1
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Riggi VS, Watson EB, Steele A, Rogers KL. Mineral-Mediated Oligoribonucleotide Condensation: Broadening the Scope of Prebiotic Possibilities on the Early Earth. Life (Basel) 2023; 13:1899. [PMID: 37763303 PMCID: PMC10532843 DOI: 10.3390/life13091899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
The origin of life on earth requires the synthesis of protobiopolymers in realistic geologic environments along strictly abiotic pathways that rely on inorganic phases (such as minerals) instead of cellular machinery to promote condensation. One such class of polymer central to biochemistry is the polynucleotides, and oligomerization of activated ribonucleotides has been widely studied. Nonetheless, the range of laboratory conditions tested to date is limited and the impact of realistic early Earth conditions on condensation reactions remains unexplored. Here, we investigate the potential for a variety of minerals to enhance oligomerization using ribonucleotide monomers as one example to model condensation under plausible planetary conditions. The results show that several minerals differing in both structure and composition enhance oligomerization. Sulfide minerals yielded oligomers of comparable lengths to those formed in the presence of clays, with galena being the most effective, yielding oligonucleotides up to six bases long. Montmorillonite continues to excel beyond other clays. Chemical pretreatment of the clay was not required, though maximum oligomer lengths decreased from ~11 to 6 bases. These results demonstrate the diversity of mineral phases that can impact condensation reactions and highlight the need for greater consideration of environmental context when assessing prebiotic synthesis and the origin of life.
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Affiliation(s)
- Vincent S. Riggi
- Rensselaer Astrobiology Research and Education Center, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; (E.B.W.); (A.S.); (K.L.R.)
- Department of Earth and Environmental Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - E. Bruce Watson
- Rensselaer Astrobiology Research and Education Center, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; (E.B.W.); (A.S.); (K.L.R.)
- Department of Earth and Environmental Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Andrew Steele
- Rensselaer Astrobiology Research and Education Center, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; (E.B.W.); (A.S.); (K.L.R.)
- Earth and Planets Laboratory, Carnegie Institution for Science, 5251 Broad Branch Rd NW, Washington, DC 20015, USA
| | - Karyn L. Rogers
- Rensselaer Astrobiology Research and Education Center, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; (E.B.W.); (A.S.); (K.L.R.)
- Department of Earth and Environmental Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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2
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Spark of Life: Role of Electrotrophy in the Emergence of Life. Life (Basel) 2023; 13:life13020356. [PMID: 36836714 PMCID: PMC9961546 DOI: 10.3390/life13020356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/20/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
The emergence of life has been a subject of intensive research for decades. Different approaches and different environmental "cradles" have been studied, from space to the deep sea. Since the recent discovery of a natural electrical current through deep-sea hydrothermal vents, a new energy source is considered for the transition from inorganic to organic. This energy source (electron donor) is used by modern microorganisms via a new trophic type, called electrotrophy. In this review, we draw a parallel between this metabolism and a new theory for the emergence of life based on this electrical electron flow. Each step of the creation of life is revised in the new light of this prebiotic electrochemical context, going from the evaluation of similar electrical current during the Hadean, the CO2 electroreduction into a prebiotic primordial soup, the production of proto-membranes, the energetic system inspired of the nitrate reduction, the proton gradient, and the transition to a planktonic proto-cell. Finally, this theory is compared to the two other theories in hydrothermal context to assess its relevance and overcome the limitations of each. Many critical factors that were limiting each theory can be overcome given the effect of electrochemical reactions and the environmental changes produced.
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3
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Guo X, Fu S, Ying J, Zhao Y. Prebiotic chemistry: a review of nucleoside phosphorylation and polymerization. Open Biol 2023; 13:220234. [PMID: 36629018 PMCID: PMC9832566 DOI: 10.1098/rsob.220234] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The phosphorylation of nucleosides and their polymerization are crucial issues concerning the origin of life. The question of how these plausible chemical processes took place in the prebiotic Earth is still perplexing, despite several studies that have attempted to explain these prebiotic processes. The purpose of this article is to review these chemical reactions with respect to chemical evolution in the primeval Earth. Meanwhile, from our perspective, the chiral properties and selection of biomolecules should be considered in the prebiotic chemical origin of life, which may contribute to further research in this field to some extent.
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Affiliation(s)
- Xiaofan Guo
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, People's Republic of China
| | - Songsen Fu
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, People's Republic of China
| | - Jianxi Ying
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, People's Republic of China
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, People's Republic of China,Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, Fujian, People's Republic of China
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4
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Kloprogge JT(T, Hartman H. Clays and the Origin of Life: The Experiments. Life (Basel) 2022; 12:259. [PMID: 35207546 PMCID: PMC8880559 DOI: 10.3390/life12020259] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/08/2022] [Accepted: 02/01/2022] [Indexed: 12/15/2022] Open
Abstract
There are three groups of scientists dominating the search for the origin of life: the organic chemists (the Soup), the molecular biologists (RNA world), and the inorganic chemists (metabolism and transient-state metal ions), all of which have experimental adjuncts. It is time for Clays and the Origin of Life to have its experimental adjunct. The clay data coming from Mars and carbonaceous chondrites have necessitated a review of the role that clays played in the origin of life on Earth. The data from Mars have suggested that Fe-clays such as nontronite, ferrous saponites, and several other clays were formed on early Mars when it had sufficient water. This raised the question of the possible role that these clays may have played in the origin of life on Mars. This has put clays front and center in the studies on the origin of life not only on Mars but also here on Earth. One of the major questions is: What was the catalytic role of Fe-clays in the origin and development of metabolism here on Earth? First, there is the recent finding of a chiral amino acid (isovaline) that formed on the surface of a clay mineral on several carbonaceous chondrites. This points to the formation of amino acids on the surface of clay minerals on carbonaceous chondrites from simpler molecules, e.g., CO2, NH3, and HCN. Additionally, there is the catalytic role of small organic molecules, such as dicarboxylic acids and amino acids found on carbonaceous chondrites, in the formation of Fe-clays themselves. Amino acids and nucleotides adsorb on clay surfaces on Earth and subsequently polymerize. All of these observations and more must be subjected to strict experimental analysis. This review provides an overview of what has happened and is now happening in the experimental clay world related to the origin of life. The emphasis is on smectite-group clay minerals, such as montmorillonite and nontronite.
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Affiliation(s)
- Jacob Teunis (Theo) Kloprogge
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Department of Chemistry, College of Arts and Sciences, University of the Philippines Visayas, Miagao 5023, Philippines
| | - Hyman Hartman
- Department of Earth Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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5
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Namani T, Snyder S, Eagan JM, Bevilacqua PC, Wesdemiotis C, Sahai N. Amino Acid Specific Nonenzymatic Montmorillonite‐Promoted RNA Polymerization. CHEMSYSTEMSCHEM 2021. [DOI: 10.1002/syst.202000060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Trishool Namani
- School of Polymer Science and Polymer Engineering The University of Akron Akron OH 44325 USA
| | - Savannah Snyder
- Department of Chemistry The University of Akron Akron OH 44325 USA
| | - James M. Eagan
- School of Polymer Science and Polymer Engineering The University of Akron Akron OH 44325 USA
| | - Philip C. Bevilacqua
- Department of Chemistry and Biochemistry Department of Microbiology and Molecular Biology Center for RNA Molecular Biology Pennsylvania State University University Park Pennsylvania PA 16802 USA
| | | | - Nita Sahai
- School of Polymer Science and Polymer Engineering The University of Akron Akron OH 44325 USA
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6
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Motsch S, Tremmel P, Richert C. Regioselective formation of RNA strands in the absence of magnesium ions. Nucleic Acids Res 2020; 48:1097-1107. [PMID: 31819977 PMCID: PMC7026634 DOI: 10.1093/nar/gkz1125] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/08/2019] [Accepted: 11/18/2019] [Indexed: 11/28/2022] Open
Abstract
The oligomerization of ribonucleotides can produce short RNA strands in the absence of enzymes. This reaction gives one of two regioisomeric phosphodiester linkages, a 2',5'- or a 3',5'-diester. The former, non-natural linkage is detrimental for duplex stability, and is known to form preferentially in oligomerizations occurring in homogeneous solution with preactivated nucleotides in the presence of magnesium cations. We have studied ribonucleotide oligomerization with in situ activation, using NMR as monitoring technique. Unexpectedly, the known preference for 2',5'-linkages in the oligomerization of AMP was reversed in the absence of magnesium ions at slightly basic pH. Further, oligomerization was surprisingly efficient in the absence of Mg2+ salts, producing oligomers long enough for duplex formation. A quantitative systems chemistry analysis then revealed that the absence of magnesium ions favors the activation of nucleotides, and that the high concentration of active species can compensate for slower coupling. Further, organocatalytic intermediates can help to overcome the unfavorable regioselectivity of the magnesium-catalyzed reactions. Our findings allay concerns that RNA may have been difficult to form in the absence of enzymes. They also show that there is an efficient path to genetic material that does not require mineral surfaces or cations known to catalyze RNA hydrolysis.
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Affiliation(s)
- Sebastian Motsch
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Peter Tremmel
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
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7
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Tremmel P, Griesser H, Steiner UE, Richert C. How Small Heterocycles Make a Reaction Network of Amino Acids and Nucleotides Efficient in Water. Angew Chem Int Ed Engl 2019; 58:13087-13092. [PMID: 31276284 PMCID: PMC6852251 DOI: 10.1002/anie.201905427] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/06/2019] [Indexed: 12/16/2022]
Abstract
Organisms use enzymes to ensure a flow of substrates through biosynthetic pathways. How the earliest form of life established biosynthetic networks and prevented hydrolysis of intermediates without enzymes is unclear. Organocatalysts may have played the role of enzymes. Quantitative analysis of reactions of adenosine 5'-monophosphate and glycine that produce peptides, pyrophosphates, and RNA chains reveals that organocapture by heterocycles gives hydrolytically stabilized intermediates with balanced reactivity. We determined rate constants for 20 reactions in aqueous solutions containing a carbodiimide and measured product formation with cyanamide as a condensing agent. Organocapture favors reactions that are kinetically slow but productive, and networks, over single transformations. Heterocycles can increase the metabolic efficiency more than two-fold, with up to 0.6 useful bonds per fuel molecule spent, boosting the efficiency of life-like reaction systems in the absence of enzymes.
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Affiliation(s)
- Peter Tremmel
- Institut für Organische ChemieUniversität Stuttgart70569StuttgartGermany
| | - Helmut Griesser
- Institut für Organische ChemieUniversität Stuttgart70569StuttgartGermany
| | | | - Clemens Richert
- Institut für Organische ChemieUniversität Stuttgart70569StuttgartGermany
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8
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Tremmel P, Griesser H, Steiner UE, Richert C. How Small Heterocycles Make a Reaction Network of Amino Acids and Nucleotides Efficient in Water. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905427] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Peter Tremmel
- Institut für Organische Chemie Universität Stuttgart 70569 Stuttgart Germany
| | - Helmut Griesser
- Institut für Organische Chemie Universität Stuttgart 70569 Stuttgart Germany
| | - Ulrich E. Steiner
- Department of Chemistry University of Konstanz 78457 Konstanz Germany
| | - Clemens Richert
- Institut für Organische Chemie Universität Stuttgart 70569 Stuttgart Germany
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9
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Yi R, Hongo Y, Fahrenbach AC. Synthesis of imidazole-activated ribonucleotides using cyanogen chloride. Chem Commun (Camb) 2018; 54:511-514. [PMID: 29264602 DOI: 10.1039/c7cc08489g] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the syntheses of ribonucleoside 5'-monophosphates activated with imidazole, using a mechanism which relies on the in situ generation of cyanogen chloride from the reaction of cyanide anion with hypochlorous acid. Cyanogen chloride reacts rapidly with imidazole to form diimidazole imine as the major product, a species which affords the activation of ribonucleoside 5'-monophosphates to their 5'-phosphorimidazolides.
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Affiliation(s)
- Ruiqin Yi
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
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10
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Tam CP, Zhou L, Fahrenbach AC, Zhang W, Walton T, Szostak JW. Synthesis of a Nonhydrolyzable Nucleotide Phosphoroimidazolide Analogue That Catalyzes Nonenzymatic RNA Primer Extension. J Am Chem Soc 2018; 140:783-792. [PMID: 29251930 PMCID: PMC6326531 DOI: 10.1021/jacs.7b11623] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
We
report the synthesis of guanosine 5′-(4-methylimidazolyl)phosphonate
(ICG), the third member of a series of nonhydrolyzable nucleoside
5′-phosphoro-2-methylimidazolide (2-MeImpN) analogues designed
for mechanistic studies of nonenzymatic RNA primer extension. The
addition of a 2-MeImpN monomer to a primer is catalyzed by the presence
of a downstream activated monomer, yet the three nonhydrolyzable analogues
do not show catalytic effects under standard mildly basic primer extension
conditions. Surprisingly, ICG, which has a pKa similar to that of 2-MeImpG, is a modest catalyst of nonenzymatic
primer extension at acidic pH. Here we show that ICG reacts with 2-MeImpC
to form a stable 5′–5′-imidazole-bridged guanosine-cytosine
dinucleotide, with both a labile nitrogen–phosphorus and a
stable carbon–phosphorus linkage flanking the central imidazole
bridge. Cognate RNA primer–template complexes react with this
GC-dinucleotide by attack of the primer 3′-hydroxyl on the
activated N–P side of the 5′-5′-imidazole bridge.
These observations support the hypothesis that 5′–5′-imidazole-bridged
dinucleotides can bind to cognate RNA primer–template duplexes
and adopt appropriate conformations for subsequent phosphodiester
bond formation, consistent with our recent mechanistic proposal that
the formation of activated 5′–5′-imidazolium-bridged
dinucleotides is responsible for 2-MeImpN-driven primer extension.
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Affiliation(s)
- Chun Pong Tam
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital , 185 Cambridge Street, Boston, Massachusetts 02114, United States.,Department of Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Lijun Zhou
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital , 185 Cambridge Street, Boston, Massachusetts 02114, United States.,Department of Genetics, Harvard Medical School , 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Albert C Fahrenbach
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital , 185 Cambridge Street, Boston, Massachusetts 02114, United States.,Department of Genetics, Harvard Medical School , 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.,Earth-Life Science Institute, Tokyo Institute of Technology , 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Wen Zhang
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital , 185 Cambridge Street, Boston, Massachusetts 02114, United States.,Department of Genetics, Harvard Medical School , 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Travis Walton
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital , 185 Cambridge Street, Boston, Massachusetts 02114, United States.,Program of Biological and Biomedical Sciences, Harvard Medical School , 25 Shattuck Street, Gordon Hall, Boston, Massachusetts 02115, United States
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital , 185 Cambridge Street, Boston, Massachusetts 02114, United States.,Department of Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, Cambridge, Massachusetts 02138, United States.,Department of Genetics, Harvard Medical School , 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.,Earth-Life Science Institute, Tokyo Institute of Technology , 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
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11
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Kawamura K, Maurel MC. Walking over 4 Gya: Chemical Evolution from Photochemistry to Mineral and Organic Chemistries Leading to an RNA World. ORIGINS LIFE EVOL B 2017; 47:281-296. [PMID: 28432500 DOI: 10.1007/s11084-017-9537-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 01/20/2017] [Indexed: 01/25/2023]
Abstract
Here we overview the chemical evolution of RNA molecules from inorganic material through mineral-mediated RNA formation compatible with the plausible early Earth environments. Pathways from the gas-phase reaction to the formation of nucleotides, activation and oligomerization of nucleotides, seem to be compatible with specific environments. However, how these steps interacted is not clear since the chemical conditions are frequently different and can be incompatible between them; thus the products would have migrated from one place to another, suitable for further chemical evolution. In this review, we summarize certain points to scrutinize the RNA World hypothesis.
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Affiliation(s)
- Kunio Kawamura
- Department of Human Environmental Studies, Hiroshima Shudo University, 1-1-1 Ozuka-higashi, Asaminami-ku, Hiroshima, 731-3195, Japan.
| | - Marie-Christine Maurel
- Institut de Systématique, Evolution, Biodiversité (ISYEB), UMR 7205 CNRS MNHN UPMC EPHE, Sorbonne Universités, 50, 57 rue Cuvier, 75005, Paris, CP, France
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12
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Kervio E, Sosson M, Richert C. The effect of leaving groups on binding and reactivity in enzyme-free copying of DNA and RNA. Nucleic Acids Res 2016; 44:5504-14. [PMID: 27235418 PMCID: PMC4937335 DOI: 10.1093/nar/gkw476] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 05/06/2016] [Accepted: 05/09/2016] [Indexed: 01/29/2023] Open
Abstract
The template-directed incorporation of nucleotides at the terminus of a growing primer is the basis of the transmission of genetic information. Nature uses polymerases-catalyzed reactions, but enzyme-free versions exist that employ nucleotides with organic leaving groups. The leaving group affects yields, but it was not clear whether inefficient extensions are due to poor binding, low reactivity toward the primer, or rapid hydrolysis. We have measured the binding of a total of 15 different activated nucleotides to DNA or RNA sequences. Further, we determined rate constants for the chemical step of primer extension involving methylimidazolides or oxyazabenzotriazolides of deoxynucleotides or ribonucleotides. Binding constants range from 10 to >500 mM and rate constants from 0.1 to 370 M(-1) h(-1) For aminoterminal primers, a fast covalent step and slow hydrolysis are the main factors leading to high yields. For monomers with weakly pairing bases, the leaving group can improve binding significantly. A detailed mechanistic picture emerges that explains why some enzyme-free primer extensions occur in high yield, while others remain recalcitrant to copying without enzymatic catalysis. A combination of tight binding and rapid extension, coupled with slow hydrolysis induces efficient enzyme-free copying.
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Affiliation(s)
- Eric Kervio
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Marilyne Sosson
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
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13
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Ertem G, Prabahar KJ, Joshi PC, Ferris JP. Bridging the prebiotic and RNA worlds: prebiotic RNA synthesis on clay. J Biomol Struct Dyn 2016; 17 Suppl 1:207-10. [PMID: 22607426 DOI: 10.1080/07391102.2000.10506623] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Abstract Progress towards the laboratory demonstration of the steps in the prebiotic origin of the RNA world is reviewed. Montmorillonite clay catalyzes the formation of RNAs containing 6-14 monomer units from the activated mononucleotides of A, C, G, I and U. The RNAs formed have 3', 5'- and 2', 5'-links, pyrophosphate links and have both linear and cyclic chains. The purine oligonucleotides have more 3', 5'- links while the pyrimidine nucleotides have more 2', 5'-linkages. Template-directed synthesis on the heterogeneous oligo(C)s formed on mont- morillonite yields the corresponding oligo(G)s. The dimer fraction formed in the reaction of a binary mixture of a purine and pyrimidine nucleotide shows sequence selectivity with about a 20 fold excess of the 5'-purine-pyrimidine dimer over that of the 5'-pyrimidine-purine dimer. RNAs as long as 50 mers are formed by the elongation of a decamer bound to montmorillonite by the daily addition of activated monomer to it over a 14-day time period.
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Affiliation(s)
- G Ertem
- a Department of Chemistry , Rensselaer Polytechnic Institute , Troy , NY , 12180
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14
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Pal A, Das RS, Zhang W, Lang M, McLaughlin LW, Szostak JW. Effect of terminal 3′-hydroxymethyl modification of an RNA primer on nonenzymatic primer extension. Chem Commun (Camb) 2016; 52:11905-11907. [DOI: 10.1039/c6cc06925h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Displacing the hydroxyl nucleophile at the 3′-end of a primer by a single methylene group drastically decreases the rate of primer extension, illustrating the importance of the precise position of the hydroxyl nucleophile.
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Affiliation(s)
- Ayan Pal
- Howard Hughes Medical Institute
- Department of Molecular Biology and Center for Computational and Integrative Biology
- Massachusetts General Hospital
- Boston
- USA
| | - Rajat S. Das
- Boston College
- Department of Chemistry
- Merkert Chemistry Center
- Chestnut Hill
- USA
| | - Weicheng Zhang
- Howard Hughes Medical Institute
- Department of Molecular Biology and Center for Computational and Integrative Biology
- Massachusetts General Hospital
- Boston
- USA
| | - Megan Lang
- Boston College
- Department of Chemistry
- Merkert Chemistry Center
- Chestnut Hill
- USA
| | - Larry W. McLaughlin
- Boston College
- Department of Chemistry
- Merkert Chemistry Center
- Chestnut Hill
- USA
| | - Jack W. Szostak
- Howard Hughes Medical Institute
- Department of Molecular Biology and Center for Computational and Integrative Biology
- Massachusetts General Hospital
- Boston
- USA
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15
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Jauker M, Griesser H, Richert C. Copying of RNA Sequences without Pre-Activation. Angew Chem Int Ed Engl 2015; 54:14559-63. [PMID: 26435291 PMCID: PMC4678514 DOI: 10.1002/anie.201506592] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 09/03/2015] [Indexed: 11/23/2022]
Abstract
Template-directed incorporation of nucleotides at the terminus of a growing complementary strand is the basis of replication. For RNA, this process can occur in the absence of enzymes, if the ribonucleotides are first converted to an active species with a leaving group. Thus far, the activation required a separate chemical step, complicating prebiotically plausible scenarios. Here we show that a combination of a carbodiimide and an organocatalyst induces near-quantitative incorporation of any of the four ribonucleotides. Upon in situ activation, adenosine monophosphate was found to also form oligomers in aqueous solution. So, both de novo strand formation and sequence-specific copying can occur without an artificial synthetic step.
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Affiliation(s)
- Mario Jauker
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany)
| | - Helmut Griesser
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany)
| | - Clemens Richert
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany).
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16
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Jauker M, Griesser H, Richert C. Kopieren von RNA-Sequenzen ohne Voraktivierung. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506592] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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17
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Martin LL, Unrau PJ, Müller UF. RNA synthesis by in vitro selected ribozymes for recreating an RNA world. Life (Basel) 2015; 5:247-68. [PMID: 25610978 PMCID: PMC4390851 DOI: 10.3390/life5010247] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 12/22/2014] [Accepted: 01/13/2015] [Indexed: 01/20/2023] Open
Abstract
The RNA world hypothesis states that during an early stage of life, RNA molecules functioned as genome and as the only genome-encoded catalyst. This hypothesis is supported by several lines of evidence, one of which is the in vitro selection of catalytic RNAs (ribozymes) in the laboratory for a wide range of reactions that might have been used by RNA world organisms. This review focuses on three types of ribozymes that could have been involved in the synthesis of RNA, the core activity in the self-replication of RNA world organisms. These ribozyme classes catalyze nucleoside synthesis, triphosphorylation, and the polymerization of nucleoside triphosphates. The strengths and weaknesses regarding each ribozyme’s possible function in a self-replicating RNA network are described, together with the obstacles that need to be overcome before an RNA world organism can be generated in the laboratory.
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Affiliation(s)
- Lyssa L Martin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
| | - Peter J Unrau
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
| | - Ulrich F Müller
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0356, USA.
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18
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Synergism and mutualism in non-enzymatic RNA polymerization. Life (Basel) 2014; 4:598-620. [PMID: 25370531 PMCID: PMC4284460 DOI: 10.3390/life4040598] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 10/15/2014] [Accepted: 10/17/2014] [Indexed: 01/19/2023] Open
Abstract
The link between non-enzymatic RNA polymerization and RNA self-replication is a key step towards the "RNA world" and still far from being solved, despite extensive research. Clay minerals, lipids and, more recently, peptides were found to catalyze the non-enzymatic synthesis of RNA oligomers. Herein, a review of the main models for the formation of the first RNA polymers is presented in such a way as to emphasize the cooperation between life's building blocks in their emergence and evolution. A logical outcome of the previous results is a combination of these models, in which RNA polymerization might have been catalyzed cooperatively by clays, lipids and peptides in one multi-component prebiotic soup. The resulting RNAs and oligopeptides might have mutualistically evolved towards functional RNAs and catalytic peptides, preceding the first RNA replication, thus supporting an RNA-peptide world. The investigation of such a system is a formidable challenge, given its complexity deriving from a tremendously large number of reactants and innumerable products. A rudimentary experimental design is outlined, which could be used in an initial attempt to study a quaternary component system.
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19
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Rouch DA. Evolution of the first genetic cells and the universal genetic code: a hypothesis based on macromolecular coevolution of RNA and proteins. J Theor Biol 2014; 357:220-44. [PMID: 24931677 DOI: 10.1016/j.jtbi.2014.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 06/02/2014] [Accepted: 06/03/2014] [Indexed: 11/19/2022]
Abstract
A qualitative hypothesis based on coevolution of protein and nucleic acid macromolecules was developed to explain the evolution of the first genetic cells, from the likely organic chemical-rich environment of early earth, through to the Last Universal Common Ancestor (LUCA). The evolution of the first genetic cell was divided into three phases, proto-genetic cells I, II and III, and the transition to each milestone is described, based on development of chemical cross-catalysis, bio-cross-catalysis, and the universal genetic code, respectively. Selection of macromolecular properties of both peptides and nucleic acids, in response to environmental factors, was likely to be a key aspect of early evolution. The development of hereditable nucleic acids with various key functions; translation, transcription and replication, is described. These functions are envisaged to have coevolved with protein enzymes, from simple organic precursors. Genetically heritable nucleotides may have developed after the local earth environment had cooled below 63 °C. Around this temperature G-C bases would have been preferentially utilized for nucleotide synthesis. Under these conditions RNA type nucleotides were then likely selected from a range of different types of nucleotide backbones through template-based synthesis. Initial development of the genetic coding system was simplified by the availability of proto-messenger RNA sequences that contained only G and C bases, and the need to encode only four amino acids. The step-wise addition of further amino acids to the code was predicted to parallel the growing metabolic complexity of the proto-genetic cell. On completion of this evolutionary process the proto-genetic cell is envisaged to have become the LUCA, the last common ancestor of bacteria, eukaryote and archaea domains. Key issues addressed by the model include: (a) the transition from non-hereditable random sequences of peptides and nucleic acids to specific proteins coded by hereditable nucleotide sequences, (b) the origin of homochiral amino acids and sugars, and (c) the mutation limits on the sizes of early nucleic acid genomes. The first genome was limited to a size of about 200 base pairs.
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Affiliation(s)
- Duncan A Rouch
- Biotechnology and Environmental Biology, RMIT University, PO Box 71, Bundoora, Melbourne, Vic 3083, Australia.
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20
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Abstract
The complexity of even the simplest known life forms makes efforts to synthesize living cells from inanimate components seem like a daunting task. However, recent progress toward the creation of synthetic cells, ranging from simple protocells to artificial cells approaching the complexity of bacteria, suggests that the synthesis of life is now a realistic goal. Protocell research, fueled by advances in the biophysics of primitive membranes and the chemistry of nucleic acid replication, is providing new insights into the origin of cellular life. Parallel efforts to construct more complex artificial cells, incorporating translational machinery and protein enzymes, are providing information about the requirements for protein-based life. We discuss recent advances and remaining challenges in the synthesis of artificial cells, the possibility of creating new forms of life distinct from existing biology, and the promise of this research for gaining a deeper understanding of the nature of living systems.
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Affiliation(s)
- J Craig Blain
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114; ,
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21
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Mamajanov I, MacDonald PJ, Ying J, Duncanson DM, Dowdy GR, Walker CA, Engelhart AE, Fernández FM, Grover MA, Hud NV, Schork FJ. Ester Formation and Hydrolysis during Wet–Dry Cycles: Generation of Far-from-Equilibrium Polymers in a Model Prebiotic Reaction. Macromolecules 2014. [DOI: 10.1021/ma402256d] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Irena Mamajanov
- School of Chemistry and Biochemistry, ‡School of Chemical & Biomolecular Engineering, and §Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Patrick J. MacDonald
- School of Chemistry and Biochemistry, ‡School of Chemical & Biomolecular Engineering, and §Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Jingya Ying
- School of Chemistry and Biochemistry, ‡School of Chemical & Biomolecular Engineering, and §Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Daniel M. Duncanson
- School of Chemistry and Biochemistry, ‡School of Chemical & Biomolecular Engineering, and §Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Garrett R. Dowdy
- School of Chemistry and Biochemistry, ‡School of Chemical & Biomolecular Engineering, and §Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Chelsea A. Walker
- School of Chemistry and Biochemistry, ‡School of Chemical & Biomolecular Engineering, and §Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Aaron E. Engelhart
- School of Chemistry and Biochemistry, ‡School of Chemical & Biomolecular Engineering, and §Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Facundo M. Fernández
- School of Chemistry and Biochemistry, ‡School of Chemical & Biomolecular Engineering, and §Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Martha A. Grover
- School of Chemistry and Biochemistry, ‡School of Chemical & Biomolecular Engineering, and §Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Nicholas V. Hud
- School of Chemistry and Biochemistry, ‡School of Chemical & Biomolecular Engineering, and §Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - F. Joseph Schork
- School of Chemistry and Biochemistry, ‡School of Chemical & Biomolecular Engineering, and §Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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22
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Abstract
The RNA world hypothesis describes a stage in the early evolution of life in which RNA served as genome and as the only genome-encoded catalyst. To test whether RNA world organisms could have used cyclic trimetaphosphate as an energy source, we developed an in vitro selection strategy for isolating ribozymes that catalyze the triphosphorylation of RNA 5′-hydroxyl groups with trimetaphosphate. Several active sequences were isolated, and one ribozyme was analyzed in more detail. The ribozyme was truncated to 96 nt, while retaining full activity. It was converted to a trans-format and reacted with rates of 0.16 min−1 under optimal conditions. The secondary structure appears to contain a four-helical junction motif. This study showed that ribozymes can use trimetaphosphate to triphosphorylate RNA 5′-hydroxyl groups and suggested that RNA world organisms could have used trimetaphosphate as their energy source.
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Affiliation(s)
- Janina E Moretti
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
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23
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Ruiz-Mirazo K, Briones C, de la Escosura A. Prebiotic Systems Chemistry: New Perspectives for the Origins of Life. Chem Rev 2013; 114:285-366. [DOI: 10.1021/cr2004844] [Citation(s) in RCA: 563] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kepa Ruiz-Mirazo
- Biophysics
Unit (CSIC-UPV/EHU), Leioa, and Department of Logic and Philosophy
of Science, University of the Basque Country, Avenida de Tolosa 70, 20080 Donostia−San Sebastián, Spain
| | - Carlos Briones
- Department
of Molecular Evolution, Centro de Astrobiología (CSIC−INTA, associated to the NASA Astrobiology Institute), Carretera de Ajalvir, Km 4, 28850 Torrejón de Ardoz, Madrid, Spain
| | - Andrés de la Escosura
- Organic
Chemistry Department, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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24
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Sliding over the blocks in enzyme-free RNA copying--one-pot primer extension in ice. PLoS One 2013; 8:e75617. [PMID: 24058695 PMCID: PMC3776762 DOI: 10.1371/journal.pone.0075617] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 08/15/2013] [Indexed: 12/02/2022] Open
Abstract
Template-directed polymerization of RNA in the absence of enzymes is the basis for an information transfer in the ‘RNA-world’ hypothesis and in novel nucleic acid based technology. Previous investigations established that only cytidine rich strands are efficient templates in bulk aqueous solutions while a few specific sequences completely block the extension of hybridized primers. We show that a eutectic water/ice system can support Pb2+/Mg2+-ion catalyzed extension of a primer across such sequences, i.e. AA, AU and AG, in a one-pot synthesis. Using mixtures of imidazole activated nucleotide 5′-monophosphates, the two first “blocking” residues could be passed during template-directed polymerization, i.e., formation of triply extended products containing a high fraction of faithful copies was demonstrated. Across the AG sequence, a mismatch sequence was formed in similar amounts to the correct product due to U·G wobble pairing. Thus, the template-directed extension occurs both across pyrimidine and purine rich sequences and insertions of pyrimidines did not inhibit the subsequent insertions. Products were mainly formed with 2′-5′-phosphodiester linkages, however, the abundance of 3′–5′-linkages was higher than previously reported for pyrimidine insertions. When enzyme-free, template-directed RNA polymerization is performed in a eutectic water ice environment, various intrinsic reaction limitations observed in bulk solution can then be overcome.
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25
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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 genetically encoded proteins were not involved as catalysts. There is now strong evidence indicating that an RNA World did indeed exist before DNA- and protein-based life. However, arguments regarding whether life on Earth began with RNA are more tenuous. It might be imagined that all of the components of RNA were available in some prebiotic pool, and that these components assembled into replicating, evolving polynucleotides without the prior existence of any evolved macromolecules. A thorough consideration of this "RNA-first" view of the origin of life must reconcile concerns regarding the intractable mixtures that are obtained in experiments designed to simulate the chemistry of the primitive Earth. Perhaps these concerns will eventually be resolved, and recent experimental findings provide some reason for optimism. However, the problem of the origin of the RNA World is far from being solved, and it is fruitful to consider the alternative possibility that RNA was preceded by some other replicating, evolving molecule, just as DNA and proteins were preceded by RNA.
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Affiliation(s)
- Michael P Robertson
- Departments of Chemistry and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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26
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Zhang N, Zhang S, Szostak JW. Activated ribonucleotides undergo a sugar pucker switch upon binding to a single-stranded RNA template. J Am Chem Soc 2012; 134:3691-4. [PMID: 22296305 PMCID: PMC3448298 DOI: 10.1021/ja212027q] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Indexed: 12/02/2022]
Abstract
Template-directed polymerization of chemically activated ribonucleotide monomers, such as nucleotide 5'-phosphorimidazolides, has been studied as a model for nonenzymatic RNA replication during the origin of life. Kinetic studies of the polymerization of various nucleotide monomers on oligonucleotide templates have suggested that the A-form (C3'-endo sugar pucker) conformation is optimal for both monomers and templates for efficient copying. However, RNA monomers are predominantly in the C2'-endo conformation when free in solution, except for cytidine, which is approximately equally distributed between the C2'-endo and C3'-endo conformations. We hypothesized that ribonucleotides undergo a switch in sugar pucker upon binding to an A-type template and that this conformational switch allows or enhances subsequent polymerization. We used transferred nuclear Overhauser effect spectroscopy (TrNOESY), which can be used for specific detection of the bound conformation of small-molecule ligands with relatively weak affinity to receptors, to study the interactions between nucleotide 5'-phosphorimidazolides and single-stranded oligonucleotide templates. We found that the sugar pucker of activated ribonucleotides switches from C2'-endo in the free state to C3'-endo upon binding to an RNA template. This switch occurs only on RNA and not on DNA templates. Furthermore, activated 2'-deoxyribonucleotides maintain a C2'-endo sugar pucker in both the free and template-bound states. Our results provide a structural explanation for the observations that activated ribonucleotides are superior to activated deoxyribonucleotides and that RNA templates are superior to DNA templates in template-directed nonenzymatic primer-extension reactions.
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Affiliation(s)
- Na Zhang
- Howard Hughes
Medical Institute and Department of Molecular
Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street,
Boston, Massachusetts 02114, United States
| | - Shenglong Zhang
- Howard Hughes
Medical Institute and Department of Molecular
Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street,
Boston, Massachusetts 02114, United States
| | - Jack W. Szostak
- Howard Hughes
Medical Institute and Department of Molecular
Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street,
Boston, Massachusetts 02114, United States
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27
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Pino S, Biasiucci M, Scardamaglia M, Gigli G, Betti MG, Mariani C, Di Mauro E. Nonenzymatic ligation of an RNA oligonucleotide analyzed by atomic force microscopy. J Phys Chem B 2011; 115:6296-303. [PMID: 21500793 DOI: 10.1021/jp200832w] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The products of ligation reaction of a 24 nucleotides long PolyA RNA adsorbed on mica were observed by atomic force microscopy. The occurrence of oligonucleotides at different degrees of polymerization has been quantitatively studied before and after ligation reaction. The microscopy images at the nanoscale show that nonenzymatic ligation of pristine RNA monomers results in the formation of supramolecular aggregates, with prevalence of dimers and tetramers. Analytical conditions were defined allowing the identification, the quantitative evaluation, and their distribution after ligation reaction, also providing an estimate of the degree of hydration of the objects. Such investigation is of particular biological relevance and provides the simplest yet model system for direct investigation of RNA reactions by advanced microscopy.
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Affiliation(s)
- Samanta Pino
- Department of Physics, Sapienza University of Rome, P.le A. Moro 2, 00185 Rome, Italy
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28
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Röthlingshöfer M, Richert C. Chemical primer extension at submillimolar concentration of deoxynucleotides. J Org Chem 2010; 75:3945-52. [PMID: 20364862 DOI: 10.1021/jo1002467] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Template-directed primer extension usually requires a polymerase, nucleoside triphosphates, and magnesium ions as cofactors. Enzyme-free, chemical primer extensions are known for preactivated nucleotides at millimolar concentrations. Based on a screen of carbodiimides, heterocyclic catalysts, and reactions conditions, we now show that near-quantitative primer conversion can be achieved at submillimolar concentration of any of the four deoxynucleotides (dAMP, dCMP, dGMP and dTMP). The new protocol relies on in situ activation with EDC and 1-methylimidazole and a magnesium-free buffer that was tested successfully for different sequence motifs. The method greatly simplifies chemical primer extension assays, further reduces the cost of such assays, and demonstrates the potential of the in situ activation approach.
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Affiliation(s)
- Manuel Röthlingshöfer
- Institute for Organic Chemistry, University of Karlsruhe/K.I.T., 76131 Karlsruhe, Germany
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29
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Abstract
Recent synthetic approaches to understanding the origin of life have yielded insights into plausible pathways for the emergence of the first cells. Here we review current experiments with implications for the origin of life, emphasizing the ability of unexpected physical processes to facilitate the self-assembly and self-replication of the first biological systems. These laboratory efforts have uncovered novel physical mechanisms for the emergence of homochirality; the concentration and purification of prebiotic building blocks; and the ability of the first cells to assemble, grow, divide, and acquire greater complexity. In the absence of evolved biochemical capabilities, such physical processes likely played an essential role in early biology.
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Affiliation(s)
- Itay Budin
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114-2696, USA
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30
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Abstract
Understanding the origin of cellular life on Earth requires the discovery of plausible pathways for the transition from complex prebiotic chemistry to simple biology, defined as the emergence of chemical assemblies capable of Darwinian evolution. We have proposed that a simple primitive cell, or protocell, would consist of two key components: a protocell membrane that defines a spatially localized compartment, and an informational polymer that allows for the replication and inheritance of functional information. Recent studies of vesicles composed of fatty-acid membranes have shed considerable light on pathways for protocell growth and division, as well as means by which protocells could take up nutrients from their environment. Additional work with genetic polymers has provided insight into the potential for chemical genome replication and compatibility with membrane encapsulation. The integration of a dynamic fatty-acid compartment with robust, generalized genetic polymer replication would yield a laboratory model of a protocell with the potential for classical Darwinian biological evolution, and may help to evaluate potential pathways for the emergence of life on the early Earth. Here we discuss efforts to devise such an integrated protocell model.
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Affiliation(s)
- Jason P Schrum
- Howard Hughes Medical Institute, Department of Molecular Biology and the Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
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31
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Abstract
Bioenergetics is central to our understanding of living systems, yet has attracted relatively little attention in origins of life research. This article focuses on energy resources available to drive primitive metabolism and the synthesis of polymers that could be incorporated into molecular systems having properties associated with the living state. The compartmented systems are referred to as protocells, each different from all the rest and representing a kind of natural experiment. The origin of life was marked when a rare few protocells happened to have the ability to capture energy from the environment to initiate catalyzed heterotrophic growth directed by heritable genetic information in the polymers. This article examines potential sources of energy available to protocells, and mechanisms by which the energy could be used to drive polymer synthesis.
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Affiliation(s)
- David Deamer
- Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, California 95064, USA.
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32
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Loakes D, Holliger P. Darwinian chemistry: towards the synthesis of a simple cell. MOLECULAR BIOSYSTEMS 2009; 5:686-94. [PMID: 19562107 DOI: 10.1039/b904024b] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The total synthesis of a simple cell is in many ways the ultimate challenge in synthetic biology. Outlined eight years ago in a visionary article by Szostak et al. (J. W. Szostak, D. P. Bartel and P. L. Luisi, Nature, 2001, 409, 387), the chances of success seemed remote. However, recent progress in nucleic acid chemistry, directed evolution and membrane biophysics have brought the prospect of a simple synthetic cell with life-like properties such as growth, division, heredity and evolution within reach. Success in this area will not only revolutionize our understanding of abiogenesis but provide a fertile test-bed for models of prebiotic chemistry and early evolution. Last but not least, a robust "living" protocell may provide a versatile and safe chassis for embedding synthetic devices and systems.
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Affiliation(s)
- David Loakes
- Medical Research Council, Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK
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33
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Röthlingshöfer M, Kervio E, Lommel T, Plutowski U, Hochgesand A, Richert C. Chemical primer extension in seconds. Angew Chem Int Ed Engl 2008; 47:6065-8. [PMID: 18613189 DOI: 10.1002/anie.200801260] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Manuel Röthlingshöfer
- Institut für Organische Chemie, Universität Karlsruhe (TH), 76131 Karlsruhe, Germany
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34
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Röthlingshöfer M, Kervio E, Lommel T, Plutowski U, Hochgesand A, Richert C. Chemical Primer Extension in Seconds. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200801260] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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35
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36
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Huang W, Ferris JP. One-step, regioselective synthesis of up to 50-mers of RNA oligomers by montmorillonite catalysis. J Am Chem Soc 2007; 128:8914-9. [PMID: 16819887 DOI: 10.1021/ja061782k] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
5'-Nucleotides of A and U with the phosphate activated with 1-methyladenine generate RNA oligomers containing 40-50 monomers in 1 day in reactions catalyzed by montmorillonite. The corresponding monomers of C give oligomers that are 20-25-mers in length after a 9-day reaction. It was not possible to determine the chain lengths of the oligomers of G since they did not give well-defined bands on gel electrophoresis. Co-oligomers of A and U as well as A, U, G, and C were also prepared. The oligo(A)s formed were separated by gel electrophoresis, and the bands of the 7-39-mers were isolated, the 3',5'-phosphodiester bonds were cleaved by RNase T(2), and the terminal phosphate groups were cleaved with alkaline phosphatase. HPLC analysis revealed that the proportions of A(5)'pp(5)'A, A, A(2)'pA, and A(2)'pA(2)'pA formed were almost the same for the long and shorter oligomers. A similar structure analysis performed on the oligo(U)s established that the proportions of U(5)'pp(5)'U, U, U(2)'pU, U(2)'pU(2)'pU, U(2)'pU(2)'pU(2)'pU, and U(2)'pU(2)'pU(2)'pU(2)'pU did not vary with chain length. The structural analysis of the oligomers of A revealed that 74% of the phosphodiester bonds were 3',5'-linked a value slightly greater than 67% observed when imidazole was the activating group. 61% of the bonds in the U oligomers were 3',5'-linked, which is almost 3 times greater than the 20% measured when imidazole was the activating group. The potential significance of these data to the origin and early evolution of life is discussed.
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Affiliation(s)
- Wenhua Huang
- Department of Chemistry and Chemical Biology and New York Center for Studies on the Origins of Life and Rensselaer Polytechnic Institute, Troy, New York 12180, USA
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37
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Costanzo G, Saladino R, Crestini C, Ciciriello F, Di Mauro E. Formamide as the main building block in the origin of nucleic acids. BMC Evol Biol 2007; 7 Suppl 2:S1. [PMID: 17767725 PMCID: PMC1963486 DOI: 10.1186/1471-2148-7-s2-s1] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The simplest molecules grouping the four most common elements of the universe H,C,O and N (with the exception of the biologically inert He) are isocyanate HNCO and formamide H2NCOH. Reasons for the availability of formamide on prebiotic Earth are presented. We review evidence showing that formamide in the presence of largely available catalysts and by moderate heating yields the complete set of nucleic bases necessary for the formation of nucleic acids. Formamide also favours the formation of acyclonucleosides and the phosphorylation and trans-phosphorylation of nucleosides, thus providing a plausible chemical frame for the passage from a simple one-carbon compound to nucleic polymers. Physico-chemical conditions exist in which formamide favours the stability of the phosphoester bonds in nucleic polymers relative to that of the same bonds in monomers. Starting from a formamide-laden environment subject only to the laws of chemistry, a hypothesis is outlined sketching the passage towards an aqueous world in which Darwinian rules apply.
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Affiliation(s)
- Giovanna Costanzo
- Istituto di Biologia e Patologia Molecolari, CNR, P.le Aldo Moro, 5, Rome 00185, Italy
| | - Raffaele Saladino
- Istituto di Biologia e Patologia Molecolari, CNR, P.le Aldo Moro, 5, Rome 00185, Italy
- Dipartimento A.B.A.C., Università della Tuscia, Via San Camillo De Lellis, Viterbo, Italy
| | - Claudia Crestini
- Marine Dipartimento di Scienze e Tecnologie Chimiche, Università "Tor Vergata", Rome 00133, Italy
| | - Fabiana Ciciriello
- Fondazione "Istituto Pasteur-Fondazione Cenci-Bolognetti" c/o Dipartimento di Genetica e Biologia Molecolare, Università "La Sapienza" di Roma, P.le Aldo Moro, 5, Rome 00185, Italy
| | - Ernesto Di Mauro
- Ernesto Di Mauro, Dipartimento di Genetica e Biologia Molecolare, Università "La Sapienza" di Roma, P.le Aldo Moro, 5, 00185 Rome, Italy
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38
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Saladino R, Crestini C, Ciciriello F, Costanzo G, Di Mauro E. Formamide chemistry and the origin of informational polymers. Chem Biodivers 2007; 4:694-720. [PMID: 17443884 DOI: 10.1002/cbdv.200790059] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Formamide (HCONH2) provides a chemical frame potentially affording all the monomeric components necessary for the formation of nucleic polymers. In the presence of the appropriate catalysts, and by moderate heating, formamide yields a complete set of nucleic bases, acyclonucleosides, and favors both phosphorylations and transphosphorylations. Physico-chemical conditions exist in which formamide favors the stability of the phosphoester bonds in nucleic polymers more than that of the same bonds in monomers. This property establishes 'thermodynamic niches' in which the polymeric forms are favored. The hypothesis that these specific attributes of formamide allowed the onset of prebiotic chemical equilibria capable of Darwinian evolution is discussed.
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Affiliation(s)
- Raffaele Saladino
- Dipartimento A. B. A. C., Università della Tuscia, Via San Camillo De Lellis, I-01100 Viterbo
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Joshi PC, Pitsch S, Ferris JP. Selectivity of montmorillonite catalyzed prebiotic reactions of D, L-nucleotides. ORIGINS LIFE EVOL B 2007; 37:3-26. [PMID: 17160436 DOI: 10.1007/s11084-006-9013-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2006] [Accepted: 02/24/2006] [Indexed: 10/23/2022]
Abstract
The montmorillonite-catalyzed reactions of the 5'-phosphorimidazolides of D, L-adenosine (D, L-ImpA) (Figure 1a. N = A, R = H) and D, L-uridine (Figure 1a., N = U, R = H) yields oligomers that were as long as 7 mers and 6 mers, respectively. The reactions of dilute solutions of D-ImpA and D-ImpU under the same conditions gave oligomers as long as 9 and 8 mers respectively. This demonstrated that oligomer formation is only partially inhibited by incorporation of both the D- and L-enantiomers. The structures of the dimers, trimers and tetramer fractions formed from D, L-ImpA was investigated by selective enzymatic hydrolysis, comparison with authentic samples and mass spectrometry. Homochiral products were present in greater amounts than would be expected if theoretical amounts of each were formed. The ratio of the proportion of homochiral products to that of the amount of each expected for the dimers (cyclic and linear), trimers and tetramers, was 1.3, 1.6, and 2.1, respectively. In the D, L-ImpU reaction homochiral products did not predominate with ratios of dimers (cyclic and linear), trimers and tetramers 0.8, 0.44, and 1.4, respectively. The proportions of cyclic dimers in the dimer fraction were 52-66% with D, L-ImpA and 44-69% with D, L-ImpU. No cyclic dimers were formed in the absence of montmorillonite. The differences in the reaction products of D, L-ImpA and D, L-ImpU are likely to be due to the difference in the orientations of the activated monomers when bound to the catalytic sites on montmorillonite. The consequences of the selectivity of montmorillonite as a prebiotic catalyst are discussed.
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Affiliation(s)
- Prakash C Joshi
- Department of Chemistry & Chemical Biology and NY Center for Studies on the Origins of Life, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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Warthaka M, Karwowska-Desaulniers P, Pflum MKH. Phosphopeptide modification and enrichment by oxidation-reduction condensation. ACS Chem Biol 2006; 1:697-701. [PMID: 17184134 DOI: 10.1021/cb6003564] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many cellular processes are regulated by the reversible phosphorylation of proteins. Despite the importance of monitoring protein phosphorylation, available methods to modify and enrich phosphopeptides from complex mixtures for subsequent mass spectrometric analysis are challenging. Here the oxidation-reduction condensation was shown for the first time to directly modify the phosphate of phosphopeptides and phosphoproteins. By coupling with a solid-phase resin, the oxidation-reduction condensation was validated for capture and recovery of phosphoserine-, phosphothreonine-, and phosphotyrosine-containing peptides from a peptide mixture. In addition, full-length phosphoproteins or phosphopeptides from a protein digestion were captured and recovered using the oxidation-reduction condensation, demonstrating its compatibility with protein mixtures. The strategy modifies all phosphopeptides, maintains high chemical selectivity, requires only two steps, and relies on commercially available reagents, suggesting that the oxidation-reduction condensation has the potential to enhance phosphopeptide enrichment methods and encourage development of efficient biochemical and proteomics tools targeting phosphorylation.
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Hagenbuch P, Kervio E, Hochgesand A, Plutowski U, Richert C. Chemical primer extension: efficiently determining single nucleotides in DNA. Angew Chem Int Ed Engl 2006; 44:6588-92. [PMID: 16175646 DOI: 10.1002/anie.200501794] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Patrizia Hagenbuch
- Institut für Organische Chemie, Universität Karlsruhe TH, 76131 Karlsruhe, Germany
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Miyakawa S, Joshi PC, Gaffey MJ, Gonzalez-Toril E, Hyland C, Ross T, Rybij K, Ferris JP. Studies in the mineral and salt-catalyzed formation of RNA oligomers. ORIGINS LIFE EVOL B 2006; 36:343-61. [PMID: 16915351 DOI: 10.1007/s11084-006-9009-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2005] [Accepted: 01/04/2006] [Indexed: 10/24/2022]
Abstract
Activated mononucleotides oligomerize in the presence of montmorillonite clay to form RNA oligomers. In the present study, effects of salts, temperature and pH on the clay-catalyzed synthesis of RNA oligomers were investigated. This reaction is favored by relatively high concentration of salts, such as 1 M NaCl. It was shown that the presence of divalent cations was not required for this reaction. High concentrations of NH4+ and HCO3- and 0.01 M HPO4(2-) inhibit the reaction. The yields of RNA oligomers decreased as the temperature was raised from 4 degrees C to 50 degrees C. A5' ppA was the major product at pH's below 6. The catalytic activity of a variety of minerals and three meteorites were investigated but none of them except galena catalyzed the oligomerization. ATP was generated from ADP but it was due to the presence of HEPES buffer and not due to the minerals. Meteorites catalyzed the hydrolysis of the pyrophosphate bonds of ATP. The results suggest that oligomers of RNA could have formed in pH 7-9 solutions of alkali metal salts in the presence of montmorillonite clay.
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Shapiro R. Small molecule interactions were central to the origin of life. QUARTERLY REVIEW OF BIOLOGY 2006; 81:105-25. [PMID: 16776061 DOI: 10.1086/506024] [Citation(s) in RCA: 136] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Many scientists believe life began with the spontaneous formation of a replicator. This idea has been supported by "prebiotic" syntheses carried out by chemists using modern apparatus and purified reagents. The probability that such reactions would take place spontaneously on the early Earth is minute. These points are illustrated here by considering the often cited oligomerization of activated RNA components by clay minerals. A more likely alternative for the origin of life is one in which a collection of small organic molecules multiply their numbers through catalyzed reaction cycles, driven by a flow of available free energy. Although a number of possible systems of this type have been discussed, no experimental demonstration has been made. The inclusion of a "driver" reaction, directly coupled to the energy source, may lead to a solution.
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Affiliation(s)
- Robert Shapiro
- Department of Chemistry, New York University New York, New York 10003-6688, USA.
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Hagenbuch P, Kervio E, Hochgesand A, Plutowski U, Richert C. Chemical Primer Extension: Efficiently Determining Single Nucleotides in DNA. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200501794] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Saladino R, Crestini C, Ciambecchini U, Ciciriello F, Costanzo G, Di Mauro E. Synthesis and degradation of nucleobases and nucleic acids by formamide in the presence of montmorillonites. Chembiochem 2005; 5:1558-66. [PMID: 15481029 DOI: 10.1002/cbic.200400119] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We describe the role of formamide, a product of the hydrolysis of hydrogen cyanide, as precursor of several components of nucleic acids under prebiotic conditions. When formamide is heated in the presence of montmorillonites, the efficient one-pot synthesis of purine, adenine, cytosine, and uracil is obtained. Along with these nucleobases, several components of the inosine pathway are obtained: 5-aminoimidazole-4-carboxamide, 5-formamidoimidazole-4-carboxamide and hypoxanthine. This almost complete catalogue of nucleic acid precursors is accompanied by N(9)-formylpurine, which, containing a masked glycosidic bond in its formyl moiety, is a plausible precursor of purine acyclonucleosides. In addition, montmorillonites differentially affect the rate of degradation of nucleobases when embedded in 2'-deoxyoligonucleotides; namely, montmorillonites protect adenine and guanine from the degradative action of formamide, while thymine degradation is enhanced. The oligonucleotide backbone reactivity to formamide is also affected; this shows that the interaction with montmorillonites modifies the rate of abstraction of the Halpha and Hbeta protons on the sugar moieties.
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Affiliation(s)
- Raffaele Saladino
- Dipartimento A.B.A.C., Università della Tuscia, Via San Camillo De Lellis, 01100 Viterbo, Italy.
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Abstract
The demonstration that ribosomal peptide synthesis is a ribozyme-catalyzed reaction makes it almost certain that there was once an RNA World. The central problem for origin-of-life studies, therefore, is to understand how a protein-free RNA World became established on the primitive Earth. We first review the literature on the prebiotic synthesis of the nucleotides, the nonenzymatic synthesis and copying of polynucleotides, and the selection of ribozyme catalysts of a kind that might have facilitated polynucleotide replication. This leads to a brief outline of the Molecular Biologists' Dream, an optimistic scenario for the origin of the RNA World. In the second part of the review we point out the many unresolved problems presented by the Molecular Biologists' Dream. This in turn leads to a discussion of genetic systems simpler than RNA that might have "invented" RNA. Finally, we review studies of prebiotic membrane formation.
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Abstract
Na-montmorillonite prepared from Volclay by the titration method facilitates the self-condensation of ImpA, the 5'-phosphorimidazolide derivative of adenosine. As was shown by AE-HPLC analysis and selective enzymatic hydrolysis of products, oligo(A)s formed in this reaction are 10 monomer units long and contain 67% 3',5'-phosphodiester bonds (Ferris and Ertem, 1992a). Under the same reaction conditions, 5'-phosphorimidazolide derivatives of cytidine, uridine and guanosine also undergo self-condensation producing oligomers containing up to 12-14 monomer units for oligo(C)s to 6 monomer units for oligo(G)s. In oligo(C)s and oligo(U)s, 75-80% of the monomers are linked by 2',5'-phosphodiester bonds. Hexamer and higher oligomers isolated from synthetic oligo(C)s formed by montmorillonite catalysis, which contain both 3',5'- and 2',5'-linkages, serve as catalysts for the non-enzymatic template directed synthesis of oligo(G)s from activated monomer 2-MeImpG, guanosine 5'-phospho-2-methylimidazolide (Ertem and Ferris, 1996). Pentamer and higher oligomers containing exclusively 2',5'-linkages, which were isolated from the synthetic oligo(C)s, also serve as templates and produce oligo(G)s with both 2',5'- and 3',5'-phosphodiester bonds. Kinetic studies on montmorillonite catalyzed elongation rates of oligomers using the computer program SIMFIT demonstrated that the rate constants for the formation of oligo(A)s increased in the order of 2-mer < 3-mer < 4-mer ... < 7-mer (Kawamura and Ferris, 1994). A decameric primer, dA(pdA)8pA bound to montmorillonite was elongated to contain up to 50 monomer units by daily addition of activated monomer ImpA to the reaction mixture (Ferris, Hill and Orgel, 1996). Analysis of dimer fractions formed in the montmorillonite catalyzed reaction of binary and quaternary mixtures of ImpA, ImpC, 2-MeImpG and ImpU suggested that only a limited number of oligomers could have formed on the primitive Earth rather than equal amounts of all possible isomers (Ertem and Ferris, 2000). Formation of phosphodiester bonds between mononucleotides by montmorillonite catalysis is a fascinating discovery, and a significant step forward in efforts to find out how the first RNA-like oligomers might have formed in the course of chemical evolution. However, as has been pointed out in several publications, these systems should be regarded as models rather than a literal representation of prebiotic chemistry (Orgel, 1998; Joyce and Orgel, 1999; Schwartz, 1999).
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Affiliation(s)
- Gözen Ertem
- Georgetown University, Lombardi Cancer Center, 3970 Reservoir Road, NW, Washington, D.C. 20057, USA.
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Kurz M, Göbel K, Hartel C, Göbel MW. Acridine-Labeled Primers as Tools for the Study of Nonenzymatic RNA Oligomerization. Helv Chim Acta 2004. [DOI: 10.1002/hlca.19980810528] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Huang W, Ferris JP. Synthesis of 35-40 mers of RNA oligomers from unblocked monomers. A simple approach to the RNA world. Chem Commun (Camb) 2003:1458-9. [PMID: 12841290 DOI: 10.1039/b303134a] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
RNA oligomers greater than 35-40 mers in length form in one day in the montmorillonite clay-catalyzed reaction of unblocked RNA monomers at 25 degrees C in aqueous solution.
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Affiliation(s)
- Wenhua Huang
- Department of Chemistry and New York Center for Studies on the Origins of Life, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
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Ferris JP. Montmorillonite catalysis of 30-50 mer oligonucleotides: laboratory demonstration of potential steps in the origin of the RNA world. ORIGINS LIFE EVOL B 2002; 32:311-32. [PMID: 12458736 DOI: 10.1023/a:1020543312109] [Citation(s) in RCA: 145] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Elongation of the primer 32pdA(pdA)8pA proceeds by the reaction of the 5'-phosphorimidazolides of adenosine and uridine in the presence of montmorillonite clay. Daily addition of the activated nucleotides for up to 14 days results in the formation of 40-50 mers using the 5'-phosphorimidazolide of adenosine (ImpA) and 25-30 mers using the 5'-phosphorimidazolide of uridine (ImpU). The limitation on the lengths of the chains formed is not due to the inhibitors formed since the same chain lengths were formed using 2-3 times the amount of montmorillonite catalyst. The shorter oligomers formed by the addition of U monomers is not due to its greater rate of decomposition since it was found that both the A and the U adducts decompose at about the same rates. Alkaline phosphatase hydrolysis studies revealed that some of the oligomers are capped at the 5'-end to form, with ImpA, Ap32pdA(pdA)8pA(pA)n. The extent of capping depends on the reaction time and the purine or pyrimidine base in the activated mononucleotide. Hydrolysis with ribonuclease T2 followed by alkaline phosphatase determined the sites of the 3', 5'- and 2', 5'-phosphodiester bonding to the primer. The potential significance of the mineral catalyzed formation of 50 mer oligonucleotides to the origin of life based on RNA (the RNA world scenario) is discussed.
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Affiliation(s)
- James P Ferris
- Department of Chemistry, Rensselaer Polytechnic Institute, Troy, New York, 12180-3590, USA.
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