1
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Kriebisch CME, Burger L, Zozulia O, Stasi M, Floroni A, Braun D, Gerland U, Boekhoven J. Template-based copying in chemically fuelled dynamic combinatorial libraries. Nat Chem 2024; 16:1240-1249. [PMID: 39014158 PMCID: PMC11321992 DOI: 10.1038/s41557-024-01570-5] [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: 03/19/2023] [Accepted: 06/06/2024] [Indexed: 07/18/2024]
Abstract
One of science's greatest challenges is determining how life can spontaneously emerge from a mixture of molecules. A complicating factor is that life and its molecules are inherently unstable-RNA and proteins are prone to hydrolysis and denaturation. For the de novo synthesis of life or to better understand its emergence at its origin, selection mechanisms are needed for unstable molecules. Here we present a chemically fuelled dynamic combinatorial library to model RNA oligomerization and deoligomerization and shine new light on selection and purification mechanisms under kinetic control. In the experiments, oligomers can only be sustained by continuous production. Hybridization is a powerful tool for selecting unstable molecules, offering feedback on oligomerization and deoligomerization rates. Moreover, we find that templation can be used to purify libraries of oligomers. In addition, template-assisted formation of oligomers within coacervate-based protocells changes its compartment's physical properties, such as their ability to fuse. Such reciprocal coupling between oligomer production and physical properties is a key step towards synthetic life.
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Affiliation(s)
- Christine M E Kriebisch
- School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching, Germany
| | - Ludwig Burger
- School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching, Germany
| | - Oleksii Zozulia
- School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching, Germany
| | - Michele Stasi
- School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching, Germany
| | - Alexander Floroni
- Systems Biophysics Center for Nano-Science and Origins Cluster Initiative, Department of Physics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Dieter Braun
- Systems Biophysics Center for Nano-Science and Origins Cluster Initiative, Department of Physics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ulrich Gerland
- School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching, Germany
| | - Job Boekhoven
- School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching, Germany.
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2
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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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3
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Ross D, Deamer D. Template-Directed Replication and Chiral Resolution during Wet-Dry Cycling in Hydrothermal Pools. Life (Basel) 2023; 13:1749. [PMID: 37629605 PMCID: PMC10456050 DOI: 10.3390/life13081749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
The commonly supposed template-based format for RNA self-replication requires both duplex assembly and disassembly. This requisite binary provision presents a challenge to the development of a serviceable self-replication model since chemical reactions are thermochemically unidirectional. We submit that a solution to this problem lies in volcanic landmasses that engage in continuous cycles of wetting and drying and thus uniquely provide the twofold state required for self-replication. Moreover, they offer conditions that initiate chain branching, and thus furnish a path to autocatalytic self-replication. The foundations of this dual thermochemical landscape arise from the broad differences in the properties of the bulk water phase on the one hand, and the air/water interfacial regions that emerge in the evaporative stages on the other. With this reaction system as a basis and employing recognized thermochemical and kinetic parameters, we present simulations displaying the spontaneous and autocatalyzed conversion of racemic and unactivated RNA monomers to necessarily homochiral duplex structures over characteristic periods of years.
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Affiliation(s)
- David Ross
- SRI International, Menlo Park, CA 94025, USA
| | - David Deamer
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA
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4
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Dagar S, Sarkar S, Rajamani S. Nonenzymatic Template-Directed Primer Extension Using 2'-3' Cyclic Nucleotides Under Wet-Dry Cycles. ORIGINS LIFE EVOL B 2023; 53:43-60. [PMID: 37243884 DOI: 10.1007/s11084-023-09636-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 04/15/2023] [Indexed: 05/29/2023]
Abstract
RNA World Hypothesis is centred around the idea of a period in the early history of life's origin, wherein nonenzymatic oligomerization and replication of RNA resulted in functional ribozymes. Previous studies in this endeavour have demonstrated template-directed primer extension using chemically modified nucleotides and primers. Nonetheless, similar studies that used non-activated nucleotides led to the formation of RNA only with abasic sites. In this study, we report template-directed primer extension with prebiotically relevant cyclic nucleotides, under dehydration-rehydration (DH-RH) cycles occurring at high temperature (90 °C) and alkaline conditions (pH 8). 2'-3' cyclic nucleoside monophosphates (cNMP) resulted in primer extension, while 3'-5' cNMP failed to do so. Intact extension of up to two nucleotide additions was observed with both canonical hydroxy-terminated (OH-primer) and activated amino-terminated (NH2-primer) primers. We demonstrate primer extension reactions using both purine and pyrimidine 2'-3' cNMPs, with higher product yield observed during cAMP additions. Further, the presence of lipid was observed to significantly enhance the extended product in cCMP reactions. In all, our study provides a proof-of-concept for nonenzymatic primer extension of RNA, using intrinsically activated prebiotically relevant cyclic nucleotides as monomers.
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Affiliation(s)
- Shikha Dagar
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Susovan Sarkar
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Sudha Rajamani
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India.
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5
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Slootbeek AD, van Haren MHI, Smokers IBA, Spruijt E. Growth, replication and division enable evolution of coacervate protocells. Chem Commun (Camb) 2022; 58:11183-11200. [PMID: 36128910 PMCID: PMC9536485 DOI: 10.1039/d2cc03541c] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 09/13/2022] [Indexed: 11/21/2022]
Abstract
Living and proliferating cells undergo repeated cycles of growth, replication and division, all orchestrated by complex molecular networks. How a minimal cell cycle emerged and helped primitive cells to evolve remains one of the biggest mysteries in modern science, and is an active area of research in chemistry. Protocells are cell-like compartments that recapitulate features of living cells and may be seen as the chemical ancestors of modern life. While compartmentalization is not strictly required for primitive, open-ended evolution of self-replicating systems, it gives such systems a clear identity by setting the boundaries and it can help them overcome three major obstacles of dilution, parasitism and compatibility. Compartmentalization is therefore widely considered to be a central hallmark of primitive life, and various types of protocells are actively investigated, with the ultimate goal of developing a protocell capable of autonomous proliferation by mimicking the well-known cell cycle of growth, replication and division. We and others have found that coacervates are promising protocell candidates in which chemical building blocks required for life are naturally concentrated, and chemical reactions can be selectively enhanced or suppressed. This feature article provides an overview of how growth, replication and division can be realized with coacervates as protocells and what the bottlenecks are. Considerations are given for designing chemical networks in coacervates that can lead to sustained growth, selective replication and controlled division, in a way that they are linked together like in the cell cycle. Ultimately, such a system may undergo evolution by natural selection of certain phenotypes, leading to adaptation and the gain of new functions, and we end with a brief discussion of the opportunities for coacervates to facilitate this.
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Affiliation(s)
- Annemiek D Slootbeek
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Merlijn H I van Haren
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Iris B A Smokers
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
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6
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Rolling Circles as a Means of Encoding Genes in the RNA World. Life (Basel) 2022; 12:life12091373. [PMID: 36143408 PMCID: PMC9505818 DOI: 10.3390/life12091373] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/17/2022] [Accepted: 08/23/2022] [Indexed: 11/25/2022] Open
Abstract
The rolling circle mechanism found in viroids and some RNA viruses is a likely way that replication could have begun in the RNA World. Here, we consider simulations of populations of protocells, each containing multiple copies of rolling circle RNAs that can replicate non-enzymatically. The mechanism requires the presence of short self-cleaving ribozymes such as hammerheads, which can cleave and re-circularize RNA strands. A rolling circle must encode a hammerhead and the complement of a hammerhead, so that both plus and minus strands can cleave. Thus, the minimal functional length is twice the length of the hammerhead sequence. Selection for speed of replication will tend to reduce circles to this minimum length. However, if sequence errors occur when copying the hammerhead sequence, this prevents cleavage at one point, but still allows cleavage on the next passage around the rolling circle. Thus, there is a natural doubling mechanism that creates strands that are multiple times the length of the minimal sequence. This can provide space for the origin of new genes with beneficial functions. We show that if a beneficial gene appears in this new space, the longer sequence with the beneficial function can be selected, even though it replicates more slowly. This provides a route for the evolution of longer circles encoding multiple genes.
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7
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Göppel T, Rosenberger JH, Altaner B, Gerland U. Thermodynamic and Kinetic Sequence Selection in Enzyme-Free Polymer Self-Assembly Inside a Non-Equilibrium RNA Reactor. Life (Basel) 2022; 12:life12040567. [PMID: 35455058 PMCID: PMC9032526 DOI: 10.3390/life12040567] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/03/2022] [Accepted: 04/06/2022] [Indexed: 11/18/2022] Open
Abstract
The RNA world is one of the principal hypotheses to explain the emergence of living systems on the prebiotic Earth. It posits that RNA oligonucleotides acted as both carriers of information as well as catalytic molecules, promoting their own replication. However, it does not explain the origin of the catalytic RNA molecules. How could the transition from a pre-RNA to an RNA world occur? A starting point to answer this question is to analyze the dynamics in sequence space on the lowest level, where mononucleotide and short oligonucleotides come together and collectively evolve into larger molecules. To this end, we study the sequence-dependent self-assembly of polymers from a random initial pool of short building blocks via templated ligation. Templated ligation requires two strands that are hybridized adjacently on a third strand. The thermodynamic stability of such a configuration crucially depends on the sequence context and, therefore, significantly influences the ligation probability. However, the sequence context also has a kinetic effect, since non-complementary nucleotide pairs in the vicinity of the ligation site stall the ligation reaction. These sequence-dependent thermodynamic and kinetic effects are explicitly included in our stochastic model. Using this model, we investigate the system-level dynamics inside a non-equilibrium ‘RNA reactor’ enabling a fast chemical activation of the termini of interacting oligomers. Moreover, the RNA reactor subjects the oligomer pool to periodic temperature changes inducing the reshuffling of the system. The binding stability of strands typically grows with the number of complementary nucleotides forming the hybridization site. While shorter strands unbind spontaneously during the cold phase, larger complexes only disassemble during the temperature peaks. Inside the RNA reactor, strand growth is balanced by cleavage via hydrolysis, such that the oligomer pool eventually reaches a non-equilibrium stationary state characterized by its length and sequence distribution. How do motif-dependent energy and stalling parameters affect the sequence composition of the pool of long strands? As a critical factor for self-enhancing sequence selection, we identify kinetic stalling due to non-complementary base pairs at the ligation site. Kinetic stalling enables cascades of self-amplification that result in a strong reduction of occupied states in sequence space. Moreover, we discuss the significance of the symmetry breaking for the transition from a pre-RNA to an RNA world.
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8
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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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9
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Giurgiu C, Fang Z, Aitken HRM, Kim SC, Pazienza L, Mittal S, Szostak JW. Structure–Activity Relationships in Nonenzymatic Template‐Directed RNA Synthesis. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Constantin Giurgiu
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Chemistry and Chemical Biology Harvard University Cambridge MA 02138 USA
| | - Ziyuan Fang
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Genetics Harvard Medical School Boston MA 02115 USA
| | - Harry R. M. Aitken
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Genetics Harvard Medical School Boston MA 02115 USA
| | - Seohyun Chris Kim
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Genetics Harvard Medical School Boston MA 02115 USA
| | - Lydia Pazienza
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Chemistry and Chemical Biology Harvard University Cambridge MA 02138 USA
| | - Shriyaa Mittal
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Chemistry and Chemical Biology Harvard University Cambridge MA 02138 USA
| | - Jack W. Szostak
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Chemistry and Chemical Biology Harvard University Cambridge MA 02138 USA
- Department of Genetics Harvard Medical School Boston MA 02115 USA
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10
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Giurgiu C, Fang Z, Aitken HRM, Kim SC, Pazienza L, Mittal S, Szostak JW. Structure-Activity Relationships in Nonenzymatic Template-Directed RNA Synthesis. Angew Chem Int Ed Engl 2021; 60:22925-22932. [PMID: 34428345 PMCID: PMC8490286 DOI: 10.1002/anie.202109714] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Indexed: 11/11/2022]
Abstract
The template-directed synthesis of RNA played an important role in the transition from prebiotic chemistry to the beginnings of RNA based life, but the mechanism of RNA copying chemistry is incompletely understood. We measured the kinetics of template copying with a set of primers with modified 3'-nucleotides and determined the crystal structures of these modified nucleotides in the context of a primer/template/substrate-analog complex. pH-rate profiles and solvent isotope effects show that deprotonation of the primer 3'-hydroxyl occurs prior to the rate limiting step, the attack of the alkoxide on the activated phosphate of the incoming nucleotide. The analogs with a 3 E ribose conformation show the fastest formation of 3'-5' phosphodiester bonds. Among those derivatives, the reaction rate is strongly correlated with the electronegativity of the 2'-substituent. We interpret our results in terms of differences in steric bulk and charge distribution in the ground vs. transition states.
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Affiliation(s)
- Constantin Giurgiu
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Ziyuan Fang
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Harry R M Aitken
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Seohyun Chris Kim
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Lydia Pazienza
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Shriyaa Mittal
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
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11
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Duzdevich D, Carr CE, Ding D, Zhang SJ, Walton TS, Szostak JW. Competition between bridged dinucleotides and activated mononucleotides determines the error frequency of nonenzymatic RNA primer extension. Nucleic Acids Res 2021; 49:3681-3691. [PMID: 33744957 PMCID: PMC8053118 DOI: 10.1093/nar/gkab173] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 02/12/2021] [Accepted: 03/05/2021] [Indexed: 12/15/2022] Open
Abstract
Nonenzymatic copying of RNA templates with activated nucleotides is a useful model for studying the emergence of heredity at the origin of life. Previous experiments with defined-sequence templates have pointed to the poor fidelity of primer extension as a major problem. Here we examine the origin of mismatches during primer extension on random templates in the simultaneous presence of all four 2-aminoimidazole-activated nucleotides. Using a deep sequencing approach that reports on millions of individual template-product pairs, we are able to examine correct and incorrect polymerization as a function of sequence context. We have previously shown that the predominant pathway for primer extension involves reaction with imidazolium-bridged dinucleotides, which form spontaneously by the reaction of two mononucleotides with each other. We now show that the sequences of correctly paired products reveal patterns that are expected from the bridged dinucleotide mechanism, whereas those associated with mismatches are consistent with direct reaction of the primer with activated mononucleotides. Increasing the ratio of bridged dinucleotides to activated mononucleotides, either by using purified components or by using isocyanide-based activation chemistry, reduces the error frequency. Our results point to testable strategies for the accurate nonenzymatic copying of arbitrary RNA sequences.
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Affiliation(s)
- Daniel Duzdevich
- To whom correspondence should be addressed. Tel: +1 617 726 5102; Fax: +1 617 643 332;
| | - Christopher E Carr
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Dian Ding
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Stephanie J Zhang
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Travis S Walton
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jack W Szostak
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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12
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Duffy K, Arangundy-Franklin S, Holliger P. Modified nucleic acids: replication, evolution, and next-generation therapeutics. BMC Biol 2020; 18:112. [PMID: 32878624 PMCID: PMC7469316 DOI: 10.1186/s12915-020-00803-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Modified nucleic acids, also called xeno nucleic acids (XNAs), offer a variety of advantages for biotechnological applications and address some of the limitations of first-generation nucleic acid therapeutics. Indeed, several therapeutics based on modified nucleic acids have recently been approved and many more are under clinical evaluation. XNAs can provide increased biostability and furthermore are now increasingly amenable to in vitro evolution, accelerating lead discovery. Here, we review the most recent discoveries in this dynamic field with a focus on progress in the enzymatic replication and functional exploration of XNAs.
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Affiliation(s)
- Karen Duffy
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | | | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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13
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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: 18] [Impact Index Per Article: 4.5] [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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14
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Roy S, Bapat NV, Derr J, Rajamani S, Sengupta S. Emergence of ribozyme and tRNA-like structures from mineral-rich muddy pools on prebiotic earth. J Theor Biol 2020; 506:110446. [PMID: 32798505 DOI: 10.1016/j.jtbi.2020.110446] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 07/21/2020] [Accepted: 08/06/2020] [Indexed: 10/23/2022]
Abstract
The RNA world hypothesis, although a viable one regarding the origin of life on earth, has so far failed to provide a compelling explanation for the synthesis of RNA enzymes from free nucleotides via abiotic processes. To tackle this long-standing problem, we develop a realistic model for the onset of the RNA world, using experimentally determined rates for polymerization reactions. We start with minimal assumptions about the initial state that only requires the presence of short oligomers or just free nucleotides and consider the effects of environmental cycling by dividing a day into a dry, semi-wet and wet phases that are distinguished by the nature of reactions they support. Long polymers, with maximum lengths sometimes exceeding 100 nucleotides, spontaneously emerge due to a combination of non-enzymatic, non-templated polymer extension and template-directed primer extension processes. The former helps in increasing the lengths of RNA strands, whereas the later helps in producing complementary copies of the strands. Strands also undergo hydrolysis in a structure-dependent manner that favour breaking of bonds connecting unpaired nucleotides. We identify the most favourable conditions needed for the emergence of ribozyme and tRNA-like structures and double stranded RNA molecules, classify all RNA strands on the basis of their secondary structures and determine their abundance in the population. Our results indicate that under suitable environmental conditions, non-enzymatic processes would have been sufficient to lead to the emergence of a variety of ribozyme-like molecules with complex secondary structures and potential catalytic functions.
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Affiliation(s)
- Suvam Roy
- Department of Physical Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur 741246, India
| | - Niraja V Bapat
- Department of Biology, Indian Institute of Science Education and Research, Pune; Dr. Homi-Bhabha Road, Pune 411008, India
| | - Julien Derr
- Laboratoire Matière et Systèmes Complexes, Université Paris Diderot, 5 Rue Thomas Mann, 75013 Paris, France.
| | - Sudha Rajamani
- Department of Biology, Indian Institute of Science Education and Research, Pune; Dr. Homi-Bhabha Road, Pune 411008, India
| | - Supratim Sengupta
- Department of Physical Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur 741246, India.
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15
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Duzdevich D, Carr CE, Szostak JW. Deep sequencing of non-enzymatic RNA primer extension. Nucleic Acids Res 2020; 48:e70. [PMID: 32427335 PMCID: PMC7337528 DOI: 10.1093/nar/gkaa400] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/02/2020] [Accepted: 05/05/2020] [Indexed: 12/02/2022] Open
Abstract
Life emerging in an RNA world is expected to propagate RNA as hereditary information, requiring some form of primitive replication without enzymes. Non-enzymatic template-directed RNA primer extension is a model of the copying step in this posited form of replication. The sequence space accessed by primer extension dictates potential pathways to self-replication and, eventually, ribozymes. Which sequences can be accessed? What is the fidelity of the reaction? Does the recently illuminated mechanism of primer extension affect the distribution of sequences that can be copied? How do sequence features respond to experimental conditions and prebiotically relevant contexts? To help answer these and related questions, we here introduce a deep-sequencing methodology for studying RNA primer extension. We have designed and vetted special RNA constructs for this purpose, honed a protocol for sample preparation and developed custom software that analyzes sequencing data. We apply this new methodology to proof-of-concept controls, and demonstrate that it works as expected and reports on key features of the sequences accessed by primer extension.
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Affiliation(s)
- Daniel Duzdevich
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Christopher E Carr
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jack W Szostak
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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16
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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: 11] [Impact Index Per Article: 2.8] [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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17
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Polyesters as a Model System for Building Primitive Biologies from Non-Biological Prebiotic Chemistry. Life (Basel) 2020; 10:life10010006. [PMID: 31963928 PMCID: PMC7175156 DOI: 10.3390/life10010006] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/22/2019] [Accepted: 01/10/2020] [Indexed: 12/14/2022] Open
Abstract
A variety of organic chemicals were likely available on prebiotic Earth. These derived from diverse processes including atmospheric and geochemical synthesis and extraterrestrial input, and were delivered to environments including oceans, lakes, and subaerial hot springs. Prebiotic chemistry generates both molecules used by modern organisms, such as proteinaceous amino acids, as well as many molecule types not used in biochemistry. As prebiotic chemical diversity was likely high, and the core of biochemistry uses a rather small set of common building blocks, the majority of prebiotically available organic compounds may not have been those used in modern biochemistry. Chemical evolution was unlikely to have been able to discriminate which molecules would eventually be used in biology, and instead, interactions among compounds were governed simply by abundance and chemical reactivity. Previous work has shown that likely prebiotically available α-hydroxy acids can combinatorially polymerize into polyesters that self-assemble to create new phases which are able to compartmentalize other molecule types. The unexpectedly rich complexity of hydroxy acid chemistry and the likely enormous structural diversity of prebiotic organic chemistry suggests chemical evolution could have been heavily influenced by molecules not used in contemporary biochemistry, and that there is a considerable amount of prebiotic chemistry which remains unexplored.
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18
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The difficult case of an RNA-only origin of life. Emerg Top Life Sci 2019; 3:469-475. [PMID: 33523163 PMCID: PMC7289000 DOI: 10.1042/etls20190024] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/08/2019] [Accepted: 08/09/2019] [Indexed: 11/17/2022]
Abstract
The RNA world hypothesis is probably the most extensively studied model for the emergence of life on Earth. Despite a large body of evidence supporting the idea that RNA is capable of kick-starting autocatalytic self-replication and thus initiating the emergence of life, seemingly insurmountable weaknesses in the theory have also been highlighted. These problems could be overcome by novel experimental approaches, including out-of-equilibrium environments, and the exploration of an early co-evolution of RNA and other key biomolecules such as peptides and DNA, which might be necessary to mitigate the shortcomings of RNA-only systems.
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19
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Morasch M, Liu J, Dirscherl CF, Ianeselli A, Kühnlein A, Le Vay K, Schwintek P, Islam S, Corpinot MK, Scheu B, Dingwell DB, Schwille P, Mutschler H, Powner MW, Mast CB, Braun D. Heated gas bubbles enrich, crystallize, dry, phosphorylate and encapsulate prebiotic molecules. Nat Chem 2019; 11:779-788. [PMID: 31358919 DOI: 10.1038/s41557-019-0299-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 06/21/2019] [Indexed: 12/19/2022]
Abstract
Non-equilibrium conditions must have been crucial for the assembly of the first informational polymers of early life, by supporting their formation and continuous enrichment in a long-lasting environment. Here, we explore how gas bubbles in water subjected to a thermal gradient, a likely scenario within crustal mafic rocks on the early Earth, drive a complex, continuous enrichment of prebiotic molecules. RNA precursors, monomers, active ribozymes, oligonucleotides and lipids are shown to (1) cycle between dry and wet states, enabling the central step of RNA phosphorylation, (2) accumulate at the gas-water interface to drastically increase ribozymatic activity, (3) condense into hydrogels, (4) form pure crystals and (5) encapsulate into protecting vesicle aggregates that subsequently undergo fission. These effects occur within less than 30 min. The findings unite, in one location, the physical conditions that were crucial for the chemical emergence of biopolymers. They suggest that heated microbubbles could have hosted the first cycles of molecular evolution.
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Affiliation(s)
- Matthias Morasch
- Physics Department, Center for Nanoscience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jonathan Liu
- Physics Department, Center for Nanoscience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Christina F Dirscherl
- Physics Department, Center for Nanoscience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Alan Ianeselli
- Physics Department, Center for Nanoscience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Alexandra Kühnlein
- Physics Department, Center for Nanoscience, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Philipp Schwintek
- Physics Department, Center for Nanoscience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Saidul Islam
- Department of Chemistry, University College London, London, UK
| | | | - Bettina Scheu
- Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Donald B Dingwell
- Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Petra Schwille
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | | | - Christof B Mast
- Physics Department, Center for Nanoscience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Dieter Braun
- Physics Department, Center for Nanoscience, Ludwig-Maximilians-Universität München, Munich, Germany.
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20
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Sosson M, Pfeffer D, Richert C. Enzyme-free ligation of dimers and trimers to RNA primers. Nucleic Acids Res 2019; 47:3836-3845. [PMID: 30869145 PMCID: PMC6486630 DOI: 10.1093/nar/gkz160] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 02/25/2019] [Accepted: 02/28/2019] [Indexed: 01/19/2023] Open
Abstract
The template-directed formation of phosphodiester bonds between two nucleic acid components is a pivotal process in biology. To induce such a reaction in the absence of enzymes is a challenge. This challenge has been met for the extension of a primer with mononucleotides, but the ligation of short oligonucleotides (dimers or trimers) has proven difficult. Here we report a method for ligating dimers and trimers of ribonucleotides using in situ activation in aqueous buffer. All 16 different dimers and two trimers were tested. Binding studies by NMR showed low millimolar dissociation constants for complexes between representative dimers and hairpins mimicking primer-template duplexes, confirming that a weak template effect is not the cause of the poor ligating properties of these short oligomers. Rather, cyclization was found to compete with ligation, with up to 90% of dimer being converted to the cyclic form during the course of an assay. This side reaction is strongly sequence dependent and more pronounced for dimers than for trimers. Under optimized reaction conditions, high yields were observed with strongly pairing purines at the 3'-terminus. These results show that short oligomers of ribonucleotides are competent reactants in enzyme-free copying.
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Affiliation(s)
- Marilyne Sosson
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Daniel Pfeffer
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
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21
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Edeleva E, Salditt A, Stamp J, Schwintek P, Boekhoven J, Braun D. Continuous nonenzymatic cross-replication of DNA strands with in situ activated DNA oligonucleotides. Chem Sci 2019; 10:5807-5814. [PMID: 31293769 PMCID: PMC6568275 DOI: 10.1039/c9sc00770a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/28/2019] [Indexed: 12/28/2022] Open
Abstract
A nonenzymatic DNA cross-replicator uses temperature cycling to overcome product inhibition and thus survives exponential dilution conditions.
Continuous enzyme-free replication of oligonucleotides is central for open-ended evolution experiments that mimic the origin of life. Here, we studied a reaction system, whereby two 24mer DNA templates cross-catalyzed each other's synthesis from four 12mer DNA fragments, two of which were in situ activated with the condensing agent 1-ethyl-3-(3-dimethylamino-propyl)carbodiimide (EDC). We circumvented the problem of product inhibition by melting the stable product duplexes for their reuse as templates in the following ligation step. The system reproduced itself through ligation/melting cycles and survived exponential dilution. We quantified EDC-induced side reactions in a detailed kinetic model. The model allowed us to analyze the effects of various reaction rates on the system's kinetics and confirmed maximal replication under the chosen conditions. The presented system enables us to study nonenzymatic open-ended evolution experiments starting from diverse sequence pools.
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Affiliation(s)
- Evgeniia Edeleva
- Systems Biophysics , Physics Department , Ludwig-Maximilians-Universität München , Amalienstraße 54 , 80799 München , Germany .
| | - Annalena Salditt
- Systems Biophysics , Physics Department , Ludwig-Maximilians-Universität München , Amalienstraße 54 , 80799 München , Germany .
| | - Julian Stamp
- Systems Biophysics , Physics Department , Ludwig-Maximilians-Universität München , Amalienstraße 54 , 80799 München , Germany .
| | - Philipp Schwintek
- Systems Biophysics , Physics Department , Ludwig-Maximilians-Universität München , Amalienstraße 54 , 80799 München , Germany .
| | - Job Boekhoven
- Chemistry Department and Institute for Advanced Study , Technical University of Munich , Lichtenbergstraße 4 , 80895 Garching , Germany
| | - Dieter Braun
- Systems Biophysics , Physics Department , Ludwig-Maximilians-Universität München , Amalienstraße 54 , 80799 München , Germany .
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22
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Le Vay K, Weise LI, Libicher K, Mascarenhas J, Mutschler H. Templated Self‐Replication in Biomimetic Systems. ACTA ACUST UNITED AC 2019; 3:e1800313. [DOI: 10.1002/adbi.201800313] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 02/06/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Kristian Le Vay
- Biomimetic SystemsMax Planck Institute of Biochemistry Martinsried Germany
| | - Laura Isabel Weise
- Biomimetic SystemsMax Planck Institute of Biochemistry Martinsried Germany
| | - Kai Libicher
- Biomimetic SystemsMax Planck Institute of Biochemistry Martinsried Germany
| | - Judita Mascarenhas
- Department of Systems and Synthetic MicrobiologyMax Planck Institute for Terrestrial Microbiology Marburg Germany
| | - Hannes Mutschler
- Biomimetic SystemsMax Planck Institute of Biochemistry Martinsried Germany
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23
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Kashida H, Kokubo Y, Makino K, Asanuma H. Selective binding of nucleosides to gapped DNA duplex revealed by orientation and distance dependence of FRET. Org Biomol Chem 2019; 17:6786-6789. [DOI: 10.1039/c9ob00946a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Herein we used orientation and distance dependence of Förster resonance energy transfer (FRET) to analyze the binding of nucleosides to a gapped DNA duplex.
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Affiliation(s)
- Hiromu Kashida
- Department of Biomolecular Engineering
- Graduate School of Engineering
- Nagoya University
- Nagoya 464-8603
- Japan
| | - Yuta Kokubo
- Department of Biomolecular Engineering
- Graduate School of Engineering
- Nagoya University
- Nagoya 464-8603
- Japan
| | - Koki Makino
- Department of Biomolecular Engineering
- Graduate School of Engineering
- Nagoya University
- Nagoya 464-8603
- Japan
| | - Hiroyuki Asanuma
- Department of Biomolecular Engineering
- Graduate School of Engineering
- Nagoya University
- Nagoya 464-8603
- Japan
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24
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Walton T, Pazienza L, Szostak JW. Template-Directed Catalysis of a Multistep Reaction Pathway for Nonenzymatic RNA Primer Extension. Biochemistry 2018; 58:755-762. [PMID: 30566332 PMCID: PMC7547881 DOI: 10.1021/acs.biochem.8b01156] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
Before
the advent of polymerase enzymes, the copying of genetic
material during the origin of life may have involved the nonenzymatic
polymerization of RNA monomers that are more reactive than the biological
nucleoside triphosphates. Activated RNA monomers such as nucleotide
5′-phosphoro-2-aminoimidazolides spontaneously form an imidazolium-bridged
dinucleotide intermediate that undergoes rapid nonenzymatic template-directed
primer extension. However, it is unknown whether the intermediate
can form on the template or only in solution and whether the intermediate
is prone to hydrolysis when bound to the template or reacts preferentially
with the primer. Here we show that an activated monomer can first
bind the template and then form an imidazolium-bridged intermediate
by reacting with a 2-aminoimidazole-activated downstream oligonucleotide.
We have also characterized the partition of the template-bound intermediate
between hydrolysis and primer extension. In the presence of the catalytic
metal ion Mg2+, >90% of the template-bound intermediate
reacts with the adjacent primer to generate the primer extension product
while less than 10% reacts with competing water. Our results indicate
that an RNA template can catalyze a multistep phosphodiester bond
formation pathway while minimizing hydrolysis with a specificity reminiscent
of an enzyme-catalyzed reaction.
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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
| | - Lydia Pazienza
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology , Massachusetts General Hospital , Boston , Massachusetts 02114 , United States.,Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States
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25
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Halami B, Shahsavari S, Nelson Z, Prehoda L, Eriyagama DNAM, Fang S. Incorporation of Sensitive Ester and Chloropurine Groups into Oligodeoxynucleotides through Solid Phase Synthesis. ChemistrySelect 2018; 3:8857-8862. [PMID: 30886889 PMCID: PMC6420219 DOI: 10.1002/slct.201801484] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/30/2018] [Indexed: 02/06/2023]
Abstract
Nucleosides containing ester groups that are sensitive to nucleophiles were incorporated into oligodeoxynucleotides (ODNs) through solid phase chemical synthesis. The sensitive esters are located on a purine nucleobase. They are the esters of ethyl, 2-methoxyethyl, 4-methoxyphenyl and phenyl groups, and a thioester. These esters cannot survive the deprotection and cleavage conditions used in known ODN synthesis technologies, which involve strong nucleophiles such as ammonium hydroxide and potassium methoxide (potassium carbonate in anhydrous methanol). To incorporate these sensitive groups into ODNs, the Dmoc phosphoramidites and linker were used for solid phase synthesis, which allowed ODN deprotection and cleavage to be carried out under non-nucleophilic oxidative conditions. Sixteen ODN sequences containing these groups were synthesized and characterized with MALDI MS. In addition, the synthesis and characterization of three ODNs containing a nucleophile sensitive 6-chloropurine using the same strategy are described.
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Affiliation(s)
- Bhaskar Halami
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
| | - Shahien Shahsavari
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
| | - Zack Nelson
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
| | - Lucas Prehoda
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
| | | | - Shiyue Fang
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
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26
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Gimenez Molina A, Barvik I, Müller S, Vasseur JJ, Smietana M. RNA-based boronate internucleosidic linkages: an entry into reversible templated ligation and loop formation. Org Biomol Chem 2018; 16:8824-8830. [DOI: 10.1039/c8ob02182a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis of a 5′-boronoribonucleotidic phosphoramidite building block has been achieved and incorporated at the 5′ extremities of RNA sequences for the templated assembly of RNA shortmers.
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Affiliation(s)
- Alejandro Gimenez Molina
- 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
| | - Sabine Müller
- Institut für Biochemie
- Ernst-Moritz-Arndt-Universität Greifswald
- D-17489 Greifswald
- Germany
| | - 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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