1
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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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2
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Okita H, Kondo S, Murayama K, Asanuma H. Rapid Chemical Ligation of DNA and Acyclic Threoninol Nucleic Acid ( aTNA) for Effective Nonenzymatic Primer Extension. J Am Chem Soc 2023; 145:17872-17880. [PMID: 37466125 PMCID: PMC10436273 DOI: 10.1021/jacs.3c04979] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Indexed: 07/20/2023]
Abstract
Previously, nonenzymatic primer extension reaction of acyclic l-threoninol nucleic acid (L-aTNA) was achieved in the presence of N-cyanoimidazole (CNIm) and Mn2+; however, the reaction conditions were not optimized and a mechanistic insight was not sufficient. Herein, we report investigation of the kinetics and reaction mechanism of the chemical ligation of L-aTNA to L-aTNA and of DNA to DNA. We found that Cd2+, Ni2+, and Co2+ accelerated ligation of both L-aTNA and DNA and that the rate-determining step was activation of the phosphate group. The activation was enhanced by duplex formation between a phosphorylated L-aTNA fragment and template, resulting in unexpectedly more effective L-aTNA ligation than DNA ligation. Under optimized conditions, an 8-mer L-aTNA primer could be elongated by ligation to L-aTNA trimers to produce a 29-mer full-length oligomer with 60% yield within 2 h at 4 °C. This highly effective chemical ligation system will allow construction of artificial genomes, robust DNA nanostructures, and xeno nucleic acids for use in selection methods. Our findings also shed light on the possible pre-RNA world.
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Affiliation(s)
- Hikari Okita
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Shuto Kondo
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Keiji Murayama
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
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3
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Mizuuchi R, Ichihashi N. Minimal RNA self-reproduction discovered from a random pool of oligomers. Chem Sci 2023; 14:7656-7664. [PMID: 37476714 PMCID: PMC10355099 DOI: 10.1039/d3sc01940c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/18/2023] [Indexed: 07/22/2023] Open
Abstract
The emergence of RNA self-reproduction from prebiotic components would have been crucial in developing a genetic system during the origins of life. However, all known self-reproducing RNA molecules are complex ribozymes, and how they could have arisen from abiotic materials remains unclear. Therefore, it has been proposed that the first self-reproducing RNA may have been short oligomers that assemble their components as templates. Here, we sought such minimal RNA self-reproduction in prebiotically accessible short random RNA pools that undergo spontaneous ligation and recombination. By examining enriched RNA families with common motifs, we identified a 20-nucleotide (nt) RNA variant that self-reproduces via template-directed ligation of two 10 nt oligonucleotides. The RNA oligomer contains a 2'-5' phosphodiester bond, which typically forms during prebiotically plausible RNA synthesis. This non-canonical linkage helps prevent the formation of inactive complexes between self-complementary oligomers while decreasing the ligation efficiency. The system appears to possess an autocatalytic property consistent with exponential self-reproduction despite the limitation of forming a ternary complex of the template and two substrates, similar to the behavior of a much larger ligase ribozyme. Such a minimal, ribozyme-independent RNA self-reproduction may represent the first step in the emergence of an RNA-based genetic system from primordial components. Simultaneously, our examination of random RNA pools highlights the likelihood that complex species interactions were necessary to initiate RNA reproduction.
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Affiliation(s)
- Ryo Mizuuchi
- Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University Shinjuku Tokyo 162-8480 Japan
- JST, FOREST Kawaguchi Saitama 332-0012 Japan
| | - Norikazu Ichihashi
- Komaba Institute for Science, The University of Tokyo Meguro Tokyo 153-8902 Japan
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo Meguro Tokyo 153-8902 Japan
- Universal Biology Institute, The University of Tokyo Meguro Tokyo 153-8902 Japan
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4
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Ding D, Zhou L, Mittal S, Szostak JW. Experimental Tests of the Virtual Circular Genome Model for Nonenzymatic RNA Replication. J Am Chem Soc 2023; 145:7504-7515. [PMID: 36963403 PMCID: PMC10080680 DOI: 10.1021/jacs.3c00612] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
The virtual circular genome (VCG) model was proposed as a means of going beyond template copying to indefinite cycles of nonenzymatic RNA replication during the origin of life. In the VCG model, the protocellular genome is a collection of short oligonucleotides that map to both strands of a virtual circular sequence. Replication is driven by templated nonenzymatic primer extensions on a subset of kinetically trapped partially base-paired configurations, followed by the shuffling of these configurations to enable continued oligonucleotide elongation. Here, we describe initial experimental studies of the feasibility of the VCG model for replication. We designed a small 12-nucleotide model VCG and synthesized all 247 oligonucleotides of lengths 2 to 12 corresponding to this genome. We experimentally monitored the fate of individual labeled primers in the pool of VCG oligonucleotides following the addition of activated nucleotides and investigated the effect of factors such as oligonucleotide length, concentration, composition, and temperature on the extent of primer extension. We observe a surprisingly prolonged equilibration process in the VCG system that enables a considerable extent of reaction. We find that environmental fluctuations would be essential for continuous templated extension of the entire VCG system since the shortest oligonucleotides can only bind to templates at low temperatures, while the longest oligonucleotides require high-temperature spikes to escape from inactive configurations. Finally, we demonstrate that primer extension is significantly enhanced when the mix of VCG oligonucleotides is preactivated. We discuss the necessity of ongoing in situ activation chemistry for continuous and accurate VCG replication.
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Affiliation(s)
- Dian Ding
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Lijun Zhou
- 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
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Shriyaa Mittal
- 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
| | - Jack W Szostak
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
- 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
- Howard Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
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5
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Dirscherl CF, Ianeselli A, Tetiker D, Matreux T, Queener RM, Mast CB, Braun D. A heated rock crack captures and polymerizes primordial DNA and RNA. Phys Chem Chem Phys 2023; 25:3375-3386. [PMID: 36633199 DOI: 10.1039/d2cp04538a] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Life is based on informational polymers such as DNA or RNA. For their polymerization, high concentrations of complex monomer building blocks are required. Therefore, the dilution by diffusion poses a major problem before early life could establish a non-equilibrium of compartmentalization. Here, we explored a natural non-equilibrium habitat to polymerize RNA and DNA. A heat flux across thin rock cracks is shown to accumulate and maintain nucleotides. This boosts the polymerization to RNA and DNA inside the crack. Moreover, the polymers remain localized, aiding both the creation of longer polymers and fostering downstream evolutionary steps. In a closed system, we found single nucleotides concentrate 104-fold at the bottom of the crack compared to the top after 24 hours. We detected enhanced polymerization for 2 different activation chemistries: aminoimidazole-activated DNA nucleotides and 2',3'-cyclic RNA nucleotides. The copolymerization of 2',3'-cGMP and 2',3'-cCMP in the thermal pore showed an increased heterogeneity in sequence composition compared to isothermal drying. Finite element models unravelled the combined polymerization and accumulation kinetics and indicated that the escape of the nucleotides from such a crack is negligible over a time span of years. The thermal non-equilibrium habitat establishes a cell-like compartment that actively accumulates nucleotides for polymerization and traps the resulting oligomers. We argue that the setting creates a pre-cellular non-equilibrium steady state for the first steps of molecular evolution.
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Affiliation(s)
- Christina F Dirscherl
- Systems Biophysics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80799 Munich, Germany.
| | - Alan Ianeselli
- Systems Biophysics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80799 Munich, Germany.
| | - Damla Tetiker
- Systems Biophysics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80799 Munich, Germany.
| | - Thomas Matreux
- Systems Biophysics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80799 Munich, Germany.
| | - Robbin M Queener
- Systems Biophysics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80799 Munich, Germany.
| | - Christof B Mast
- Systems Biophysics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80799 Munich, Germany.
| | - Dieter Braun
- Systems Biophysics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80799 Munich, Germany.
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6
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Leveau G, Pfeffer D, Altaner B, Kervio E, Welsch F, Gerland U, Richert C. Enzyme‐Free Copying of 12 Bases of RNA with Dinucleotides. Angew Chem Int Ed Engl 2022; 61:e202203067. [PMID: 35445525 PMCID: PMC9401581 DOI: 10.1002/anie.202203067] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [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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Xiu D, Zhao S, Li Z, Xu Y, Wang Y, Zhu Z, Zhang M, Snow CD, Belfiore LA, Tang J. Conditionally designed luminescent DNA crystals doped by Ln 3+(Eu 3+/Tb 3+) complexes or fluorescent proteins with smart drug sensing property. J Mater Chem B 2022; 10:6443-6452. [PMID: 35703105 DOI: 10.1039/d2tb00847e] [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
In this work, a designed porous DNA crystal with high intrinsic biocompatibility was used as the scaffold material to load fluorescent guest molecules to detect anti-cancer drugs. It is shown here that the synthesized crystals have the characteristics consistent with the designed large solvent channels, and can therefore accommodate guest molecules such as fluorescent proteins that cannot be accommodated by less porous crystals. Eu(TTA)3phen and Tb(acac)3phen lanthanide complexes were individually noncovalently loaded into the porous crystals, resulting in hybrid luminescent DNA crystals. Emodin, an anti-cancer, anti-tumor, anti-inflammatory drug, was found to quench lanthanide complexes in solution or in crystals. Notably, emodin is the active ingredient of Lianhua Qingwen Capsule, an anti-COVID-19 drug candidate. Therefore, the porous DNA crystals reported here have potential applications as a biocompatible and theranostic delivery biomaterial for functional macromolecules.
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Affiliation(s)
- Dan Xiu
- Institute of Hybrid Materials, National Center of International Research for Hybrid Materials Technology, National Base of International Science & Technology Cooperation, College of Materials Science and Engineering, Qingdao University, Qingdao, 266071, P. R. China.
| | - Sibo Zhao
- Institute of Hybrid Materials, National Center of International Research for Hybrid Materials Technology, National Base of International Science & Technology Cooperation, College of Materials Science and Engineering, Qingdao University, Qingdao, 266071, P. R. China.
| | - Zhenhua Li
- Institute of Hybrid Materials, National Center of International Research for Hybrid Materials Technology, National Base of International Science & Technology Cooperation, College of Materials Science and Engineering, Qingdao University, Qingdao, 266071, P. R. China.
| | - Yanan Xu
- Institute of Hybrid Materials, National Center of International Research for Hybrid Materials Technology, National Base of International Science & Technology Cooperation, College of Materials Science and Engineering, Qingdao University, Qingdao, 266071, P. R. China.
| | - Yao Wang
- Institute of Hybrid Materials, National Center of International Research for Hybrid Materials Technology, National Base of International Science & Technology Cooperation, College of Materials Science and Engineering, Qingdao University, Qingdao, 266071, P. R. China.
| | - Zhijun Zhu
- Institute of Hybrid Materials, National Center of International Research for Hybrid Materials Technology, National Base of International Science & Technology Cooperation, College of Materials Science and Engineering, Qingdao University, Qingdao, 266071, P. R. China.
| | - Min Zhang
- Institute of Hybrid Materials, National Center of International Research for Hybrid Materials Technology, National Base of International Science & Technology Cooperation, College of Materials Science and Engineering, Qingdao University, Qingdao, 266071, P. R. China.
| | - Christopher D Snow
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado, 80523, USA.
| | - Laurence A Belfiore
- Institute of Hybrid Materials, National Center of International Research for Hybrid Materials Technology, National Base of International Science & Technology Cooperation, College of Materials Science and Engineering, Qingdao University, Qingdao, 266071, P. R. China. .,Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado, 80523, USA.
| | - Jianguo Tang
- Institute of Hybrid Materials, National Center of International Research for Hybrid Materials Technology, National Base of International Science & Technology Cooperation, College of Materials Science and Engineering, Qingdao University, Qingdao, 266071, P. R. China.
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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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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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10
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Roberts SJ, Liu Z, Sutherland JD. Potentially Prebiotic Synthesis of Aminoacyl-RNA via a Bridging Phosphoramidate-Ester Intermediate. J Am Chem Soc 2022; 144:4254-4259. [PMID: 35230111 PMCID: PMC9097472 DOI: 10.1021/jacs.2c00772] [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] [Indexed: 11/28/2022]
Abstract
![]()
Translation
according to the genetic code is made possible by selectivity
both in aminoacylation of tRNA and in anticodon/codon recognition.
In extant biology, tRNAs are selectively aminoacylated by enzymes
using high-energy intermediates, but how this might have been achieved
prior to the advent of protein synthesis has been a largely unanswered
question in prebiotic chemistry. We have now elucidated a novel, prebiotically
plausible stereoselective aminoacyl-RNA synthesis, which starts from
RNA-amino acid phosphoramidates and proceeds via phosphoramidate-ester
intermediates that subsequently undergo conversion to aminoacyl-esters
by mild acid hydrolysis. The chemistry avoids the intermediacy of
high-energy mixed carboxy-phosphate anhydrides and is greatly favored
under eutectic conditions, which also potentially allow for the requisite
pH fluctuation through the variable solubility of CO2 in
solid/liquid water.
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Affiliation(s)
- Samuel J Roberts
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K
| | - Ziwei Liu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K
| | - John D Sutherland
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K
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11
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Genome Evolution from Random Ligation of RNAs of Autocatalytic Sets. Int J Mol Sci 2021; 22:ijms222413526. [PMID: 34948321 PMCID: PMC8707343 DOI: 10.3390/ijms222413526] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/08/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022] Open
Abstract
The evolutionary origin of the genome remains elusive. Here, I hypothesize that its first iteration, the protogenome, was a multi-ribozyme RNA. It evolved, likely within liposomes (the protocells) forming in dry-wet cycling environments, through the random fusion of ribozymes by a ligase and was amplified by a polymerase. The protogenome thereby linked, in one molecule, the information required to seed the protometabolism (a combination of RNA-based autocatalytic sets) in newly forming protocells. If this combination of autocatalytic sets was evolutionarily advantageous, the protogenome would have amplified in a population of multiplying protocells. It likely was a quasispecies with redundant information, e.g., multiple copies of one ribozyme. As such, new functionalities could evolve, including a genetic code. Once one or more components of the protometabolism were templated by the protogenome (e.g., when a ribozyme was replaced by a protein enzyme), and/or addiction modules evolved, the protometabolism became dependent on the protogenome. Along with increasing fidelity of the RNA polymerase, the protogenome could grow, e.g., by incorporating additional ribozyme domains. Finally, the protogenome could have evolved into a DNA genome with increased stability and storage capacity. I will provide suggestions for experiments to test some aspects of this hypothesis, such as evaluating the ability of ribozyme RNA polymerases to generate random ligation products and testing the catalytic activity of linked ribozyme domains.
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12
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Lozoya-Colinas A, Clifton BE, Grover MA, Hud NV. Urea and Acetamide Rich Solutions Circumvent the Strand Inhibition Problem to Allow Multiple Rounds of DNA and RNA Copying. Chembiochem 2021; 23:e202100495. [PMID: 34797020 DOI: 10.1002/cbic.202100495] [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: 09/18/2021] [Revised: 11/18/2021] [Indexed: 11/08/2022]
Abstract
For decades prebiotic chemists have attempted to achieve replication of RNA under prebiotic conditions with only limited success. One of the long-recognized impediments to achieving true replication of a duplex (copying of both strands) is the so-called strand inhibition problem. Specifically, while the two strands of an RNA (or DNA) duplex can be separated by heating, upon cooling the strands of a duplex will reanneal before mononucleotide or oligonucleotide substrates can bind to the individual strands. Here we demonstrate that a class of plausible prebiotic solvents, when coupled with thermal cycling and varying levels of hydration, circumvents the strand inhibition problem, and allows multiple rounds of information transfer from both strands of a duplex (replication). Replication was achieved by simultaneous ligation of oligomers that bind to their templates with the aid of the solvents. The solvents used consisted of concentrated solutions of urea and acetamide in water (UAcW), components that were likely abundant on the early Earth. The UAcW solvent system favors the annealing of shorter strands over the re-annealing of long strands, thereby circumventing strand inhibition. We observed an improvement of DNA and RNA replication yields by a factor of 100× over aqueous buffer. Information transfer in the UAcW solvent system is robust, being achieved for a range of solvent component ratios, various drying conditions, and in the absence or presence of added salts.
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Affiliation(s)
- Adriana Lozoya-Colinas
- NSF/NASA Center for Chemical Evolution, GA 30332, Atlanta, USA.,School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, GA 30332, Atlanta, USA
| | - Bryce E Clifton
- NSF/NASA Center for Chemical Evolution, GA 30332, Atlanta, USA.,School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, GA 30332, Atlanta, USA
| | - Martha A Grover
- NSF/NASA Center for Chemical Evolution, GA 30332, Atlanta, USA.,School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, GA 30332, Atlanta, USA
| | - Nicholas V Hud
- NSF/NASA Center for Chemical Evolution, GA 30332, Atlanta, USA.,School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, GA 30332, Atlanta, USA
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13
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Structured sequences emerge from random pool when replicated by templated ligation. Proc Natl Acad Sci U S A 2021; 118:2018830118. [PMID: 33593911 PMCID: PMC7923349 DOI: 10.1073/pnas.2018830118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The structure of life emerged from randomness. This is attributed to selection by molecular Darwinian evolution. This study found that random templated ligation led to the simultaneous elongation and sequence selection of oligomers. Product strands showed highly structured sequence motifs which inhibited self-folding and built self-templating reaction networks. By the reduction of the sequence space, the kinetics of duplex formation increased and led to a faster replication through the ligation process. These findings imply that elementary binding properties of nucleotides can lead to an early selection of sequences even before the onset of Darwinian evolution. This suggests that such a simplification of sequence space could result in faster downstream selection for sequence-based function for the origin of life. The central question in the origin of life is to understand how structure can emerge from randomness. The Eigen theory of replication states, for sequences that are copied one base at a time, that the replication fidelity has to surpass an error threshold to avoid that replicated specific sequences become random because of the incorporated replication errors [M. Eigen, Naturwissenschaften 58 (10), 465–523 (1971)]. Here, we showed that linking short oligomers from a random sequence pool in a templated ligation reaction reduced the sequence space of product strands. We started from 12-mer oligonucleotides with two bases in all possible combinations and triggered enzymatic ligation under temperature cycles. Surprisingly, we found the robust creation of long, highly structured sequences with low entropy. At the ligation site, complementary and alternating sequence patterns developed. However, between the ligation sites, we found either an A-rich or a T-rich sequence within a single oligonucleotide. Our modeling suggests that avoidance of hairpins was the likely cause for these two complementary sequence pools. What emerged was a network of complementary sequences that acted both as templates and substrates of the reaction. This self-selecting ligation reaction could be restarted by only a few majority sequences. The findings showed that replication by random templated ligation from a random sequence input will lead to a highly structured, long, and nonrandom sequence pool. This is a favorable starting point for a subsequent Darwinian evolution searching for higher catalytic functions in an RNA world scenario.
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Rolling-circle and strand-displacement mechanisms for non-enzymatic RNA replication at the time of the origin of life. J Theor Biol 2021; 527:110822. [PMID: 34214567 DOI: 10.1016/j.jtbi.2021.110822] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 06/11/2021] [Accepted: 06/26/2021] [Indexed: 11/21/2022]
Abstract
It is likely that RNA replication began non-enzymatically, and that polymerases were later selected to speed up the process. We consider replication mechanisms in modern viruses and ask which of these is possible non-enzymatically, using mathematical models and experimental data found in the literature to estimate rates of RNA synthesis and replication. Replication via alternating plus and minus strands is found in some single-stranded RNA viruses. However, if this occurred non-enzymatically it would lead to double-stranded RNA that would not separate. With some form of environmental cycling, such as temperature, salinity, or pH cycling, double-stranded RNA can be melted to form single-stranded RNA, although re-annealing of existing strands would then occur much faster than synthesis of new strands. We show that re-annealing blocks this form of replication at a very low concentration of strands. Other kinds of viruses synthesize linear double strands from single strands and then make new single strands from double strands via strand-displacement. This does not require environmental cycling and is not blocked by re-annealing. However, under non-enzymatic conditions, if strand-displacement occurs from a linear template, we expect the incomplete new strand to be almost always displaced by the tail end of the old strand through toehold-mediated displacement. A third kind of replication in viruses and viroids is rolling-circle replication which occurs via strand-displacement on a circular template. Rolling-circle replication does not require environmental cycling and is not prevented by toehold-mediated displacement. Rolling-circle replication is therefore expected to occur non-enzymatically and is a likely starting point for the evolution of polymerase-catalysed replication.
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Song EY, Jiménez EI, Lin H, Le Vay K, Krishnamurthy R, Mutschler H. Prebiotically Plausible RNA Activation Compatible with Ribozyme-Catalyzed Ligation. Angew Chem Int Ed Engl 2021; 60:2952-2957. [PMID: 33128282 PMCID: PMC7898671 DOI: 10.1002/anie.202010918] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 10/29/2020] [Indexed: 01/04/2023]
Abstract
RNA-catalyzed RNA ligation is widely believed to be a key reaction for primordial biology. However, since typical chemical routes towards activating RNA substrates are incompatible with ribozyme catalysis, it remains unclear how prebiotic systems generated and sustained pools of activated building blocks needed to form increasingly larger and complex RNA. Herein, we demonstrate in situ activation of RNA substrates under reaction conditions amenable to catalysis by the hairpin ribozyme. We found that diamidophosphate (DAP) and imidazole drive the formation of 2',3'-cyclic phosphate RNA mono- and oligonucleotides from monophosphorylated precursors in frozen water-ice. This long-lived activation enables iterative enzymatic assembly of long RNAs. Our results provide a plausible scenario for the generation of higher-energy substrates required to fuel ribozyme-catalyzed RNA synthesis in the absence of a highly evolved metabolism.
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Affiliation(s)
- Emilie Yeonwha Song
- Max Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Eddy Ivanhoe Jiménez
- Department of ChemistryThe Scripps Research Institute10550 North Torrey Pines RoadLa JollaCA92037USA
| | - Huacan Lin
- Department of ChemistryThe Scripps Research Institute10550 North Torrey Pines RoadLa JollaCA92037USA
| | - Kristian Le Vay
- Max Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | | | - Hannes Mutschler
- Max Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
- Technical University DortmundOtto-Hahn-Strasse 4a44227DortmundGermany
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16
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Song EY, Jiménez EI, Lin H, Le Vay K, Krishnamurthy R, Mutschler H. Präbiotisch plausible RNA‐Aktivierung kompatibel mit ribozymkatalysierter Ligation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202010918] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Emilie Yeonwha Song
- Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Deutschland
| | - Eddy Ivanhoe Jiménez
- Department of Chemistry The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Huacan Lin
- Department of Chemistry The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Kristian Le Vay
- Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Deutschland
| | | | - Hannes Mutschler
- Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Deutschland
- TU Dortmund University Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
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17
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Libicher K, Mutschler H. Probing self-regeneration of essential protein factors required for in vitro translation activity by serial transfer. Chem Commun (Camb) 2020; 56:15426-15429. [PMID: 33241808 DOI: 10.1039/d0cc06515c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The bottom-up construction of bio-inspired systems capable of self-maintenance and reproduction is a central goal in systems chemistry and synthetic biology. A particular challenge in such systems is the continuous regeneration of key proteins required for macromolecular synthesis. Here, we probe self-maintenance of a reconstituted in vitro translation system challenged by serial transfer of selected key proteins. We find that the system can simultaneously regenerate multiple essential polypeptides, which then contribute to the maintenance of protein expression after serial transfer. The presented strategy offers a robust methodology for probing and optimizing continuous self-regeneration of proteins in cell-free environments.
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Affiliation(s)
- Kai Libicher
- Biomimetic Systems, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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Obianyor C, Newnam G, Clifton BE, Grover MA, Hud NV. Towards Efficient Nonenzymatic DNA Ligation: Comparing Key Parameters for Maximizing Ligation Rates and Yields with Carbodiimide Activation**. Chembiochem 2020; 21:3359-3370. [DOI: 10.1002/cbic.202000335] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/21/2020] [Indexed: 01/14/2023]
Affiliation(s)
- Chiamaka Obianyor
- Georgia Institute of Technology School of Chemical and Biomolecular Engineering Atlanta Georgia 30332-0400 USA
| | - Gary Newnam
- Georgia Institute of Technology, Chemistry and Biochemistry 311 Ferst Drive Atlanta Georgia 30332-0400 USA
| | - Bryce E. Clifton
- Georgia Institute of Technology, Chemistry and Biochemistry 311 Ferst Drive Atlanta Georgia 30332-0400 USA
| | - Martha A. Grover
- Georgia Institute of Technology School of Chemical and Biomolecular Engineering Atlanta Georgia 30332-0400 USA
| | - Nicholas V. Hud
- Georgia Institute of Technology, Chemistry and Biochemistry 311 Ferst Drive Atlanta Georgia 30332-0400 USA
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Bhowmik S, Krishnamurthy R. The role of sugar-backbone heterogeneity and chimeras in the simultaneous emergence of RNA and DNA. Nat Chem 2019; 11:1009-1018. [PMID: 31527850 PMCID: PMC6815252 DOI: 10.1038/s41557-019-0322-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 07/31/2019] [Indexed: 01/01/2023]
Abstract
Hypotheses of the origins of RNA and DNA are generally centred on the prebiotic synthesis of a pristine system (pre-RNA or RNA), which gives rise to its descendent. However, a lack of specificity in the synthesis of genetic polymers would probably result in chimeric sequences; the roles and fate of such sequences are unknown. Here, we show that chimeras, exemplified by mixed threose nucleic acid (TNA)-RNA and RNA-DNA oligonucleotides, preferentially bind to, and act as templates for, homogeneous TNA, RNA and DNA ligands. The chimeric templates can act as a catalyst that mediates the ligation of oligomers to give homogeneous backbone sequences, and the regeneration of the chimeric templates potentiates a scenario for a possible cross-catalytic cycle with amplification. This process provides a proof-of-principle demonstration of a heterogeneity-to-homogeneity scenario and also gives credence to the idea that DNA could appear concurrently with RNA, instead of being its later descendent.
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Affiliation(s)
- Subhendu Bhowmik
- The Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
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Niether D, Wiegand S. Thermodiffusion and hydrolysis of 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC). THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2019; 42:117. [PMID: 31486949 DOI: 10.1140/epje/i2019-11880-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 08/01/2019] [Indexed: 06/10/2023]
Abstract
Presently, microfluidic traps are designed mimicking the environment of hydrothermal pores, where a combination of thermophoresis and convection leads to accumulation so that high concentrations of organic matter can be reached. Such a setup is interesting in the context of the origin of life to observe accumulation and possible further synthesis of small organic molecules or prebiotic molecules such as nucleotides or RNA-fragments, but could also be used to replicate DNA-strands. The addition of coupling agents for the activation of carboxyl or phosphate groups such as 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) and EDC-hydrochloride (EDC-HCl) is necessary in order to speed up the process. This work characterizes the thermophoretic properties of EDC and EDC-HCl needed to optimize the design of the traps. At p H 4-6 spontaneous hydrolysis of EDC is observed, which also leads to a neutralisation of the p H. In order to evaluate the thermodiffusion measurements the rate constants were measured at 23 and [Formula: see text] C and the activation energy of the hydrolysis calculated.
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Affiliation(s)
- Doreen Niether
- ICS-3 Soft Condensed Matter, Forschungszentrum Jülich GmbH, D-52428, Jülich, Germany.
| | - Simone Wiegand
- ICS-3 Soft Condensed Matter, Forschungszentrum Jülich GmbH, D-52428, Jülich, Germany
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