XNA) world essentially requires template-directed synthesis of XNA polymers. In this study, we demonstrate template-directed synthesis of an acyclic XNA, acyclic L-threoninol nucleic acid (L-aTNA), via chemical ligation mediated by N-cyanoimidazole. The ligation of an L-aTNA fragment on an L-aTNA template is significantly faster and occurs in considerably higher yield than DNA ligation. Both L-aTNA ligation on a DNA template and DNA ligation on an L-aTNA template are also observed. High efficiency ligation of trimer L-aTNA fragments to a template-bound primer is achieved. Furthermore, a pseudo primer extension reaction is demonstrated using a pool of random L-aTNA trimers as substrates. To the best of our knowledge, this is the first example of polymerase-like primer extension of XNA with all four nucleobases, generating phosphodiester bonding without any special modification. This technique paves the way for a genetic system of the L-aTNA world.
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Affiliation(s)
- Keiji Murayama
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan.
| | - Hikari Okita
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Takumi Kuriki
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan.
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12
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Zhang SJ, Duzdevich D, Szostak JW. Potentially Prebiotic Activation Chemistry Compatible with Nonenzymatic RNA Copying. J Am Chem Soc 2020; 142:14810-14813. [PMID: 32794700 PMCID: PMC9594304 DOI: 10.1021/jacs.0c05300] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
The nonenzymatic replication of ribonucleic
acid (RNA) may have
enabled the propagation of genetic information during the origin of
life. RNA copying can be initiated in the laboratory with chemically
activated nucleotides, but continued copying requires a source of
chemical energy for in situ nucleotide activation.
Recent work has illuminated a potentially prebiotic cyanosulfidic
chemistry that activates nucleotides, but its application to nonenzymatic
RNA copying had not been demonstrated. Here, we report a novel pathway
that activates RNA nucleotides in a manner compatible with template-directed
nonenzymatic copying. We show that this pathway, which we refer to
as bridge-forming activation, selectively yields the reactive imidazolium-bridged
dinucleotide intermediate required for copying. Our results will enable
more realistic simulations of RNA propagation based on continuous in situ nucleotide activation.
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Affiliation(s)
- Stephanie J Zhang
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Daniel Duzdevich
- 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
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States.,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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13
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Motsch S, Pfeffer D, Richert C. 2'/3' Regioselectivity of Enzyme-Free Copying of RNA Detected by NMR. Chembiochem 2020; 21:2013-2018. [PMID: 32017335 PMCID: PMC7497262 DOI: 10.1002/cbic.202000014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Indexed: 11/06/2022]
Abstract
The RNA-templated extension of oligoribonucleotides by nucleotides produces either a 3',5' or a 2',5'-phosphodiester. Nature controls the regioselectivity during RNA chain growth with polymerases, but enzyme-free versions of genetic copying have modest specificity. Thus far, enzymatic degradation of products, combined with chromatography or electrophoresis, has been the preferred mode of detecting 2',5'-diesters produced in enzyme-free reactions. This approach hinges on the substrate specificity of nucleases, and is not suitable for in situ monitoring. Here we report how 1 H NMR spectroscopy can be used to detect the extension of self-templating RNA hairpins and that this reveals the regioisomeric nature of the newly formed phosphodiesters. We studied several modes of activating nucleotides, including imidazolides, a pyridinium phosphate, an active ester, and in situ activation with carbodiimide and organocatalyst. Conversion into the desired extension product ranged from 20 to 90 %, depending on the leaving group. Integration of the resonances of H1' protons of riboses and H5 protons of pyrimidines gave regioselectivities ranging from 40:60 to 85:15 (3',5' to 2',5' diester), but no simple correlation between 3',5' selectivity and yield. Our results show how monitoring with a high-resolution technique sheds a new light on a process that may have played an important role during the emergence of life.
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Affiliation(s)
- Sebastian Motsch
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Daniel Pfeffer
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
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14
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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: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [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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15
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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: 41] [Impact Index Per Article: 8.2] [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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16
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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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17
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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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18
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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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19
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Zhang W, Walton T, Li L, Szostak JW. Crystallographic observation of nonenzymatic RNA primer extension. eLife 2018; 7:36422. [PMID: 29851379 PMCID: PMC5980232 DOI: 10.7554/elife.36422] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 04/26/2018] [Indexed: 12/31/2022] Open
Abstract
The importance of genome replication has inspired detailed crystallographic studies of enzymatic DNA/RNA polymerization. In contrast, the mechanism of nonenzymatic polymerization is less well understood, despite its critical role in the origin of life. Here we report the direct observation of nonenzymatic RNA primer extension through time-resolved crystallography. We soaked crystals of an RNA primer-template-dGMP complex with guanosine-5′-phosphoro-2-aminoimidazolide for increasing times. At early times we see the activated ribonucleotides bound to the template, followed by formation of the imidazolium-bridged dinucleotide intermediate. At later times, we see a new phosphodiester bond forming between the primer and the incoming nucleotide. The intermediate is pre-organized because of the constraints of base-pairing with the template and hydrogen bonding between the imidazole amino group and both flanking phosphates. Our results provide atomic-resolution insight into the mechanism of nonenzymatic primer extension, and set the stage for further structural dissection and optimization of the RNA copying process. Enzymes speed up chemical reactions that are essential to life. Most enzymes are proteins, but some are molecules of ribonucleic acid or RNA. Like DNA, RNA is made from a chain of building blocks called nucleotides. In modern organisms, protein-based enzymes build RNAs by linking nucleotides together, while the building blocks of proteins are linked by an RNA-based enzyme at the heart of a structure called a ribosome. The earliest life on Earth most likely relied only on RNA-based enzymes, but during the emergence of life, scientists believe that RNA molecules must have replicated spontaneously before dedicated RNA-based enzymes had evolved. How RNA could replicate without enzymes has been a puzzle for decades. Recently, scientists discovered a previously unsuspected chemical intermediate that forms during the process, and hypothesized that this molecule’s special structure is what enables the chemical reaction that adds new nucleotides to a growing strand of RNA. To test this hypothesis, Zhang et al. diffused free RNA nucleotides into a crystalized complex containing template strands of RNA attached to short pieces of RNA called primers, which kick-start replication. Then, the crystals were frozen at various intervals and viewed using X-rays. This allowed Zhang et al. to observe the structural changes that occurred over time as the compounds reacted. The approach first revealed that the free nucleotides had paired with complementary nucleotides on the RNA template strands. Then, pairs of free nucleotides reacted with each other to form the intermediate. Finally, the intermediate reacted with the primer, forming a new bond that connects the RNA primer to one of the nucleotides of the intermediate, while the other nucleotide of the intermediate was released as a free nucleotide. This experiment confirms that the specific structure of the intermediate molecule promotes RNA replication without help from enzymes. These findings will benefit chemists and biologists who study how RNA evolves and replicates. Future research building upon this work will deepen scientific understanding of the environmental conditions that were required for life to appear on Earth.
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Affiliation(s)
- Wen Zhang
- Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, United States.,Department of Genetics, Harvard Medical School, Boston, United States.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States
| | - Travis Walton
- Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, United States.,Department of Genetics, Harvard Medical School, Boston, United States.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States
| | - Li Li
- Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, United States.,Department of Genetics, Harvard Medical School, Boston, United States.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States
| | - Jack W Szostak
- Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, United States.,Department of Genetics, Harvard Medical School, Boston, United States.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States
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20
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Attwater J, Raguram A, Morgunov AS, Gianni E, Holliger P. Ribozyme-catalysed RNA synthesis using triplet building blocks. eLife 2018; 7:35255. [PMID: 29759114 PMCID: PMC6003772 DOI: 10.7554/elife.35255] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 05/09/2018] [Indexed: 12/18/2022] Open
Abstract
RNA-catalyzed RNA replication is widely believed to have supported a primordial biology. However, RNA catalysis is dependent upon RNA folding, and this yields structures that can block replication of such RNAs. To address this apparent paradox, we have re-examined the building blocks used for RNA replication. We report RNA-catalysed RNA synthesis on structured templates when using trinucleotide triphosphates (triplets) as substrates, catalysed by a general and accurate triplet polymerase ribozyme that emerged from in vitro evolution as a mutualistic RNA heterodimer. The triplets cooperatively invaded and unraveled even highly stable RNA secondary structures, and support non-canonical primer-free and bidirectional modes of RNA synthesis and replication. Triplet substrates thus resolve a central incongruity of RNA replication, and here allow the ribozyme to synthesise its own catalytic subunit ‘+’ and ‘–’ strands in segments and assemble them into a new active ribozyme. Life as we know it relies on three types of molecules: DNA, which stores genetic information; proteins that carry out the chemical reactions necessary for life; and RNA, which relays information between the two. However, some scientists think that before life adopted DNA and proteins, it relied primarily on RNA. Like DNA, strands of RNA contain genetic data. Yet, some RNA strands can also fold to form ribozymes, 3D structures that could have guided life’s chemical processes the way proteins do now. For early life to be built on RNA, though, this molecule must have had the ability to make copies of itself. This duplication is a chemical reaction that could be driven by an ‘RNA replicase’ ribozyme. RNA strands are made of four different letters attached to each other in a specific order. When RNA is copied, one strand acts as a template, and a replicase ribozyme would accurately guide which letters are added to the strand under construction. However, no replicase ribozyme has been observed in existing life forms; this has led scientists to try to artificially create RNA replicase ribozymes that could copy themselves. Until now, the best approaches have assumed that a replicase would add building blocks formed of a single letter one by one to grow a new strand. Yet, although ribozymes can be made to copy straight RNA templates this way, folded RNA templates – including the replicase ribozyme itself – impede copying. In this apparent paradox, a ribozyme needs to fold to copy RNA, but when folded, is itself copied poorly. Here, Attwater et al. wondered if choosing different building blocks might overcome this contradiction. Biochemical techniques were used to engineer a ribozyme that copies RNA strands by adding letters not one-by-one, but three-by-three. Using three-letter ‘triplet’ building blocks, this new ribozyme can copy various folded RNA strands, including the active part of its own sequence. This is because triplet building blocks have different, and sometimes unexpected, chemical properties compared to single-letter blocks. For example, these triplets work together to bind tightly to RNA strands and unravel structures that block RNA copying. All life on Earth today uses a triplet RNA code to make proteins from DNA, and these experiments showed how RNA triplets might have helped RNA sustain early life forms. Further work is now needed to improve the ribozyme designed by Attwater et al. for efficient self-copying.
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Affiliation(s)
- James Attwater
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Aditya Raguram
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Alexey S Morgunov
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Edoardo Gianni
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
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21
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Sosson M, Richert C. Enzyme-free genetic copying of DNA and RNA sequences. Beilstein J Org Chem 2018; 14:603-617. [PMID: 29623122 PMCID: PMC5870163 DOI: 10.3762/bjoc.14.47] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 02/20/2018] [Indexed: 11/23/2022] Open
Abstract
The copying of short DNA or RNA sequences in the absence of enzymes is a fascinating reaction that has been studied in the context of prebiotic chemistry. It involves the incorporation of nucleotides at the terminus of a primer and is directed by base pairing. The reaction occurs in aqueous medium and leads to phosphodiester formation after attack of a nucleophilic group of the primer. Two aspects of this reaction will be discussed in this review. One is the activation of the phosphate that drives what is otherwise an endergonic reaction. The other is the improved mechanistic understanding of enzyme-free primer extension that has led to a quantitative kinetic model predicting the yield of the reaction over the time course of an assay. For a successful modeling of the reaction, the strength of the template effect, the inhibitory effect of spent monomers, and the rate constants of the chemical steps have to be determined experimentally. While challenges remain for the high fidelity copying of long stretches of DNA or RNA, the available data suggest that enzyme-free primer extension is a more powerful reaction than previously thought.
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Affiliation(s)
- 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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22
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Zhang W, Tam CP, Zhou L, Oh SS, Wang J, Szostak JW. Structural Rationale for the Enhanced Catalysis of Nonenzymatic RNA Primer Extension by a Downstream Oligonucleotide. J Am Chem Soc 2018; 140:2829-2840. [PMID: 29411978 PMCID: PMC6326529 DOI: 10.1021/jacs.7b11750] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Indexed: 01/28/2023]
Abstract
Nonenzymatic RNA primer extension by activated mononucleotides has long served as a model for the study of prebiotic RNA copying. We have recently shown that the rate of primer extension is greatly enhanced by the formation of an imidazolium-bridged dinucleotide between the incoming monomer and a second, downstream activated monomer. However, the rate of primer extension is further enhanced if the downstream monomer is replaced by an activated oligonucleotide. Even an unactivated downstream oligonucleotide provides a modest enhancement in the rate of reaction of a primer with a single activated monomer. Here we study the mechanism of these effects through crystallographic studies of RNA complexes with the recently synthesized nonhydrolyzable substrate analog, guanosine 5'-(4-methylimidazolyl)-phosphonate (ICG). ICG mimics 2-methylimidazole activated guanosine-5'-phosphate (2-MeImpG), a commonly used substrate in nonenzymatic primer extension experiments. We present crystal structures of primer-template complexes with either one or two ICG residues bound downstream of a primer. In both cases, the aryl-phosphonate moiety of the ICG adjacent to the primer is disordered. To investigate the effect of a downstream oligonucleotide, we transcribed a short RNA oligonucleotide with either a 5'-ICG residue, a 5'-phosphate or a 5'-hydroxyl. We then determined crystal structures of primer-template complexes with a bound ICG monomer sandwiched between the primer and each of the three downstream oligonucleotides. Surprisingly, all three oligonucleotides rigidify the ICG monomer conformation and position it for attack by the primer 3'-hydroxyl. Furthermore, when GpppG, an analog of the imidazolium-bridged intermediate, is sandwiched between an upstream primer and a downstream helper oligonucleotide, or covalently linked to the 5'-end of the downstream oligonucleotide, the complex is better preorganized for primer extension than in the absence of a downstream oligonucleotide. Our results suggest that a downstream helper oligonucleotide contributes to the catalysis of primer extension by favoring a reactive conformation of the primer-template-intermediate complex.
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Affiliation(s)
- Wen Zhang
- Howard
Hughes Medical Institute and Center for Computational and Integrative
Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department
of Genetics, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Chun Pong Tam
- Howard
Hughes Medical Institute 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 and Center for Computational and Integrative
Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department
of Genetics, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Seung Soo Oh
- Howard
Hughes Medical Institute and Center for Computational and Integrative
Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department
of Genetics, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Jiawei Wang
- School
of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jack W. Szostak
- Howard
Hughes Medical Institute and Center for Computational and Integrative
Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department
of Genetics, Harvard Medical School, Boston, Massachusetts 02114, United States
- Department
of Chemistry and Chemical Biology, Harvard
University, Cambridge, Massachusetts 02138, United States
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23
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Tam CP, Zhou L, Fahrenbach AC, Zhang W, Walton T, Szostak JW. Synthesis of a Nonhydrolyzable Nucleotide Phosphoroimidazolide Analogue That Catalyzes Nonenzymatic RNA Primer Extension. J Am Chem Soc 2018; 140:783-792. [PMID: 29251930 PMCID: PMC6326531 DOI: 10.1021/jacs.7b11623] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
We
report the synthesis of guanosine 5′-(4-methylimidazolyl)phosphonate
(ICG), the third member of a series of nonhydrolyzable nucleoside
5′-phosphoro-2-methylimidazolide (2-MeImpN) analogues designed
for mechanistic studies of nonenzymatic RNA primer extension. The
addition of a 2-MeImpN monomer to a primer is catalyzed by the presence
of a downstream activated monomer, yet the three nonhydrolyzable analogues
do not show catalytic effects under standard mildly basic primer extension
conditions. Surprisingly, ICG, which has a pKa similar to that of 2-MeImpG, is a modest catalyst of nonenzymatic
primer extension at acidic pH. Here we show that ICG reacts with 2-MeImpC
to form a stable 5′–5′-imidazole-bridged guanosine-cytosine
dinucleotide, with both a labile nitrogen–phosphorus and a
stable carbon–phosphorus linkage flanking the central imidazole
bridge. Cognate RNA primer–template complexes react with this
GC-dinucleotide by attack of the primer 3′-hydroxyl on the
activated N–P side of the 5′-5′-imidazole bridge.
These observations support the hypothesis that 5′–5′-imidazole-bridged
dinucleotides can bind to cognate RNA primer–template duplexes
and adopt appropriate conformations for subsequent phosphodiester
bond formation, consistent with our recent mechanistic proposal that
the formation of activated 5′–5′-imidazolium-bridged
dinucleotides is responsible for 2-MeImpN-driven primer extension.
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Affiliation(s)
- Chun Pong Tam
- 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.,Department of Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, 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 , 185 Cambridge Street, Boston, Massachusetts 02114, United States.,Department of Genetics, Harvard Medical School , 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Albert C Fahrenbach
- 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.,Department of Genetics, Harvard Medical School , 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.,Earth-Life Science Institute, Tokyo Institute of Technology , 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - 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.,Department of Genetics, Harvard Medical School , 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Travis Walton
- 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.,Program of Biological and Biomedical Sciences, Harvard Medical School , 25 Shattuck Street, Gordon Hall, 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 , 185 Cambridge Street, Boston, Massachusetts 02114, United States.,Department of Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, Cambridge, Massachusetts 02138, United States.,Department of Genetics, Harvard Medical School , 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.,Earth-Life Science Institute, Tokyo Institute of Technology , 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
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24
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Tam CP, Fahrenbach AC, Björkbom A, Prywes N, Izgu EC, Szostak JW. Downstream Oligonucleotides Strongly Enhance the Affinity of GMP to RNA Primer-Template Complexes. J Am Chem Soc 2017; 139:571-574. [PMID: 28055190 PMCID: PMC7547879 DOI: 10.1021/jacs.6b09760] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Indexed: 11/29/2022]
Abstract
Origins of life hypotheses often invoke a transitional phase of nonenzymatic template-directed RNA replication prior to the emergence of ribozyme-catalyzed copying of genetic information. Here, using NMR and ITC, we interrogate the binding affinity of guanosine 5'-monophosphate (GMP) for primer-template complexes when either another GMP, or a helper oligonucleotide, can bind downstream. Binding of GMP to a primer-template complex cannot be significantly enhanced by the possibility of downstream monomer binding, because the affinity of the downstream monomer is weaker than that of the first monomer. Strikingly, GMP binding affinity can be enhanced by ca. 2 orders of magnitude when a helper oligonucleotide is stably bound downstream of the monomer binding site. We compare these thermodynamic parameters to those previously reported for T7 RNA polymerase-mediated replication to help address questions of binding affinity in related nonenzymatic processes.
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Affiliation(s)
- Chun Pong Tam
- 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
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
| | - Albert C. Fahrenbach
- 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
- Earth
Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Anders Björkbom
- 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
- Department
of Biosciences, Åbo Akademi University, Åbo FI-20520, Finland
| | - Noam Prywes
- 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
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
| | - Enver Cagri Izgu
- 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
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
- Earth
Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
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25
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Reverte M, Barvik I, Vasseur JJ, Smietana M. RNA-directed off/on switch of RNase H activity using boronic ester formation. Org Biomol Chem 2017; 15:8204-8210. [DOI: 10.1039/c7ob02145c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new concept to modulate RNase H activity is presented based on the boronic acid/boronate switch.
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Affiliation(s)
- Maëva Reverte
- Institut des Biomolecules Max Mousseron
- IBMM UMR 5247 CNRS
- Université de Montpellier
- ENSCM
- 34095 Montpellier
| | - Ivan Barvik
- Institute of Physics
- Faculty of Mathematics and Physics
- Charles University
- 121 16 Prague 2
- Czech Republic
| | - Jean-Jacques Vasseur
- Institut des Biomolecules Max Mousseron
- IBMM UMR 5247 CNRS
- Université de Montpellier
- ENSCM
- 34095 Montpellier
| | - Michael Smietana
- Institut des Biomolecules Max Mousseron
- IBMM UMR 5247 CNRS
- Université de Montpellier
- ENSCM
- 34095 Montpellier
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26
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Benner SA. Unusual Hydrogen Bonding Patterns and the Role of the Backbone in Nucleic Acid Information Transfer. ACS CENTRAL SCIENCE 2016; 2:882-884. [PMID: 28058276 PMCID: PMC5200930 DOI: 10.1021/acscentsci.6b00344] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
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27
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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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28
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Walton T, Szostak JW. A Highly Reactive Imidazolium-Bridged Dinucleotide Intermediate in Nonenzymatic RNA Primer Extension. J Am Chem Soc 2016; 138:11996-2002. [PMID: 27552367 PMCID: PMC6326528 DOI: 10.1021/jacs.6b07977] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Because
of its importance for the origin of life, the nonenzymatic
copying of RNA templates has been the subject of intense study for
several decades. Previous characterizations of template-directed primer
extension using 5′-phosphoryl-2-methylimidazole-activated nucleotides
(2-MeImpNs) as substrates have assumed a classical in-line nucleophilic
substitution mechanism, in which the 3′-hydroxyl of the primer
attacks the phosphate of the incoming monomer, displacing the 2-methylimidazole
leaving group. However, we have found that the initial rate of primer
extension depends on the pH and concentration at which the activated
monomer is maintained prior to the primer extension reaction. These
and other results suggest an alternative mechanism, in which two monomers
react with each other to form an imidazolium-bridged dinucleotide
intermediate, which then binds to the template. Subsequent attack
of the 3′-hydroxyl of the primer displaces an activated nucleotide
as the leaving group and results in extension of the primer by one
nucleotide. Analysis of monomer solutions by NMR indicates formation
of the proposed imidazolium-bridged dinucleotide in the expected pH-dependent
manner. We have used synthetic methods to prepare material that is
enriched in this proposed intermediate and show that it is a highly
reactive substrate for primer extension. The formation of an imidazolium-bridged
dinucleotide intermediate provides a mechanistic interpretation of
previously observed catalysis by an activated nucleotide located downstream
from the site of primer extension.
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Affiliation(s)
- Travis Walton
- 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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29
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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: 39] [Impact Index Per Article: 4.9] [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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30
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Pal A, Das RS, Zhang W, Lang M, McLaughlin LW, Szostak JW. Effect of terminal 3′-hydroxymethyl modification of an RNA primer on nonenzymatic primer extension. Chem Commun (Camb) 2016; 52:11905-11907. [DOI: 10.1039/c6cc06925h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Displacing the hydroxyl nucleophile at the 3′-end of a primer by a single methylene group drastically decreases the rate of primer extension, illustrating the importance of the precise position of the hydroxyl nucleophile.
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Affiliation(s)
- Ayan Pal
- Howard Hughes Medical Institute
- Department of Molecular Biology and Center for Computational and Integrative Biology
- Massachusetts General Hospital
- Boston
- USA
| | - Rajat S. Das
- Boston College
- Department of Chemistry
- Merkert Chemistry Center
- Chestnut Hill
- USA
| | - Weicheng Zhang
- Howard Hughes Medical Institute
- Department of Molecular Biology and Center for Computational and Integrative Biology
- Massachusetts General Hospital
- Boston
- USA
| | - Megan Lang
- Boston College
- Department of Chemistry
- Merkert Chemistry Center
- Chestnut Hill
- USA
| | - Larry W. McLaughlin
- Boston College
- Department of Chemistry
- Merkert Chemistry Center
- Chestnut Hill
- USA
| | - Jack W. Szostak
- Howard Hughes Medical Institute
- Department of Molecular Biology and Center for Computational and Integrative Biology
- Massachusetts General Hospital
- Boston
- USA
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31
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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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32
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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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33
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Adamala K, Engelhart AE, Szostak JW. Generation of functional RNAs from inactive oligonucleotide complexes by non-enzymatic primer extension. J Am Chem Soc 2014; 137:483-9. [PMID: 25521912 PMCID: PMC4984999 DOI: 10.1021/ja511564d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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The earliest genomic RNAs had to
be short enough for efficient
replication, while simultaneously serving as unfolded templates and
effective ribozymes. A partial solution to this paradox may lie in
the fact that many functional RNAs can self-assemble from multiple
fragments. Therefore, in early evolution, genomic RNA fragments could
have been significantly shorter than unimolecular functional RNAs.
Here, we show that unstable, nonfunctional complexes assembled from
even shorter 3′-truncated oligonucleotides can be stabilized
and gain function via non-enzymatic primer extension. Such short RNAs
could act as good templates due to their minimal length and complex-forming
capacity, while their minimal length would facilitate replication
by relatively inefficient polymerization reactions. These RNAs could
also assemble into nascent functional RNAs and undergo conversion
to catalytically active forms, by the same polymerization chemistry
used for replication that generated the original short RNAs. Such
phenomena could have substantially relaxed requirements for copying
efficiency in early nonenzymatic replication systems.
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Affiliation(s)
- Katarzyna Adamala
- Howard Hughes Medical Institute and 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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34
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Synergism and mutualism in non-enzymatic RNA polymerization. Life (Basel) 2014; 4:598-620. [PMID: 25370531 PMCID: PMC4284460 DOI: 10.3390/life4040598] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 10/15/2014] [Accepted: 10/17/2014] [Indexed: 01/19/2023] Open
Abstract
The link between non-enzymatic RNA polymerization and RNA self-replication is a key step towards the "RNA world" and still far from being solved, despite extensive research. Clay minerals, lipids and, more recently, peptides were found to catalyze the non-enzymatic synthesis of RNA oligomers. Herein, a review of the main models for the formation of the first RNA polymers is presented in such a way as to emphasize the cooperation between life's building blocks in their emergence and evolution. A logical outcome of the previous results is a combination of these models, in which RNA polymerization might have been catalyzed cooperatively by clays, lipids and peptides in one multi-component prebiotic soup. The resulting RNAs and oligopeptides might have mutualistically evolved towards functional RNAs and catalytic peptides, preceding the first RNA replication, thus supporting an RNA-peptide world. The investigation of such a system is a formidable challenge, given its complexity deriving from a tremendously large number of reactants and innumerable products. A rudimentary experimental design is outlined, which could be used in an initial attempt to study a quaternary component system.
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35
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Cafferty BJ, Hud NV. Abiotic synthesis of RNA in water: a common goal of prebiotic chemistry and bottom-up synthetic biology. Curr Opin Chem Biol 2014; 22:146-57. [PMID: 25438801 DOI: 10.1016/j.cbpa.2014.09.015] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 09/13/2014] [Indexed: 01/01/2023]
Abstract
For more than half a century chemists have searched for a plausible prebiotic synthesis of RNA. The initial advances of the 1960s and 1970s were followed by decades of measured progress and a growing pessimism about overcoming remaining challenges. Fortunately, the past few years have provided a number of important advances, including new abiotic routes for the synthesis of nucleobases, nucleosides, and nucleotides. Recent discoveries also provide additional support for the hypothesis that RNA is the product of evolution, being preceded by ancestral genetic polymers, or pre-RNAs, that are synthesized more easily than RNA. In some cases, parallel searches for plausible prebiotic routes to RNA and pre-RNAs have provided more than one experimentally verified synthesis of RNA substructures and possible predecessors. Just as the synthesis of a contemporary biological molecule cannot be understood without knowledge of cellular metabolism, it is likely that an integrated approach that takes into account both plausible prebiotic reactions and plausible prebiotic environments will ultimately provide the most satisfactory and unifying chemical scenarios for the origin of nucleic acids. In this context, recent advances towards the abiotic synthesis of RNA and candidates for pre-RNAs are beginning to suggest that some molecules (e.g., urea) were multi-faceted contributors to the origin of nucleic acids, and the origin of life.
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Affiliation(s)
- Brian J Cafferty
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Nicholas V Hud
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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36
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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: 42] [Impact Index Per Article: 4.2] [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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37
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Abstract
The complexity of even the simplest known life forms makes efforts to synthesize living cells from inanimate components seem like a daunting task. However, recent progress toward the creation of synthetic cells, ranging from simple protocells to artificial cells approaching the complexity of bacteria, suggests that the synthesis of life is now a realistic goal. Protocell research, fueled by advances in the biophysics of primitive membranes and the chemistry of nucleic acid replication, is providing new insights into the origin of cellular life. Parallel efforts to construct more complex artificial cells, incorporating translational machinery and protein enzymes, are providing information about the requirements for protein-based life. We discuss recent advances and remaining challenges in the synthesis of artificial cells, the possibility of creating new forms of life distinct from existing biology, and the promise of this research for gaining a deeper understanding of the nature of living systems.
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Affiliation(s)
- J Craig Blain
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114; ,
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38
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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: 21] [Impact Index Per Article: 1.9] [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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39
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Zhang S, Zhang N, Blain JC, Szostak JW. Synthesis of N3'-P5'-linked phosphoramidate DNA by nonenzymatic template-directed primer extension. J Am Chem Soc 2013; 135:924-32. [PMID: 23252395 PMCID: PMC3548433 DOI: 10.1021/ja311164j] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
![]()
A fast and accurate pathway for nonenzymatic RNA replication
would
simplify models for the emergence of the RNA world from the prebiotic
chemistry of the early earth. However, numerous difficulties stand
in the way of an experimental demonstration of effective nonenzymatic
RNA replication. To gain insight into the necessary properties of
potentially self-replicating informational polymers, we have studied
several model systems based on amino–sugar nucleotides. Here
we describe the synthesis of N3′–P5′-linked phosphoramidate
DNA (3′-NP-DNA) by the template-directed polymerization of
activated 3′-amino-2′,3′-dideoxyribonucleotides.
3′-NP-DNA is an interesting model because of its very RNA-like
A-type duplex conformation and because activated 3′-amino-2′,3′-dideoxyribonucleotides
are much more reactive than the corresponding activated ribonucleotides.
In contrast to our previous studies with 2′-amino-2′,3′-dideoxyribonucleotides
(for which G and C but not A and T exhibit efficient template copying),
we have found that all four canonical 3′-amino-2′,3′-dideoxyribonucleotides
(G, C, A, and T) polymerize efficiently on RNA templates. RNA templates
are generally superior to DNA templates, and oligo-ribo-T templates
are superior to oligo-ribo-U templates, which are the least efficient
of the RNA homopolymer templates. We have also found that activation
of 3′-aminonucleotides with 2-methylimidazole results in a
ca. 10-fold higher polymerization rate relative to activation with
imidazole, an observation that parallels earlier findings with ribonucleotides.
We discuss the implications of our experiments for the possibility
of self-replication in the 3′-NP-DNA and RNA systems.
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Affiliation(s)
- Shenglong Zhang
- Howard Hughes Medical Institute and Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA
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40
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41
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Abstract
Synthetic life: the origin of life on the early Earth, and the ex novo transition of non-living matter to artificial living systems are deep scientific challenges that provide a context for the development of new chemistries with unknown technological consequences. This Essay attempts to re-frame some of the epistemological difficulties associated with these questions into an integrative framework of proto-life science. Chemistry is at the heart of this endeavour.
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Affiliation(s)
- Stephen Mann
- Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol, UK.
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42
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Kaiser A, Spies S, Lommel T, Richert C. Template-Directed Synthesis in 3′- and 5′-Direction with Reversible Termination. Angew Chem Int Ed Engl 2012; 51:8299-303. [DOI: 10.1002/anie.201203859] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Indexed: 01/21/2023]
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43
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Kaiser A, Spies S, Lommel T, Richert C. Template-Directed Synthesis in 3′- and 5′-Direction with Reversible Termination. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201203859] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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44
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Gwiazda S, Salomon K, Appel B, Müller S. RNA self-ligation: From oligonucleotides to full length ribozymes. Biochimie 2012; 94:1457-63. [DOI: 10.1016/j.biochi.2012.03.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 03/15/2012] [Indexed: 02/06/2023]
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45
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Zhang N, Zhang S, Szostak JW. Activated ribonucleotides undergo a sugar pucker switch upon binding to a single-stranded RNA template. J Am Chem Soc 2012; 134:3691-4. [PMID: 22296305 PMCID: PMC3448298 DOI: 10.1021/ja212027q] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Indexed: 12/02/2022]
Abstract
Template-directed polymerization of chemically activated ribonucleotide monomers, such as nucleotide 5'-phosphorimidazolides, has been studied as a model for nonenzymatic RNA replication during the origin of life. Kinetic studies of the polymerization of various nucleotide monomers on oligonucleotide templates have suggested that the A-form (C3'-endo sugar pucker) conformation is optimal for both monomers and templates for efficient copying. However, RNA monomers are predominantly in the C2'-endo conformation when free in solution, except for cytidine, which is approximately equally distributed between the C2'-endo and C3'-endo conformations. We hypothesized that ribonucleotides undergo a switch in sugar pucker upon binding to an A-type template and that this conformational switch allows or enhances subsequent polymerization. We used transferred nuclear Overhauser effect spectroscopy (TrNOESY), which can be used for specific detection of the bound conformation of small-molecule ligands with relatively weak affinity to receptors, to study the interactions between nucleotide 5'-phosphorimidazolides and single-stranded oligonucleotide templates. We found that the sugar pucker of activated ribonucleotides switches from C2'-endo in the free state to C3'-endo upon binding to an RNA template. This switch occurs only on RNA and not on DNA templates. Furthermore, activated 2'-deoxyribonucleotides maintain a C2'-endo sugar pucker in both the free and template-bound states. Our results provide a structural explanation for the observations that activated ribonucleotides are superior to activated deoxyribonucleotides and that RNA templates are superior to DNA templates in template-directed nonenzymatic primer-extension reactions.
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Affiliation(s)
- Na Zhang
- Howard Hughes
Medical Institute and Department of Molecular
Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street,
Boston, Massachusetts 02114, United States
| | - Shenglong Zhang
- Howard Hughes
Medical Institute and 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 and 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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46
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47
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Leu K, Obermayer B, Rajamani S, Gerland U, Chen IA. The prebiotic evolutionary advantage of transferring genetic information from RNA to DNA. Nucleic Acids Res 2011; 39:8135-47. [PMID: 21724606 PMCID: PMC3185426 DOI: 10.1093/nar/gkr525] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 06/07/2011] [Accepted: 06/07/2011] [Indexed: 11/13/2022] Open
Abstract
In the early 'RNA world' stage of life, RNA stored genetic information and catalyzed chemical reactions. However, the RNA world eventually gave rise to the DNA-RNA-protein world, and this transition included the 'genetic takeover' of information storage by DNA. We investigated evolutionary advantages for using DNA as the genetic material. The error rate of replication imposes a fundamental limit on the amount of information that can be stored in the genome, as mutations degrade information. We compared misincorporation rates of RNA and DNA in experimental non-enzymatic polymerization and calculated the lowest possible error rates from a thermodynamic model. Both analyses found that RNA replication was intrinsically error-prone compared to DNA, suggesting that total genomic information could increase after the transition to DNA. Analysis of the transitional RNA/DNA hybrid duplexes showed that copying RNA into DNA had similar fidelity to RNA replication, so information could be maintained during the genetic takeover. However, copying DNA into RNA was very error-prone, suggesting that attempts to return to the RNA world would result in a considerable loss of information. Therefore, the genetic takeover may have been driven by a combination of increased chemical stability, increased genome size and irreversibility.
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Affiliation(s)
- Kevin Leu
- FAS Center for Systems Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA and Department of Physics, Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians Universität München, Munich, Germany
| | - Benedikt Obermayer
- FAS Center for Systems Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA and Department of Physics, Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians Universität München, Munich, Germany
| | - Sudha Rajamani
- FAS Center for Systems Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA and Department of Physics, Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians Universität München, Munich, Germany
| | - Ulrich Gerland
- FAS Center for Systems Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA and Department of Physics, Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians Universität München, Munich, Germany
| | - Irene A. Chen
- FAS Center for Systems Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA and Department of Physics, Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians Universität München, Munich, Germany
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48
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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: 108] [Impact Index Per Article: 8.3] [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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49
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Nierth A, Jäschke A. Radioactive phosphorylation of alcohols to monitor biocatalytic Diels-Alder reactions. PLoS One 2011; 6:e21391. [PMID: 21731729 PMCID: PMC3120863 DOI: 10.1371/journal.pone.0021391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Accepted: 05/26/2011] [Indexed: 11/17/2022] Open
Abstract
Nature has efficiently adopted phosphorylation for numerous biological key processes, spanning from cell signaling to energy storage and transmission. For the bioorganic chemist the number of possible ways to attach a single phosphate for radioactive labeling is surprisingly small. Here we describe a very simple and fast one-pot synthesis to phosphorylate an alcohol with phosphoric acid using trichloroacetonitrile as activating agent. Using this procedure, we efficiently attached the radioactive phosphorus isotope (32)P to an anthracene diene, which is a substrate for the Diels-Alderase ribozyme-an RNA sequence that catalyzes the eponymous reaction. We used the (32)P-substrate for the measurement of RNA-catalyzed reaction kinetics of several dye-labeled ribozyme variants for which precise optical activity determination (UV/vis, fluorescence) failed due to interference of the attached dyes. The reaction kinetics were analyzed by thin-layer chromatographic separation of the (32)P-labeled reaction components and densitometric analysis of the substrate and product radioactivities, thereby allowing iterative optimization of the dye positions for future single-molecule studies. The phosphorylation strategy with trichloroacetonitrile may be applicable for labeling numerous other compounds that contain alcoholic hydroxyl groups.
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Affiliation(s)
- Alexander Nierth
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
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Röthlingshöfer M, Richert C. Chemical primer extension at submillimolar concentration of deoxynucleotides. J Org Chem 2010; 75:3945-52. [PMID: 20364862 DOI: 10.1021/jo1002467] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Template-directed primer extension usually requires a polymerase, nucleoside triphosphates, and magnesium ions as cofactors. Enzyme-free, chemical primer extensions are known for preactivated nucleotides at millimolar concentrations. Based on a screen of carbodiimides, heterocyclic catalysts, and reactions conditions, we now show that near-quantitative primer conversion can be achieved at submillimolar concentration of any of the four deoxynucleotides (dAMP, dCMP, dGMP and dTMP). The new protocol relies on in situ activation with EDC and 1-methylimidazole and a magnesium-free buffer that was tested successfully for different sequence motifs. The method greatly simplifies chemical primer extension assays, further reduces the cost of such assays, and demonstrates the potential of the in situ activation approach.
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Affiliation(s)
- Manuel Röthlingshöfer
- Institute for Organic Chemistry, University of Karlsruhe/K.I.T., 76131 Karlsruhe, Germany
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