1
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Agmon I. Three Biopolymers and Origin of Life Scenarios. Life (Basel) 2024; 14:277. [PMID: 38398786 PMCID: PMC10890401 DOI: 10.3390/life14020277] [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: 12/28/2023] [Revised: 02/08/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024] Open
Abstract
To track down the possible roots of life, various models for the initial living system composed of different combinations of the three extant biopolymers, RNA, DNA, and proteins, are presented. The suitability of each molecular set is assessed according to its ability to emerge autonomously, sustain, and evolve continuously towards life as we know it. The analysis incorporates current biological knowledge gained from high-resolution structural data and large sequence datasets, together with experimental results concerned with RNA replication and with the activity demonstrated by standalone constructs of the ribosomal Peptidyl Transferase Center region. The scrutiny excludes the DNA-protein combination and assigns negligible likelihood to the existence of an RNA-DNA world, as well as to an RNA world that contained a replicase made of RNA. It points to the precedence of an RNA-protein system, whose model of emergence suggests specific processes whereby a coded proto-ribosome ribozyme, specifically aminoacylated proto-tRNAs and a proto-polymerase enzyme, could have autonomously emerged, cross-catalyzing the formation of each other. This molecular set constitutes a feasible starting point for a continuous evolutionary path, proceeding via natural processes from the inanimate matter towards life as we know it.
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Affiliation(s)
- Ilana Agmon
- Institute for Advanced Studies in Theoretical Chemistry, Schulich Faculty of Chemistry, Technion—Israel Institute of Technology, Haifa 3200003, Israel;
- Fritz Haber Research Center for Molecular Dynamics, Hebrew University, Jerusalem 9190401, Israel
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2
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Nogal N, Sanz-Sánchez M, Vela-Gallego S, Ruiz-Mirazo K, de la Escosura A. The protometabolic nature of prebiotic chemistry. Chem Soc Rev 2023; 52:7359-7388. [PMID: 37855729 PMCID: PMC10614573 DOI: 10.1039/d3cs00594a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Indexed: 10/20/2023]
Abstract
The field of prebiotic chemistry has been dedicated over decades to finding abiotic routes towards the molecular components of life. There is nowadays a handful of prebiotically plausible scenarios that enable the laboratory synthesis of most amino acids, fatty acids, simple sugars, nucleotides and core metabolites of extant living organisms. The major bottleneck then seems to be the self-organization of those building blocks into systems that can self-sustain. The purpose of this tutorial review is having a close look, guided by experimental research, into the main synthetic pathways of prebiotic chemistry, suggesting how they could be wired through common intermediates and catalytic cycles, as well as how recursively changing conditions could help them engage in self-organized and dissipative networks/assemblies (i.e., systems that consume chemical or physical energy from their environment to maintain their internal organization in a dynamic steady state out of equilibrium). In the article we also pay attention to the implications of this view for the emergence of homochirality. The revealed connectivity between those prebiotic routes should constitute the basis for a robust research program towards the bottom-up implementation of protometabolic systems, taken as a central part of the origins-of-life problem. In addition, this approach should foster further exploration of control mechanisms to tame the combinatorial explosion that typically occurs in mixtures of various reactive precursors, thus regulating the functional integration of their respective chemistries into self-sustaining protocellular assemblies.
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Affiliation(s)
- Noemí Nogal
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
| | - Marcos Sanz-Sánchez
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
| | - Sonia Vela-Gallego
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
| | - Kepa Ruiz-Mirazo
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, Leioa, Spain
- Department of Philosophy, University of the Basque Country, Leioa, Spain
| | - Andrés de la Escosura
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
- Institute for Advanced Research in Chemistry (IAdChem), Campus de Cantoblanco, 28049, Madrid, Spain
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3
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Pavlinova P, Lambert CN, Malaterre C, Nghe P. Abiogenesis through gradual evolution of autocatalysis into template-based replication. FEBS Lett 2023; 597:344-379. [PMID: 36203246 DOI: 10.1002/1873-3468.14507] [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: 07/15/2022] [Revised: 09/20/2022] [Accepted: 09/29/2022] [Indexed: 11/11/2022]
Abstract
How life emerged from inanimate matter is one of the most intriguing questions posed to modern science. Central to this research are experimental attempts to build systems capable of Darwinian evolution. RNA catalysts (ribozymes) are a promising avenue, in line with the RNA world hypothesis whereby RNA pre-dated DNA and proteins. Since evolution in living organisms relies on template-based replication, the identification of a ribozyme capable of replicating itself (an RNA self-replicase) has been a major objective. However, no self-replicase has been identified to date. Alternatively, autocatalytic systems involving multiple RNA species capable of ligation and recombination may enable self-reproduction. However, it remains unclear how evolution could emerge in autocatalytic systems. In this review, we examine how experimentally feasible RNA reactions catalysed by ribozymes could implement the evolutionary properties of variation, heredity and reproduction, and ultimately allow for Darwinian evolution. We propose a gradual path for the emergence of evolution, initially supported by autocatalytic systems leading to the later appearance of RNA replicases.
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Affiliation(s)
- Polina Pavlinova
- Laboratoire de Biophysique et Evolution, UMR CNRS-ESPCI 8231 Chimie Biologie Innovation, PSL University, Paris, France
| | - Camille N Lambert
- Laboratoire de Biophysique et Evolution, UMR CNRS-ESPCI 8231 Chimie Biologie Innovation, PSL University, Paris, France
| | - Christophe Malaterre
- Laboratory of Philosophy of Science (LAPS) and Centre Interuniversitaire de Recherche sur la Science et la Technologie (CIRST), Université du Québec à Montréal (UQAM), Canada
| | - Philippe Nghe
- Laboratoire de Biophysique et Evolution, UMR CNRS-ESPCI 8231 Chimie Biologie Innovation, PSL University, Paris, France
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4
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A liquid crystal world for the origins of life. Emerg Top Life Sci 2022; 6:557-569. [PMID: 36373852 DOI: 10.1042/etls20220081] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/23/2022] [Accepted: 10/27/2022] [Indexed: 11/16/2022]
Abstract
Nucleic acids (NAs) in modern biology accomplish a variety of tasks, and the emergence of primitive nucleic acids is broadly recognized as a crucial step for the emergence of life. While modern NAs have been optimized by evolution to accomplish various biological functions, such as catalysis or transmission of genetic information, primitive NAs could have emerged and been selected based on more rudimental chemical-physical properties, such as their propensity to self-assemble into supramolecular structures. One such supramolecular structure available to primitive NAs are liquid crystal (LC) phases, which are the outcome of the collective behavior of short DNA or RNA oligomers or monomers that self-assemble into linear aggregates by combinations of pairing and stacking. Formation of NA LCs could have provided many essential advantages for a primitive evolving system, including the selection of potential genetic polymers based on structure, protection by compartmentalization, elongation, and recombination by enhanced abiotic ligation. Here, we review recent studies on NA LC assembly, structure, and functions with potential prebiotic relevance. Finally, we discuss environmental or geological conditions on early Earth that could have promoted (or inhibited) primitive NA LC formation and highlight future investigation axes essential to further understanding of how LCs could have contributed to the emergence of life.
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5
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Saha A, Yi R, Fahrenbach AC, Wang A, Jia TZ. A Physicochemical Consideration of Prebiotic Microenvironments for Self-Assembly and Prebiotic Chemistry. LIFE (BASEL, SWITZERLAND) 2022; 12:life12101595. [PMID: 36295030 PMCID: PMC9604842 DOI: 10.3390/life12101595] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/07/2022] [Accepted: 10/08/2022] [Indexed: 11/06/2022]
Abstract
The origin of life on Earth required myriads of chemical and physical processes. These include the formation of the planet and its geological structures, the formation of the first primitive chemicals, reaction, and assembly of these primitive chemicals to form more complex or functional products and assemblies, and finally the formation of the first cells (or protocells) on early Earth, which eventually evolved into modern cells. Each of these processes presumably occurred within specific prebiotic reaction environments, which could have been diverse in physical and chemical properties. While there are resources that describe prebiotically plausible environments or nutrient availability, here, we attempt to aggregate the literature for the various physicochemical properties of different prebiotic reaction microenvironments on early Earth. We introduce a handful of properties that can be quantified through physical or chemical techniques. The values for these physicochemical properties, if they are known, are then presented for each reaction environment, giving the reader a sense of the environmental variability of such properties. Such a resource may be useful for prebiotic chemists to understand the range of conditions in each reaction environment, or to select the medium most applicable for their targeted reaction of interest for exploratory studies.
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Affiliation(s)
- Arpita Saha
- Blue Marble Space Institute of Science, 600 1st Ave, Floor 1, Seattle, WA 98104, USA
- Amity Institute of Applied Sciences, Amity University, Kolkata 700135, India
| | - Ruiqin Yi
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Albert C. Fahrenbach
- School of Chemistry, UNSW Sydney, Sydney, NSW 2052, Australia
- Australian Centre for Astrobiology, UNSW Sydney, Sydney, NSW 2052, Australia
- UNSW RNA Institute, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Anna Wang
- School of Chemistry, UNSW Sydney, Sydney, NSW 2052, Australia
- Australian Centre for Astrobiology, UNSW Sydney, Sydney, NSW 2052, Australia
- UNSW RNA Institute, UNSW Sydney, Sydney, NSW 2052, Australia
- Correspondence: (A.W.); (T.Z.J.)
| | - Tony Z. Jia
- Blue Marble Space Institute of Science, 600 1st Ave, Floor 1, Seattle, WA 98104, USA
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Correspondence: (A.W.); (T.Z.J.)
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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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Müller UF, Elsila J, Trail D, DasGupta S, Giese CC, Walton CR, Cohen ZR, Stolar T, Krishnamurthy R, Lyons TW, Rogers KL, Williams LD. Frontiers in Prebiotic Chemistry and Early Earth Environments. ORIGINS LIFE EVOL B 2022; 52:165-181. [PMID: 35796897 PMCID: PMC9261198 DOI: 10.1007/s11084-022-09622-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/29/2022] [Indexed: 11/28/2022]
Abstract
The Prebiotic Chemistry and Early Earth Environments (PCE3) Consortium is a community of researchers seeking to understand the origins of life on Earth and in the universe. PCE3 is one of five Research Coordination Networks (RCNs) within NASA’s Astrobiology Program. Here we report on the inaugural PCE3 workshop, intended to cross-pollinate, transfer information, promote cooperation, break down disciplinary barriers, identify new directions, and foster collaborations. This workshop, entitled, “Building a New Foundation”, was designed to propagate current knowledge, identify possibilities for multidisciplinary collaboration, and ultimately define paths for future collaborations. Presentations addressed the likely conditions on early Earth in ways that could be incorporated into prebiotic chemistry experiments and conceptual models to improve their plausibility and accuracy. Additionally, the discussions that followed among workshop participants helped to identify within each subdiscipline particularly impactful new research directions. At its core, the foundational knowledge base presented in this workshop should underpin future workshops and enable collaborations that bridge the many disciplines that are part of PCE3.
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Affiliation(s)
| | - Jamie Elsila
- NASA/Goddard Space Flight Center, Greenbelt, United States
| | - Dustin Trail
- University of Rochester, Rochester, United States
| | | | - Claudia-Corina Giese
- Leiden University, Leiden, The Netherlands.,Utrecht University, Utrecht, The Netherlands
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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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Kristoffersen EL, Burman M, Noy A, Holliger P. Rolling circle RNA synthesis catalysed by RNA. eLife 2022; 11:75186. [PMID: 35108196 PMCID: PMC8937235 DOI: 10.7554/elife.75186] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/01/2022] [Indexed: 11/13/2022] Open
Abstract
RNA-catalyzed RNA replication is widely considered a key step in the emergence of life’s first genetic system. However, RNA replication can be impeded by the extraordinary stability of duplex RNA products, which must be dissociated for re-initiation of the next replication cycle. Here, we have explored rolling circle synthesis (RCS) as a potential solution to this strand separation problem. We observe sustained RCS by a triplet polymerase ribozyme beyond full-length circle synthesis with strand displacement yielding concatemeric RNA products. Furthermore, we show RCS of a circular Hammerhead ribozyme capable of self-cleavage and re-circularization. Thus, all steps of a viroid-like RNA replication pathway can be catalyzed by RNA alone. Finally, we explore potential RCS mechanisms by molecular dynamics simulations, which indicate a progressive build-up of conformational strain upon RCS with destabilization of nascent strand 5′- and 3′-ends. Our results have implications for the emergence of RNA replication and for understanding the potential of RNA to support complex genetic processes. Many organisms today rely on a trio of molecules for their survival: DNA, to store their genetic information; proteins, to conduct the biological processes required for growth or replication; and RNA, to mainly act as an intermediary between DNA and proteins. Yet, how these inanimate molecules first came together to form a living system remains unclear. Circumstantial evidence suggests that the first lifeforms relied to a much greater exrtent on RNA to conduct all necessary biological processes. There is no trace of this ‘RNA world’ today, but molecular ‘fossils’ may exist in current biology. Viroids, for example, are agents which can infect and replicate inside plant cells. They are formed of nothing but a circular strand of RNA that serves not only as genetic storage but also as ribozymes (RNA-based enzymes). Viroids need proteins from the host plant to replicate, but scientists have been able to engineer ribozymes that can copy complex RNA strands. This suggests that viroid-like replication could be achieved using only RNA. Kristoffersen et al. put this idea to the test and showed that it is possible to use RNA enzymatic activity alone to carry out all the steps of a viroid-like copying mechanism. This process included copying a viroid-like RNA circle with RNA, followed by trimming the copy to the right size and reforming the circle. These two latter steps could be carried out by a ribozyme that could itself be encoded on the RNA circle. A computer simulation indicated that RNA synthesis on the circle caused increasing tension that could ease some of the barriers to replication. These results increase our understanding of how RNA copying by RNA could be possible. This may lead to developing molecular models of a primordial RNA-based replication, which could be used to investigate early genetic systems and may have potential applications in synthetic biology.
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Affiliation(s)
| | - Matthew Burman
- Department of Physics, University of York, York, United Kingdom
| | - Agnes Noy
- Department of Physics, University of York, York, United Kingdom
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10
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Takahashi S, Matsumoto S, Chilka P, Ghosh S, Okura H, Sugimoto N. Dielectricity of a molecularly crowded solution accelerates NTP misincorporation during RNA-dependent RNA polymerization by T7 RNA polymerase. Sci Rep 2022; 12:1149. [PMID: 35064200 PMCID: PMC8782835 DOI: 10.1038/s41598-022-05136-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/06/2022] [Indexed: 11/09/2022] Open
Abstract
In biological systems, the synthesis of nucleic acids, such as DNA and RNA, is catalyzed by enzymes in various aqueous solutions. However, substrate specificity is derived from the chemical properties of the residues, which implies that perturbations of the solution environment may cause changes in the fidelity of the reaction. Here, we investigated non-promoter-based synthesis of RNA using T7 RNA polymerase (T7 RNAP) directed by an RNA template in the presence of polyethylene glycol (PEG) of various molecular weights, which can affect polymerization fidelity by altering the solution properties. We found that the mismatch extensions of RNA propagated downstream polymerization. Furthermore, PEG promoted the polymerization of non-complementary ribonucleoside triphosphates, mainly due to the decrease in the dielectric constant of the solution. These results indicate that the mismatch extension of RNA-dependent RNA polymerization by T7 RNAP is driven by the stacking interaction of bases of the primer end and the incorporated nucleotide triphosphates (NTP) rather than base pairing between them. Thus, proteinaceous RNA polymerase may display different substrate specificity with changes in dielectricity caused by molecular crowding conditions, which can result in increased genetic diversity without proteinaceous modification.
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Affiliation(s)
- Shuntaro Takahashi
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan
| | - Saki Matsumoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan
| | - Pallavi Chilka
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan
| | - Saptarshi Ghosh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan
| | - Hiromichi Okura
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan.
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan.
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11
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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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12
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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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13
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Schuster GB, Cafferty BJ, Karunakaran SC, Hud NV. Water-Soluble Supramolecular Polymers of Paired and Stacked Heterocycles: Assembly, Structure, Properties, and a Possible Path to Pre-RNA. J Am Chem Soc 2021; 143:9279-9296. [PMID: 34152760 DOI: 10.1021/jacs.0c13081] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The hypothesis that RNA and DNA are products of chemical and biological evolution has motivated our search for alternative nucleic acids that may have come earlier in the emergence of life-polymers that possess a proclivity for covalent and non-covalent self-assembly not exhibited by RNA. Our investigations have revealed a small set of candidate ancestral nucleobases that self-assemble into hexameric rosettes that stack in water to form long, twisted, rigid supramolecular polymers. These structures exhibit properties that provide robust solutions to long-standing problems that have stymied the search for a prebiotic synthesis of nucleic acids. Moreover, their examination by experimental and computational methods provides insight into the chemical and physical principles that govern a particular class of water-soluble one-dimensional supramolecular polymers. In addition to efficient self-assembly, their lengths and polydispersity are modulated by a wide variety of positively charged, planar compounds; their assembly and disassembly are controlled over an exceedingly narrow pH range; they exhibit spontaneous breaking of symmetry; and homochirality emerges through non-covalent cross-linking during hydrogel formation. Some of these candidate ancestral nucleobases spontaneously form glycosidic bonds with ribose and other sugars, and, most significantly, functionalized forms of these heterocycles form supramolecular structures and covalent polymers under plausibly prebiotic conditions. This Perspective recounts a journey of discovery that continues to reveal attractive answers to questions concerning the origins of life and to uncover the principles that control the structure and properties of water-soluble supramolecular polymers.
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Affiliation(s)
- Gary B Schuster
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
| | - Brian J Cafferty
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
| | - Suneesh C Karunakaran
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
| | - Nicholas V Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
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14
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Guo W, Kinghorn AB, Zhang Y, Li Q, Poonam AD, Tanner JA, Shum HC. Non-associative phase separation in an evaporating droplet as a model for prebiotic compartmentalization. Nat Commun 2021; 12:3194. [PMID: 34045455 PMCID: PMC8160217 DOI: 10.1038/s41467-021-23410-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 04/22/2021] [Indexed: 11/13/2022] Open
Abstract
The synthetic pathways of life’s building blocks are envisaged to be through a series of complex prebiotic reactions and processes. However, the strategy to compartmentalize and concentrate biopolymers under prebiotic conditions remains elusive. Liquid-liquid phase separation is a mechanism by which membraneless organelles form inside cells, and has been hypothesized as a potential mechanism for prebiotic compartmentalization. Associative phase separation of oppositely charged species has been shown to partition RNA, but the strongly negative charge exhibited by RNA suggests that RNA-polycation interactions could inhibit RNA folding and its functioning inside the coacervates. Here, we present a prebiotically plausible pathway for non-associative phase separation within an evaporating all-aqueous sessile droplet. We quantitatively investigate the kinetic pathway of phase separation triggered by the non-uniform evaporation rate, together with the Marangoni flow-driven hydrodynamics inside the sessile droplet. With the ability to undergo liquid-liquid phase separation, the drying droplets provide a robust mechanism for formation of prebiotic membraneless compartments, as demonstrated by localization and storage of nucleic acids, in vitro transcription, as well as a three-fold enhancement of ribozyme activity. The compartmentalization mechanism illustrated in this model system is feasible on wet organophilic silica-rich surfaces during early molecular evolution. Prebiotic compartmentalization could prove essential for the evolution of life. Guo et al. show that liquid-liquid separation in an aqueous two-phase system driven by evaporation may already suffice to facilitate chemical processes required for the RNA world hypothesis.
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Affiliation(s)
- Wei Guo
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong (SAR), Hong Kong, China
| | - Andrew B Kinghorn
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong (SAR), Hong Kong, China
| | - Yage Zhang
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong (SAR), Hong Kong, China
| | - Qingchuan Li
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong (SAR), Hong Kong, China.,School of Chemistry & Chemical Engineering, National Engineering Research Center for Colloidal Materials, Shandong University, Jinan, 250100, China
| | - Aditi Dey Poonam
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong (SAR), Hong Kong, China
| | - Julian A Tanner
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong (SAR), Hong Kong, China. .,Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong (SAR), Hong Kong, China.
| | - Ho Cheung Shum
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong (SAR), Hong Kong, China. .,Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong (SAR), Hong Kong, China.
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15
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Liquid Crystal Peptide/DNA Coacervates in the Context of Prebiotic Molecular Evolution. CRYSTALS 2020. [DOI: 10.3390/cryst10110964] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Liquid–liquid phase separation (LLPS) phenomena are ubiquitous in biological systems, as various cellular LLPS structures control important biological processes. Due to their ease of in vitro assembly into membraneless compartments and their presence within modern cells, LLPS systems have been postulated to be one potential form that the first cells on Earth took on. Recently, liquid crystal (LC)-coacervate droplets assembled from aqueous solutions of short double-stranded DNA (s-dsDNA) and poly-L-lysine (PLL) have been reported. Such LC-coacervates conjugate the advantages of an associative LLPS with the relevant long-range ordering and fluidity properties typical of LC, which reflect and propagate the physico-chemical properties of their molecular constituents. Here, we investigate the structure, assembly, and function of DNA LC-coacervates in the context of prebiotic molecular evolution and the emergence of functional protocells on early Earth. We observe through polarization microscopy that LC-coacervate systems can be dynamically assembled and disassembled based on prebiotically available environmental factors including temperature, salinity, and dehydration/rehydration cycles. Based on these observations, we discuss how LC-coacervates can in principle provide selective pressures effecting and sustaining chemical evolution within partially ordered compartments. Finally, we speculate about the potential for LC-coacervates to perform various biologically relevant properties, such as segregation and concentration of biomolecules, catalysis, and scaffolding, potentially providing additional structural complexity, such as linearization of nucleic acids and peptides within the LC ordered matrix, that could have promoted more efficient polymerization. While there are still a number of remaining open questions regarding coacervates, as protocell models, including how modern biologies acquired such membraneless organelles, further elucidation of the structure and function of different LLPS systems in the context of origins of life and prebiotic chemistry could provide new insights for understanding new pathways of molecular evolution possibly leading to the emergence of the first cells on Earth.
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16
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Menor Salván C, Bouza M, Fialho DM, Burcar BT, Fernández FM, Hud NV. Prebiotic Origin of Pre‐RNA Building Blocks in a Urea “Warm Little Pond” Scenario. Chembiochem 2020; 21:3504-3510. [DOI: 10.1002/cbic.202000510] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Indexed: 11/07/2022]
Affiliation(s)
- C. Menor Salván
- NSF-NASA Center for Chemical Evolution Georgia Institute of Technology Atlanta GA 30302 USA
- Dep. de Biología de Sistemas/IQAR Universidad de Alcalá 28806 Madrid Spain
| | - Marcos Bouza
- NSF-NASA Center for Chemical Evolution Georgia Institute of Technology Atlanta GA 30302 USA
- School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta GA 30302 USA
| | - David M. Fialho
- NSF-NASA Center for Chemical Evolution Georgia Institute of Technology Atlanta GA 30302 USA
- School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta GA 30302 USA
| | - Bradley T. Burcar
- NSF-NASA Center for Chemical Evolution Georgia Institute of Technology Atlanta GA 30302 USA
- School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta GA 30302 USA
| | - Facundo M. Fernández
- NSF-NASA Center for Chemical Evolution Georgia Institute of Technology Atlanta GA 30302 USA
- School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta GA 30302 USA
| | - Nicholas V. Hud
- NSF-NASA Center for Chemical Evolution Georgia Institute of Technology Atlanta GA 30302 USA
- School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta GA 30302 USA
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17
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Chien CY, Yu SS. Ester-mediated peptide formation promoted by deep eutectic solvents: a facile pathway to proto-peptides. Chem Commun (Camb) 2020; 56:11949-11952. [PMID: 32929424 DOI: 10.1039/d0cc03319g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The ester-amide exchange reaction enables spontaneous formation of prebiotic proto-peptides under mild conditions. However, this reaction also leads to oligomers with a vast sequence diversity of ester and amide linkages. Here, we demonstrate using deep eutectic solvents as a universal strategy to regulate the reaction pathways and promote the formation of amino acid-enriched oligomers with peptide backbones.
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Affiliation(s)
- Chen-Yu Chien
- Department of Chemical Engineering, National Cheng Kung University, No. 1 University Road, Tainan City, 70101, Taiwan, Republic of China.
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18
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Zhou L, O'Flaherty DK, Szostak JW. Template-Directed Copying of RNA by Non-enzymatic Ligation. Angew Chem Int Ed Engl 2020; 59:15682-15687. [PMID: 32558121 PMCID: PMC7496532 DOI: 10.1002/anie.202004934] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 06/04/2020] [Indexed: 12/12/2022]
Abstract
The non-enzymatic replication of the primordial genetic material is thought to have enabled the evolution of early forms of RNA-based life. However, the replication of oligonucleotides long enough to encode catalytic functions is problematic due to the low efficiency of template copying with mononucleotides. We show that template-directed ligation can assemble long RNAs from shorter oligonucleotides, which would be easier to replicate. The rate of ligation can be greatly enhanced by employing a 3'-amino group at the 3'-end of each oligonucleotide, in combination with an N-alkyl imidazole organocatalyst. These modifications enable the copying of RNA templates by the multistep ligation of tetranucleotide building blocks, as well as the assembly of long oligonucleotides using short splint oligonucleotides. We also demonstrate the formation of long oligonucleotides inside model prebiotic vesicles, which suggests a potential route to the assembly of artificial cells capable of evolution.
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Affiliation(s)
- Lijun Zhou
- Howard Hughes Medical InstituteDepartment of Molecular BiologyCenter for Computational and Integrative BiologyMassachusetts General HospitalBostonMA02114 (USA), E
| | - Derek K. O'Flaherty
- Howard Hughes Medical InstituteDepartment of Molecular BiologyCenter for Computational and Integrative BiologyMassachusetts General HospitalBostonMA02114 (USA), E
- Present address: Alnylam PharmaceuticalsCambridgeMA02142USA
| | - Jack W. Szostak
- Howard Hughes Medical InstituteDepartment of Molecular BiologyCenter for Computational and Integrative BiologyMassachusetts General HospitalBostonMA02114 (USA), E
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19
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Zhou L, O'Flaherty DK, Szostak JW. Template‐Directed Copying of RNA by Non‐enzymatic Ligation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004934] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Lijun Zhou
- Howard Hughes Medical Institute Department of Molecular Biology Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 (USA), E
| | - Derek K. O'Flaherty
- Howard Hughes Medical Institute Department of Molecular Biology Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 (USA), E
- Present address: Alnylam Pharmaceuticals Cambridge MA 02142 USA
| | - Jack W. Szostak
- Howard Hughes Medical Institute Department of Molecular Biology Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 (USA), E
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20
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Núñez-Pertíñez S, Wilks TR. Deep Eutectic Solvents as Media for the Prebiotic DNA-Templated Synthesis of Peptides. Front Chem 2020; 8:41. [PMID: 32083058 PMCID: PMC7005209 DOI: 10.3389/fchem.2020.00041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 01/14/2020] [Indexed: 12/25/2022] Open
Abstract
Translation of genetic information into peptide products is one of the fundamental processes of biology. How this occurred prebiotically, in the absence of enzyme catalysts, is an intriguing question. Nucleic acid-templated synthesis (NATS) promotes reactions by bringing building blocks tethered to complementary DNA strands into close proximity and has been shown to enable peptide synthesis without enzymes—it could therefore serve as a model for prebiotic translation of information stored in nucleic acid sequences into functional peptides. The decomposition of highly reactive DNA adapters has so far limited the effectiveness of NATS, but these studies have been performed exclusively in aqueous solution. Deep eutectic solvents (DESs) have been proposed as a feasible solvent for prebiotic replication of nucleic acids, and here are studied as media for prebiotic translation using NATS as a model. DESs are shown to enhance the stability of DNA-conjugated activated esters, the precursors of peptides. However, this enhanced stability was coupled with decreased amine reactivity that hampered the formation of peptide bonds in DESs. These properties are exploited to demonstrate the storage of DNA-conjugated activated esters in a DES followed by transfer into aqueous buffer to activate the NATS of peptides “on demand.” These findings, together with the reported functions of DESs in prebiotic processes, shed light on how DESs could have facilitated the non-enzymatic translation of genetic information into functional peptides on the early Earth.
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Affiliation(s)
| | - Thomas R Wilks
- School of Chemistry, University of Birmingham, Birmingham, United Kingdom
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21
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Le Vay K, Salibi E, Song EY, Mutschler H. Nucleic Acid Catalysis under Potential Prebiotic Conditions. Chem Asian J 2020; 15:214-230. [PMID: 31714665 PMCID: PMC7003795 DOI: 10.1002/asia.201901205] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 11/05/2019] [Indexed: 01/25/2023]
Abstract
Catalysis by nucleic acids is indispensable for extant cellular life, and it is widely accepted that nucleic acid enzymes were crucial for the emergence of primitive life 3.5-4 billion years ago. However, geochemical conditions on early Earth must have differed greatly from the constant internal milieus of today's cells. In order to explore plausible scenarios for early molecular evolution, it is therefore essential to understand how different physicochemical parameters, such as temperature, pH, and ionic composition, influence nucleic acid catalysis and to explore to what extent nucleic acid enzymes can adapt to non-physiological conditions. In this article, we give an overview of the research on catalysis of nucleic acids, in particular catalytic RNAs (ribozymes) and DNAs (deoxyribozymes), under extreme and/or unusual conditions that may relate to prebiotic environments.
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Affiliation(s)
- Kristian Le Vay
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Elia Salibi
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Emilie Y. Song
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Hannes Mutschler
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
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22
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He C, Lozoya-Colinas A, Gállego I, Grover MA, Hud NV. Solvent viscosity facilitates replication and ribozyme catalysis from an RNA duplex in a model prebiotic process. Nucleic Acids Res 2020; 47:6569-6577. [PMID: 31170298 PMCID: PMC6649698 DOI: 10.1093/nar/gkz496] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/22/2019] [Accepted: 05/24/2019] [Indexed: 11/24/2022] Open
Abstract
The RNA World hypothesis posits that RNA was once responsible for genetic information storage and catalysis. However, a prebiotic mechanism has yet to be reported for the replication of duplex RNA that could have operated before the emergence of polymerase ribozymes. Previously, we showed that a viscous solvent enables information transfer from one strand of long RNA duplex templates, overcoming ‘the strand inhibition problem'. Here, we demonstrate that the same approach allows simultaneous information transfer from both strands of long duplex templates. An additional challenge for the RNA World is that structured RNAs (like those with catalytic activity) function poorly as templates in model prebiotic RNA synthesis reactions, raising the question of how a single sequence could serve as both a catalyst and as a replication template. Here, we show that a viscous solvent also facilitates the transition of a newly synthesized hammerhead ribozyme sequence from its inactive, duplex state to its active, folded state. These results demonstrate how fluctuating environmental conditions can allow a ribozyme sequence to alternate between acting as a template for replication and functioning as a catalyst, and illustrate the potential for temporally changing environments to enable molecular processes necessary for the origin of life.
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Affiliation(s)
- Christine He
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0100, USA
| | - Adriana Lozoya-Colinas
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA
| | - Isaac Gállego
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA
| | - Martha A Grover
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0100, USA
| | - Nicholas V Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA
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23
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Zhou L, Kim SC, Ho KH, O'Flaherty DK, Giurgiu C, Wright TH, Szostak JW. Non-enzymatic primer extension with strand displacement. eLife 2019; 8:e51888. [PMID: 31702557 PMCID: PMC6872209 DOI: 10.7554/elife.51888] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 11/07/2019] [Indexed: 12/20/2022] Open
Abstract
Non-enzymatic RNA self-replication is integral to the emergence of the 'RNA World'. Despite considerable progress in non-enzymatic template copying, demonstrating a full replication cycle remains challenging due to the difficulty of separating the strands of the product duplex. Here, we report a prebiotically plausible approach to strand displacement synthesis in which short 'invader' oligonucleotides unwind an RNA duplex through a toehold/branch migration mechanism, allowing non-enzymatic primer extension on a template that was previously occupied by its complementary strand. Kinetic studies of single-step reactions suggest that following invader binding, branch migration results in a 2:3 partition of the template between open and closed states. Finally, we demonstrate continued primer extension with strand displacement by employing activated 3'-aminonucleotides, a more reactive proxy for ribonucleotides. Our study suggests that complete cycles of non-enzymatic replication of the primordial genetic material may have been facilitated by short RNA oligonucleotides.
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Affiliation(s)
- Lijun Zhou
- Department of Molecular BiologyHoward Hughes Medical Institute, Massachusetts General HospitalBostonUnited States
- Center for Computational and IntegrativeBiologyMassachusetts General HospitalBostonUnited States
- Department of GeneticsHarvard Medical SchoolBostonUnited States
| | - Seohyun Chris Kim
- Department of Molecular BiologyHoward Hughes Medical Institute, Massachusetts General HospitalBostonUnited States
- Center for Computational and IntegrativeBiologyMassachusetts General HospitalBostonUnited States
- Department of GeneticsHarvard Medical SchoolBostonUnited States
| | - Katherine H Ho
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
| | - Derek K O'Flaherty
- Department of Molecular BiologyHoward Hughes Medical Institute, Massachusetts General HospitalBostonUnited States
- Center for Computational and IntegrativeBiologyMassachusetts General HospitalBostonUnited States
- Department of GeneticsHarvard Medical SchoolBostonUnited States
| | - Constantin Giurgiu
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
| | - Tom H Wright
- Department of Molecular BiologyHoward Hughes Medical Institute, Massachusetts General HospitalBostonUnited States
- Center for Computational and IntegrativeBiologyMassachusetts General HospitalBostonUnited States
- Department of GeneticsHarvard Medical SchoolBostonUnited States
| | - Jack W Szostak
- Department of Molecular BiologyHoward Hughes Medical Institute, Massachusetts General HospitalBostonUnited States
- Center for Computational and IntegrativeBiologyMassachusetts General HospitalBostonUnited States
- Department of GeneticsHarvard Medical SchoolBostonUnited States
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
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24
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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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25
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Zhang L, Zhang YQ, Chen Z, Lin T, Paszkiewicz M, Hellwig R, Huang T, Ruben M, Barth JV, Klappenberger F. On-Surface Activation of Trimethylsilyl-Terminated Alkynes on Coinage Metal Surfaces. Chemphyschem 2019; 20:2382-2393. [PMID: 31120616 DOI: 10.1002/cphc.201900249] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/14/2019] [Indexed: 11/11/2022]
Abstract
The controlled attachment of protecting groups combined with the ability to selectively abstract them is central to organic synthesis. The trimethylsilyl (TMS) functional group is a popular protecting group in solution. However, insights on its activation behavior under ultra-high vacuum (UHV) and surface-confined conditions are scarce. Here we investigate a series of TMS-protected alkyne precursors via scanning tunneling microscopy (STM) regarding their compatibility with organic molecular beam epitaxy (OMBE) and their potential deprotection on various coinage metal surfaces. After in-situ evaporation on the substrates held in UHV at room temperature, we find that all molecules arrived and adsorbed as intact units forming ordered supramolecular aggregates stabilized by non-covalent interactions. Thus, TMS-functionalized alkyne precursors with weights up to 1100 atomic mass units are stable against OMBE evaporation in UHV. Furthermore, the TMS activation through thermal annealing is investigated with STM and X-ray photoelectron spectroscopy (XPS). We observe that deprotection starts to occur between 400 K and 500 K on the copper and gold surfaces, respectively. In contrast, on silver surfaces, the TMS-alkyne bond remains stable up to temperatures where molecular desorption sets in (≈600 K). Hence, TMS functional groups can be utilized as leaving groups on copper and gold surfaces while they serve as protecting groups on silver surfaces.
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Affiliation(s)
- Liding Zhang
- Physics Department E20, Technical University of Munich (TUM), 85748, Garching, Germany
| | - Yi-Qi Zhang
- Physics Department E20, Technical University of Munich (TUM), 85748, Garching, Germany
| | - Zhi Chen
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany
| | - Tao Lin
- Physics Department E20, Technical University of Munich (TUM), 85748, Garching, Germany.,College of New Materials and New Energies, Shenzhen Technology University, 518118, Shenzhen, China
| | - Mateusz Paszkiewicz
- Physics Department E20, Technical University of Munich (TUM), 85748, Garching, Germany
| | - Raphael Hellwig
- Physics Department E20, Technical University of Munich (TUM), 85748, Garching, Germany
| | - Tianjiao Huang
- Physics Department E20, Technical University of Munich (TUM), 85748, Garching, Germany
| | - Mario Ruben
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany.,Département des Matériaux Organiques (DMO), Institut de Physique et Chimie des Matériaux de Strasbourg (IPCMS), 67034, Strasbourg, France
| | - Johannes V Barth
- Physics Department E20, Technical University of Munich (TUM), 85748, Garching, Germany
| | - Florian Klappenberger
- Physics Department E20, Technical University of Munich (TUM), 85748, Garching, Germany
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26
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Zhao Y, Yuan B, Li C, Zhang P, Mai Y, Guan D, Li Y, Zheng H, Liu C, Wang S, Jia J. On-Surface Synthesis of Iron Phthalocyanine Using Metal-Organic Coordination Templates. Chemphyschem 2019; 20:2394-2397. [PMID: 31025456 DOI: 10.1002/cphc.201900238] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 04/19/2019] [Indexed: 11/06/2022]
Abstract
On-surface synthesis provides a convenient route to many kinds of conjugated molecular nanostructures, but it has remained challenging to precisely control the reaction pathway for using multicomponent precursors. Herein, we demonstrate a two-step strategy to synthesize iron phthalocyanine (FePc) molecules using metal-organic coordination for templating by using high-resolution scanning tunnelling microscopy and non-contact atomic force microscopy. In a first step, 1,2,4,5-tetracyanobenzene (TCNB) precursors and Fe atoms self-assembly into Fe(TCNB)4 coordination complexes on a clean Au(111) surface. The Fe(TCNB)4 complexes further undergo cyclic tetramerization upon thermal annealing, forming single FePc molecules. We expect that our demonstrated synthetic strategy may shed light on the design and synthesis of two-dimensional extended conjugated systems.
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Affiliation(s)
- Yan Zhao
- Key Laboratory of Artificial Structures and Quantum Control (Ministry of Education), School of Physics and Astronomy, Shanghai Jiao Tong University, 800 DongChuan Road, Shanghai, 200240, China
| | - Bingkai Yuan
- Key Laboratory of Artificial Structures and Quantum Control (Ministry of Education), School of Physics and Astronomy, Shanghai Jiao Tong University, 800 DongChuan Road, Shanghai, 200240, China
| | - Can Li
- Key Laboratory of Artificial Structures and Quantum Control (Ministry of Education), School of Physics and Astronomy, Shanghai Jiao Tong University, 800 DongChuan Road, Shanghai, 200240, China
| | - Pengfei Zhang
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 DongChuan Road, Shanghai, 200240, China
| | - Yiyong Mai
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 DongChuan Road, Shanghai, 200240, China
| | - Dandan Guan
- Key Laboratory of Artificial Structures and Quantum Control (Ministry of Education), School of Physics and Astronomy, Shanghai Jiao Tong University, 800 DongChuan Road, Shanghai, 200240, China
| | - Yaoyi Li
- Key Laboratory of Artificial Structures and Quantum Control (Ministry of Education), School of Physics and Astronomy, Shanghai Jiao Tong University, 800 DongChuan Road, Shanghai, 200240, China
| | - Hao Zheng
- Key Laboratory of Artificial Structures and Quantum Control (Ministry of Education), School of Physics and Astronomy, Shanghai Jiao Tong University, 800 DongChuan Road, Shanghai, 200240, China
| | - Canhua Liu
- Key Laboratory of Artificial Structures and Quantum Control (Ministry of Education), School of Physics and Astronomy, Shanghai Jiao Tong University, 800 DongChuan Road, Shanghai, 200240, China
| | - Shiyong Wang
- Key Laboratory of Artificial Structures and Quantum Control (Ministry of Education), School of Physics and Astronomy, Shanghai Jiao Tong University, 800 DongChuan Road, Shanghai, 200240, China
| | - Jinfeng Jia
- Key Laboratory of Artificial Structures and Quantum Control (Ministry of Education), School of Physics and Astronomy, Shanghai Jiao Tong University, 800 DongChuan Road, Shanghai, 200240, China
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27
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Li J, Lampart S, Siegel JS, Ernst K, Wäckerlin C. Graphene Grown from Flat and Bowl Shaped Polycyclic Aromatic Hydrocarbons on Cu(111). Chemphyschem 2019; 20:2354-2359. [DOI: 10.1002/cphc.201900291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/06/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Jingyi Li
- Swiss Federal Laboratories for Materials Science and Technology Überlandstr. 129 Dübendorf Switzerland
| | - Samuel Lampart
- Department of ChemistryUniversity of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Jay S. Siegel
- School of Pharmaceutical Science and TechnologyTianjin University 92 Weijin Road, Nankai District Tianjin- 3000072 China
| | - Karl‐Heinz Ernst
- Swiss Federal Laboratories for Materials Science and Technology Überlandstr. 129 Dübendorf Switzerland
- Department of ChemistryUniversity of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
- Institute of Physics of the Czech Academy of Sciences Cukrovarnická 10 162 00 Praha 6 Czech Republic
| | - Christian Wäckerlin
- Swiss Federal Laboratories for Materials Science and Technology Überlandstr. 129 Dübendorf Switzerland
- Institute of Physics of the Czech Academy of Sciences Cukrovarnická 10 162 00 Praha 6 Czech Republic
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28
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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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29
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Takahashi S, Okura H, Sugimoto N. Bisubstrate Function of RNA Polymerases Triggered by Molecular Crowding Conditions. Biochemistry 2019; 58:1081-1093. [DOI: 10.1021/acs.biochem.8b01204] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Shuntaro Takahashi
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 minatojima-Minamimachi, Kobe 650-0047, Japan
| | - Hiromichi Okura
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 minatojima-Minamimachi, Kobe 650-0047, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 minatojima-Minamimachi, Kobe 650-0047, Japan
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 minatojima-Minamimachi, Kobe 650-0047, Japan
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30
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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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31
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Shu CH, Xie YL, Wang A, Shi KJ, Zhang WF, Li DY, Liu PN. On-surface reactions of aryl chloride and porphyrin macrocycles via merging two reactive sites into a single precursor. Chem Commun (Camb) 2018; 54:12626-12629. [PMID: 30351327 DOI: 10.1039/c8cc07652a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The reaction of aryl chloride and porphyrin macrocycles, which are merged into a single precursor, has been achieved on Cu(111). Scanning tunneling microscopy analysis of the oligomer products showed that the adjacent porphyrin moieties linked mainly by the phenyl group with the porphyrin macrocycle.
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Affiliation(s)
- Chen-Hui Shu
- Shanghai Key Laboratory of Functional Materials Chemistry, State Key Laboratory of Chemical Engineering, School of Chemistry & Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
| | - Yu-Li Xie
- Shanghai Key Laboratory of Functional Materials Chemistry, State Key Laboratory of Chemical Engineering, School of Chemistry & Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
| | - An Wang
- Shanghai Key Laboratory of Functional Materials Chemistry, State Key Laboratory of Chemical Engineering, School of Chemistry & Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
| | - Ke-Ji Shi
- Shanghai Key Laboratory of Functional Materials Chemistry, State Key Laboratory of Chemical Engineering, School of Chemistry & Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
| | - Wei-Feng Zhang
- Key Laboratory of Photovoltaic Materials of Henan Province, Henan University, Kaifeng 475004, China.
| | - Deng-Yuan Li
- Shanghai Key Laboratory of Functional Materials Chemistry, State Key Laboratory of Chemical Engineering, School of Chemistry & Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
| | - Pei-Nian Liu
- Shanghai Key Laboratory of Functional Materials Chemistry, State Key Laboratory of Chemical Engineering, School of Chemistry & Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
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32
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Yadav A, Iost RM, Neubert TJ, Baylan S, Schmid T, Balasubramanian K. Selective electrochemical functionalization of the graphene edge. Chem Sci 2018; 10:936-942. [PMID: 30774888 PMCID: PMC6346287 DOI: 10.1039/c8sc04083d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 11/04/2018] [Indexed: 12/23/2022] Open
Abstract
We report the direct exclusive modification of the edge of a single graphene monolayer with nanoparticles or organic functionalities under ambient conditions.
We present a versatile and simple method using electrochemistry for the exclusive functionalization of the edge of a graphene monolayer with metal nanoparticles or polymeric amino groups. The attachment of metal nanoparticles allows us to exploit surface-enhanced Raman scattering to characterize the chemistry of both the pristine and the functionalized graphene edge. For the pristine patterned graphene edge, we observe the typical edge-related modes, while for the functionalized graphene edge we identify the chemical structure of the functional layer by vibrational fingerprinting. The ability to obtain single selectively functionalized graphene edges routinely on an insulating substrate opens an avenue for exploring the effect of edge chemistry on graphene properties systematically.
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Affiliation(s)
- Anur Yadav
- School of Analytical Sciences Adlershof (SALSA) , Humboldt Universität zu Berlin , 10099 Berlin , Germany . nano.anchem-at-hu-berlin.de.,Department of Chemistry , IRIS Adlershof , Humboldt Universität zu Berlin , 10099 Berlin , Germany
| | - Rodrigo M Iost
- School of Analytical Sciences Adlershof (SALSA) , Humboldt Universität zu Berlin , 10099 Berlin , Germany . nano.anchem-at-hu-berlin.de.,Department of Chemistry , IRIS Adlershof , Humboldt Universität zu Berlin , 10099 Berlin , Germany
| | - Tilmann J Neubert
- School of Analytical Sciences Adlershof (SALSA) , Humboldt Universität zu Berlin , 10099 Berlin , Germany . nano.anchem-at-hu-berlin.de.,Department of Chemistry , IRIS Adlershof , Humboldt Universität zu Berlin , 10099 Berlin , Germany.,Helmholtz-Zentrum Berlin für Materialien und Energie GmbH , Institut für Silizium-Photovolatik , Kekuléstr. 5 , 12489 Berlin , Germany
| | - Sema Baylan
- School of Analytical Sciences Adlershof (SALSA) , Humboldt Universität zu Berlin , 10099 Berlin , Germany . nano.anchem-at-hu-berlin.de
| | - Thomas Schmid
- School of Analytical Sciences Adlershof (SALSA) , Humboldt Universität zu Berlin , 10099 Berlin , Germany . nano.anchem-at-hu-berlin.de.,BAM , Federal Institute for Materials Research and Testing , Richard-Willstätter-Str. 11 , 12489 Berlin , Germany
| | - Kannan Balasubramanian
- School of Analytical Sciences Adlershof (SALSA) , Humboldt Universität zu Berlin , 10099 Berlin , Germany . nano.anchem-at-hu-berlin.de.,Department of Chemistry , IRIS Adlershof , Humboldt Universität zu Berlin , 10099 Berlin , Germany.,BAM , Federal Institute for Materials Research and Testing , Richard-Willstätter-Str. 11 , 12489 Berlin , Germany
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33
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Macedo LJA, Iost RM, Hassan A, Balasubramanian K, Crespilho FN. Bioelectronics and Interfaces Using Monolayer Graphene. ChemElectroChem 2018. [DOI: 10.1002/celc.201800934] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Lucyano J. A. Macedo
- São Carlos Institute of Chemistry; University of São Paulo; São Carlos SP 13560-970 Brazil
| | - Rodrigo M. Iost
- Department of Chemistry School of Analytical Sciences Adlershof (SALSA) and IRIS Adlershof; Humboldt-Universität zu Berlin; Berlin 10099 Germany
| | - Ayaz Hassan
- São Carlos Institute of Chemistry; University of São Paulo; São Carlos SP 13560-970 Brazil
| | - Kannan Balasubramanian
- Department of Chemistry School of Analytical Sciences Adlershof (SALSA) and IRIS Adlershof; Humboldt-Universität zu Berlin; Berlin 10099 Germany
| | - Frank N. Crespilho
- São Carlos Institute of Chemistry; University of São Paulo; São Carlos SP 13560-970 Brazil
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34
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Matsubara YJ, Kaneko K. Kinetic Selection of Template Polymer with Complex Sequences. PHYSICAL REVIEW LETTERS 2018; 121:118101. [PMID: 30265117 DOI: 10.1103/physrevlett.121.118101] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 06/21/2018] [Indexed: 06/08/2023]
Abstract
The emergence and maintenance of polymers with complex sequences pose a major question in the study of the origin of life. To answer this, we study a model polymerization reaction, where polymers are synthesized by stepwise ligation from two types of monomers, catalyzed by a long polymer as a template. Direct stochastic simulation and dynamical systems analysis reveal that the most dominant polymer sequence in a population successively changes, depending on the flow rate of monomers to the system, with more complex sequences selected at a lower flow rate. We discuss the relevance of this kinetic sequence selection through nonequilibrium flow to the origin of complex polymers.
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Affiliation(s)
- Yoshiya J Matsubara
- Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Kunihiko Kaneko
- Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
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35
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Decreased water activity in nanoconfinement contributes to the folding of G-quadruplex and i-motif structures. Proc Natl Acad Sci U S A 2018; 115:9539-9544. [PMID: 30181280 DOI: 10.1073/pnas.1805939115] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Due to the small size of a nanoconfinement, the property of water contained inside is rather challenging to probe. Herein, we measured the amount of water molecules released during the folding of individual G-quadruplex and i-motif structures, from which water activities are estimated in the DNA nanocages prepared by 5 × 5 to 7 × 7 helix bundles (cross-sections, 9 × 9 to 15 × 15 nm). We found water activities decrease with reducing cage size. In the 9 × 9-nm cage, water activity was reduced beyond the reach of regular cosolutes such as polyethylene glycol (PEG). With this set of nanocages, we were able to retrieve the change in water molecules throughout the folding trajectory of G-quadruplex or i-motif. We found that water molecules absorbed from the unfolded to the transition states are much fewer than those lost from the transition to the folded states. The overall loss of water therefore drives the folding of G-quadruplex or i-motif in nanocages with reduced water activities.
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36
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Abstract
The general notion of an "RNA world" is that, in the early development of life on the Earth, genetic continuity was assured by the replication of RNA, and RNA molecules were the chief agents of catalytic function. Assuming that all of the components of RNA were available in some prebiotic locale, these components could have assembled into activated nucleotides that condensed to form RNA polymers, setting the stage for the chemical replication of polynucleotides through RNA-templated RNA polymerization. If a sufficient diversity of RNAs could be copied with reasonable rate and fidelity, then Darwinian evolution would begin with RNAs that facilitated their own reproduction enjoying a selective advantage. The concept of a "protocell" refers to a compartment where replication of the primitive genetic material took place and where primitive catalysts gave rise to products that accumulated locally for the benefit of the replicating cellular entity. Replication of both the protocell and its encapsulated genetic material would have enabled natural selection to operate based on the differential fitness of competing cellular entities, ultimately giving rise to modern cellular life.
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Affiliation(s)
- Gerald F Joyce
- The Salk Institute for Biological Studies, La Jolla, California 92037
| | - Jack W Szostak
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114
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37
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Mönig H. Copper-oxide tip functionalization for submolecular atomic force microscopy. Chem Commun (Camb) 2018; 54:9874-9888. [PMID: 30124700 DOI: 10.1039/c8cc05332d] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Establishing submolecular imaging in real-space by non-contact atomic force microscopy (NC-AFM) has been a major breakthrough in the field of organic surface chemistry. The key for the drastically increased resolution in these experiments is to functionalize a metallic tip apex with an inert probe particle. However, due to their weak bonding at the metal apex, these probe particles show a pronounced dynamic lateral deflection in the measurements. This constitutes a major limitation of this approach as it involves image distortions, an overestimation of bond lengths, and even artificial bond-like contrast features where actually no bonds exist. In this contribution, recent progress by using an alternative approach by copper-oxide tip functionalization is reviewed. Copper-oxide tips (CuOx tips) consist of a bulk copper apex, terminated by a covalently connected single oxygen atom, which chemically passivates the tip. Such CuOx tips can be identified by contrast analysis at specific surface sites and allow for submolecular resolution. A comparative analysis of data recorded with flexible tips allows a detailed discussion of the contrast mechanisms and related artificial effects. It is concluded with an assessment of limitations, future challenges and opportunities in such experiments.
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Affiliation(s)
- Harry Mönig
- Physikalisches Institut, Westfälische Wilhelms-Universität Münster, Wilhelm-Klemm-Strasse 10, 48149 Münster, Germany.
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38
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Ranjan S, Todd ZR, Sutherland JD, Sasselov DD. Sulfidic Anion Concentrations on Early Earth for Surficial Origins-of-Life Chemistry. ASTROBIOLOGY 2018; 18:1023-1040. [PMID: 29627997 PMCID: PMC6225604 DOI: 10.1089/ast.2017.1770] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 01/19/2018] [Indexed: 05/16/2023]
Abstract
A key challenge in origin-of-life studies is understanding the environmental conditions on early Earth under which abiogenesis occurred. While some constraints do exist (e.g., zircon evidence for surface liquid water), relatively few constraints exist on the abundances of trace chemical species, which are relevant to assessing the plausibility and guiding the development of postulated prebiotic chemical pathways which depend on these species. In this work, we combine literature photochemistry models with simple equilibrium chemistry calculations to place constraints on the plausible range of concentrations of sulfidic anions (HS-, HSO3-, SO32-) available in surficial aquatic reservoirs on early Earth due to outgassing of SO2 and H2S and their dissolution into small shallow surface water reservoirs like lakes. We find that this mechanism could have supplied prebiotically relevant levels of SO2-derived anions, but not H2S-derived anions. Radiative transfer modeling suggests UV light would have remained abundant on the planet surface for all but the largest volcanic explosions. We apply our results to the case study of the proposed prebiotic reaction network of Patel et al. ( 2015 ) and discuss the implications for improving its prebiotic plausibility. In general, epochs of moderately high volcanism could have been especially conducive to cyanosulfidic prebiotic chemistry. Our work can be similarly applied to assess and improve the prebiotic plausibility of other postulated surficial prebiotic chemistries that are sensitive to sulfidic anions, and our methods adapted to study other atmospherically derived trace species.
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Affiliation(s)
- Sukrit Ranjan
- Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts, USA
- MIT Department of Earth, Atmospheric, and Planetary Sciences, Cambridge, Massachusetts, USA
| | - Zoe R. Todd
- Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts, USA
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39
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Exploration of RNA Sequence Space in the Absence of a Replicase. J Mol Evol 2018; 86:264-276. [PMID: 29748740 DOI: 10.1007/s00239-018-9846-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 05/04/2018] [Indexed: 12/29/2022]
Abstract
It is generally considered that if an RNA World ever existed that it would be driven by an RNA capable of RNA replication. Whether such a catalytic RNA could emerge in an RNA World or not, there would need to be prior routes to increasing complexity in order to produce it. It is hypothesized here that increasing sequence variety, if not complexity, can in fact readily emerge in response to a dynamic equilibrium between synthesis and degradation. A model system in which T4 RNA ligase catalyzes synthesis and Benzonase catalyzes degradation was constructed. An initial 20-mer served as a seed and was subjected to 180 min of simultaneous ligation and degradation. The seed RNA rapidly disappeared and was replaced by an increasing number and variety of both larger and smaller variants. Variants of 40-80 residues were consistently seen, typically representing 2-4% of the unique sequences. In a second experiment with four individual 9-mers, numerous variants were again produced. These included variants of the individual 9-mers as well as sequences that contained sequence segments from two or more 9-mers. In both cases, the RNA products lack large numbers of point mutations but instead incorporate additions and subtractions of fragments of the original RNAs. The system demonstrates that if such equilibrium were established in a prebiotic world it would result in significant exploration of RNA sequence space and likely increased complexity. It remains to be seen if the variety of products produced is affected by the presence of small peptide oligomers.
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40
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Mineral Surface-Templated Self-Assembling Systems: Case Studies from Nanoscience and Surface Science towards Origins of Life Research. Life (Basel) 2018; 8:life8020010. [PMID: 29738443 PMCID: PMC6027067 DOI: 10.3390/life8020010] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 04/26/2018] [Accepted: 05/03/2018] [Indexed: 01/20/2023] Open
Abstract
An increasing body of evidence relates the wide range of benefits mineral surfaces offer for the development of early living systems, including adsorption of small molecules from the aqueous phase, formation of monomeric subunits and their subsequent polymerization, and supramolecular assembly of biopolymers and other biomolecules. Each of these processes was likely a necessary stage in the emergence of life on Earth. Here, we compile evidence that templating and enhancement of prebiotically-relevant self-assembling systems by mineral surfaces offers a route to increased structural, functional, and/or chemical complexity. This increase in complexity could have been achieved by early living systems before the advent of evolvable systems and would not have required the generally energetically unfavorable formation of covalent bonds such as phosphodiester or peptide bonds. In this review we will focus on various case studies of prebiotically-relevant mineral-templated self-assembling systems, including supramolecular assemblies of peptides and nucleic acids, from nanoscience and surface science. These fields contain valuable information that is not yet fully being utilized by the origins of life and astrobiology research communities. Some of the self-assemblies that we present can promote the formation of new mineral surfaces, similar to biomineralization, which can then catalyze more essential prebiotic reactions; this could have resulted in a symbiotic feedback loop by which geology and primitive pre-living systems were closely linked to one another even before life’s origin. We hope that the ideas presented herein will seed some interesting discussions and new collaborations between nanoscience/surface science researchers and origins of life/astrobiology researchers.
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41
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Poudyal R, Cakmak FP, Keating CD, Bevilacqua PC. Physical Principles and Extant Biology Reveal Roles for RNA-Containing Membraneless Compartments in Origins of Life Chemistry. Biochemistry 2018; 57:2509-2519. [PMID: 29560725 PMCID: PMC7276092 DOI: 10.1021/acs.biochem.8b00081] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
This Perspective focuses on RNA in biological and nonbiological compartments resulting from liquid-liquid phase separation (LLPS), with an emphasis on origins of life. In extant cells, intracellular liquid condensates, many of which are rich in RNAs and intrinsically disordered proteins, provide spatial regulation of biomolecular interactions that can result in altered gene expression. Given the diversity of biogenic and abiogenic molecules that undergo LLPS, such membraneless compartments may have also played key roles in prebiotic chemistries relevant to the origins of life. The RNA World hypothesis posits that RNA may have served as both a genetic information carrier and a catalyst during the origin of life. Because of its polyanionic backbone, RNA can undergo LLPS by complex coacervation in the presence of polycations. Phase separation could provide a mechanism for concentrating monomers for RNA synthesis and selectively partition longer RNAs with enzymatic functions, thus driving prebiotic evolution. We introduce several types of LLPS that could lead to compartmentalization and discuss potential roles in template-mediated non-enzymatic polymerization of RNA and other related biomolecules, functions of ribozymes and aptamers, and benefits or penalties imparted by liquid demixing. We conclude that tiny liquid droplets may have concentrated precious biomolecules and acted as bioreactors in the RNA World.
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Affiliation(s)
- Raghav Poudyal
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Fatma Pir Cakmak
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Christine D. Keating
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Philip C. Bevilacqua
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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42
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Wang A, Ye J, Humphrey MG, Zhang C. Graphene and Carbon-Nanotube Nanohybrids Covalently Functionalized by Porphyrins and Phthalocyanines for Optoelectronic Properties. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1705704. [PMID: 29450914 DOI: 10.1002/adma.201705704] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 11/02/2017] [Indexed: 06/08/2023]
Abstract
In recent years, there has been a rapid growth in studies of the optoelectronic properties of graphene, carbon nanotubes (CNTs), and their derivatives. The chemical functionalization of graphene and CNTs is a key requirement for the development of this field, but it remains a significant challenge. The focus here is on recent advances in constructing nanohybrids of graphene or CNTs covalently linked to porphyrins or phthalocyanines, as well as their application in nonlinear optics. Following a summary of the syntheses of nanohybrids constructed from graphene or CNTs and porphyrins or phthalocyanines, explicit intraconjugate electronic interactions between photoexcited porphyrins/phthalocyanines and graphene/CNTs are introduced classified by energy transfer, electron transfer, and charge transfer, and their optoelectronic applications are also highlighted. The major current challenges for the development of covalently linked nanohybrids of porphyrins or phthalocyanines and carbon nanostructures are also presented.
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Affiliation(s)
- Aijian Wang
- China-Australia Joint Research Center for Functional Molecular Materials, School of Chemical Science and Engineering, Tongji University, Shanghai, 200092, P. R. China
| | - Jun Ye
- China-Australia Joint Research Center for Functional Molecular Materials, School of Chemical Science and Engineering, Tongji University, Shanghai, 200092, P. R. China
| | - Mark G Humphrey
- China-Australia Joint Research Center for Functional Molecular Materials, School of Chemical Science and Engineering, Tongji University, Shanghai, 200092, P. R. China
| | - Chi Zhang
- China-Australia Joint Research Center for Functional Molecular Materials, School of Chemical Science and Engineering, Tongji University, Shanghai, 200092, P. R. China
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43
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Leng X, Lu Y, Feng G, Wang Z, Li W, Liu X, Zhang R, Zhang N, Wang L. Surface-assisted dehydrogenative homocoupling and cyclodehydrogenation of mesityl groups on a copper surface. Chem Commun (Camb) 2018; 53:9151-9154. [PMID: 28765848 DOI: 10.1039/c7cc03950f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We present for the first time an adjacent dehydrogenative homocoupling and cyclodehydrogenation reaction of mesityl groups to form a synthetic nanoribbon on Cu(110). Submolecular resolution scanning tunneling microscopy (STM) observations and density functional theory (DFT) calculations confirm the formation of an ethylene (-CH[double bond, length as m-dash]CH-) unit or an aromatic six-membered ring group.
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Affiliation(s)
- Xinli Leng
- Department of Physics, Nanchang University, Nanchang 330031, P. R. China.
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44
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Synthesis of armchair graphene nanoribbons from the 10,10'-dibromo-9,9'-bianthracene molecules on Ag(111): the role of organometallic intermediates. Sci Rep 2018; 8:3506. [PMID: 29472611 PMCID: PMC5823938 DOI: 10.1038/s41598-018-21704-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 02/01/2018] [Indexed: 11/08/2022] Open
Abstract
We investigate the bottom-up growth of N = 7 armchair graphene nanoribbons (7-AGNRs) from the 10,10′-dibromo-9,9′-bianthracene (DBBA) molecules on Ag(111) with the focus on the role of the organometallic (OM) intermediates. It is demonstrated that DBBA molecules on Ag(111) are partially debrominated at room temperature and lose all bromine atoms at elevated temperatures. Similar to DBBA on Cu(111), debrominated molecules form OM chains on Ag(111). Nevertheless, in contrast with the Cu(111) substrate, formation of polyanthracene chains from OM intermediates via an Ullmann-type reaction is feasible on Ag(111). Cleavage of C–Ag bonds occurs before the thermal threshold for the surface-catalyzed activation of C–H bonds on Ag(111) is reached, while on Cu(111) activation of C–H bonds occurs in parallel with the cleavage of the stronger C–Cu bonds. Consequently, while OM intermediates obstruct the Ullmann reaction between DBBA molecules on the Cu(111) substrate, they are required for the formation of polyanthracene chains on Ag(111). If the Ullmann-type reaction on Ag(111) is inhibited, heating of the OM chains produces nanographenes instead. Heating of the polyanthracene chains produces 7-AGNRs, while heating of nanographenes causes the formation of the disordered structures with the possible admixture of short GNRs.
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45
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Menor-Salván C. From the Dawn of Organic Chemistry to Astrobiology: Urea as a Foundational Component in the Origin of Nucleobases and Nucleotides. PREBIOTIC CHEMISTRY AND CHEMICAL EVOLUTION OF NUCLEIC ACIDS 2018. [DOI: 10.1007/978-3-319-93584-3_4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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46
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Zeng J, Chen KQ. A nearly perfect spin filter and a spin logic gate based on a porphyrin/graphene hybrid material. Phys Chem Chem Phys 2018; 20:3997-4004. [DOI: 10.1039/c7cp07795e] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We propose experimentally feasible spintronic devices using the porphyrin/graphene hybrid material, and find a nearly perfect spin polarization effect.
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Affiliation(s)
- Jing Zeng
- College of Physics and Electronic Engineering, Hengyang Normal University
- Hengyang 421002
- People's Republic of China
- Hunan Provincial Key Laboratory of Intelligent Information Processing and Application
- Hengyang 421002
| | - Ke-Qiu Chen
- Department of Applied Physics, School of Physics and Electronics, Hunan University
- Changsha 410082
- People's Republic of China
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47
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Walton T, Szostak JW. A Kinetic Model of Nonenzymatic RNA Polymerization by Cytidine-5'-phosphoro-2-aminoimidazolide. Biochemistry 2017; 56:5739-5747. [PMID: 29022704 PMCID: PMC6340129 DOI: 10.1021/acs.biochem.7b00792] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The
nonenzymatic polymerization of RNA may have enabled copying
of functional sequences during the origin of life. Recent progress
utilizing 5′-phosphoro-2-aminoimidazole activation has reinvigorated
the possibility of using nonenzymatic RNA polymerization for copying
arbitrary sequences. However, the reasons why 2-aminoimidazole (AI)
is a superior activation group remain unclear. Here we report that
the predominant mechanism of polymerization using cytidine-5′-phosphoro-2-aminoimidazolide
(Cp*) involves a 2-aminoimidazolium-bridged dinucleotide (Cp*pC) intermediate.
To explore the role of this intermediate, we first identify and quantify
four reactions involving the synthesis and breakdown of Cp*pC that
occur in the absence of the primer–template duplex. We then
analyze the dependence of the rate of polymerization on the concentration
of the Cp*pC intermediate in the presence and absence of the competitive
inhibitor Cp. We also show that the contribution of the monomer Cp*
to the polymerization rate is negligible under our primer extension
conditions. Finally, we use the experimentally determined rate constants
of these reactions to develop a kinetic model that helps explain the
changing rate of nonenzymatic RNA polymerization over time. Our model
accounts for the concentration of Cp*pC formed by Cp* under primer
extension conditions. The model does not completely account for the
decline in polymerization rate observed over long times, which indicates
that additional important inhibitory processes have not yet been identified.
Our results suggest that the superiority of 2-aminoimidazole over
the traditional 2-methylimidazole activation is mostly due to the
higher level of accumulation of the imidazolium-bridged intermediate
under primer extension conditions.
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Affiliation(s)
- Travis Walton
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital , Boston, Massachusetts 02114, United States
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital , Boston, Massachusetts 02114, United States
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48
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Beierle JM, Ura Y, Ghadiri MR, Leman LJ. Templated Self-Assembly of Dynamic Peptide Nucleic Acids. Biochemistry 2017; 57:160-172. [PMID: 28832127 DOI: 10.1021/acs.biochem.7b00656] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Template-directed macromolecule synthesis is a hallmark of living systems. Inspired by this natural process, several fundamentally novel mechanisms for template-directed assembly of nucleic acid analogues have been developed. Although these approaches have broad significance, including potential applications in biotechnology and implications for the origins of life, there are unresolved challenges in how to characterize in detail the complex assembly equilibria associated with dynamic templated reactions. Here we describe mechanistic studies of template-directed dynamic assembly for thioester peptide nucleic acid (tPNA), an informational polymer that responds to selection pressures under enzyme-free conditions. To overcome some of the inherent challenges of mechanistic studies of dynamic oligomers, we designed, synthesized, and implemented tPNA-DNA conjugates. The DNA primer region affords a high level of control over the location and register of the tPNA backbone in relation to the template strand. We characterized the degree and kinetics of dynamic nucleobase mismatch correction at defined backbone positions. Furthermore, we report the fidelity of dynamic assembly in tPNA as a function of position along the peptide backbone. Finally, we present theoretical studies that explore the level of fidelity that can be expected for an oligomer having a given hybridization affinity in dynamic templated reactions and provide guidance for the future development of sequence self-editing polymers and materials. As our results demonstrate, the use of molecular conjugates of constitutionally static and dynamic polymers establishes a new methodology for expediting the characterization of the complex chemical equilibria that underlie the assembly of dynamic informational polymers.
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Affiliation(s)
- John M Beierle
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yasuyuki Ura
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - M Reza Ghadiri
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Luke J Leman
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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Sun Q, Tran BV, Cai L, Ma H, Yu X, Yuan C, Stöhr M, Xu W. On-Surface Formation of Cumulene by Dehalogenative Homocoupling of Alkenyl gem
-Dibromides. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706104] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Qiang Sun
- Interdisciplinary Materials Research Center; Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials; College of Materials Science and Engineering; Tongji University; Shanghai 201804 P. R. China
| | - Bay V. Tran
- Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Liangliang Cai
- Interdisciplinary Materials Research Center; Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials; College of Materials Science and Engineering; Tongji University; Shanghai 201804 P. R. China
| | - Honghong Ma
- Interdisciplinary Materials Research Center; Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials; College of Materials Science and Engineering; Tongji University; Shanghai 201804 P. R. China
| | - Xin Yu
- Interdisciplinary Materials Research Center; Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials; College of Materials Science and Engineering; Tongji University; Shanghai 201804 P. R. China
| | - Chunxue Yuan
- Interdisciplinary Materials Research Center; Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials; College of Materials Science and Engineering; Tongji University; Shanghai 201804 P. R. China
| | - Meike Stöhr
- Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Wei Xu
- Interdisciplinary Materials Research Center; Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials; College of Materials Science and Engineering; Tongji University; Shanghai 201804 P. R. China
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50
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Sun Q, Tran BV, Cai L, Ma H, Yu X, Yuan C, Stöhr M, Xu W. On-Surface Formation of Cumulene by Dehalogenative Homocoupling of Alkenyl gem-Dibromides. Angew Chem Int Ed Engl 2017; 56:12165-12169. [PMID: 28772061 DOI: 10.1002/anie.201706104] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Indexed: 11/09/2022]
Abstract
The on-surface activation of carbon-halogen groups is an efficient route to produce radicals for constructing various hydrocarbons and carbon nanostructures. To date, the employed halide precursors have only one halogen attached to a carbon atom. It is thus of interest to study the effect of attaching more than one halogen atom to a carbon atom with the aim of producing multiple unpaired electrons. By introducing an alkenyl gem-dibromide, cumulene products were fabricated on a Au(111) surface by dehalogenative homocoupling reactions. The reaction products and pathways were unambiguously characterized by a combination of high-resolution scanning tunneling microscopy and non-contact atomic force microscopy measurements together with density functional calculations. This study further supplements the database of on-surface synthesis strategies and provides a facile manner for incorporation of more complicated carbon scaffolds into surface nanostructures.
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Affiliation(s)
- Qiang Sun
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University, Shanghai, 201804, P. R. China
| | - Bay V Tran
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Liangliang Cai
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University, Shanghai, 201804, P. R. China
| | - Honghong Ma
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University, Shanghai, 201804, P. R. China
| | - Xin Yu
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University, Shanghai, 201804, P. R. China
| | - Chunxue Yuan
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University, Shanghai, 201804, P. R. China
| | - Meike Stöhr
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Wei Xu
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University, Shanghai, 201804, P. R. China
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