1
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2021-2022. MASS SPECTROMETRY REVIEWS 2024. [PMID: 38925550 DOI: 10.1002/mas.21873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/05/2024] [Accepted: 02/12/2024] [Indexed: 06/28/2024]
Abstract
The use of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry for the analysis of carbohydrates and glycoconjugates is a well-established technique and this review is the 12th update of the original article published in 1999 and brings coverage of the literature to the end of 2022. As with previous review, this review also includes a few papers that describe methods appropriate to analysis by MALDI, such as sample preparation, even though the ionization method is not MALDI. The review follows the same format as previous reviews. It is divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of computer software for structural identification. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other general areas such as medicine, industrial processes, natural products and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. MALDI is still an ideal technique for carbohydrate analysis, particularly in its ability to produce single ions from each analyte and advancements in the technique and range of applications show little sign of diminishing.
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2
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Bizzarri BM, Fanelli A, Ciprini S, Giorgi A, De Angelis M, Fioravanti R, Nencioni L, Saladino R. Multicomponent Synthesis of Diaminopurine and Guanine PNA's Analogues Active against Influenza A Virus from Prebiotic Compounds. ACS OMEGA 2022; 7:45253-45264. [PMID: 36530301 PMCID: PMC9753540 DOI: 10.1021/acsomega.2c05754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/24/2022] [Indexed: 06/17/2023]
Abstract
Peptide nucleic acids (PNAs) play a key role in prebiotic chemistry as a chimera between RNA and proteins. We developed an alternative synthesis of bioactive PNA's diaminopurine and guanine analogues from prebiotic compounds, such as aminomalononitrile (AMN), urea, and guanidine, using a two-step multicomponent microwave-assisted and solvent-free approach in the presence of selected amino acids. The novel derivatives showed selective inhibitory activity against influenza virus A/Puerto Rico/8/34 H1N1 encompassing the range of nanomolar activity. Derivatives decorated with the tyrosine residue showed the highest inhibitory activity against the virus.
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Affiliation(s)
- Bruno Mattia Bizzarri
- Department
of Biological and Ecological Sciences, University
of Tuscia, Viterbo 01100, Italy
| | - Angelica Fanelli
- Department
of Biological and Ecological Sciences, University
of Tuscia, Viterbo 01100, Italy
| | - Stefania Ciprini
- Department
of Biological and Ecological Sciences, University
of Tuscia, Viterbo 01100, Italy
| | - Alessandra Giorgi
- Department
of Biological and Ecological Sciences, University
of Tuscia, Viterbo 01100, Italy
| | - Marta De Angelis
- Department
of Public Health and Infectious Diseases, Laboratory Affiliated to
Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Rome 00185, Italy
| | - Raoul Fioravanti
- Department
of Public Health and Infectious Diseases, Laboratory Affiliated to
Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Rome 00185, Italy
| | - Lucia Nencioni
- Department
of Public Health and Infectious Diseases, Laboratory Affiliated to
Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Rome 00185, Italy
| | - Raffaele Saladino
- Department
of Biological and Ecological Sciences, University
of Tuscia, Viterbo 01100, Italy
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3
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Pastorek A, Clark VHJ, Yurchenko SN, Ferus M, Civiš S. New physical insights: Formamide discharge decomposition and the role of fragments in the formation of large biomolecules. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 278:121322. [PMID: 35537261 DOI: 10.1016/j.saa.2022.121322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 04/21/2022] [Accepted: 04/25/2022] [Indexed: 06/14/2023]
Abstract
In this work we present a time-resolved FTIR spectroscopic study on kinetics of atomic and molecular species, specifically CO, CN radical, N2, HCN and CO2 generated in a glow discharge of formamide-nitrogen-water mixture in a helium buffer gas. Radicals such as NH, CH and OH have been proven to be fundamental stones of subsequent chemical reactions having a crucial role in a prebiotic synthesis of large organic molecules. This work contains three main goals. Firstly, we present our time-resolved spectra of formamide decomposition products and discuss the mechanism of collisional excitations between specific species. Secondly, according to our time resolution, we demonstrate and explain the band shape of CO's first overtone and the energy transfer between excited nitrogen and CO, present in our spectra. Lastly, we present theoretical results for the non-LTE modelling of the spectra using bi-temperature approach and a 1D harmonic Franck-Condon approach for the multi-molecule spectra of the formamide decomposition process in the 1800-5600 cm-1 spectral range.
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Affiliation(s)
- Adam Pastorek
- J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 2155/3, 18200 Prague 8, Czech Republic; Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Břehová 78/7, 11519 Prague 1, Czech Republic
| | - Victoria H J Clark
- Faculty of Mathematics and Physical Sciences, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Sergei N Yurchenko
- Faculty of Mathematics and Physical Sciences, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Martin Ferus
- J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 2155/3, 18200 Prague 8, Czech Republic
| | - Svatopluk Civiš
- J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 2155/3, 18200 Prague 8, Czech Republic.
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4
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Prosdocimi F, de Farias ST, José MV. Prebiotic chemical refugia: multifaceted scenario for the formation of biomolecules in primitive Earth. Theory Biosci 2022; 141:339-347. [PMID: 36042123 DOI: 10.1007/s12064-022-00377-7] [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: 03/11/2020] [Accepted: 08/17/2022] [Indexed: 11/25/2022]
Abstract
The origin of life was a cosmic event happened on primitive Earth. A critical problem to better understand the origins of life in Earth is the search for chemical scenarios on which the basic building blocks of biological molecules could be produced. Classic works in pre-biotic chemistry frequently considered early Earth as an homogeneous atmosphere constituted by chemical elements such as methane (CH4), ammonia (NH3), water (H2O), hydrogen (H2) and hydrogen sulfide (H2S). Under that scenario, Stanley Miller was capable to produce amino acids and solved the question about the abiotic origin of proteins. Conversely, the origin of nucleic acids has tricked scientists for decades once nucleotides are complex, though necessary molecules to allow the existence of life. Here we review possible chemical scenarios that allowed not only the formation of nucleotides but also other significant biomolecules. We aim to provide a theoretical solution for the origin of biomolecules at specific sites named "Prebiotic Chemical Refugia." Prebiotic chemical refugium should therefore be understood as a geographic site in prebiotic Earth on which certain chemical elements were accumulated in higher proportion than expected, facilitating the production of basic building blocks for biomolecules. This higher proportion should not be understood as static, but dynamic; once the physicochemical conditions of our planet changed periodically. These different concentration of elements, together with geochemical and astronomical changes along days, synodic months and years provided somewhat periodic changes in temperature, pressure, electromagnetic fields, and conditions of humidity, among other features. Recent and classic works suggesting most likely prebiotic refugia on which the main building blocks for biological molecules might be accumulated are reviewed and discussed.
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Affiliation(s)
- Francisco Prosdocimi
- Laboratório de Biologia Teórica E de Sistemas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal Do Rio de Janeiro, 21.941-902, Rio de Janeiro, Brazil. .,Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, CDMX, Mexico.
| | - Sávio Torres de Farias
- Laboratório de Genética Evolutiva Paulo Leminsk, Departamento de Biologia Molecular, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil
| | - Marco V José
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, CDMX, Mexico.
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5
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Evolution of Realistic Organic Mixtures for the Origins of Life through Wet–Dry Cycling. SCI 2022. [DOI: 10.3390/sci4020022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
One of the challenges in understanding chemical evolution is the large number of starting organics and environments that were plausible on early Earth. Starting with realistic organic mixtures and using chemical analyses that are not biologically biased, understanding the interplay between organic composition and environment can be approached using statistical analysis. In this work, a mixture of 73 organics was cycled through dehydrating conditions five times, considering environmental parameters of pH, salinity, and rehydration solution. Products were analyzed by HPLC, amide and ester assays, and phosphatase and esterase assays. While all environmental factors were found to influence chemical evolution, salinity was found to play a large role in the evolution of these mixtures, with samples diverging at very high sea salt concentrations. This framework should be expanded and formalized to improve our understanding of abiogenesis.
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6
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Bizzarri BM, Fanelli A, Botta L, De Angelis M, Palamara AT, Nencioni L, Saladino R. Aminomalononitrile inspired prebiotic chemistry as a novel multicomponent tool for the synthesis of imidazole and purine derivatives with anti-influenza A virus activity. RSC Adv 2021; 11:30020-30029. [PMID: 35480240 PMCID: PMC9040849 DOI: 10.1039/d1ra05240c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/30/2021] [Indexed: 12/21/2022] Open
Abstract
Amino imidazole carbonitrile derivatives decorated with α-amino acid side-chains have been synthesized by a multicomponent microwave assisted reaction inspired by the prebiotic chemistry of aminomalononitrile as a tool for generating high chemical diversity. These compounds were used as annulation synthons for the preparation of 8,9-disubstituted-6,9-dihydro-1H-purin-6-ones by reaction with formic acid as a simple C-1 donor reagent. The novel heterocycles were characterized by significant activity against influenza A virus, amino imidazole carbonitrile derivatives showing the highest activity. Thus, the chemical complexity generated by prebiotic chemistry furnished a general tool for the identification of novel antiviral agents. Amino imidazole carbonitrile derivatives decorated with α-amino acid side-chains have been synthesized by a multicomponent microwave assisted reaction inspired by the prebiotic chemistry of aminomalononitrile for generating high chemical diversity.![]()
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Affiliation(s)
- Bruno Mattia Bizzarri
- Ecological and Biological Sciences Department (DEB), University of Tuscia Via S. Camillo de Lellis snc 01100 Viterbo Italy
| | - Angelica Fanelli
- Ecological and Biological Sciences Department (DEB), University of Tuscia Via S. Camillo de Lellis snc 01100 Viterbo Italy
| | - Lorenzo Botta
- Ecological and Biological Sciences Department (DEB), University of Tuscia Via S. Camillo de Lellis snc 01100 Viterbo Italy
| | - Marta De Angelis
- Department of Public Health and Infectious Diseases, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome Piazzale Aldo Moro, 5 00185 Rome Italy
| | - Anna Teresa Palamara
- Department of Public Health and Infectious Diseases, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome Piazzale Aldo Moro, 5 00185 Rome Italy .,Department of Infectious Diseases, Istituto Superiore di Sanità Viale Regina Elena, 299 00161 Rome Italy
| | - Lucia Nencioni
- Department of Public Health and Infectious Diseases, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome Piazzale Aldo Moro, 5 00185 Rome Italy
| | - Raffaele Saladino
- Ecological and Biological Sciences Department (DEB), University of Tuscia Via S. Camillo de Lellis snc 01100 Viterbo Italy
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7
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Szabla R, Zdrowowicz M, Spisz P, Green NJ, Stadlbauer P, Kruse H, Šponer J, Rak J. 2,6-diaminopurine promotes repair of DNA lesions under prebiotic conditions. Nat Commun 2021; 12:3018. [PMID: 34021158 PMCID: PMC8139960 DOI: 10.1038/s41467-021-23300-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 04/20/2021] [Indexed: 01/04/2023] Open
Abstract
High-yielding and selective prebiotic syntheses of RNA and DNA nucleotides involve UV irradiation to promote the key reaction steps and eradicate biologically irrelevant isomers. While these syntheses were likely enabled by UV-rich prebiotic environment, UV-induced formation of photodamages in polymeric nucleic acids, such as cyclobutane pyrimidine dimers (CPDs), remains the key unresolved issue for the origins of RNA and DNA on Earth. Here, we demonstrate that substitution of adenine with 2,6-diaminopurine enables repair of CPDs with yields reaching 92%. This substantial self-repairing activity originates from excellent electron donating properties of 2,6-diaminopurine in nucleic acid strands. We also show that the deoxyribonucleosides of 2,6-diaminopurine and adenine can be formed under the same prebiotic conditions. Considering that 2,6-diaminopurine was previously shown to increase the rate of nonenzymatic RNA replication, this nucleobase could have played critical roles in the formation of functional and photostable RNA/DNA oligomers in UV-rich prebiotic environments. UV-induced photodamage that likely occurred during the prebiotic synthesis of DNA and RNA is still an untackled issue for their origin on early Earth. Here, the authors show that substitution of 2,6-diaminopurine for adenine enables repair of cyclobutane pyrimidine dimers with high yields, and demonstrate that both 2,6-diaminopurine and adenine nucleosides can be formed under the same prebiotic conditions.
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Affiliation(s)
- Rafał Szabla
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK. .,Institute of Physics, Polish Academy of Sciences, Warsaw, Poland.
| | | | - Paulina Spisz
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | | | - Petr Stadlbauer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Janusz Rak
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
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8
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Bizzarri BM, Saladino R, Delfino I, García-Ruiz JM, Di Mauro E. Prebiotic Organic Chemistry of Formamide and the Origin of Life in Planetary Conditions: What We Know and What Is the Future. Int J Mol Sci 2021; 22:ijms22020917. [PMID: 33477625 PMCID: PMC7831497 DOI: 10.3390/ijms22020917] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/14/2021] [Accepted: 01/17/2021] [Indexed: 11/18/2022] Open
Abstract
The goal of prebiotic chemistry is the depiction of molecular evolution events preceding the emergence of life on Earth or elsewhere in the cosmos. Plausible experimental models require geochemical scenarios and robust chemistry. Today we know that the chemical and physical conditions for life to flourish on Earth were at work much earlier than thought, i.e., earlier than 4.4 billion years ago. In recent years, a geochemical model for the first five hundred million years of the history of our planet has been devised that would work as a cradle for life. Serpentinization processes in the Hadean eon affording self-assembled structures and vesicles provides the link between the catalytic properties of the inorganic environment and the impressive chemical potential of formamide to produce complete panels of organic molecules relevant in pre-genetic and pre-metabolic processes. Based on an interdisciplinary approach, we propose basic transformations connecting geochemistry to the chemistry of formamide, and we hint at the possible extension of this perspective to other worlds.
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Affiliation(s)
- Bruno Mattia Bizzarri
- Ecological and Biological Sciences Department (DEB), University of Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy; (B.M.B.); (I.D.); (E.D.M.)
| | - Raffaele Saladino
- Ecological and Biological Sciences Department (DEB), University of Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy; (B.M.B.); (I.D.); (E.D.M.)
- Correspondence: (R.S.); (J.M.G.-R.)
| | - Ines Delfino
- Ecological and Biological Sciences Department (DEB), University of Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy; (B.M.B.); (I.D.); (E.D.M.)
| | - Juan Manuel García-Ruiz
- Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la Tierra, Consejo Superior de Investigaciones Científicas–Universidad de Granada, Avenida de las Palmeras 4, Armilla, 18100 Granada, Spain
- Correspondence: (R.S.); (J.M.G.-R.)
| | - Ernesto Di Mauro
- Ecological and Biological Sciences Department (DEB), University of Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy; (B.M.B.); (I.D.); (E.D.M.)
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9
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Bizzarri BM, Fanelli A, Kapralov M, Krasavin E, Saladino R. Meteorite-catalyzed intermolecular trans-glycosylation produces nucleosides under proton beam irradiation. RSC Adv 2021; 11:19258-19264. [PMID: 35478633 PMCID: PMC9033569 DOI: 10.1039/d1ra02379a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/14/2021] [Indexed: 11/23/2022] Open
Abstract
Di-glycosylated adenines act as glycosyl donors in the intermolecular trans-glycosylation of pyrimidine nucleobases under proton beam irradiation conditions. Formamide and chondrite meteorite NWA 1465 increased the yield and the selectivity of the reaction. The glycosyl transfer process was highly regioselective in yielding canonical N1-pyrimidine nucleosides, the natural β-anomers prevailing in the presence of formamide and NWA 1465. These data highlight the possible role of intermolecular trans-glycosylation in the prebiotic formation of purine and pyrimidine nucleosides, avoiding the occurrence of independent synthetic pathways. Di-glycosylated adenines act as glycosyl donors in the intermolecular trans-glycosylation of pyrimidine nucleobases under proton beam irradiation conditions.![]()
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Affiliation(s)
| | - Angelica Fanelli
- Ecological and Biological Sciences Department (DEB)
- University of Tuscia
- Viterbo
- Italy
| | - Michail Kapralov
- Joint Institute for Nuclear Research
- JINR's Laboratory of Radiation Biology
- Russia
- Dubna State University
- Ulitsa Universitetskaya
| | - Eugene Krasavin
- Joint Institute for Nuclear Research
- JINR's Laboratory of Radiation Biology
- Russia
- Dubna State University
- Ulitsa Universitetskaya
| | - Raffaele Saladino
- Ecological and Biological Sciences Department (DEB)
- University of Tuscia
- Viterbo
- Italy
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10
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Prebiotic chemistry and origins of life research with atomistic computer simulations. Phys Life Rev 2020; 34-35:105-135. [DOI: 10.1016/j.plrev.2018.09.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 09/10/2018] [Indexed: 02/02/2023]
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11
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Pastorek A, Ferus M, Čuba V, Šrámek O, Ivanek O, Civiš S. Primordial Radioactivity and Prebiotic Chemical Evolution: Effect of γ Radiation on Formamide-Based Synthesis. J Phys Chem B 2020; 124:8951-8959. [PMID: 32970439 DOI: 10.1021/acs.jpcb.0c05233] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although the effect of ionizing radiation on prebiotic chemistry is often overlooked, primordial natural radioactivity might have been an important source of energy for various chemical transformations. Estimates of the abundances of short-lived radionuclides on early Earth suggest that the primordial intensity of endogenous terrestrial radioactivity was up to 4 × 103 times higher than it is today. Therefore, we assume that chemical substances in contact with radioactive rocks should therefore undergo radiolysis. The calculations are followed by research investigating the influence of ionizing γ radiation on basic prebiotic substances, including formamide mixed with various clays, which might have played the role of a catalyst and an agent that partially blocked radiation that was potentially destructive for the products. Our explorations of this effect have shown that the irradiation of formamide-clay mixtures at doses of ∼6 kGy produces significant amounts of urea (up to the maximal concentration of approximately 250 mg L-1), which plays a role in HCN-based prebiotic chemistry.
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Affiliation(s)
- Adam Pastorek
- J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 2155/3, 18200 Prague, Prague 8, Czech Republic.,Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Břehová 78/7, 11519 Prague, Prague 1, Czech Republic
| | - Martin Ferus
- J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 2155/3, 18200 Prague, Prague 8, Czech Republic
| | - Václav Čuba
- Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Břehová 78/7, 11519 Prague, Prague 1, Czech Republic
| | - Ondřej Šrámek
- Department of Geophysics, Faculty of Mathematics and Physics, Charles University, V Holešovičkách 2, 18000 Prague, Prague 8, Czech Republic
| | - Ondřej Ivanek
- J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 2155/3, 18200 Prague, Prague 8, Czech Republic
| | - Svatopluk Civiš
- J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 2155/3, 18200 Prague, Prague 8, Czech Republic
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12
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Saladino R. Computational investigation of the primordial soup: Comment on "Prebiotic chemistry and origin of life research with atomistic computer simulations" by A. Pérez-Villa, F. Pietrucci, and A. M. Saitta. Phys Life Rev 2020; 34-35:149-152. [PMID: 31974057 DOI: 10.1016/j.plrev.2020.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 01/10/2020] [Indexed: 10/25/2022]
Affiliation(s)
- Raffaele Saladino
- Department of Ecological and Biological Sciences, Via S. Camillo de Lellis, University of Tuscia, 01100, Viterbo, Italy.
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13
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Bizzarri BM, Šponer JE, Šponer J, Cassone G, Kapralov M, Timoshenko GN, Krasavin E, Fanelli G, Timperio AM, Di Mauro E, Saladino R. Meteorite‐Assisted Phosphorylation of Adenosine Under Proton Irradiation Conditions. CHEMSYSTEMSCHEM 2019. [DOI: 10.1002/syst.201900039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Bruno M. Bizzarri
- Department of Ecological and Biological SciencesUniversity of Tuscia Via S. Camillo de Lellis 01100 Viterbo Italy
| | - Judit E. Šponer
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 CZ-61265 Brno Czech Republic
- Regional Centre of Advanced Technologies and Materials Faculty of SciencePalacky University 17 listopadu 771 46 Olomouc Czech Republic
| | - Jiri Šponer
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 CZ-61265 Brno Czech Republic
- Regional Centre of Advanced Technologies and Materials Faculty of SciencePalacky University 17 listopadu 771 46 Olomouc Czech Republic
| | - Giuseppe Cassone
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 CZ-61265 Brno Czech Republic
| | - Michail Kapralov
- Joint Institute for Nuclear ResearchJINR's Laboratory of Radiation Biology Dubna Russia
| | - Gennady N. Timoshenko
- Joint Institute for Nuclear ResearchJINR's Laboratory of Radiation Biology Dubna Russia
| | - Eugene Krasavin
- Joint Institute for Nuclear ResearchJINR's Laboratory of Radiation Biology Dubna Russia
| | - Giuseppina Fanelli
- Department of Science and Technology for Agriculture, Forestry, Nature, and EnergyUniversity of Tuscia Via S. Camillo de Lellis 01100 Viterbo Italy
| | - Anna Maria Timperio
- Department of Ecological and Biological SciencesUniversity of Tuscia Via S. Camillo de Lellis 01100 Viterbo Italy
| | - Ernesto Di Mauro
- Department of Ecological and Biological SciencesUniversity of Tuscia Via S. Camillo de Lellis 01100 Viterbo Italy
| | - Raffaele Saladino
- Department of Ecological and Biological SciencesUniversity of Tuscia Via S. Camillo de Lellis 01100 Viterbo Italy
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14
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Šponer JE, Šponer J, Di Mauro E. Structural and Energetic Compatibility: The Driving Principles of Molecular Evolution. ASTROBIOLOGY 2019; 19:1117-1122. [PMID: 31045430 DOI: 10.1089/ast.2018.1978] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In this work, we provide an answer to the question formulated by Albert Eschenmoser: "How would you envisage the bridge between potentially primordial geochemistry that had been disordered and one that gradually became self-organizing?" Analysis of the free-energy profiles of some of the key reactions leading to formation of nucleotides and their oligomers shows that, whereas the first part of the pathway, up to nucleotides, is energy-driven, in the second low-energy part entropic control in the form of structural compatibility becomes more important. We suggest that the birth of modern metabolism requires structural compatibility, which is enabled by the commensurability of the thermodynamics of the synthetic steps with the stabilizing effect of those intermolecular interactions that play a key role in dictating entropic control of these reactions.
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Affiliation(s)
- Judit E Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Ernesto Di Mauro
- Institute for Molecular Biology and Pathology, CNR, c/o Università Sapienza, Roma, Italy
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15
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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.
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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
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16
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Saladino R, Di Mauro E, García‐Ruiz JM. A Universal Geochemical Scenario for Formamide Condensation and Prebiotic Chemistry. Chemistry 2019; 25:3181-3189. [PMID: 30230056 PMCID: PMC6470889 DOI: 10.1002/chem.201803889] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/14/2018] [Indexed: 11/06/2022]
Abstract
The condensation of formamide has been shown to be a robust chemical pathway affording molecules necessary for the origin of life. It has been experimentally demonstrated that condensation reactions of formamide are catalyzed by a number of minerals, including silicates, phosphates, sulfides, zirconia, and borates, and by cosmic dusts and meteorites. However, a critical discussion of the catalytic power of the tested minerals, and the geochemical conditions under which the condensation would occur, is still missing. We show here that mineral self-assembled structures forming under alkaline silica-rich solutions are excellent catalysts for the condensation of formamide with respect to other minerals. We also propose that these structures were likely forming as early as 4.4 billion years ago when the whole earth surface was a reactor, a global scale factory, releasing large amounts of organic compounds. Our experimental results suggest that the conditions required for the synthesis of the molecular bricks from which life self-assembles, rather than being local and bizarre, appears to be universal and geologically rather conventional.
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Affiliation(s)
- Raffaele Saladino
- Dipartimento di Scienze Ecologiche e BiologicheUniversità della TusciaVia San Camillo De Lellis01100ViterboItaly
| | - Ernesto Di Mauro
- Dipartimento di Scienze Ecologiche e BiologicheUniversità della TusciaVia San Camillo De Lellis01100ViterboItaly
| | - Juan Manuel García‐Ruiz
- Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la TierraCSIC-Universidad de GranadaAv. De las Palmeras 4ArmillaGranadaSpain
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17
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Bacchus-Montabonel MC. Role of sulfur in proton-induced collisions of RNA prebiotic precursors. Phys Chem Chem Phys 2019; 21:1428-1434. [PMID: 30601542 DOI: 10.1039/c8cp07204c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A main objective in the synthesis of prebiotic compounds is to remain consistent with reasonable geochemical scenarios, while avoiding concomitant formation of undesirable by-products. In this context, 2-aminothiazole has shown enhanced selectivity in the addition reaction with sugars promoting interest in this sulfur species compared to its oxygenated analogue, 2-aminooxazole. More generally, the role of sulfur in prebiotic chemistry needs to be widely investigated with regard to the numerous sulfur-containing molecules detected recently in different astrophysical environments. However, in parallel to the problematic formation of building blocks of life, how prebiotic molecules could survive under extreme astrophysical conditions remains an open question. Intense UV radiation or ion bombardment may indeed lead to fragmentation and the specific behaviour of sulfur compounds has to be addressed. Focusing on its potentiality in prebiotic multistep synthesis, a detailed analysis of the proton impact on 2-aminothiazole has been investigated theoretically in a wide collision energy range chosen to model various astrophysical environments. The comparison with its oxygenated analogue may suggest qualitative trends on their respective stability under such processes which could be of crucial interest for prebiotic synthesis.
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18
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Sleep NH. Geological and Geochemical Constraints on the Origin and Evolution of Life. ASTROBIOLOGY 2018; 18:1199-1219. [PMID: 30124324 DOI: 10.1089/ast.2017.1778] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The traditional tree of life from molecular biology with last universal common ancestor (LUCA) branching into bacteria and archaea (though fuzzy) is likely formally valid enough to be a basis for discussion of geological processes on the early Earth. Biologists infer likely properties of nodal organisms within the tree and, hence, the environment they inhabited. Geologists both vet tenuous trees and putative origin of life scenarios for geological and ecological reasonability and conversely infer geological information from trees. The latter approach is valuable as geologists have only weakly constrained the time when the Earth became habitable and the later time when life actually existed to the long interval between ∼4.5 and ∼3.85 Ga where no intact surface rocks are known. With regard to vetting, origin and early evolution hypotheses from molecular biology have recently centered on serpentinite settings in marine and alternatively land settings that are exposed to ultraviolet sunlight. The existence of these niches on the Hadean Earth is virtually certain. With regard to inferring geological environment from genomics, nodes on the tree of life can arise from true bottlenecks implied by the marine serpentinite origin scenario and by asteroid impact. Innovation of a very useful trait through a threshold allows the successful organism to quickly become very abundant and later root a large clade. The origin of life itself, that is, the initial Darwinian ancestor, the bacterial and archaeal roots as free-living cellular organisms that independently escaped hydrothermal chimneys above marine serpentinite or alternatively from shallow pore-water environments on land, the Selabacteria root with anoxygenic photosynthesis, and the Terrabacteria root colonizing land are attractive examples that predate the geological record. Conversely, geological reasoning presents likely events for appraisal by biologists. Asteroid impacts may have produced bottlenecks by decimating life. Thermophile roots of bacteria and archaea as well as a thermophile LUCA are attractive.
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Affiliation(s)
- Norman H Sleep
- Department of Geophysics, Stanford University , Stanford, California
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19
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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.
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20
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Saladino R, Botta L, Di Mauro E. The Prevailing Catalytic Role of Meteorites in Formamide Prebiotic Processes. Life (Basel) 2018; 8:life8010006. [PMID: 29470412 PMCID: PMC5871938 DOI: 10.3390/life8010006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 01/26/2018] [Accepted: 02/18/2018] [Indexed: 01/03/2023] Open
Abstract
Meteorites are consensually considered to be involved in the origin of life on this Planet for several functions and at different levels: (i) as providers of impact energy during their passage through the atmosphere; (ii) as agents of geodynamics, intended both as starters of the Earth’s tectonics and as activators of local hydrothermal systems upon their fall; (iii) as sources of organic materials, at varying levels of limited complexity; and (iv) as catalysts. The consensus about the relevance of these functions differs. We focus on the catalytic activities of the various types of meteorites in reactions relevant for prebiotic chemistry. Formamide was selected as the chemical precursor and various sources of energy were analyzed. The results show that all the meteorites and all the different energy sources tested actively afford complex mixtures of biologically-relevant compounds, indicating the robustness of the formamide-based prebiotic chemistry involved. Although in some cases the yields of products are quite small, the diversity of the detected compounds of biochemical significance underlines the prebiotic importance of meteorite-catalyzed condensation of formamide.
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Affiliation(s)
- Raffaele Saladino
- Biological and Ecological Department, University of Tuscia, 01100 Viterbo, Italy.
| | - Lorenzo Botta
- Biological and Ecological Department, University of Tuscia, 01100 Viterbo, Italy.
| | - Ernesto Di Mauro
- Biological and Ecological Department, University of Tuscia, 01100 Viterbo, Italy.
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21
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Becker S, Schneider C, Okamura H, Crisp A, Amatov T, Dejmek M, Carell T. Wet-dry cycles enable the parallel origin of canonical and non-canonical nucleosides by continuous synthesis. Nat Commun 2018; 9:163. [PMID: 29323115 PMCID: PMC5765019 DOI: 10.1038/s41467-017-02639-1] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 12/14/2017] [Indexed: 12/28/2022] Open
Abstract
The molecules of life were created by a continuous physicochemical process on an early Earth. In this hadean environment, chemical transformations were driven by fluctuations of the naturally given physical parameters established for example by wet-dry cycles. These conditions might have allowed for the formation of (self)-replicating RNA as the fundamental biopolymer during chemical evolution. The question of how a complex multistep chemical synthesis of RNA building blocks was possible in such an environment remains unanswered. Here we report that geothermal fields could provide the right setup for establishing wet-dry cycles that allow for the synthesis of RNA nucleosides by continuous synthesis. Our model provides both the canonical and many ubiquitous non-canonical purine nucleosides in parallel by simple changes of physical parameters such as temperature, pH and concentration. The data show that modified nucleosides were potentially formed as competitor molecules. They could in this sense be considered as molecular fossils.
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Affiliation(s)
- Sidney Becker
- Center for Integrated Protein Science Munich CiPSM at the Department of Chemistry, Ludwig-Maximilians-Universität München, 81377, Munich, Germany
| | - Christina Schneider
- Center for Integrated Protein Science Munich CiPSM at the Department of Chemistry, Ludwig-Maximilians-Universität München, 81377, Munich, Germany
| | - Hidenori Okamura
- Center for Integrated Protein Science Munich CiPSM at the Department of Chemistry, Ludwig-Maximilians-Universität München, 81377, Munich, Germany
| | - Antony Crisp
- Center for Integrated Protein Science Munich CiPSM at the Department of Chemistry, Ludwig-Maximilians-Universität München, 81377, Munich, Germany
| | - Tynchtyk Amatov
- Center for Integrated Protein Science Munich CiPSM at the Department of Chemistry, Ludwig-Maximilians-Universität München, 81377, Munich, Germany
| | - Milan Dejmek
- Institute of Organic Chemistry and Biochemistry ASCR, 16610, Prague 6, Czech Republic
| | - Thomas Carell
- Center for Integrated Protein Science Munich CiPSM at the Department of Chemistry, Ludwig-Maximilians-Universität München, 81377, Munich, Germany.
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