1
|
Coulon R, Papoušková B, Mohammadi E, Otyepka M, Wunnava S, Šponer J, Šponer JE. Prebiotic Synthesis of 3',5'-Cyclic Adenosine and Guanosine Monophosphates through Carbodiimide-Assisted Cyclization. Chembiochem 2023; 24:e202300510. [PMID: 37747702 DOI: 10.1002/cbic.202300510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/25/2023] [Accepted: 09/25/2023] [Indexed: 09/26/2023]
Abstract
3',5'-Cyclic nucleotides play a fundamental role in modern biochemical processes and have been suggested to have played a central role at the origin of terrestrial life. In this work, we suggest that a formamide-based systems chemistry might account for their availability on the early Earth. In particular, we demonstrate that in a liquid formamide environment at elevated temperatures 3',5'-cyclic nucleotides are obtained in good yield and selectivity upon intramolecular cyclization of 5'-phosphorylated nucleosides in the presence of carbodiimides.
Collapse
Affiliation(s)
- Rémi Coulon
- CATRIN - Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc, Šlechtitelů 27, 77900, Olomouc, Czech Republic
- Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, 17. listopadu 12, 77146, Olomouc, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200, Brno, Czech Republic
| | - Barbora Papoušková
- CATRIN - Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc, Šlechtitelů 27, 77900, Olomouc, Czech Republic
- Department of Analytical Chemistry, Faculty of Science, Palacký University Olomouc, 17. listopadu 12, 77146, Olomouc, Czech Republic
| | - Elmira Mohammadi
- CATRIN - Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc, Šlechtitelů 27, 77900, Olomouc, Czech Republic
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, V6T 1Z1, BC, Canada
| | - Michal Otyepka
- CATRIN - Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc, Šlechtitelů 27, 77900, Olomouc, Czech Republic
- IT4Innovations, VSB - Technical University of Ostrava, 17. listopadu 2172/15, 708 00, Ostrava, Poruba, Czech Republic
| | - Sreekar Wunnava
- Department of Physics, NanoSystems Initiative Munich and Center for Nanoscience, Ludwig-Maximilians-Universität München, Amalienstrasse 54, 80799, Munich, Germany
| | - Jiří Šponer
- CATRIN - Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc, Šlechtitelů 27, 77900, Olomouc, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200, Brno, Czech Republic
| | - Judit E Šponer
- CATRIN - Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc, Šlechtitelů 27, 77900, Olomouc, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200, Brno, Czech Republic
| |
Collapse
|
2
|
Cruz HA, Jiménez EI, Krishnamurthy R. Enhancing Prebiotic Phosphorylation and Modulating the Regioselectivity of Nucleosides with Diamidophosphate†. J Am Chem Soc 2023; 145:23781-23793. [PMID: 37856825 DOI: 10.1021/jacs.3c08539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Among the many prebiotic phosphorylation chemistries investigated, diamidophosphate (DAP) has shown promising potential for nucleoside phosphorylation. Herein, we show that DAP's phosphorylation capability is enhanced significantly (up to 90%) in wet-dry cycles by a range of prebiotically plausible pHs (6-10) and temperatures (up to 80 °C) in the presence of additives such as formamide, cyanamide, urea, guanidine, 2-aminoimidazole, and hydantoin. For ribonucleosides, the main products are the 2',3'-cyclic phosphates along with the corresponding 2'- and 3'-phosphates, while deoxyribonucleosides form 5'- and 3'-phosphates, the ratios of which are affected by cycles and the presence and nature of the additives. A simple change of temperature to 80 °C with additives leads to higher conversion yields (≈80-90%) with an increased level of 5'-phosphorylation (≈40-49%). This demonstration of enhancing and controlling the regioselectivity of DAP-mediated phosphorylation by a range of additives and conditions potentiates transitioning to the search for more efficient catalysts, enabling regiospecific phosphorylations and oligonucleotide formation in the same milieu and setting.
Collapse
Affiliation(s)
- Harold A Cruz
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Eddy I Jiménez
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| |
Collapse
|
3
|
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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 12/06/2022] [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.
Collapse
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
| |
Collapse
|
4
|
Bechtel M, Hümmer E, Trapp O. Selective Phosphorylation of RNA‐ and DNA‐Nucleosides under Prebiotically Plausible Conditions. CHEMSYSTEMSCHEM 2022. [DOI: 10.1002/syst.202200020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Maximilian Bechtel
- Department of Chemistry Ludwig-Maximilians-University Munich Butenandtstr. 5–13 81377 Munich Germany
| | - Eva Hümmer
- Department of Chemistry Ludwig-Maximilians-University Munich Butenandtstr. 5–13 81377 Munich Germany
| | - Oliver Trapp
- Department of Chemistry Ludwig-Maximilians-University Munich Butenandtstr. 5–13 81377 Munich Germany
- Max-Planck-Institute for Astronomy Königstuhl 17 69117 Heidelberg Germany
| |
Collapse
|
5
|
Lozoya-Colinas A, Clifton BE, Grover MA, Hud NV. Urea and Acetamide Rich Solutions Circumvent the Strand Inhibition Problem to Allow Multiple Rounds of DNA and RNA Copying. Chembiochem 2021; 23:e202100495. [PMID: 34797020 DOI: 10.1002/cbic.202100495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 11/18/2021] [Indexed: 11/08/2022]
Abstract
For decades prebiotic chemists have attempted to achieve replication of RNA under prebiotic conditions with only limited success. One of the long-recognized impediments to achieving true replication of a duplex (copying of both strands) is the so-called strand inhibition problem. Specifically, while the two strands of an RNA (or DNA) duplex can be separated by heating, upon cooling the strands of a duplex will reanneal before mononucleotide or oligonucleotide substrates can bind to the individual strands. Here we demonstrate that a class of plausible prebiotic solvents, when coupled with thermal cycling and varying levels of hydration, circumvents the strand inhibition problem, and allows multiple rounds of information transfer from both strands of a duplex (replication). Replication was achieved by simultaneous ligation of oligomers that bind to their templates with the aid of the solvents. The solvents used consisted of concentrated solutions of urea and acetamide in water (UAcW), components that were likely abundant on the early Earth. The UAcW solvent system favors the annealing of shorter strands over the re-annealing of long strands, thereby circumventing strand inhibition. We observed an improvement of DNA and RNA replication yields by a factor of 100× over aqueous buffer. Information transfer in the UAcW solvent system is robust, being achieved for a range of solvent component ratios, various drying conditions, and in the absence or presence of added salts.
Collapse
Affiliation(s)
- Adriana Lozoya-Colinas
- NSF/NASA Center for Chemical Evolution, GA 30332, Atlanta, USA.,School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, GA 30332, Atlanta, USA
| | - Bryce E Clifton
- NSF/NASA Center for Chemical Evolution, GA 30332, Atlanta, USA.,School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, GA 30332, Atlanta, USA
| | - Martha A Grover
- NSF/NASA Center for Chemical Evolution, GA 30332, Atlanta, USA.,School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, GA 30332, Atlanta, USA
| | - Nicholas V Hud
- NSF/NASA Center for Chemical Evolution, GA 30332, Atlanta, USA.,School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, GA 30332, Atlanta, USA
| |
Collapse
|
6
|
Fialho DM, Roche TP, Hud NV. Prebiotic Syntheses of Noncanonical Nucleosides and Nucleotides. Chem Rev 2020; 120:4806-4830. [PMID: 32421316 DOI: 10.1021/acs.chemrev.0c00069] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The origin of nucleotides is a major question in origins-of-life research. Given the central importance of RNA in biology and the influential RNA World hypothesis, a great deal of this research has focused on finding possible prebiotic syntheses of the four canonical nucleotides of coding RNA. However, the use of nucleotides in other roles across the tree of life might be evidence that nucleotides have been used in noncoding roles for even longer than RNA has been used as a genetic polymer. Likewise, it is possible that early life utilized nucleotides other than the extant nucleotides as the monomers of informational polymers. Therefore, finding plausible prebiotic syntheses of potentially ancestral noncanonical nucleotides may be of great importance for understanding the origins and early evolution of life. Experimental investigations into abiotic noncanonical nucleotide synthesis reveal that many noncanonical nucleotides and related glycosides are formed much more easily than the canonical nucleotides. An analysis of the mechanisms by which nucleosides and nucleotides form in the solution phase or in drying-heating reactions from pre-existing sugars and heterocycles suggests that a wide variety of noncanonical nucleotides and related glycosides would have been present on the prebiotic Earth, if any such molecules were present.
Collapse
Affiliation(s)
- David M Fialho
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0440, United States
| | - Tyler P Roche
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0440, United States
| | - Nicholas V Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0440, United States
| |
Collapse
|
7
|
d'Ischia M, Manini P, Moracci M, Saladino R, Ball V, Thissen H, Evans RA, Puzzarini C, Barone V. Astrochemistry and Astrobiology: Materials Sciencein Wonderland? Int J Mol Sci 2019; 20:E4079. [PMID: 31438518 PMCID: PMC6747172 DOI: 10.3390/ijms20174079] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/14/2019] [Accepted: 08/19/2019] [Indexed: 02/04/2023] Open
Abstract
Astrochemistry and astrobiology, the fascinating disciplines that strive to unravel the origin of life, have opened unprecedented and unpredicted vistas into exotic compounds as well as extreme or complex reaction conditions of potential relevance for a broad variety of applications. Representative, and so far little explored sources of inspiration include complex organic systems, such as polycyclic aromatic hydrocarbons (PAHs) and their derivatives; hydrogen cyanide (HCN) and formamide (HCONH2) oligomers and polymers, like aminomalononitrile (AMN)-derived species; and exotic processes, such as solid-state photoreactions on mineral surfaces, phosphorylation by minerals, cold ice irradiation and proton bombardment, and thermal transformations in fumaroles. In addition, meteorites and minerals like forsterite, which dominate dust chemistry in the interstellar medium, may open new avenues for the discovery of innovative catalytic processes and unconventional methodologies. The aim of this review was to offer concise and inspiring, rather than comprehensive, examples of astrochemistry-related materials and systems that may be of relevance in areas such as surface functionalization, nanostructures, and hybrid material design, and for innovative technological solutions. The potential of computational methods to predict new properties from spectroscopic data and to assess plausible reaction pathways on both kinetic and thermodynamic grounds has also been highlighted.
Collapse
Affiliation(s)
- Marco d'Ischia
- Department of Chemical Sciences, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Via Cupa Nuova Cinthia 21, 80126 Naples, Italy.
| | - Paola Manini
- Department of Chemical Sciences, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Via Cupa Nuova Cinthia 21, 80126 Naples, Italy
| | - Marco Moracci
- Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Via Cupa Nuova Cinthia 21, 80126 Naples, Italy
- Institute of Biosciences and BioResources, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy
| | - Raffaele Saladino
- Department of Ecological and Biological Sciences, Via S. Camillo de Lellis, University of Tuscia, 01100 Viterbo, Italy
| | - Vincent Ball
- Institut National de la Santé et de la RechercheMédicale, 11 rue Humann, 67085 Strasbourg Cedex, France
- Faculté de Chirurgie Dentaire, Université de Strasbourg, 1 Place de l'Hôpital, 67000 Strasbourg, France
| | - Helmut Thissen
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Manufacturing, Clayton, VIC 3168, Australia
| | - Richard A Evans
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Manufacturing, Clayton, VIC 3168, Australia
| | - Cristina Puzzarini
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| |
Collapse
|
8
|
Ziegler EW, Kim HJ, Benner SA. Molybdenum(VI)-Catalyzed Rearrangement of Prebiotic Carbohydrates in Formamide, a Candidate Prebiotic Solvent. ASTROBIOLOGY 2018; 18:1159-1170. [PMID: 30204496 DOI: 10.1089/ast.2017.1742] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
It has been four decades since formamide was first suggested to perform roles as a precursor and/or a solvent in prebiotic chemistry. However, little work has sought to integrate formamide into larger prebiotic schemes that might create prebiotic RNA, often proposed to have been the first Darwinian biopolymer. Here, we report that formamide can be used as a solvent to perform the Bílik reaction, which uses molybdenum(VI) oxo species as catalysts at near-neutral pH to rearrange branched carbohydrates to give linear carbohydrates; the branched carbohydrates are produced from formaldehyde (HCHO) in alkaline mixtures containing borate, whereas the linear carbohydrates are the precursors needed for ribonucleosides and ribonucleotides. Under conditions wherein the Bílik reaction does this rearrangement, carbohydrate reaction products do not require stabilization by borate. These results, therefore, connect aqueous and formamide-based processes for the prebiotic formation of RNA components. Based on data from Hadean zircons that show that the mantle of the early Earth was near the fayalite-quartz-magnetite fugacity, molybdenum in its 6+ oxidation state was likely available in the Hadean. Together, these allow us to conjecture a process that delivers ribonucleosides and ribonucleotides from hydrogen cyanide and HCHO from a Hadean atmosphere on a Hadean geosphere, without needing precisely timed transitions from one solvent system to the other.
Collapse
Affiliation(s)
- Eric W Ziegler
- 1 Firebird Biomolecular Sciences , Alachua, Florida
- 2 Department of Chemistry, Florida Institute of Technology , Melbourne, Florida
| | - Hyo-Joong Kim
- 1 Firebird Biomolecular Sciences , Alachua, Florida
- 3 Foundation for Applied Molecular Evolution , Alachua, Florida
| | - Steven A Benner
- 1 Firebird Biomolecular Sciences , Alachua, Florida
- 3 Foundation for Applied Molecular Evolution , Alachua, Florida
| |
Collapse
|
9
|
Chemomimesis and Molecular Darwinism in Action: From Abiotic Generation of Nucleobases to Nucleosides and RNA. Life (Basel) 2018; 8:life8020024. [PMID: 29925796 PMCID: PMC6027154 DOI: 10.3390/life8020024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 06/14/2018] [Accepted: 06/19/2018] [Indexed: 01/26/2023] Open
Abstract
Molecular Darwinian evolution is an intrinsic property of reacting pools of molecules resulting in the adaptation of the system to changing conditions. It has no a priori aim. From the point of view of the origin of life, Darwinian selection behavior, when spontaneously emerging in the ensembles of molecules composing prebiotic pools, initiates subsequent evolution of increasingly complex and innovative chemical information. On the conservation side, it is a posteriori observed that numerous biological processes are based on prebiotically promptly made compounds, as proposed by the concept of Chemomimesis. Molecular Darwinian evolution and Chemomimesis are principles acting in balanced cooperation in the frame of Systems Chemistry. The one-pot synthesis of nucleosides in radical chemistry conditions is possibly a telling example of the operation of these principles. Other indications of similar cases of molecular evolution can be found among biogenic processes.
Collapse
|
10
|
Šponer JE, Szabla R, Góra RW, Saitta AM, Pietrucci F, Saija F, Di Mauro E, Saladino R, Ferus M, Civiš S, Šponer J. Prebiotic synthesis of nucleic acids and their building blocks at the atomic level - merging models and mechanisms from advanced computations and experiments. Phys Chem Chem Phys 2018; 18:20047-66. [PMID: 27136968 DOI: 10.1039/c6cp00670a] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The origin of life on Earth is one of the most fascinating questions of contemporary science. Extensive research in the past decades furnished diverse experimental proposals for the emergence of first informational polymers that could form the basis of the early terrestrial life. Side by side with the experiments, the fast development of modern computational chemistry methods during the last 20 years facilitated the use of in silico modelling tools to complement the experiments. Modern computations can provide unique atomic-level insights into the structural and electronic aspects as well as the energetics of key prebiotic chemical reactions. Many of these insights are not directly obtainable from the experimental techniques and the computations are thus becoming indispensable for proper interpretation of many experiments and for qualified predictions. This review illustrates the synergy between experiment and theory in the origin of life research focusing on the prebiotic synthesis of various nucleic acid building blocks and on the self-assembly of nucleotides leading to the first functional oligonucleotides.
Collapse
Affiliation(s)
- Judit E Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic. and CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Rafał Szabla
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic.
| | - Robert W Góra
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - A Marco Saitta
- Sorbonne Universités, Université Pierre et Marie Curie Paris 6, CNRS, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d'Histoire Naturelle, Institut de Recherche pour le Développement, UMR 7590, F-75005 Paris, France
| | - Fabio Pietrucci
- Sorbonne Universités, Université Pierre et Marie Curie Paris 6, CNRS, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d'Histoire Naturelle, Institut de Recherche pour le Développement, UMR 7590, F-75005 Paris, France
| | - Franz Saija
- CNR-IPCF, Viale Ferdinando Stagno d'Alcontres 37, 98158 Messina, Italy
| | - Ernesto Di Mauro
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", "Sapienza" Università di Roma, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Raffaele Saladino
- Dipartimento di Scienze Ecologiche e Biologiche Università della Tuscia, Via San Camillo De Lellis, 01100 Viterbo, Italy
| | - Martin Ferus
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague 8, Czech Republic
| | - Svatopluk Civiš
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague 8, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic. and CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, CZ-62500 Brno, Czech Republic
| |
Collapse
|
11
|
Adam ZR, Hongo Y, Cleaves HJ, Yi R, Fahrenbach AC, Yoda I, Aono M. Estimating the capacity for production of formamide by radioactive minerals on the prebiotic Earth. Sci Rep 2018; 8:265. [PMID: 29321594 PMCID: PMC5762809 DOI: 10.1038/s41598-017-18483-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/12/2017] [Indexed: 12/11/2022] Open
Abstract
Water creates special problems for prebiotic chemistry, as it is thermodynamically favorable for amide and phosphodiester bonds to hydrolyze. The availability of alternative solvents with more favorable properties for the formation of prebiotic molecules on the early Earth may have helped bypass this so-called "water paradox". Formamide (FA) is one such solvent, and can serve as a nucleobase precursor, but it is difficult to envision how FA could have been generated in large quantities or accumulated in terrestrial surface environments. We report here the conversion of aqueous acetonitrile (ACN) via hydrogen cyanide (HCN) as an intermediate into FA by γ-irradiation under conditions mimicking exposure to radioactive minerals. We estimate that a radioactive placer deposit could produce 0.1‒0.8 mol FA km-2 year-1. A uraninite fission zone comparable to the Oklo reactors in Gabon can produce 0.1‒1 mol m-2 year-1, orders of magnitude greater than other scenarios of FA production or delivery for which reaching sizeable concentrations of FA are problematic. Radioactive mineral deposits may be favorable settings for prebiotic compound formation through emergent geologic processes and FA-mediated organic chemistry.
Collapse
Affiliation(s)
- Zachary R Adam
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA.
- Blue Marble Space Institute of Science, Seattle, WA, USA.
| | - Yayoi Hongo
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - H James Cleaves
- Blue Marble Space Institute of Science, Seattle, WA, USA
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Institute for Advanced Study, Princeton, NJ, 08540, USA
- Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Ruiqin Yi
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | | | - Isao Yoda
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - Masashi Aono
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Faculty of Environment and Information Studies, Keio University, Kanagawa, Japan
| |
Collapse
|
12
|
Saladino R, Šponer JE, Šponer J, Di Mauro E. Rewarming the Primordial Soup: Revisitations and Rediscoveries in Prebiotic Chemistry. Chembiochem 2018; 19:22-25. [PMID: 29164768 PMCID: PMC5768021 DOI: 10.1002/cbic.201700534] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Indexed: 01/11/2023]
Abstract
A short history of Campbell's primordial soup: In this essay we try to disclose some of the historical connections between the studies that have contributed to our current understanding of the emergence of catalytic RNA molecules and their components from an inanimate matter.
Collapse
Affiliation(s)
- Raffaele Saladino
- Dipartimento di Scienze Ecologiche e BiologicheUniversità della TusciaVia San Camillo De Lellis01100ViterboItaly
| | - Judit E. Šponer
- Institute of Biophysics of the Czech Academy of SciencesKrálovopolská 13561265BrnoCzech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of SciencesKrálovopolská 13561265BrnoCzech Republic
| | - Ernesto Di Mauro
- Dipartimento di Scienze Ecologiche e BiologicheUniversità della TusciaVia San Camillo De Lellis01100ViterboItaly
| |
Collapse
|
13
|
Fernández-García C, Coggins AJ, Powner MW. A Chemist's Perspective on the Role of Phosphorus at the Origins of Life. Life (Basel) 2017; 7:E31. [PMID: 28703763 PMCID: PMC5617956 DOI: 10.3390/life7030031] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 07/06/2017] [Accepted: 07/11/2017] [Indexed: 11/17/2022] Open
Abstract
The central role that phosphates play in biological systems, suggests they also played an important role in the emergence of life on Earth. In recent years, numerous important advances have been made towards understanding the influence that phosphates may have had on prebiotic chemistry, and here, we highlight two important aspects of prebiotic phosphate chemistry. Firstly, we discuss prebiotic phosphorylation reactions; we specifically contrast aqueous electrophilic phosphorylation, and aqueous nucleophilic phosphorylation strategies, with dry-state phosphorylations that are mediated by dissociative phosphoryl-transfer. Secondly, we discuss the non-structural roles that phosphates can play in prebiotic chemistry. Here, we focus on the mechanisms by which phosphate has guided prebiotic reactivity through catalysis or buffering effects, to facilitating selective transformations in neutral water. Several prebiotic routes towards the synthesis of nucleotides, amino acids, and core metabolites, that have been facilitated or controlled by phosphate acting as a general acid-base catalyst, pH buffer, or a chemical buffer, are outlined. These facile and subtle mechanisms for incorporation and exploitation of phosphates to orchestrate selective, robust prebiotic chemistry, coupled with the central and universally conserved roles of phosphates in biochemistry, provide an increasingly clear message that understanding phosphate chemistry will be a key element in elucidating the origins of life on Earth.
Collapse
|
14
|
Šponer JE, Šponer J, Nováková O, Brabec V, Šedo O, Zdráhal Z, Costanzo G, Pino S, Saladino R, Di Mauro E. Emergence of the First Catalytic Oligonucleotides in a Formamide-Based Origin Scenario. Chemistry 2016; 22:3572-86. [PMID: 26807661 DOI: 10.1002/chem.201503906] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Indexed: 02/02/2023]
Abstract
50 years after the historical Miller-Urey experiment, the formamide-based scenario is perhaps the most powerful concurrent hypothesis for the origin of life on our planet besides the traditional HCN-based concept. The information accumulated during the last 15 years in this topic is astonishingly growing and nowadays the formamide-based model represents one of the most complete and coherent pathways leading from simple prebiotic precursors up to the first catalytically active RNA molecules. In this work, we overview the major events of this long pathway that have emerged from recent experimental and theoretical studies, mainly concentrating on the mechanistic, methodological, and structural aspects of this research.
Collapse
Affiliation(s)
- Judit E Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic. .,CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 62500, Brno, Czech Republic.
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic.,CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 62500, Brno, Czech Republic
| | - Olga Nováková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic
| | - Viktor Brabec
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic
| | - Ondrej Šedo
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 62500, Brno, Czech Republic
| | - Zbyněk Zdráhal
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 62500, Brno, Czech Republic
| | - Giovanna Costanzo
- Istituto di Biologia e Patologia Molecolari, CNR, P.le Aldo Moro, 5, Rome, 00185, Italy
| | - Samanta Pino
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", "Sapienza" Università di Roma, Piazzale Aldo Moro, 5, Rome, 00185, Italy
| | - Raffaele Saladino
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia, Via San Camillo De Lellis, 01100, Viterbo, Italy
| | - Ernesto Di Mauro
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", "Sapienza" Università di Roma, Piazzale Aldo Moro, 5, Rome, 00185, Italy
| |
Collapse
|
15
|
Furukawa Y, Kim HJ, Hutter D, Benner SA. Abiotic regioselective phosphorylation of adenosine with borate in formamide. ASTROBIOLOGY 2015; 15:259-67. [PMID: 25826074 DOI: 10.1089/ast.2014.1209] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Nearly 40 years ago, Schoffstall and his coworkers used formamide as a solvent to permit the phosphorylation of nucleosides by inorganic phosphate to give nucleoside phosphates, which (due to their thermodynamic instability with respect to hydrolysis) cannot be easily created in water by an analogous phosphorylation (the "water problem" in prebiotic chemistry). More recently, we showed that borate could stabilize certain carbohydrates against degradation (the "asphalt problem"). Here, we combine the two concepts to show that borate can work in formamide to guide the reactivity of nucleosides under conditions where they are phosphorylated. Specifically, reaction of adenosine in formamide with inorganic phosphate and pyrophosphate in the presence of borate gives adenosine-5'-phosphate as the only detectable phosphorylated product, with formylation (as opposed to hydrolysis) being the competing reaction.
Collapse
Affiliation(s)
- Yoshihiro Furukawa
- 1 Department of Earth Science, Graduate School of Science, Tohoku University , Sendai, Japan
| | | | | | | |
Collapse
|
16
|
Cafferty BJ, Hud NV. Abiotic synthesis of RNA in water: a common goal of prebiotic chemistry and bottom-up synthetic biology. Curr Opin Chem Biol 2014; 22:146-57. [PMID: 25438801 DOI: 10.1016/j.cbpa.2014.09.015] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 09/13/2014] [Indexed: 01/01/2023]
Abstract
For more than half a century chemists have searched for a plausible prebiotic synthesis of RNA. The initial advances of the 1960s and 1970s were followed by decades of measured progress and a growing pessimism about overcoming remaining challenges. Fortunately, the past few years have provided a number of important advances, including new abiotic routes for the synthesis of nucleobases, nucleosides, and nucleotides. Recent discoveries also provide additional support for the hypothesis that RNA is the product of evolution, being preceded by ancestral genetic polymers, or pre-RNAs, that are synthesized more easily than RNA. In some cases, parallel searches for plausible prebiotic routes to RNA and pre-RNAs have provided more than one experimentally verified synthesis of RNA substructures and possible predecessors. Just as the synthesis of a contemporary biological molecule cannot be understood without knowledge of cellular metabolism, it is likely that an integrated approach that takes into account both plausible prebiotic reactions and plausible prebiotic environments will ultimately provide the most satisfactory and unifying chemical scenarios for the origin of nucleic acids. In this context, recent advances towards the abiotic synthesis of RNA and candidates for pre-RNAs are beginning to suggest that some molecules (e.g., urea) were multi-faceted contributors to the origin of nucleic acids, and the origin of life.
Collapse
Affiliation(s)
- Brian J Cafferty
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Nicholas V Hud
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| |
Collapse
|
17
|
Hud NV, Cafferty BJ, Krishnamurthy R, Williams LD. The origin of RNA and "my grandfather's axe". ACTA ACUST UNITED AC 2013; 20:466-74. [PMID: 23601635 DOI: 10.1016/j.chembiol.2013.03.012] [Citation(s) in RCA: 150] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 03/20/2013] [Accepted: 03/22/2013] [Indexed: 12/27/2022]
Abstract
The origin of RNA is one of the most formidable problems facing prebiotic chemists. We consider RNA as a product of evolution, as opposed to the more conventional view of RNA as originally being the product of abiotic processes. We have come to accept that life's informational polymers have changed in chemical structure since their emergence, which presents a quandary similar to the paradox of "My Grandfather's Axe". Here, we discuss reasons why all contemporary components of RNA--the nucleobases, ribose, and phosphate--are not likely the original components of the first informational polymer(s) of life. We also evaluate three distinct models put forth as pathways for how the earliest informational polymers might have assembled. We see the quest to uncover the ancestors of RNA as an exciting scientific journey, one that is already providing additional chemical constraints on the origin of life and one that has the potential to produce self-assembling materials, novel catalysis, and bioactive compounds.
Collapse
Affiliation(s)
- Nicholas V Hud
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | | | | | | |
Collapse
|
18
|
Neveu M, Kim HJ, Benner SA. The "strong" RNA world hypothesis: fifty years old. ASTROBIOLOGY 2013; 13:391-403. [PMID: 23551238 DOI: 10.1089/ast.2012.0868] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
This year marks the 50(th) anniversary of a proposal by Alex Rich that RNA, as a single biopolymer acting in two capacities, might have supported both genetics and catalysis at the origin of life. We review here both published and previously unreported experimental data that provide new perspectives on this old proposal. The new data include evidence that, in the presence of borate, small amounts of carbohydrates can fix large amounts of formaldehyde that are expected in an environment rich in carbon dioxide. Further, we consider other species, including arsenate, arsenite, phosphite, and germanate, that might replace phosphate as linkers in genetic biopolymers. While linkages involving these oxyanions are judged to be too unstable to support genetics on Earth, we consider the possibility that they might do so in colder semi-aqueous environments more exotic than those found on Earth, where cosolvents such as ammonia might prevent freezing at temperatures well below 273 K. These include the ammonia-water environments that are possibly present at low temperatures beneath the surface of Titan, Saturn's largest moon.
Collapse
Affiliation(s)
- Marc Neveu
- Foundation for Applied Molecular Evolution, Gainesville, Florida 32601, USA
| | | | | |
Collapse
|
19
|
Benner SA, Kim HJ, Carrigan MA. Asphalt, water, and the prebiotic synthesis of ribose, ribonucleosides, and RNA. Acc Chem Res 2012; 45:2025-34. [PMID: 22455515 DOI: 10.1021/ar200332w] [Citation(s) in RCA: 157] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
RNA has been called a "prebiotic chemist's nightmare" because of its combination of large size, carbohydrate building blocks, bonds that are thermodynamically unstable in water, and overall intrinsic instability. However, a discontinuous synthesis model is well-supported by experimental work that might produce RNA from atmospheric CO(2), H(2)O, and N(2). For example, electrical discharge in such atmospheres gives formaldehyde (HCHO) in large amounts and glycolaldehyde (HOCH(2)CHO) in small amounts. When rained into alkaline aquifers generated by serpentinizing rocks, these substances were undoubtedly converted to carbohydrates including ribose. Likewise, atmospherically generated HCN was undoubtedly converted in these aquifers to formamide and ammonium formate, precursors for RNA nucleobases. Finally, high reduction potentials maintained by mantle-derived rocks and minerals would allow phosphite to be present in equilibrium with phosphate, mobilizing otherwise insoluble phosphorus for the prebiotic synthesis of phosphite and phosphate esters after oxidation. So why does the community not view this discontinuous synthesis model as compelling evidence for the RNA-first hypothesis for the origin of life? In part, the model is deficient because no experiments have joined together those steps without human intervention. Further, many steps in the model have problems. Some are successful only if reactive compounds are presented in a specific order in large amounts. Failing controlled addition, the result produces complex mixtures that are inauspicious precursors for biology, a situation described as the "asphalt problem". Many bonds in RNA are thermodynamically unstable with respect to hydrolysis in water, creating a "water problem". Finally, some bonds in RNA appear to be "impossible" to form under any conditions considered plausible for early Earth. To get a community-acceptable "RNA first" model for the origin of life, the discontinuous synthesis model must be developed. In particular, the model must be refined so that it yields oligomeric RNA from CO(2), H(2)O, and N(2) without human intervention. This Account describes our efforts in this direction. Our hypothesis centers on a geological model that synthesizes RNA in a prebiotic intermountain dry valley (not in a marine environment). This valley receives high pH run-off from a watershed rich in serpentinizing olivines and eroding borate minerals. The runoff contains borate-stabilized carbohydrates, formamide, and ammonium formate. As atmospheric CO(2) dissolves in the subaerial aquifer, the pH of the aquifer is lowered. In the desert valley, evaporation of water, a solvent with a nucleophilic "background reactivity", leaves behind formamide, a solvent with an electrophilic "background reactivity". As a result, nucleobases, formylated nucleobases, and formylated carbohydrates, including formylated ribose, can form. Well-known chemistry transforms these structures into nucleosides, nucleotides, and partially formylated oligomeric RNA.
Collapse
Affiliation(s)
- Steven A. Benner
- Foundation for Applied Molecular Evolution, Gainesville, Florida 32604, United States
| | - Hyo-Joong Kim
- Foundation for Applied Molecular Evolution, Gainesville, Florida 32604, United States
| | - Matthew A. Carrigan
- Foundation for Applied Molecular Evolution, Gainesville, Florida 32604, United States
| |
Collapse
|
20
|
Saladino R, Botta G, Pino S, Costanzo G, Di Mauro E. Genetics first or metabolism first? The formamide clue. Chem Soc Rev 2012; 41:5526-65. [PMID: 22684046 DOI: 10.1039/c2cs35066a] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Life is made of the intimate interaction of metabolism and genetics, both built around the chemistry of the most common elements of the Universe (hydrogen, oxygen, nitrogen, and carbon). The transmissible interaction of metabolic and genetic cycles results in the hypercycles of organization and de-organization of chemical information, of living and non-living. The origin-of-life quest has long been split into several attitudes exemplified by the aphorisms "genetics-first" or "metabolism-first". Recently, the opposition between these approaches has been solved by more unitary theoretical and experimental frames taking into account energetic, evolutionary, proto-metabolic and environmental aspects. Nevertheless, a unitary and simple chemical frame is still needed that could afford both the precursors of the synthetic pathways eventually leading to RNA and to the key components of the central metabolic cycles, possibly connected with the synthesis of fatty acids. In order to approach the problem of the origin of life it is therefore reasonable to start from the assumption that both metabolism and genetics had a common origin, shared a common chemical frame, and were embedded under physical-chemical conditions favourable for the onset of both. The singleness of such a prebiotically productive chemical process would partake of Darwinian advantages over more complex fragmentary chemical systems. The prebiotic chemistry of formamide affords in a single and simple physical-chemical frame nucleic bases, acyclonucleosides, nucleotides, biogenic carboxylic acids, sugars, amino sugars, amino acids and condensing agents. Thus, we suggest the possibility that formamide could have jointly provided the main components for the onset of both (pre)genetic and (pre)metabolic processes. As a note of caution, we discuss the fact that these observations only indicate possible solutions at the level of organic substrates, not at the systemic chemical level.
Collapse
Affiliation(s)
- Raffaele Saladino
- Dipartimento di Agrobiologia ed Agrochimica, Università della Tuscia, Via San Camillo De Lellis, 01100 Viterbo, Italy.
| | | | | | | | | |
Collapse
|
21
|
Saladino R, Botta G, Pino S, Costanzo G, Di Mauro E. From the one-carbon amide formamide to RNA all the steps are prebiotically possible. Biochimie 2012; 94:1451-6. [PMID: 22738728 DOI: 10.1016/j.biochi.2012.02.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 02/16/2012] [Indexed: 01/07/2023]
Abstract
Formamide provides the raw material and the reaction leads connecting hydrogen cyanide HCN chemistry with higher complexity molecular structures. Formamide is liquid between 4 and 210 °C and, upon heating in the presence of one of several catalysts, affords nucleic bases, acyclonucleosides, carboxylic acids and aminoacids. In formamide in the presence of a source of phosphate, nucleosides are non-fastidiously phosphorylated in every position of the sugar residue, also yielding cyclic nucleotides. Guanine 3',5' cyclic nucleotide monophosphates polymerize to oligonucleotides, up to 30 nucleotides long. Adenine 3',5' cyclic nucleotide monophosphate reacts similarly but less efficiently. Preformed oligonucleotides may undergo terminal ligation in the absence of enzymes, thus allowing the formation of abiotically obtained long RNA chains.
Collapse
Affiliation(s)
- Raffaele Saladino
- Dipartimento di Agrobiologia ed Agrochimica, Università della Tuscia, Via San Camillo De Lellis, 01100 Viterbo, Italy
| | | | | | | | | |
Collapse
|
22
|
Pino S, Costanzo G, Giorgi A, Di Mauro E. Sequence complementarity-driven nonenzymatic ligation of RNA. Biochemistry 2011; 50:2994-3003. [PMID: 21361363 DOI: 10.1021/bi101981z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report two reactions of RNA G:C sequences occurring nonenzymatically in water in the absence of any added cofactor or metal ion: (a) sequence complementarity-driven terminal ligation and (b) complementary sequence adaptor-driven multiple tandemization. The two abiotic reactions increase the chemical complexity of the resulting pool of RNA molecules and change the Shannon information of the initial population of sequences.
Collapse
Affiliation(s)
- Samanta Pino
- Dipartimento di Biologia e Biotecnologie Charles Darwin, Sapienza Università di Roma, P.le Aldo Moro, 5, Rome 00185, Italy
| | | | | | | |
Collapse
|
23
|
Ciciriello F, Costanzo G, Crestini C, Saladino R, Di Mauro E. Origin of informational polymers and the search for non-terran life: protection of the polymeric state of DNA by phosphate minerals. ASTROBIOLOGY 2007; 7:616-30. [PMID: 17723093 DOI: 10.1089/ast.2006.0044] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
An in-depth analysis of the effects exerted on the DNA backbone by 25 crystal phosphate minerals is reported. Degradation of DNA oligomers was performed with two different reactions: Hydrolysis following Nucleophilic Degradation (HND), initiated by the nucleophilic addition of formamide on both purine and pyrimidine nucleobases, and Hydrolysis following Nucleophilic Substitution (HNS) carried on by water and starting with the removal of a nondegraded base. A complete panel of effects on the phosphoester bonds, from protection to enhanced instability to absence of interference, is described. These effects differ in the different degradation pathways and in different physical-chemical conditions. The relationship between the hardness of the mineral and its protective ability is discussed. In addition to its interest per se, this study was prompted by the observed catalytic abilities of soluble and mineral phosphates (Saladino et al., 2006c) on the synthetic reactions by formamide. The relevance of these observations in the search for nonterran life is discussed.
Collapse
Affiliation(s)
- Fabiana Ciciriello
- Dipartimento di Genetica e Biologia Molecolare, Università La Sapienza di Roma, Piazzale Aldo Moro, Rome, Italy
| | | | | | | | | |
Collapse
|
24
|
Costanzo G, Saladino R, Crestini C, Ciciriello F, Di Mauro E. Nucleoside phosphorylation by phosphate minerals. J Biol Chem 2007; 282:16729-35. [PMID: 17412692 DOI: 10.1074/jbc.m611346200] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the presence of formamide, crystal phosphate minerals may act as phosphate donors to nucleosides, yielding both 5'- and, to a lesser extent, 3'-phosphorylated forms. With the mineral Libethenite the formation of 5'-AMP can be as high as 6% of the adenosine input and last for at least 10(3) h. At high concentrations, soluble non-mineral phosphate donors (KH(2)PO(4) or 5'-CMP) afford 2'- and 2':3'-cyclic AMP in addition to 5'-and 3'-AMP. The phosphate minerals analyzed were Herderite Ca[BePO(4)F], Hureaulite Mn(2+)(5)(PO(3)(OH)(2)(PO(4))(2)(H(2)O)(4), Libethenite Cu(2+)(2)(PO(4))(OH), Pyromorphite Pb(5)(PO(4))(3)Cl, Turquoise Cu(2+)Al(6)(PO(4))(4)(OH)(8)(H(2)O)(4), Fluorapatite Ca(5)(PO(4))(3)F, Hydroxylapatite Ca(5)(PO(4))(3)OH, Vivianite Fe(2+)(3)(PO(4))(2)(H(2)O)(8), Cornetite Cu(2+)(3)(PO(4))(OH)(3), Pseudomalachite Cu(2+)(5)(PO(4))(2)(OH)(4), Reichenbachite Cu(2+)(5)(PO(4))(2)(OH)(4), and Ludjibaite Cu(2+)(5)(PO(4))(2)(OH)(4)). Based on their behavior in the formamide-driven nucleoside phosphorylation reaction, these minerals can be characterized as: 1) inactive, 2) low level phosphorylating agents, or 3) active phosphorylating agents. Instances were detected (Libethenite and Hydroxylapatite) in which phosphorylation occurs on the mineral surface, followed by release of the phosphorylated compounds. Libethenite and Cornetite markedly protect the beta-glycosidic bond. Thus, activated nucleic monomers can form in a liquid non-aqueous environment in conditions compatible with the thermodynamics of polymerization, providing a solution to the standard-state Gibbs free energy change (DeltaG degrees ') problem, the major obstacle for polymerizations in the liquid phase in plausible prebiotic scenarios.
Collapse
Affiliation(s)
- Giovanna Costanzo
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Pizalle Aldo Moro, 5, 00185 Rome, Italy
| | | | | | | | | |
Collapse
|
25
|
Saladino R, Crestini C, Neri V, Ciciriello F, Costanzo G, Di Mauro E. Origin of informational polymers: The concurrent roles of formamide and phosphates. Chembiochem 2007; 7:1707-14. [PMID: 17051657 DOI: 10.1002/cbic.200600139] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Formamide chemistry provides a unitary system by gathering all of the precursors needed to synthesise pregenetic informational polymers in a single milieu. This is not observed with HCN chemistry. With common catalysts, formamide affords all of the precursor nucleobases, photochemically condenses into acyclonucleosides, favours transphosphorylation and enhances micellar aggregation of surfactants. Also, formamide provides a set of physicochemical conditions that thermodynamically favour the polymeric state of nucleotides over the monomers. In the origin-of-informational-polymers scenario, formamide acts in every step, the least characterised being the set of its reactions with phosphates. On this matter, we report two complementary sets of results: 1) the synthesis of prebiotic precursors from formamide, which are catalysed by soluble and mineral phosphates-we observed the formation of rich mixtures that include uracil, 9H-purine, cytosine, dihydrouracil, hypoxanthine, adenosine, urea, parabanic acid, the amino acid N-formylglycine and the peptide-condensing agent carbodiimide; and 2) the protection of ribo- and deoxyribophosphoester bonds by phosphates. The relevance of these effects with respect to the origin of informational polymers is discussed.
Collapse
Affiliation(s)
- Raffaele Saladino
- Dipartimento A.B.A.C., Università della Tuscia, Via San Camillo De Lellis, 01100 Viterbo, Italy.
| | | | | | | | | | | |
Collapse
|
26
|
Saladino R, Crestini C, Ciciriello F, Costanzo G, Di Mauro E. About a formamide-based origin of informational polymers: syntheses of nucleobases and favourable thermodynamic niches for early polymers. ORIGINS LIFE EVOL B 2006; 36:523-31. [PMID: 17136429 DOI: 10.1007/s11084-006-9053-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Formamide NH(2)CHO chemistry provides a unitary frame into which several pieces of the origin-of-life puzzle may be adjusted. Synthetic processes were uncovered which, starting from formamide and prebiotically easily available common catalysts, yield all the necessary nucleic bases precursors, including acyclonucleosides. Formamide allows phosphorylations and trans-phosphorylations, favours the micellar aggregation of surfactants and, most importantly, determines conditions in which the formation of nucleic polymers is thermodynamically favoured. In the detected conditions, the phosphoester bonds are more stable in the polymeric than in the monomeric form, thus allowing formation and survival of informational nucleic polymers.
Collapse
Affiliation(s)
- Raffaele Saladino
- Dipartimento A.B.A.C., Università della Tuscia, Via San Camillo De Lellis, Viterbo 01100, Italy.
| | | | | | | | | |
Collapse
|
27
|
Schulze-Makuch D, Irwin LN. The prospect of alien life in exotic forms on other worlds. Naturwissenschaften 2006; 93:155-72. [PMID: 16525788 DOI: 10.1007/s00114-005-0078-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2005] [Accepted: 12/12/2005] [Indexed: 11/29/2022]
Abstract
The nature of life on Earth provides a singular example of carbon-based, water-borne, photosynthesis-driven biology. Within our understanding of chemistry and the physical laws governing the universe, however, lies the possibility that alien life could be based on different chemistries, solvents, and energy sources from the one example provided by Terran biology. In this paper, we review some of these possibilities. Silanes may be used as functional analogs to carbon molecules in environments very different from Earth; solvents other than water may be compatible for life-supporting processes, especially in cold environments, and a variety of energy sources may be utilized, some of which have no Terran analog. We provide a detailed discussion of two possible habitats for alien life which are generally not considered as such: the lower cloud level of the Venusian atmosphere and Titan's surface environment.
Collapse
Affiliation(s)
- Dirk Schulze-Makuch
- Department of Geology, Washington State University, Pullman, WA 99164-2812, USA.
| | | |
Collapse
|
28
|
Abstract
A review of organic chemistry suggests that life, a chemical system capable of Darwinian evolution, may exist in a wide range of environments. These include non-aqueous solvent systems at low temperatures, or even supercritical dihydrogen-helium mixtures. The only absolute requirements may be a thermodynamic disequilibrium and temperatures consistent with chemical bonding. A solvent system, availability of elements such as carbon, hydrogen, oxygen and nitrogen, certain thermodynamic features of metabolic pathways, and the opportunity for isolation, may also define habitable environments. If we constrain life to water, more specific criteria can be proposed, including soluble metabolites, genetic materials with repeating charges, and a well defined temperature range.
Collapse
Affiliation(s)
- Steven A Benner
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA.
| | | | | |
Collapse
|