1
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Williamson MP. Autocatalytic Selection as a Driver for the Origin of Life. Life (Basel) 2024; 14:590. [PMID: 38792611 PMCID: PMC11122578 DOI: 10.3390/life14050590] [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: 04/03/2024] [Revised: 04/29/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024] Open
Abstract
Darwin's theory of evolution by natural selection was revolutionary because it provided a mechanism by which variation could be selected. This mechanism can only operate on living systems and thus cannot be applied to the origin of life. Here, we propose a viable alternative mechanism for prebiotic systems: autocatalytic selection, in which molecules catalyze reactions and processes that lead to increases in their concentration. Crucially, this provides a driver for increases in concentrations of molecules to a level that permits prebiotic metabolism. We show how this can produce high levels of amino acids, sugar phosphates, nucleotides and lipids and then lead on to polymers. Our outline is supported by a set of guidelines to support the identification of the most likely prebiotic routes. Most of the steps in this pathway are already supported by experimental results. These proposals generate a coherent and viable set of pathways that run from established Hadean geochemistry to the beginning of life.
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Affiliation(s)
- Mike P Williamson
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
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2
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Dirscherl CF, Ianeselli A, Tetiker D, Matreux T, Queener RM, Mast CB, Braun D. A heated rock crack captures and polymerizes primordial DNA and RNA. Phys Chem Chem Phys 2023; 25:3375-3386. [PMID: 36633199 DOI: 10.1039/d2cp04538a] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Life is based on informational polymers such as DNA or RNA. For their polymerization, high concentrations of complex monomer building blocks are required. Therefore, the dilution by diffusion poses a major problem before early life could establish a non-equilibrium of compartmentalization. Here, we explored a natural non-equilibrium habitat to polymerize RNA and DNA. A heat flux across thin rock cracks is shown to accumulate and maintain nucleotides. This boosts the polymerization to RNA and DNA inside the crack. Moreover, the polymers remain localized, aiding both the creation of longer polymers and fostering downstream evolutionary steps. In a closed system, we found single nucleotides concentrate 104-fold at the bottom of the crack compared to the top after 24 hours. We detected enhanced polymerization for 2 different activation chemistries: aminoimidazole-activated DNA nucleotides and 2',3'-cyclic RNA nucleotides. The copolymerization of 2',3'-cGMP and 2',3'-cCMP in the thermal pore showed an increased heterogeneity in sequence composition compared to isothermal drying. Finite element models unravelled the combined polymerization and accumulation kinetics and indicated that the escape of the nucleotides from such a crack is negligible over a time span of years. The thermal non-equilibrium habitat establishes a cell-like compartment that actively accumulates nucleotides for polymerization and traps the resulting oligomers. We argue that the setting creates a pre-cellular non-equilibrium steady state for the first steps of molecular evolution.
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Affiliation(s)
- Christina F Dirscherl
- Systems Biophysics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80799 Munich, Germany.
| | - Alan Ianeselli
- Systems Biophysics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80799 Munich, Germany.
| | - Damla Tetiker
- Systems Biophysics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80799 Munich, Germany.
| | - Thomas Matreux
- Systems Biophysics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80799 Munich, Germany.
| | - Robbin M Queener
- Systems Biophysics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80799 Munich, Germany.
| | - Christof B Mast
- Systems Biophysics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80799 Munich, Germany.
| | - Dieter Braun
- Systems Biophysics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80799 Munich, Germany.
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3
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Magalhães ÁF, Powner MW. Prebiotic triose glycolysis promoted by co-catalytic proline and phosphate in neutral water. Chem Commun (Camb) 2022; 58:13519-13522. [PMID: 36398592 DOI: 10.1039/d2cc05466c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Proline and phosphate promote a near-quantitative aldol reaction between glycolaldehyde phosphate and formaldehyde at neutral pH in water. Our results demonstrate the important role of general acid-base catalysis in water and underscore the essential role that amino acid catalysis may have played in early evolution of life's core metabolic pathways.
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Affiliation(s)
- Álvaro F Magalhães
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK.
| | - Matthew W Powner
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK.
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4
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Ben Chouikha I, Kerkeni B, Ouerfelli G, Makroni L, Nyman G. Quantum chemical study of the reaction paths and kinetics of acetaldehyde formation on a methanol-water ice model. RSC Adv 2022; 12:18994-19005. [PMID: 35873325 PMCID: PMC9241153 DOI: 10.1039/d2ra03555c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 06/15/2022] [Indexed: 12/03/2022] Open
Abstract
Acetaldehyde (CH3CHO) is ubiquitous in interstellar space and is important for astrochemistry as it can contribute to the formation of amino acids through reaction with nitrogen containing chemical species. Quantum chemical and reaction kinetics studies are reported for acetaldehyde formation from the chemical reaction of C(3P) with a methanol molecule adsorbed at the eighth position of a cubic water cluster. We present extensive quantum chemical calculations for total spin S = 1 and S = 0. The UωB97XD/6-311++G(2d,p) model chemistry is employed to optimize the structures, compute minimum energy paths and zero-point vibrational energies of all reaction steps. For the optimized structures, the calculated energies are refined by CCSD(T) single point computations. We identify four transition states on the triplet potential energy surface (PES), and one on the singlet PES. The reaction mechanism involves the intermediate formation of CH3OCH adsorbed on the ice cluster. The rate limiting step for forming acetaldehyde is the C–O bond breaking in CH3OCH to form adsorbed CH3 and HCO. We find two positions on the reaction path where spin crossing may be possible such that acetaldehyde can form in its singlet spin state. Using variational transition-state theory with multidimensional tunnelling we provide thermal rate constants for the energetically rate limiting step for both spin states and discuss two routes to acetaldehyde formation. As expected, quantum effects are important at low temperatures. Acetaldehyde (CH3CHO) is ubiquitous in interstellar space and is important for astrochemistry as it can contribute to the formation of amino acids. The reaction mechanism for its formation on a methanol ice grain may involve intersystem spin crossing.![]()
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Affiliation(s)
- Islem Ben Chouikha
- Département de Physique, LPMC, Faculté des Sciences de Tunis, Université de Tunis el Manar Tunis 2092 Tunisia
| | - Boutheïna Kerkeni
- Département de Physique, LPMC, Faculté des Sciences de Tunis, Université de Tunis el Manar Tunis 2092 Tunisia .,ISAMM, Université de la Manouba La Manouba 2010 Tunisia
| | - Ghofrane Ouerfelli
- Département de Physique, LPMC, Faculté des Sciences de Tunis, Université de Tunis el Manar Tunis 2092 Tunisia .,Taif University Taif Saudi Arabia
| | - Lily Makroni
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an Shaanxi 710119 China
| | - Gunnar Nyman
- Department of Chemistry and Molecular Biology, University of Gothenburg Sweden
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5
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Chatterjee A, Reja A, Pal S, Das D. Systems chemistry of peptide-assemblies for biochemical transformations. Chem Soc Rev 2022; 51:3047-3070. [PMID: 35316323 DOI: 10.1039/d1cs01178b] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
During the billions of years of the evolutionary journey, primitive polymers, involved in proto metabolic pathways with low catalytic activity, played critical roles in the emergence of modern enzymes with remarkable substrate specificity. The precise positioning of amino acid residues and the complex orchestrated interplay in the binding pockets of evolved enzymes promote covalent and non-covalent interactions to foster a diverse set of complex catalytic transformations. Recent efforts to emulate the structural and functional information of extant enzymes by minimal peptide based assemblies have attempted to provide a holistic approach that could help in discerning the prebiotic origins of catalytically active binding pockets of advanced proteins. In addition to the impressive sets of advanced biochemical transformations, catalytic promiscuity and cascade catalysis by such small molecule based dynamic systems can foreshadow the ancestral catalytic processes required for the onset of protometabolism. Looking beyond minimal systems that work close to equilibrium, catalytic systems and compartments under non-equilibrium conditions utilizing simple prebiotically relevant precursors have attempted to shed light on how bioenergetics played an essential role in chemical emergence of complex behaviour. Herein, we map out these recent works and progress where diverse sets of complex enzymatic transformations were demonstrated by utilizing minimal peptide based self-assembled systems. Further, we have attempted to cover the examples of peptide assemblies that could feature promiscuous activity and promote complex multistep cascade reaction networks. The review also covers a few recent examples of minimal transient catalytic assemblies under non-equilibrium conditions. This review attempts to provide a broad perspective for potentially programming functionality via rational selection of amino acid sequences leading towards minimal catalytic systems that resemble the traits of contemporary enzymes.
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Affiliation(s)
- Ayan Chatterjee
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
| | - Antara Reja
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
| | - Sumit Pal
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
| | - Dibyendu Das
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
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6
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Kawasaki T, Kubo H, Nishiyama S, Saijo T, Yokoi R, Tokunaga Y. Quantitative Difference in Solubility of Diastereomeric ( 2H/ 1H)-Isotopomers. J Am Chem Soc 2021; 143:19525-19531. [PMID: 34738466 PMCID: PMC8630799 DOI: 10.1021/jacs.1c09253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Many achiral organic compounds become chiral by an isotopic substitution of one of the enantiotopic moieties in their structures. Although spectroscopic methods can recognize the molecular chirality due to an isotopic substitution, the effects of isotopically chiral compounds in enantioselective reactions have remained unsolved because the small chirality arises only from the difference between the number of neutrons in the atomic nuclei. The difference between the diastereomeric isotopomers of reactive sources should be the key to these effects. However, the energy difference between them is difficult to calculate, even using present computational methods, and differences in physical properties have not yet been reported. Here, we demonstrate that the small energy difference between the diastereomeric isotopomers at the molecular level can be enhanced to appear as a solubility difference between the diastereomeric (2H/1H) isotopomers of α-aminonitriles, synthesized from an isotopically chiral amine, achiral aldehyde, and HCN. This small, but measurable, difference induces the chiral (d/l) imbalance in the suspended α-aminonitrile; therefore, a second enhancement in the solid-state chirality proceeds to afford a highly stereoimproved aminonitrile (>99% selectivity) whose handedness arises completely from the excess enantiomer of isotopically chiral amine, even in a low enantiomeric excess and low deuterium-labeling ratio. Because α-aminonitriles can be hydrolyzed to chiral α-amino acids with the removal of an isotope-labeling moiety, the current sequence of reactions represents a highly enantioselective Strecker amino acid synthesis induced by the chiral hydrogen (2H/1H) isotopomer. Thus, hydrogen isotopic chirality links directly with the homochirality of α-amino acids via a double enhancement of α-aminonitrile, the chiral intermediate of a proposed prebiotic mechanism.
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Affiliation(s)
- Tsuneomi Kawasaki
- Department of Applied Chemistry, Tokyo University of Science, Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan
| | - Hiroki Kubo
- Department of Applied Chemistry, Tokyo University of Science, Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan
| | - Satoshi Nishiyama
- Department of Materials Science and Engineering, University of Fukui, Bunkyo, Fukui 910-8507, Japan
| | - Taiki Saijo
- Department of Applied Chemistry, Tokyo University of Science, Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan
| | - Rintaro Yokoi
- Department of Applied Chemistry, Tokyo University of Science, Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan
| | - Yuji Tokunaga
- Department of Materials Science and Engineering, University of Fukui, Bunkyo, Fukui 910-8507, Japan
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7
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Joseph V, Levine M. Ronald C.D. Breslow (1931-2017): A career in review. Bioorg Chem 2021; 115:104868. [PMID: 34523507 DOI: 10.1016/j.bioorg.2021.104868] [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: 02/02/2021] [Accepted: 03/23/2021] [Indexed: 11/26/2022]
Abstract
Reviewed herein are key research accomplishments of Professor Ronald Charles D. Breslow (1931-2017) throughout his more than 60 year research career. These accomplishments span a wide range of topics, most notably physical organic chemistry, medicinal chemistry, and bioorganic chemistry. These topics are reviewed, as are topics of molecular electronics and origin of chirality, which combine to make up the bulk of this review. Also reviewed briefly are Breslow's contributions to the broader chemistry profession, including his work for the American Chemical Society and his work promoting gender equity. Throughout the article, efforts are made to put Breslow's accomplishments in the context of other work being done at the time, as well as to include subsequent iterations and elaborations of the research.
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Affiliation(s)
- Vincent Joseph
- Department of Chemical Sciences, Ariel University, Israel
| | - Mindy Levine
- Department of Chemical Sciences, Ariel University, Israel.
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8
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Cassone G, Sponer J, Saija F. Ab Initio Molecular Dynamics Studies of the Electric-Field-Induced Catalytic Effects on Liquids. Top Catal 2021. [DOI: 10.1007/s11244-021-01487-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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9
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Legnani L, Darù A, Jones AX, Blackmond DG. Mechanistic Insight into the Origin of Stereoselectivity in the Ribose-Mediated Strecker Synthesis of Alanine. J Am Chem Soc 2021; 143:7852-7858. [PMID: 33979125 DOI: 10.1021/jacs.1c03552] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enantioenriched amino acids are produced in a hydrolytic kinetic resolution of racemic aminonitriles mediated by chiral pentose sugars. Experimental kinetic and spectroscopic results combined with DFT computational studies and microkinetic modeling help to identify the nature of the intermediate species and provide insight into the stereoselectivity of their hydrolysis in the prebiotically relevant ribose-alanine system. These studies support a synergistic role for sugars and amino acids in the emergence of homochirality in biological molecules.
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Affiliation(s)
- Luca Legnani
- Department of Chemistry, Scripps Research, La Jolla, California 92037, United States
| | - Andrea Darù
- Department of Chemistry, Scripps Research, La Jolla, California 92037, United States
| | - Alexander X Jones
- Department of Chemistry, Scripps Research, La Jolla, California 92037, United States
| | - Donna G Blackmond
- Department of Chemistry, Scripps Research, La Jolla, California 92037, United States
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10
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Dass AV, Georgelin T, Westall F, Foucher F, De Los Rios P, Busiello DM, Liang S, Piazza F. Equilibrium and non-equilibrium furanose selection in the ribose isomerisation network. Nat Commun 2021; 12:2749. [PMID: 33980850 PMCID: PMC8115175 DOI: 10.1038/s41467-021-22818-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 03/19/2021] [Indexed: 11/08/2022] Open
Abstract
The exclusive presence of β-D-ribofuranose in nucleic acids is still a conundrum in prebiotic chemistry, given that pyranose species are substantially more stable at equilibrium. However, a precise characterisation of the relative furanose/pyranose fraction at temperatures higher than about 50 °C is still lacking. Here, we employ a combination of NMR measurements and statistical mechanics modelling to predict a population inversion between furanose and pyranose at equilibrium at high temperatures. More importantly, we show that a steady temperature gradient may steer an open isomerisation network into a non-equilibrium steady state where furanose is boosted beyond the limits set by equilibrium thermodynamics. Moreover, we demonstrate that nonequilibrium selection of furanose is maximum at optimal dissipation, as gauged by the temperature gradient and energy barriers for isomerisation. The predicted optimum is compatible with temperature drops found in hydrothermal vents associated with extremely fresh lava flows on the seafloor.
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Affiliation(s)
- Avinash Vicholous Dass
- Centre de Biophysique Moléculaire, CNRS-UPR4301, Rue C. Sadron, Orléans, France
- Department of Physics, Ludwig Maximilians University, München, Germany
| | - Thomas Georgelin
- Centre de Biophysique Moléculaire, CNRS-UPR4301, Rue C. Sadron, Orléans, France
- Laboratoire de Réactivité de Surface, UMR 7197, Sorbonne Université, Paris, France
| | - Frances Westall
- Centre de Biophysique Moléculaire, CNRS-UPR4301, Rue C. Sadron, Orléans, France
| | - Frédéric Foucher
- Centre de Biophysique Moléculaire, CNRS-UPR4301, Rue C. Sadron, Orléans, France
| | - Paolo De Los Rios
- Institute of Physics, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne-EPFL, Lausanne, Switzerland
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne-EPFL, Lausanne, Switzerland
| | - Daniel Maria Busiello
- Institute of Physics, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne-EPFL, Lausanne, Switzerland
| | - Shiling Liang
- Institute of Physics, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne-EPFL, Lausanne, Switzerland
| | - Francesco Piazza
- Centre de Biophysique Moléculaire, CNRS-UPR4301, Rue C. Sadron, Orléans, France.
- Université d'Orléans, UFR CoST Sciences et Techniques, Orléans, France.
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11
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Jiménez EI, Gibard C, Krishnamurthy R. Prebiotic Phosphorylation and Concomitant Oligomerization of Deoxynucleosides to form DNA. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015910] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Eddy I. Jiménez
- The Department of Chemistry The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Clémentine Gibard
- The Department of Chemistry The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Ramanarayanan Krishnamurthy
- The Department of Chemistry The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
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12
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Jiménez EI, Gibard C, Krishnamurthy R. Prebiotic Phosphorylation and Concomitant Oligomerization of Deoxynucleosides to form DNA. Angew Chem Int Ed Engl 2021; 60:10775-10783. [PMID: 33325148 DOI: 10.1002/anie.202015910] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Indexed: 12/14/2022]
Abstract
Recent demonstrations of RNA-DNA chimeras (RDNA) enabling RNA and DNA replication, coupled with prebiotic co-synthesis of deoxyribo- and ribo-nucleotides, have resurrected the hypothesis of co-emergence of RNA and DNA. As further support, we show that diamidophosphate (DAP) with 2-aminoimidazole (amido)phosphorylates and oligomerizes deoxynucleosides to form DNA-under conditions similar to those of ribonucleosides. The pyrimidine deoxynucleoside 5'-O-amidophosphates are formed in good (≈60 %) yields. Intriguingly, the presence of pyrimidine deoxynucleos(t)ides increased the yields of purine deoxynucleotides (≈20 %). Concomitantly, oligomerization (≈18-31 %) is observed with predominantly 3',5'-phosphodiester DNA linkages, and some (<5 %) pyrophosphates. Combined with previous observations of DAP-mediated chemistries and the constructive role of RDNA chimeras, the results reported here help set the stage for systematic investigation of a systems chemistry approach of RNA-DNA coevolution.
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Affiliation(s)
- Eddy I Jiménez
- The Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Clémentine Gibard
- The Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Ramanarayanan Krishnamurthy
- The Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
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13
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The Role of Glycerol and Its Derivatives in the Biochemistry of Living Organisms, and Their Prebiotic Origin and Significance in the Evolution of Life. Catalysts 2021. [DOI: 10.3390/catal11010086] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The emergence and evolution of prebiotic biomolecules on the early Earth remain a question that is considered crucial to understanding the chemistry of the origin of life. Amongst prebiotic molecules, glycerol is significant due to its ubiquity in biochemistry. In this review, we discuss the significance of glycerol and its various derivatives in biochemistry, their plausible roles in the origin and evolution of early cell membranes, and significance in the biochemistry of extremophiles, followed by their prebiotic origin on the early Earth and associated catalytic processes that led to the origin of these compounds. We also discuss various scenarios for the prebiotic syntheses of glycerol and its derivates and evaluate these to determine their relevance to early Earth biochemistry and geochemistry, and recapitulate the utilization of various minerals (including clays), condensation agents, and solvents that could have led to the successful prebiotic genesis of these biomolecules. Furthermore, important prebiotic events such as meteoritic delivery and prebiotic synthesis reactions under astrophysical conditions are also discussed. Finally, we have also highlighted some novel features of glycerol, including glycerol nucleic acid (GNA), in the origin and evolution of the life.
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14
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Kleimeier NF, Turner AM, Fortenberry RC, Kaiser RI. On the Formation of the Popcorn Flavorant 2,3-Butanedione (CH 3 COCOCH 3 ) in Acetaldehyde-Containing Interstellar Ices. Chemphyschem 2020; 21:1531-1540. [PMID: 32458552 DOI: 10.1002/cphc.202000116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/25/2020] [Indexed: 11/06/2022]
Abstract
Acetaldehyde (CH3 CHO) is ubiquitous throughout the interstellar medium and has been observed in cold molecular clouds, star forming regions, and in meteorites such as Murchison. As the simplest methyl-bearing aldehyde, acetaldehyde constitutes a critical precursor to prebiotic molecules such as the sugar deoxyribose and amino acids via the Strecker synthesis. In this study, we reveal the first laboratory detection of 2,3-butanedione (diacetyl, CH3 COCOCH3 ) - a butter and popcorn flavorant - synthesized within acetaldehyde-based interstellar analog ices exposed to ionizing radiation at 5 K. Detailed isotopic substitution experiments combined with tunable vacuum ultraviolet (VUV) photoionization of the subliming molecules demonstrate that 2,3-butanedione is formed predominantly via the barrier-less radical-radical reaction of two acetyl radicals (CH3 ĊO). These processes are of fundamental importance for a detailed understanding of how complex organic molecules (COMs) are synthesized in deep space thus constraining the molecular structures and complexity of molecules forming in extraterrestrial ices containing acetaldehyde through a vigorous galactic cosmic ray driven non-equilibrium chemistry.
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Affiliation(s)
- N Fabian Kleimeier
- Department of Chemistry and W. M. Keck Research Laboratory in Astrochemistry, University of Hawai'i at Manoa 2545 McCarthy Mall, Honolulu, HI, 96822, USA
| | - Andrew M Turner
- Department of Chemistry and W. M. Keck Research Laboratory in Astrochemistry, University of Hawai'i at Manoa 2545 McCarthy Mall, Honolulu, HI, 96822, USA
| | - Ryan C Fortenberry
- Department of Chemistry & Biochemistry, University of Mississippi, 322 Coulter Hall, University, MS, 38677-1848, USA
| | - Ralf I Kaiser
- Department of Chemistry and W. M. Keck Research Laboratory in Astrochemistry, University of Hawai'i at Manoa 2545 McCarthy Mall, Honolulu, HI, 96822, USA
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15
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Hawkins K, Patterson AK, Clarke PA, Smith DK. Catalytic Gels for a Prebiotically Relevant Asymmetric Aldol Reaction in Water: From Organocatalyst Design to Hydrogel Discovery and Back Again. J Am Chem Soc 2020; 142:4379-4389. [PMID: 32023044 PMCID: PMC7146862 DOI: 10.1021/jacs.9b13156] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Indexed: 12/14/2022]
Abstract
This paper reports an investigation into organocatalytic hydrogels as prebiotically relevant systems. Gels are interesting prebiotic reaction media, combining heterogeneous and homogeneous characteristics with a structurally organized active "solid-like" catalyst separated from the surrounding environment, yet in intimate contact with the solution phase and readily accessible via "liquid-like" diffusion. A simple self-assembling glutamine amide derivative 1 was initially found to catalyze a model aldol reaction between cyclohexanone and 4-nitrobenzaldehyde, but it did not maintain its gel structure during reaction. In this study, it was observed that compound 1 could react directly with the benzaldehyde to form a hydrogel in situ based on Schiff base 2 as a low-molecular-weight gelator (LMWG). This new dynamic gel is a rare example of a two-component self-assembled LMWG hydrogel and was fully characterized. It was demonstrated that glutamine amide 1 could select an optimal aldehyde component and preferentially assemble from mixtures. In the hunt for an organocatalyst, reductive conditions were applied to the Schiff base to yield secondary amine 3, which is also a highly effective hydrogelator at very low loadings with a high degree of nanoscale order. Most importantly, the hydrogel based on 3 catalyzed the prebiotically relevant aldol dimerization of glycolaldehyde to give threose and erythrose. In buffered conditions, this reaction gave excellent conversions, good diastereoselectivity, and some enantioselectivity. Catalysis using the hydrogel of 3 was much better than that using non-assembled 3-demonstrating a clear benefit of self-assembly. The results suggest that hydrogels offer a potential strategy by which prebiotic reactions can be promoted using simple, prebiotically plausible LMWGs that can selectively self-organize from complex mixtures. Such processes may have been of prebiotic importance.
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Affiliation(s)
- Kirsten Hawkins
- Department of Chemistry, University
of York, Heslington, York YO10 5DD, U.K.
| | - Anna K. Patterson
- Department of Chemistry, University
of York, Heslington, York YO10 5DD, U.K.
| | - Paul A. Clarke
- Department of Chemistry, University
of York, Heslington, York YO10 5DD, U.K.
| | - David K. Smith
- Department of Chemistry, University
of York, Heslington, York YO10 5DD, U.K.
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Abstract
The chemistry of abiotic nucleotide synthesis of RNA and DNA in the context of their prebiotic origins on early earth is a continuing challenge. How did (or how can) the nucleotides form and assemble from the small molecule inventories and under conditions that prevailed on early earth 3.5-4 billion years ago? This review provides a background and up-to-date progress that will allow the reader to judge where the field stands currently and what remains to be achieved. We start with a brief primer on the biological synthesis of nucleotides, followed by an extensive focus on the prebiotic formation of the components of nucleotides-either via the synthesis of ribose and the canonical nucleobases and then joining them together or by building both the conjoined sugar and nucleobase, part-by-part-toward the ultimate goal of forming RNA and DNA by polymerization. The review will emphasize that there are-and will continue to be-many more questions than answers from the synthetic, mechanistic, and analytical perspectives. We wrap up the review with a cautionary note in this context about coming to conclusions as to whether the problem of chemistry of prebiotic nucleotide synthesis has been solved.
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Affiliation(s)
- Mahipal Yadav
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
| | - Ravi Kumar
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
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17
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Wang W, Yang J, Sun Y, Li Z, You C. Artificial ATP-Free in Vitro Synthetic Enzymatic Biosystems Facilitate Aldolase-Mediated C–C Bond Formation for Biomanufacturing. ACS Catal 2019. [DOI: 10.1021/acscatal.9b04696] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wei Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Jiangang Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Yuanxia Sun
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, People’s Republic of China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Zhimin Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai 200237, China
| | - Chun You
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, People’s Republic of China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
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18
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Aiba S, Tanaka Y, Tokunaga Y, Kawasaki T. Self-Replication of Chiral α-Amino Acids in Strecker-Type Synthesis via Asymmetric Induction and Amplification of Their Own Chiral Intermediate α-Aminonitriles. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20190116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Shohei Aiba
- Department of Materials Science and Engineering, University of Fukui, Bunkyo, Fukui 910-8507, Japan
| | - Yudai Tanaka
- Department of Applied Chemistry, Tokyo University of Science, Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan
| | - Yuji Tokunaga
- Department of Materials Science and Engineering, University of Fukui, Bunkyo, Fukui 910-8507, Japan
| | - Tsuneomi Kawasaki
- Department of Applied Chemistry, Tokyo University of Science, Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan
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19
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Kim HJ, Kim J. A Prebiotic Synthesis of Canonical Pyrimidine and Purine Ribonucleotides. ASTROBIOLOGY 2019; 19:669-674. [PMID: 30698463 PMCID: PMC6486662 DOI: 10.1089/ast.2018.1935] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The "RNA first" model for the origin of life holds that RNA emerged spontaneously on early Earth and developed into life through its dual capabilities for genetics and catalysis. The model's central weakness is the difficulty of making its building blocks, in particular, the glycosidic bond joining nucleobases to ribose. Thus, the focus of much of the modern literature on the topic is directed toward solving this difficulty and includes elegant, though indirect, methods for making this bond. Here, we report that the glycosidic bond in canonical pyrimidine and purine ribonucleotides can be formed by direct coupling of cyclic carbohydrate phosphates with free nucleobases, all reported to be available by experimentally supported pathways that might have operated on early Earth.
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Affiliation(s)
- Hyo-Joong Kim
- Firebird Biomolecular Sciences LLC, Alachua, Florida
- Address correspondence to: Hyo-Joong Kim, Firebird Biomolecular Sciences LLC, 13709 Progress Blvd N104, Alachua, FL 32615
| | - Justin Kim
- Firebird Biomolecular Sciences LLC, Alachua, Florida
- Buchholz High School, Gainesville, Florida
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20
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Cassone G, Sponer J, Sponer JE, Pietrucci F, Saitta AM, Saija F. Synthesis of (d)-erythrose from glycolaldehyde aqueous solutions under electric field. Chem Commun (Camb) 2018; 54:3211-3214. [DOI: 10.1039/c8cc00045j] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A Miller-like numerical experiment demonstrates that ubiquitarious molecules such as water and glycolaldehyde can synthesize (d)-erythrose, one of the direct precursors of ribose.
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Affiliation(s)
- Giuseppe Cassone
- Institute of Biophysics, Czech Academy of Sciences
- 61265 Brno
- Czech Republic
| | - Jiri Sponer
- Institute of Biophysics, Czech Academy of Sciences
- 61265 Brno
- Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University
- 77146 Olomouc
| | - Judit E. Sponer
- Institute of Biophysics, Czech Academy of Sciences
- 61265 Brno
- Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University
- 77146 Olomouc
| | - Fabio Pietrucci
- Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, CNRS, Muséum national d’Histoire naturelle, Institut de Recherche pour le Développement
- F-75005 Paris
- France
| | - A. Marco Saitta
- Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, CNRS, Muséum national d’Histoire naturelle, Institut de Recherche pour le Développement
- F-75005 Paris
- France
| | - Franz Saija
- CNR-IPCF, Viale Ferdinando Stagno d’Alcontres 37
- 98158 Messina
- Italy
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21
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Todd ZR, Fahrenbach AC, Magnani CJ, Ranjan S, Björkbom A, Szostak JW, Sasselov DD. Solvated-electron production using cyanocuprates is compatible with the UV-environment on a Hadean–Archaean Earth. Chem Commun (Camb) 2018; 54:1121-1124. [PMID: 29334083 PMCID: PMC9631354 DOI: 10.1039/c7cc07748c] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
UV-driven photoredox processing of cyanocuprates can generate simple sugars necessary for prebiotic synthesis. We investigate the wavelength dependence of this process from 215 to 295 nm and generally observe faster rates at shorter wavelengths. The most efficient wavelengths are accessible to a range of potential prebiotic atmospheres, supporting the potential role of cyanocuprate photochemistry in prebiotic synthesis on the early Earth. Simple sugars necessary for the synthesis of prebiotic molecules can be generated from UV-driven cyanocuprate photoprocessing under conditions consistent with those expected on the surface of the early Earth.![]()
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Affiliation(s)
- Zoe R. Todd
- Department of Astronomy
- Harvard-Smithsonian Center for Astrophysics
- 60 Garden Street
- Cambridge
- USA
| | - Albert C. Fahrenbach
- Howard Hughes Medical Institute
- Department of Molecular Biology and Center for Computational and Integrative Biology
- Massachusetts General Hospital
- 185 Cambridge Street
- Boston
| | - Christopher J. Magnani
- Department of Astronomy
- Harvard-Smithsonian Center for Astrophysics
- 60 Garden Street
- Cambridge
- USA
| | - Sukrit Ranjan
- Department of Astronomy
- Harvard-Smithsonian Center for Astrophysics
- 60 Garden Street
- Cambridge
- USA
| | - Anders Björkbom
- Howard Hughes Medical Institute
- Department of Molecular Biology and Center for Computational and Integrative Biology
- Massachusetts General Hospital
- 185 Cambridge Street
- Boston
| | - Jack W. Szostak
- Howard Hughes Medical Institute
- Department of Molecular Biology and Center for Computational and Integrative Biology
- Massachusetts General Hospital
- 185 Cambridge Street
- Boston
| | - Dimitar D. Sasselov
- Department of Astronomy
- Harvard-Smithsonian Center for Astrophysics
- 60 Garden Street
- Cambridge
- USA
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