1
|
Węgrzyn E, Mejdrová I, Carell T. Gradual evolution of a homo-l-peptide world on homo-d-configured RNA and DNA. Chem Sci 2024:d4sc03384a. [PMID: 39129775 PMCID: PMC11306956 DOI: 10.1039/d4sc03384a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 07/26/2024] [Indexed: 08/13/2024] Open
Abstract
Modern life requires the translation of genetic information - encoded by nucleic acids - into proteins, which establishes the essential link between genotype and phenotype. During translation, exclusively l-amino acids are loaded onto transfer RNA molecules (tRNA), which are then connected at the ribosome to give homo-l-proteins. In contrast to the homo-l-configuration of amino acids and proteins, the oligonucleotides involved are all d-configured (deoxy)ribosides. Previously, others and us have shown that if peptide synthesis occurs at homo d-configured oligonucleotides, a pronounced l-amino acid selectivity is observed, which reflects the d-sugar/l-amino acid world that evolved in nature. Here we further explore this astonishing selectivity. We show a peptide-synthesis/recapture-cycle that can lead to a gradual enrichment and hence selection of a homo-l-peptide world. We show that even if peptides with a mixed l/d-stereochemistry are formed, they are not competitive against the homo-l-counterparts. We also demonstrate that this selectivity is not limited to RNA but that peptide synthesis on DNA features the same l-amino acid preference. In total, the data bring us a step closer to an understanding of how homochirality on Earth once evolved.
Collapse
Affiliation(s)
- Ewa Węgrzyn
- Department of Chemistry, Center for Nucleic Acids Therapies at the Institute for Chemical Epigenetics (ICE-M), Ludwig-Maximilians-Universität (LMU) München Butenandtstrasse 5-13 81377 Munich Germany
| | - Ivana Mejdrová
- Department of Chemistry, Center for Nucleic Acids Therapies at the Institute for Chemical Epigenetics (ICE-M), Ludwig-Maximilians-Universität (LMU) München Butenandtstrasse 5-13 81377 Munich Germany
| | - Thomas Carell
- Department of Chemistry, Center for Nucleic Acids Therapies at the Institute for Chemical Epigenetics (ICE-M), Ludwig-Maximilians-Universität (LMU) München Butenandtstrasse 5-13 81377 Munich Germany
| |
Collapse
|
2
|
Takano Y, Naraoka H, Dworkin JP, Koga T, Sasaki K, Sato H, Oba Y, Ogawa NO, Yoshimura T, Hamase K, Ohkouchi N, Parker ET, Aponte JC, Glavin DP, Furukawa Y, Aoki J, Kano K, Nomura SIM, Orthous-Daunay FR, Schmitt-Kopplin P, Yurimoto H, Nakamura T, Noguchi T, Okazaki R, Yabuta H, Sakamoto K, Yada T, Nishimura M, Nakato A, Miyazaki A, Yogata K, Abe M, Okada T, Usui T, Yoshikawa M, Saiki T, Tanaka S, Terui F, Nakazawa S, Watanabe SI, Tsuda Y, Tachibana S. Primordial aqueous alteration recorded in water-soluble organic molecules from the carbonaceous asteroid (162173) Ryugu. Nat Commun 2024; 15:5708. [PMID: 38987536 PMCID: PMC11237059 DOI: 10.1038/s41467-024-49237-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 05/29/2024] [Indexed: 07/12/2024] Open
Abstract
We report primordial aqueous alteration signatures in water-soluble organic molecules from the carbonaceous asteroid (162173) Ryugu by the Hayabusa2 spacecraft of JAXA. Newly identified low-molecular-weight hydroxy acids (HO-R-COOH) and dicarboxylic acids (HOOC-R-COOH), such as glycolic acid, lactic acid, glyceric acid, oxalic acid, and succinic acid, are predominant in samples from the two touchdown locations at Ryugu. The quantitative and qualitative profiles for the hydrophilic molecules between the two sampling locations shows similar trends within the order of ppb (parts per billion) to ppm (parts per million). A wide variety of structural isomers, including α- and β-hydroxy acids, are observed among the hydrophilic molecules. We also identify pyruvic acid and dihydroxy and tricarboxylic acids, which are biochemically important intermediates relevant to molecular evolution, such as the primordial TCA (tricarboxylic acid) cycle. Here, we find evidence that the asteroid Ryugu samples underwent substantial aqueous alteration, as revealed by the presence of malonic acid during keto-enol tautomerism in the dicarboxylic acid profile. The comprehensive data suggest the presence of a series for water-soluble organic molecules in the regolith of Ryugu and evidence of signatures in coevolutionary aqueous alteration between water and organics in this carbonaceous asteroid.
Collapse
Affiliation(s)
- Yoshinori Takano
- Biogeochemistry Research Center (BGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima, Yokosuka, 237-0061, Japan.
- Institute for Advanced Biosciences (IAB), Keio University, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan.
| | - Hiroshi Naraoka
- Department of Earth and Planetary Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Jason P Dworkin
- Solar System Exploration Division, NASA Goddard Space Flight Center, Greenbelt, MD, 20771, USA
| | - Toshiki Koga
- Biogeochemistry Research Center (BGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima, Yokosuka, 237-0061, Japan
| | - Kazunori Sasaki
- Institute for Advanced Biosciences (IAB), Keio University, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
- Human Metabolome Technologies Inc., Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
| | - Hajime Sato
- Human Metabolome Technologies Inc., Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
| | - Yasuhiro Oba
- Institute of Low Temperature Science (ILTS), Hokkaido University, N19W8 Kita-ku, Sapporo, 060-0819, Japan
| | - Nanako O Ogawa
- Biogeochemistry Research Center (BGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima, Yokosuka, 237-0061, Japan
| | - Toshihiro Yoshimura
- Biogeochemistry Research Center (BGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima, Yokosuka, 237-0061, Japan
| | - Kenji Hamase
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, 812-0054, Japan
| | - Naohiko Ohkouchi
- Biogeochemistry Research Center (BGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima, Yokosuka, 237-0061, Japan
| | - Eric T Parker
- Solar System Exploration Division, NASA Goddard Space Flight Center, Greenbelt, MD, 20771, USA
| | - José C Aponte
- Solar System Exploration Division, NASA Goddard Space Flight Center, Greenbelt, MD, 20771, USA
| | - Daniel P Glavin
- Solar System Exploration Division, NASA Goddard Space Flight Center, Greenbelt, MD, 20771, USA
| | - Yoshihiro Furukawa
- Department of Earth Material Science, Tohoku University, Sendai, 980-8578, Japan
| | - Junken Aoki
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Tokyo, 113-0033, Japan
| | - Kuniyuki Kano
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Tokyo, 113-0033, Japan
| | - Shin-Ichiro M Nomura
- Department of Robotics Graduate school of Engineering, Tohoku University, Sendai, 980-8579, Japan
| | - Francois-Regis Orthous-Daunay
- Université Grenoble Alpes, Centre National de la Recherche Scientifique (CNRS), Centre National d'Etudes Spatiales, L'Institut de Planétologie et d'Astrophysique de Grenoble, 38000, Grenoble, France
| | - Philippe Schmitt-Kopplin
- Technische Universitӓt München, Analytische Lebensmittel Chemie, 85354, Freising, Germany
- Max Planck Institute for Extraterrestrial Physics, 85748, Garching bei München, Germany
- Center for Research and Exploration in Space Science and Technology, NASA Goddard Space Flight Center, Greenbelt, MD, 20771, USA
| | - Hisayoshi Yurimoto
- Department of Earth and Planetary Sciences, Hokkaido University, Sapporo, 060-0810, Japan
| | - Tomoki Nakamura
- Department of Earth Material Science, Tohoku University, Sendai, 980-8578, Japan
| | - Takaaki Noguchi
- Department of Earth and Planetary Sciences, Kyoto University, Kyoto, 606-8502, Japan
| | - Ryuji Okazaki
- Department of Earth and Planetary Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Hikaru Yabuta
- Department of Earth and Planetary Sciences, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
| | - Kanako Sakamoto
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Toru Yada
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Masahiro Nishimura
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Aiko Nakato
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Akiko Miyazaki
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Kasumi Yogata
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Masanao Abe
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Tatsuaki Okada
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Tomohiro Usui
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Makoto Yoshikawa
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Takanao Saiki
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Satoshi Tanaka
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Fuyuto Terui
- Kanagawa Institute of Technology, Atsugi, 243-0292, Japan
| | - Satoru Nakazawa
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Sei-Ichiro Watanabe
- Department of Earth and Environment Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | - Yuichi Tsuda
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Shogo Tachibana
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
- UTokyo Organization for Planetary and Space Science (UTOPS), University of Tokyo, 7-3-1 Hongo, Tokyo, 113-0033, Japan
| |
Collapse
|
3
|
Li Z, Duan S, Liu B. Freezing Functional Nucleic Acids: From Molecular Reactions to Surface Immobilization. Chembiochem 2024:e202400416. [PMID: 38979890 DOI: 10.1002/cbic.202400416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 07/08/2024] [Accepted: 07/08/2024] [Indexed: 07/10/2024]
Abstract
Biochemical reactions are typically slowed down by decreasing temperature. However, accelerated reaction kinetics have been observed for a long time. More recent examples have highlighted the unique role of freezing in fabricating supermaterials, degrading environmental contaminants, and accelerating bioreactions. Functional nucleic acids are DNA or RNA oligonucleotides with versatile properties, including target recognition, catalysis, and molecular co4mputing. In this review, we discuss the current observations and understanding of freezing-facilitated reactions involving functional nucleic acids. Molecular reactions such as ligation/conjugation, cleavage, and hybridization are discussed. Moreover, freezing-induced DNA-nanoparticle conjugations are introduced. Then, we describe our effect in immobilizing DNA on bulk surfaces. Finally, we address some critical questions and research opportunities in the field.
Collapse
Affiliation(s)
- Zhenglian Li
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Siyi Duan
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Biwu Liu
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| |
Collapse
|
4
|
Stolar T, Pearce BK, Etter M, Truong KN, Ostojić T, Krajnc A, Mali G, Rossi B, Molčanov K, Lončarić I, Meštrović E, Užarević K, Grisanti L. Base-pairing of uracil and 2,6-diaminopurine: from cocrystals to photoreactivity. iScience 2024; 27:109894. [PMID: 38783999 PMCID: PMC11112615 DOI: 10.1016/j.isci.2024.109894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/18/2023] [Accepted: 05/01/2024] [Indexed: 05/25/2024] Open
Abstract
We show that the non-canonical nucleobase 2,6-diaminopurine (D) spontaneously base pairs with uracil (U) in water and the solid state without the need to be attached to the ribose-phosphate backbone. Depending on the reaction conditions, D and U assemble in thermodynamically stable hydrated and anhydrated D-U base-paired cocrystals. Under UV irradiation, an aqueous solution of D-U base-pair undergoes photochemical degradation, while a pure aqueous solution of U does not. Our simulations suggest that D may trigger the U photodimerization and show that complementary base-pairing modifies the photochemical properties of nucleobases, which might have implications for prebiotic chemistry.
Collapse
Affiliation(s)
- Tomislav Stolar
- Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia
- Federal Institute for Materials Research and Testing (BAM), Richard-Willstätter-Straße 11, 12489 Berlin, Germany
| | - Ben K.D. Pearce
- Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Martin Etter
- Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, 22607 Hamburg, Germany
| | - Khai-Nghi Truong
- Rigaku Europe SE, Hugenottenallee 167, 63263 Neu-Isenburg, Germany
| | - Tea Ostojić
- Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia
| | - Andraž Krajnc
- National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Gregor Mali
- National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Barbara Rossi
- Elettra Sincrotrone Trieste, Strada Statale 14 km 163.5, 34149 Trieste, Italy
| | | | - Ivor Lončarić
- Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia
| | - Ernest Meštrović
- Faculty of Chemical Engineering and Technology, University of Zagreb, Trg Marka Marulića 19, 10000 Zagreb, Croatia
| | | | - Luca Grisanti
- Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia
- National Research Council - Materials Foundry Institute (CNR-IOM) c/o SISSA (International School for Advanced Studies), Via Bonomea 265, 34136 Trieste, Italy
| |
Collapse
|
5
|
Rodriguez LE, Altair T, Hermis NY, Jia TZ, Roche TP, Steller LH, Weber JM. Chapter 4: A Geological and Chemical Context for the Origins of Life on Early Earth. ASTROBIOLOGY 2024; 24:S76-S106. [PMID: 38498817 DOI: 10.1089/ast.2021.0139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Within the first billion years of Earth's history, the planet transformed from a hot, barren, and inhospitable landscape to an environment conducive to the emergence and persistence of life. This chapter will review the state of knowledge concerning early Earth's (Hadean/Eoarchean) geochemical environment, including the origin and composition of the planet's moon, crust, oceans, atmosphere, and organic content. It will also discuss abiotic geochemical cycling of the CHONPS elements and how these species could have been converted to biologically relevant building blocks, polymers, and chemical networks. Proposed environments for abiogenesis events are also described and evaluated. An understanding of the geochemical processes under which life may have emerged can better inform our assessment of the habitability of other worlds, the potential complexity that abiotic chemistry can achieve (which has implications for putative biosignatures), and the possibility for biochemistries that are vastly different from those on Earth.
Collapse
Affiliation(s)
- Laura E Rodriguez
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- Lunar and Planetary Institute, Universities Space Research Association, Houston, Texas, USA. (Current)
| | - Thiago Altair
- Institute of Chemistry of São Carlos, Universidade de São Paulo, São Carlos, Brazil
- Department of Chemistry, College of the Atlantic, Bar Harbor, Maine, USA. (Current)
| | - Ninos Y Hermis
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- Department of Physics and Space Sciences, University of Granada, Granada Spain. (Current)
| | - Tony Z Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo, Japan
- Blue Marble Space Institute of Science, Seattle, Washington, USA
| | - Tyler P Roche
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Luke H Steller
- Australian Centre for Astrobiology, and School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, Australia
| | - Jessica M Weber
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| |
Collapse
|
6
|
Guerrero-Méndez L, Lema-Saavedra A, Jiménez E, Fernández-Ramos A, Martínez-Núñez E. Gas-phase formation of glycolonitrile in the interstellar medium. Phys Chem Chem Phys 2023; 25:20988-20996. [PMID: 37503548 DOI: 10.1039/d3cp02379f] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Our automated reaction discovery program, AutoMeKin, has been utilized to investigate the formation of glycolonitrile (HOCH2CN) in the gas phase under the low temperatures of the interstellar medium (ISM). The feasibility of a proposed pathway depends on the absence of barriers above the energy of reactants and the availability of the suggested precursors in the ISM. Based on these criteria, several radical-radical reactions and a radical-molecule reaction have been identified as viable formation routes in the ISM. Among the radical-radical reactions, OH + CH2CN appears to be the most relevant, considering the energy of the radicals and its ability to produce glycolonitrile in a single step. However, our analysis reveals that this reaction produces hydrogen isocyanide (HNC) and formaldehyde (CH2O), with rate coefficients ranging from (7.3-11.5) × 10-10 cm3 molecule-1 s-1 across the temperature range of 10-150 K. Furthermore, the identification of this remarkably efficient pathway for HNC elimination from glycolonitrile significantly broadens the possibilities for any radical-radical mechanism proposed in our research to be considered as a feasible pathway for the formation of HNC in the ISM. This finding is particularly interesing given the persistently unexplained overabundance of hydrogen isocyanide in the ISM. Among the radical-molecule reactions investigated, the most promising one is OH + CH2CHNH, which forms glycolonitrile and atomic hydrogen with rate coefficients in the range (0.3-6.6) × 10-10 cm3 molecule-1 s-1 within the 10-150 K temperature range. Our calculations indicate that the formation of both hydrogen isocyanide and glycolonitrile is efficient under the harsh conditions of the ISM.
Collapse
Affiliation(s)
- Luis Guerrero-Méndez
- Departamento de Química Física, Facultade de Química, Universidade de Santiago de Compostela, Avda. das Ciencias s/n 15782, Santiago de Compostela, Spain.
| | - Anxo Lema-Saavedra
- Centro Singular de Investigación en Química Biológica y Materiales Moleculares (CIQUS), Universidade de Santiago de Compostela, C/Jenaro de la Fuente s/n, 15782, Santiago de Compostela, Spain
| | - Elena Jiménez
- Departamento de Química Física, Facultad de Ciencias y Tecnologías Químicas, Universidad de Castilla-La Mancha, Avda. Camilo José Cela 1b, 13071, Ciudad Real, Spain
- Instituto de Investigación en Combustión y Contaminación Atmosférica (ICCA), Universidad de Castilla-La Mancha, Camino de Moledores s/n, 13071, Ciudad Real, Spain
| | - Antonio Fernández-Ramos
- Departamento de Química Física, Facultade de Química, Universidade de Santiago de Compostela, Avda. das Ciencias s/n 15782, Santiago de Compostela, Spain.
- Centro Singular de Investigación en Química Biológica y Materiales Moleculares (CIQUS), Universidade de Santiago de Compostela, C/Jenaro de la Fuente s/n, 15782, Santiago de Compostela, Spain
| | - Emilio Martínez-Núñez
- Departamento de Química Física, Facultade de Química, Universidade de Santiago de Compostela, Avda. das Ciencias s/n 15782, Santiago de Compostela, Spain.
| |
Collapse
|
7
|
Salibi E, Peter B, Schwille P, Mutschler H. Periodic temperature changes drive the proliferation of self-replicating RNAs in vesicle populations. Nat Commun 2023; 14:1222. [PMID: 36869058 PMCID: PMC9984477 DOI: 10.1038/s41467-023-36940-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 02/24/2023] [Indexed: 03/05/2023] Open
Abstract
Growth and division of biological cells are based on the complex orchestration of spatiotemporally controlled reactions driven by highly evolved proteins. In contrast, it remains unknown how their primordial predecessors could achieve a stable inheritance of cytosolic components before the advent of translation. An attractive scenario assumes that periodic changes of environmental conditions acted as pacemakers for the proliferation of early protocells. Using catalytic RNA (ribozymes) as models for primitive biocatalytic molecules, we demonstrate that the repeated freezing and thawing of aqueous solutions enables the assembly of active ribozymes from inactive precursors encapsulated in separate lipid vesicle populations. Furthermore, we show that encapsulated ribozyme replicators can overcome freezing-induced content loss and successive dilution by freeze-thaw driven propagation in feedstock vesicles. Thus, cyclic freezing and melting of aqueous solvents - a plausible physicochemical driver likely present on early Earth - provides a simple scenario that uncouples compartment growth and division from RNA self-replication, while maintaining the propagation of these replicators inside new vesicle populations.
Collapse
Affiliation(s)
- Elia Salibi
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Benedikt Peter
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
| | - Hannes Mutschler
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany.
| |
Collapse
|
8
|
Dujardin A, Himbert S, Pudritz R, Rheinstädter MC. The Formation of RNA Pre-Polymers in the Presence of Different Prebiotic Mineral Surfaces Studied by Molecular Dynamics Simulations. LIFE (BASEL, SWITZERLAND) 2022; 13:life13010112. [PMID: 36676060 PMCID: PMC9860743 DOI: 10.3390/life13010112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/21/2022] [Accepted: 12/24/2022] [Indexed: 01/04/2023]
Abstract
We used all-atom Molecular Dynamics (MD) computer simulations to study the formation of pre-polymers between the four nucleotides in RNA (AMP, UMP, CMP, GMP) in the presence of different substrates that could have been present in a prebiotic environment. Pre-polymers are C3'-C5' hydrogen-bonded nucleotides that have been suggested to be the precursors of phosphodiester-bonded RNA polymers. We simulated wet-dry cycles by successively removing water molecules from the simulations, from ~60 to 3 water molecules per nucleotide. The nine substrates in this study include three clay minerals, one mica, one phosphate mineral, one silica, and two metal oxides. The substrates differ in their surface charge and ability to form hydrogen bonds with the nucleotides. From the MD simulations, we quantify the interactions between different nucleotides, and between nucleotides and substrates. For comparison, we included graphite as an inert substrate, which is not charged and cannot form hydrogen bonds. We also simulated the dehydration of a nucleotide-only system, which mimics the drying of small droplets. The number of hydrogen bonds between nucleotides and nucleotides and substrates was found to increase significantly when water molecules were removed from the systems. The largest number of C3'-C5' hydrogen bonds between nucleotides occurred in the graphite and nucleotide-only systems. While the surface of the substrates led to an organization and periodic arrangement of the nucleotides, none of the substrates was found to be a catalyst for pre-polymer formation, neither at full hydration, nor when dehydrated. While confinement and dehydration seem to be the main drivers for hydrogen bond formation, substrate interactions reduced the interactions between nucleotides in all cases. Our findings suggest that small supersaturated water droplets that could have been produced by geysers or springs on the primitive Earth may play an important role in non-enzymatic RNA polymerization.
Collapse
Affiliation(s)
- Alix Dujardin
- Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4M1, Canada
- Origins Institute, McMaster University, Hamilton, ON L8S 4M1, Canada
| | - Sebastian Himbert
- Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4M1, Canada
- Origins Institute, McMaster University, Hamilton, ON L8S 4M1, Canada
| | - Ralph Pudritz
- Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4M1, Canada
- Origins Institute, McMaster University, Hamilton, ON L8S 4M1, Canada
| | - Maikel C. Rheinstädter
- Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4M1, Canada
- Origins Institute, McMaster University, Hamilton, ON L8S 4M1, Canada
- Correspondence: ; Tel.: +1-(905)-525-9140-23134; Fax: +1-(905)-546-1252
| |
Collapse
|
9
|
Holden DT, Morato NM, Cooks RG. Aqueous microdroplets enable abiotic synthesis and chain extension of unique peptide isomers from free amino acids. Proc Natl Acad Sci U S A 2022; 119:e2212642119. [PMID: 36191178 PMCID: PMC9586328 DOI: 10.1073/pnas.2212642119] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/27/2022] [Indexed: 12/13/2022] Open
Abstract
Amide bond formation, the essential condensation reaction underlying peptide synthesis, is hindered in aqueous systems by the thermodynamic constraints associated with dehydration. This represents a key difficulty for the widely held view that prebiotic chemical evolution leading to the formation of the first biomolecules occurred in an oceanic environment. Recent evidence for the acceleration of chemical reactions at droplet interfaces led us to explore aqueous amino acid droplet chemistry. We report the formation of dipeptide isomer ions from free glycine or L-alanine at the air-water interface of aqueous microdroplets emanating from a single spray source (with or without applied potential) during their flight toward the inlet of a mass spectrometer. The proposed isomeric dipeptide ion is an oxazolidinone that takes fully covalent and ion-neutral complex forms. This structure is consistent with observed fragmentation patterns and its conversion to authentic dipeptide ions upon gentle collisions and for its formation from authentic dipeptides at ultra-low concentrations. It also rationalizes the results of droplet fusion experiments that show that the dipeptide isomer facilitates additional amide bond formation events, yielding authentic tri- through hexapeptides. We propose that the interface of aqueous microdroplets serves as a drying surface that shifts the equilibrium between free amino acids in favor of dehydration via stabilization of the dipeptide isomers. These findings offer a possible solution to the water paradox of biopolymer synthesis in prebiotic chemistry.
Collapse
Affiliation(s)
- Dylan T. Holden
- Department of Chemistry, Purdue University, West Lafayette, IN 47907
| | - Nicolás M. Morato
- Department of Chemistry, Purdue University, West Lafayette, IN 47907
| | - R. Graham Cooks
- Department of Chemistry, Purdue University, West Lafayette, IN 47907
| |
Collapse
|
10
|
Arias A, Gómez S, Rojas-Valencia N, Núñez-Zarur F, Cappelli C, Murillo-López JA, Restrepo A. Formation and evolution of C-C, C-O, C[double bond, length as m-dash]O and C-N bonds in chemical reactions of prebiotic interest. RSC Adv 2022; 12:28804-28817. [PMID: 36320504 PMCID: PMC9549586 DOI: 10.1039/d2ra06000k] [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: 09/22/2022] [Accepted: 09/27/2022] [Indexed: 11/18/2022] Open
Abstract
A series of prebiotic chemical reactions yielding the precursor building blocks of amino acids, proteins and carbohydrates, starting solely from HCN and water is studied here. We closely follow the formation and evolution of the pivotal C-C, C-O, C[double bond, length as m-dash]O, and C-N bonds, which dictate the chemistry of the molecules of life. In many cases, formation of these bonds is set in motion by proton transfers in which individual water molecules act as catalysts so that water atoms end up in the products. Our results indicate that the prebiotic formation of carbon dioxide, formaldehyde, formic acid, formaldimine, glycolaldehyde, glycine, glycolonitrile, and oxazole derivatives, among others, are best described as highly nonsynchronous concerted single step processes. Nonetheless, for all reactions involving double proton transfer, the formation and breaking of O-H bonds around a particular O atom occur in a synchronous fashion, apparently independently from other primitive processes. For the most part, the first process to initiate seems to be the double proton transfer in the reactions where they are present, then bond breaking/formation around the reactive carbon in the carbonyl group and finally rupture of the C-N bonds in the appropriate cases, which are the most reluctant to break. Remarkably, within the limitations of our non-dynamical computational model, the wide ranges of temperature and pressure in which these reactions occur, downplay the problematic determination of the exact constraints on the early Earth.
Collapse
Affiliation(s)
- Alejandro Arias
- Instituto de Química, Universidad de Antioquia UdeACalle 70 No. 52-21MedellínColombia
| | - Sara Gómez
- Scuola Normale Superiore, Classe di ScienzePiazza dei Cavalieri 7Pisa56126Italy
| | - Natalia Rojas-Valencia
- Instituto de Química, Universidad de Antioquia UdeACalle 70 No. 52-21MedellínColombia,Escuela de Ciencias y Humanidades, Departamento de Ciencias Básicas, Universidad EafitMedellínAA 3300Colombia
| | - Francisco Núñez-Zarur
- Facultad de Ciencias Básicas, Universidad de MedellínCarrera 87 No. 30-65Medellín050026Colombia
| | - Chiara Cappelli
- Scuola Normale Superiore, Classe di ScienzePiazza dei Cavalieri 7Pisa56126Italy
| | - Juliana A. Murillo-López
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres BelloAutopista, Concepción-TalcahuanoTalcahuano 7100Chile
| | - Albeiro Restrepo
- Instituto de Química, Universidad de Antioquia UdeACalle 70 No. 52-21MedellínColombia
| |
Collapse
|
11
|
Root-Bernstein R, Brown AW. Novel Apparatuses for Incorporating Natural Selection Processes into Origins-of-Life Experiments to Produce Adaptively Evolving Chemical Ecosystems. Life (Basel) 2022; 12:1508. [PMID: 36294944 PMCID: PMC9605314 DOI: 10.3390/life12101508] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 11/21/2022] Open
Abstract
Origins-of-life chemical experiments usually aim to produce specific chemical end-products such as amino acids, nucleic acids or sugars. The resulting chemical systems do not evolve or adapt because they lack natural selection processes. We have modified Miller origins-of-life apparatuses to incorporate several natural, prebiotic physicochemical selection factors that can be tested individually or in tandem: freezing-thawing cycles; drying-wetting cycles; ultraviolet light-dark cycles; and catalytic surfaces such as clays or minerals. Each process is already known to drive important origins-of-life chemical reactions such as the production of peptides and synthesis of nucleic acid bases and each can also destroy various reactants and products, resulting selection within the chemical system. No previous apparatus has permitted all of these selection processes to work together. Continuous synthesis and selection of products can be carried out over many months because the apparatuses can be re-gassed. Thus, long-term chemical evolution of chemical ecosystems under various combinations of natural selection may be explored for the first time. We argue that it is time to begin experimenting with the long-term effects of such prebiotic natural selection processes because they may have aided biotic life to emerge by taming the combinatorial chemical explosion that results from unbounded chemical syntheses.
Collapse
Affiliation(s)
| | - Adam W. Brown
- Department of Art, Art History and Design, Michigan State University, East Lansing, MI 48824, USA
| |
Collapse
|
12
|
Christensen ZA, Pearcy AC, Mason KA, El-Shall MS. Gas-Phase External Solvation of Protonated Benzonitrile by Eight Methanol Molecules. J Phys Chem A 2022; 126:5160-5166. [PMID: 35917155 DOI: 10.1021/acs.jpca.2c03715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The gas-phase sequential association of methanol onto protonated benzonitrile (C6H5CNH+) and the proton-bound dimer (C6H5CN)2H+ have been examined experimentally by equilibrium thermochemical measurements and computationally by density functional theory (DFT). The bonding enthalpy (ΔH°) for the association of methanol with protonated benzonitrile (25.2 kcal mol-1) reflects the strong electrostatic interaction provided by the formation of an ionic hydrogen bond in the C6H5CNH+OHCH3 cluster in excellent agreement with a DFT-calculated binding energy of 24.9 kcal mol-1. The sequential bonding enthalpy within the (C6H5CN)H+(OHCH3)n clusters decreases from 25.2 to 10.6 kcal mol-1 for the eighth solvation step (n = 8), which remains more than 25% above the enthalpy of vaporization of liquid methanol (8.4 kcal mol-1). The nonbulk convergence of ΔH°n-1,n with eight solvent molecules is attributed to the external solvation of a benzonitrile molecule by an extended hydrogen bonding network of protonated methanol clusters H+(CH3OH)n. In the external solvation of protonated benzonitrile by methanol, the proton resides on the methanol subcluster and the neutral benzonitrile molecule remains outside and bonded to the surface of the protonated methanol cluster. The bonding enthalpy of methanol to the proton-bound benzonitrile dimer (C6H5CN)H+(NCC6H5) is measured to be 18.0 kcal mol-1, in good agreement with a DFT-calculated value of 17.1 kcal mol-1, which reflects the association of the proton with the lower proton affinity methanol molecule, thus forming a highly stable structure of protonated methanol terminated by two ionic hydrogen bonds to the two benzonitrile molecules. The external solvation of benzonitrile by methanol ices in space allows benzonitrile to remain on the ice grain surface rather than being isolated inside the ice. This could provide accessibility for reactions with incoming ions and molecules or for photochemical processes by UV irradiation, leading to the formation of complex organics on the surface of ice grains.
Collapse
Affiliation(s)
- Zachary A Christensen
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, United States
| | - Adam C Pearcy
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, United States
| | - Kyle A Mason
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, United States
| | - M Samy El-Shall
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, United States
| |
Collapse
|
13
|
Menor‐Salván C, Burcar BT, Bouza M, Fialho DM, Fernández FM, Hud NV. A Shared Prebiotic Formation of Neopterins and Guanine Nucleosides from Pyrimidine Bases. Chemistry 2022; 28:e202200714. [PMID: 35537135 PMCID: PMC9401002 DOI: 10.1002/chem.202200714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Indexed: 11/09/2022]
Abstract
The prebiotic origins of biopolymers and metabolic co-factors are key questions in Origins of Life studies. In a simple warm-little-pond model, using a drying phase to produce a urea-enriched solution, we present a prebiotic synthetic path for the simultaneous formation of neopterins and tetrahydroneopterins, along with purine nucleosides. We show that, in the presence of ribose and in a formylating environment consisting of urea, ammonium formate, and water (UAFW), the formation of neopterins from pyrimidine precursors is robust, while the simultaneous formation of guanosine requires a significantly higher ribose concentration. Furthermore, these reactions provide a tetrahydropterin-pterin redox pair. This model suggests a prebiotic link in the origin of purine nucleosides and pterin cofactors that provides a possible deep prebiotic temporal connection for the emergence of nucleic acids and metabolic cofactors.
Collapse
Affiliation(s)
- César Menor‐Salván
- NSF-NASA Center for Chemical EvolutionGeorgia Institute of TechnologyAtlanta30302 GAUSA
- Dept. de Biología de Sistemas/IQARUniversidad de Alcalá28806MadridSpain
| | - Bradley T. Burcar
- Dept. de Biología de Sistemas/IQARUniversidad de Alcalá28806MadridSpain
- NASA HQ/Georgetown University/GSFCGreenbeltMD 20771
| | - Marcos Bouza
- Dept. de Biología de Sistemas/IQARUniversidad de Alcalá28806MadridSpain
- Dept. of Physical and Analytical ChemistryUniversidad de JaenJaén23071 JaenSpain
| | - David M. Fialho
- School of Chemistry and BiochemistryGeorgia Institute of TechnologyAtlanta30302 GAUSA
- Dept. de Biología de Sistemas/IQARUniversidad de Alcalá28806MadridSpain
| | - Facundo M. Fernández
- School of Chemistry and BiochemistryGeorgia Institute of TechnologyAtlanta30302 GAUSA
- Dept. de Biología de Sistemas/IQARUniversidad de Alcalá28806MadridSpain
| | - Nicholas V. Hud
- School of Chemistry and BiochemistryGeorgia Institute of TechnologyAtlanta30302 GAUSA
- Dept. de Biología de Sistemas/IQARUniversidad de Alcalá28806MadridSpain
| |
Collapse
|
14
|
Mason KA, Pearcy AC, Christensen ZA, Attah IK, Meot-Ner Mautner M, El-Shall MS. Water-Assisted Proton Transfer in the Sequential Hydration of Benzonitrile Radical Cation C 6H 5CN •+(H 2O) n: Transition to Hydrated Distonic Cation •C 6H 4CNH +(H 2O) n with n ≥ 4. J Am Chem Soc 2022; 144:9684-9694. [PMID: 35609235 DOI: 10.1021/jacs.2c01143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The stepwise hydration of the benzonitrile•+ radical cation with one-seven H2O molecules was investigated experimentally and computationally with density functional theory in C6H5CN•+(H2O)n clusters. The stepwise binding energies (ΔHn-1,n°) were determined by equilibrium measurements for C6H5CN•+(H2O) and for •C6H4CNH+(H2O)n with n = 5, 6, and 7 to be 8.8 and 11.3, 11.0, and 10.0 kcal/mol, respectively. The populations of n = 2 and 3 of the C6H5CN•+(H2O)n clusters were observed only in trace abundance due to fast depletion processes leading to the formation of the hydrated distonic cations •C6H4CNH+(H2O)n with n = 4-7. The observed transition occurs between conventional radical cations hydrated on the ring in C6H5CN•+(H2O)n clusters with n = 1-3 and the protonated radical •C6H4CNH+ (distonic ion) formed by a proton transfer to the CN nitrogen and ionic hydrogen bonding to water molecules in •C6H4CNH+(H2O)n clusters with n = 4-7. The measured binding energy of the hydrated ion C6H5CN•+(H2O) (8.8 kcal/mol) is similar to that of the hydrated benzene radical cation (8.5 kcal/mol) that involves a relatively weak CHδ+···O hydrogen bonding interaction. Also, the measured binding energies of the •C6H4CNH+(H2O)n clusters with n = 5-7 are similar to those of the protonated benzonitrile (methanol)n clusters [C6H5CNH+(CH3OH)n, n = 5-7] that involve CNH+···O ionic hydrogen bonds. The proton shift from the para-•C ring carbon to the nitrogen of the benzonitrile radical cation is endothermic without solvent but thermoneutral for n = 1 and exothermic for n = 2-4 in C6H5CN•+(H2O)n clusters to form the distonic •C6H4CN···H+(OH2)n clusters. The distonic clusters •C6H4CN···H+(OH2)n constitute a new class of structures in radical ion/solvent clusters.
Collapse
Affiliation(s)
- Kyle A Mason
- Department of Chemistry, Virginia Commonwealth University, Richmond 23284-2006 Virginia, United States
| | - Adam C Pearcy
- Department of Chemistry, Virginia Commonwealth University, Richmond 23284-2006 Virginia, United States
| | - Zachary A Christensen
- Department of Chemistry, Virginia Commonwealth University, Richmond 23284-2006 Virginia, United States
| | - Isaac K Attah
- Department of Chemistry, Virginia Commonwealth University, Richmond 23284-2006 Virginia, United States
| | - Michael Meot-Ner Mautner
- Department of Chemistry, Virginia Commonwealth University, Richmond 23284-2006 Virginia, United States
| | - M Samy El-Shall
- Department of Chemistry, Virginia Commonwealth University, Richmond 23284-2006 Virginia, United States
| |
Collapse
|
15
|
Freeze-thaw cycles enable a prebiotically plausible and continuous pathway from nucleotide activation to nonenzymatic RNA copying. Proc Natl Acad Sci U S A 2022; 119:e2116429119. [PMID: 35446612 PMCID: PMC9169909 DOI: 10.1073/pnas.2116429119] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The replication of RNA without the aid of evolved enzymes may have enabled the inheritance of useful molecular functions during the origin of life. Template-directed RNA copying is a posited step in RNA replication. Key steps on the path to copying of RNA templates have been studied in isolation, including chemical nucleotide activation, generation of a key reactive intermediate, and template-directed polymerization. Here we report a prebiotically plausible scenario under which these reactions can happen together under mutually compatible conditions. Thus, this pathway could potentially have operated in nature without the complicating requirement for exchange of materials between distinct environments. Nonenzymatic template-directed RNA copying using chemically activated nucleotides is thought to have played a key role in the emergence of genetic information on the early Earth. A longstanding question concerns the number and nature of different environments that might have been necessary to enable all of the steps from nucleotide synthesis to RNA copying. Here we explore three sequential steps from this overall pathway: nucleotide activation, synthesis of imidazolium-bridged dinucleotides, and template-directed RNA copying. We find that all three steps can take place in one reaction mixture undergoing multiple freeze-thaw cycles. Recent experiments have demonstrated a potentially prebiotic methyl isocyanide-based nucleotide activation chemistry. However, the original version of this approach is incompatible with nonenzymatic RNA copying because the high required concentration of the imidazole activating group prevents the accumulation of the essential imidazolium-bridged dinucleotide. Here we report that ice eutectic phase conditions facilitate not only the methyl isocyanide-based activation of ribonucleotide 5′-monophosphates with stoichiometric 2-aminoimidazole, but also the subsequent conversion of these activated mononucleotides into imidazolium-bridged dinucleotides. Furthermore, this one-pot approach is compatible with template-directed RNA copying in the same reaction mixture. Our results suggest that the simple and common environmental fluctuation of freeze-thaw cycles could have played an important role in prebiotic nucleotide activation and nonenzymatic RNA copying.
Collapse
|
16
|
From amino acid mixtures to peptides in liquid sulphur dioxide on early Earth. Nat Commun 2021; 12:7182. [PMID: 34893619 PMCID: PMC8664857 DOI: 10.1038/s41467-021-27527-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 11/18/2021] [Indexed: 01/01/2023] Open
Abstract
The formation of peptide bonds is one of the most important biochemical reaction steps. Without the development of structurally and catalytically active polymers, there would be no life on our planet. However, the formation of large, complex oligomer systems is prevented by the high thermodynamic barrier of peptide condensation in aqueous solution. Liquid sulphur dioxide proves to be a superior alternative for copper-catalyzed peptide condensations. Compared to water, amino acids are activated in sulphur dioxide, leading to the incorporation of all 20 proteinogenic amino acids into proteins. Strikingly, even extremely low initial reactant concentrations of only 50 mM are sufficient for extensive peptide formation, yielding up to 2.9% of dialanine in 7 days. The reactions carried out at room temperature and the successful use of the Hadean mineral covellite (CuS) as a catalyst, suggest a volcanic environment for the formation of the peptide world on early Earth. Peptide bond formation is one of the key biochemical reactions needed for the formation of life, but is thermodynamically unfavoured in water. Here, the authors report on the possibility of complex oligomer formation in liquid sulphur dioxide which may have existed on early Earth at the emergence of life.
Collapse
|
17
|
Chirumbolo S, Vella A. Molecules, Information and the Origin of Life: What Is Next? Molecules 2021; 26:molecules26041003. [PMID: 33672848 PMCID: PMC7917628 DOI: 10.3390/molecules26041003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/20/2022] Open
Abstract
How life did originate and what is life, in its deepest foundation? The texture of life is known to be held by molecules and their chemical-physical laws, yet a thorough elucidation of the aforementioned questions still stands as a puzzling challenge for science. Focusing solely on molecules and their laws has indirectly consolidated, in the scientific knowledge, a mechanistic (reductionist) perspective of biology and medicine. This occurred throughout the long historical path of experimental science, affecting subsequently the onset of the many theses and speculations about the origin of life and its maintenance. Actually, defining what is life, asks for a novel epistemology, a ground on which living systems’ organization, whose origin is still questioned via chemistry, physics and even philosophy, may provide a new key to focus onto the complex nature of the human being. In this scenario, many issues, such as the role of information and water structure, have been long time neglected from the theoretical basis on the origin of life and marginalized as a kind of scenic backstage. On the contrary, applied science and technology went ahead on considering molecules as the sole leading components in the scenery. Water physics and information dynamics may have a role in living systems much more fundamental than ever expected. Can an organism be simply explained by a mechanistic view of its nature or we need “something else”? Probably, we can earn sound foundations about life by simply changing our prejudicial view about living systems simply as complex, highly ordered machines. In this manuscript we would like to reappraise many fundamental aspects of molecular and chemical biology and reading them through a new paradigm, which includes Prigogine’s dissipative structures and informational dissipation (Shannon dissipation). This would provide readers with insightful clues about how biology and chemistry may be thoroughly revised, referring to new models, such as informational dissipation. We trust they are enabled to address a straightforward contribution in elucidating what life is for science. This overview is not simply a philosophical speculation, but it would like to affect deeply our way to conceive and describe the foundations of organisms’ life, providing intriguing suggestions for readers in the field.
Collapse
Affiliation(s)
- Salvatore Chirumbolo
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy
- Correspondence: ; Tel.: +39-0458027645
| | - Antonio Vella
- Verona-Unit of Immunology, Azienda Ospedaliera Universitaria Integrata, 37134 Verona, Italy;
| |
Collapse
|
18
|
Clark BC, Kolb VM. Macrobiont: Cradle for the Origin of Life and Creation of a Biosphere. Life (Basel) 2020; 10:life10110278. [PMID: 33198206 PMCID: PMC7697624 DOI: 10.3390/life10110278] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 11/09/2020] [Accepted: 11/09/2020] [Indexed: 02/06/2023] Open
Abstract
Although the cellular microorganism is the fundamental unit of biology, the origin of life (OoL) itself is unlikely to have occurred in a microscale environment. The macrobiont (MB) is the macro-scale setting where life originated. Guided by the methodologies of Systems Analysis, we focus on subaerial ponds of scale 3 to 300 m diameter. Within such ponds, there can be substantial heterogeneity, on the vertical, horizontal, and temporal scales, which enable multi-pot prebiotic chemical evolution. Pond size-sensitivities for several figures of merit are mathematically formulated, leading to the expectation that the optimum pond size for the OoL is intermediate, but biased toward smaller sizes. Sensitivities include relative access to nutrients, energy sources, and catalysts, as sourced from geological, atmospheric, hydrospheric, and astronomical contributors. Foreshores, especially with mudcracks, are identified as a favorable component for the success of the macrobiont. To bridge the gap between inanimate matter and a planetary-scale biosphere, five stages of evolution within the macrobiont are hypothesized: prebiotic chemistry → molecular replicator → protocell → macrobiont cell → colonizer cell. Comparison of ponds with other macrobionts, including hydrothermal and meteorite settings, allows a conclusion that more than one possible macrobiont locale could enable an OoL.
Collapse
Affiliation(s)
- Benton C. Clark
- Space Science Institute, Boulder, CO 80301, USA
- Correspondence:
| | - Vera M. Kolb
- Department of Chemistry, University of Wisconsin—Parkside, Kenosha, WI 53141, USA;
| |
Collapse
|
19
|
Abstract
Either stereo reactants or stereo catalysis from achiral or chiral molecules are a prerequisite to obtain pure enantiomeric lipid derivatives. We reviewed a few plausibly organic syntheses of phospholipids under prebiotic conditions with special attention paid to the starting materials as pro-chiral dihydroxyacetone and dihydroxyacetone phosphate (DHAP), which are the key molecules to break symmetry in phospholipids. The advantages of homochiral membranes compared to those of heterochiral membranes were analysed in terms of specific recognition, optimal functions of enzymes, membrane fluidity and topological packing. All biological membranes contain enantiomerically pure lipids in modern bacteria, eukarya and archaea. The contemporary archaea, comprising of methanogens, halobacteria and thermoacidophiles, are living under extreme conditions reminiscent of primitive environment and may indicate the origin of one ancient evolution path of lipid biosynthesis. The analysis of the known lipid metabolism reveals that all modern cells including archaea synthetize enantiomerically pure lipid precursors from prochiral DHAP. Sn-glycerol-1-phosphate dehydrogenase (G1PDH), usually found in archaea, catalyses the formation of sn-glycerol-1-phosphate (G1P), while sn-glycerol-3-phosphate dehydrogenase (G3PDH) catalyses the formation of sn-glycerol-3-phosphate (G3P) in bacteria and eukarya. The selective enzymatic activity seems to be the main strategy that evolution retained to obtain enantiomerically pure lipids. The occurrence of two genes encoding for G1PDH and G3PDH served to build up an evolutionary tree being the basis of our hypothesis article focusing on the evolution of these two genes. Gene encoding for G3PDH in eukarya may originate from G3PDH gene found in rare archaea indicating that archaea appeared earlier in the evolutionary tree than eukarya. Archaea and bacteria evolved probably separately, due to their distinct respective genes coding for G1PDH and G3PDH. We propose that prochiral DHAP is an essential molecule since it provides a convergent link between G1DPH and G3PDH. The synthesis of enantiopure phospholipids from DHAP appeared probably firstly in the presence of chemical catalysts, before being catalysed by enzymes which were the products of later Darwinian selection. The enzymes were probably selected for their efficient catalytic activities during evolution from large libraries of vesicles containing amino acids, carbohydrates, nucleic acids, lipids, and meteorite components that induced symmetry imbalance.
Collapse
|
20
|
Rajkoomar N, Murugesan A, Prabu S, Gengan RM. Synthesis of methyl piperazinyl-quinolinyl α-aminophosphonates derivatives under microwave irradiation with Pd–SrTiO 3 catalyst and their antibacterial and antioxidant activities. PHOSPHORUS SULFUR 2020. [DOI: 10.1080/10426507.2020.1799366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Nikisha Rajkoomar
- Department of Chemistry, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa
| | - Arul Murugesan
- Department of Chemistry, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa
| | - Samikannu Prabu
- Department of Chemistry, Chung-Yuan Christian University, Zhongli, Taiwan, R.O.C
| | - Robert M. Gengan
- Department of Chemistry, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa
| |
Collapse
|
21
|
Chen L, Liu X, Zou Y. Recent Advances in the Construction of Phosphorus‐Substituted Heterocycles, 2009–2019. Adv Synth Catal 2020. [DOI: 10.1002/adsc.201901540] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Long Chen
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of AntibioticsChengdu University 168 Hua Guan Road Chengdu 610052 Peoples's Republic of China
| | - Xiao‐Yan Liu
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of AntibioticsChengdu University 168 Hua Guan Road Chengdu 610052 Peoples's Republic of China
| | - Yun‐Xiang Zou
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of AntibioticsChengdu University 168 Hua Guan Road Chengdu 610052 Peoples's Republic of China
| |
Collapse
|
22
|
Hawkins K, Patterson AK, Clarke PA, Smith DK. Catalytic Gels for a Prebiotically Relevant Asymmetric Aldol Reaction in Water: From Organocatalyst Design to Hydrogel Discovery and Back Again. J Am Chem Soc 2020; 142:4379-4389. [PMID: 32023044 PMCID: PMC7146862 DOI: 10.1021/jacs.9b13156] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Indexed: 12/14/2022]
Abstract
This paper reports an investigation into organocatalytic hydrogels as prebiotically relevant systems. Gels are interesting prebiotic reaction media, combining heterogeneous and homogeneous characteristics with a structurally organized active "solid-like" catalyst separated from the surrounding environment, yet in intimate contact with the solution phase and readily accessible via "liquid-like" diffusion. A simple self-assembling glutamine amide derivative 1 was initially found to catalyze a model aldol reaction between cyclohexanone and 4-nitrobenzaldehyde, but it did not maintain its gel structure during reaction. In this study, it was observed that compound 1 could react directly with the benzaldehyde to form a hydrogel in situ based on Schiff base 2 as a low-molecular-weight gelator (LMWG). This new dynamic gel is a rare example of a two-component self-assembled LMWG hydrogel and was fully characterized. It was demonstrated that glutamine amide 1 could select an optimal aldehyde component and preferentially assemble from mixtures. In the hunt for an organocatalyst, reductive conditions were applied to the Schiff base to yield secondary amine 3, which is also a highly effective hydrogelator at very low loadings with a high degree of nanoscale order. Most importantly, the hydrogel based on 3 catalyzed the prebiotically relevant aldol dimerization of glycolaldehyde to give threose and erythrose. In buffered conditions, this reaction gave excellent conversions, good diastereoselectivity, and some enantioselectivity. Catalysis using the hydrogel of 3 was much better than that using non-assembled 3-demonstrating a clear benefit of self-assembly. The results suggest that hydrogels offer a potential strategy by which prebiotic reactions can be promoted using simple, prebiotically plausible LMWGs that can selectively self-organize from complex mixtures. Such processes may have been of prebiotic importance.
Collapse
Affiliation(s)
- Kirsten Hawkins
- Department of Chemistry, University
of York, Heslington, York YO10 5DD, U.K.
| | - Anna K. Patterson
- Department of Chemistry, University
of York, Heslington, York YO10 5DD, U.K.
| | - Paul A. Clarke
- Department of Chemistry, University
of York, Heslington, York YO10 5DD, U.K.
| | - David K. Smith
- Department of Chemistry, University
of York, Heslington, York YO10 5DD, U.K.
| |
Collapse
|
23
|
Das T, Ghule S, Vanka K. Insights Into the Origin of Life: Did It Begin from HCN and H 2O? ACS CENTRAL SCIENCE 2019; 5:1532-1540. [PMID: 31572780 PMCID: PMC6764159 DOI: 10.1021/acscentsci.9b00520] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Indexed: 05/14/2023]
Abstract
The seminal Urey-Miller experiments showed that molecules crucial to life such as HCN could have formed in the reducing atmosphere of the Hadean Earth and then dissolved in the oceans. Subsequent proponents of the "RNA World" hypothesis have shown aqueous HCN to be the starting point for the formation of the precursors of RNA and proteins. However, the conditions of early Earth suggest that aqueous HCN would have had to react under a significant number of constraints. Therefore, given the limiting conditions, could RNA and protein precursors still have formed from aqueous HCN? If so, what mechanistic routes would have been followed? The current computational study, with the aid of the ab initio nanoreactor (AINR), a powerful new tool in computational chemistry, addresses these crucial questions. Gratifyingly, not only do the results from the AINR approach show that aqueous HCN could indeed have been the source of RNA and protein precursors, but they also indicate that just the interaction of HCN with water would have sufficed to begin a series of reactions leading to the precursors. The current work therefore provides important missing links in the story of prebiotic chemistry and charts the road from aqueous HCN to the precursors of RNA and proteins.
Collapse
Affiliation(s)
- Tamal Das
- Physical and Materials Chemistry Division,
CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha
Road, Pashan, Pune 411008, India
- Academy of Scientific and Innovative
Research (AcSIR), Ghaziabad 201002, India
| | - Siddharth Ghule
- Physical and Materials Chemistry Division,
CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha
Road, Pashan, Pune 411008, India
- Academy of Scientific and Innovative
Research (AcSIR), Ghaziabad 201002, India
| | - Kumar Vanka
- Physical and Materials Chemistry Division,
CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha
Road, Pashan, Pune 411008, India
- Academy of Scientific and Innovative
Research (AcSIR), Ghaziabad 201002, India
- E-mail:
| |
Collapse
|
24
|
Lamour S, Pallmann S, Haas M, Trapp O. Prebiotic Sugar Formation Under Nonaqueous Conditions and Mechanochemical Acceleration. Life (Basel) 2019; 9:life9020052. [PMID: 31226799 PMCID: PMC6617062 DOI: 10.3390/life9020052] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 12/26/2022] Open
Abstract
Monosaccharides represent one of the major building blocks of life. One of the plausible prebiotic synthesis routes is the formose network, which generates sugars from C1 and C2 carbon sources in basic aqueous solution. We report on the feasibility of the formation of monosaccharides under physical forces simulated in a ball mill starting from formaldehyde, glycolaldehyde, DL-glyceraldehyde as prebiotically available substrates using catalytically active, basic minerals. We investigated the influence of the mechanic energy input on our model system using calcium hydroxide in an oscillatory ball mill. We show that the synthesis of monosaccharides is kinetically accelerated under mechanochemical conditions. The resulting sugar mixture contains monosaccharides with straight and branched carbon chains as well as decomposition products. In comparison to the sugar formation in water, the monosaccharides formed under mechanochemical conditions are more stable and selectively synthesized. Our results imply the possibility of a prebiotic monosaccharide origin in geochemical environments scant or devoid of water promoted by mechanochemical forces such as meteorite impacts or lithospheric activity.
Collapse
Affiliation(s)
- Saskia Lamour
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany.
- Max-Planck-Institut für Astronomie, Königstuhl 17, 69117 Heidelberg, Germany.
| | - Sebastian Pallmann
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany.
| | - Maren Haas
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany.
- Max-Planck-Institut für Astronomie, Königstuhl 17, 69117 Heidelberg, Germany.
| | - Oliver Trapp
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany.
- Max-Planck-Institut für Astronomie, Königstuhl 17, 69117 Heidelberg, Germany.
| |
Collapse
|
25
|
Zeng S, Quénard D, Jiménez-Serra I, Martín-Pintado J, Rivilla VM, Testi L, Martín-Doménech R. First detection of the pre-biotic molecule glycolonitrile (HOCH2CN) in the interstellar medium. ACTA ACUST UNITED AC 2019. [DOI: 10.1093/mnrasl/slz002] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- S Zeng
- School of Physics and Astronomy, Queen Mary University of London, Mile End Road, E1 4NS London, United Kingdom
| | - D Quénard
- School of Physics and Astronomy, Queen Mary University of London, Mile End Road, E1 4NS London, United Kingdom
| | - I Jiménez-Serra
- Centro de Astrobiología (CSIC, INTA), Ctra. de Ajalvir, km. 4, Torrejón de Ardoz, E-28850 Madrid, Spain
| | - J Martín-Pintado
- Centro de Astrobiología (CSIC, INTA), Ctra. de Ajalvir, km. 4, Torrejón de Ardoz, E-28850 Madrid, Spain
| | - V M Rivilla
- INAF-Osservatorio Astrofisico di Arcetri, Largo Enrico Fermi 5, I-50125 Florence, Italy
| | - L Testi
- INAF-Osservatorio Astrofisico di Arcetri, Largo Enrico Fermi 5, I-50125 Florence, Italy
- Excellence Cluster ‘Universe’, Boltzmann str. 2, D-85748 Garching bei Muenchen, Germany
- ESO/European Southern Observatory, Karl Schwarzschild str. 2, D-85748 Garching, Germany
| | - R Martín-Doménech
- Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, MA 02138 Cambridge, USA
| |
Collapse
|
26
|
Kasprzyk W, Swiergosz T, Bednarz S, Walas K, Bashmakova NV, Bogdał D. Luminescence phenomena of carbon dots derived from citric acid and urea - a molecular insight. NANOSCALE 2018; 10:13889-13894. [PMID: 29999091 DOI: 10.1039/c8nr03602k] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
In this report, we present the results of our investigations into the elucidation of the chemical structure of moieties responsible for the blue and green luminescence of CDs derived from the microwave-assisted pyrolysis of citric acid in the presence of urea. The molecular fluorophore that forms during the synthesis of green fluorescing CDs is 4-hydroxy-1H-pyrrolo[3,4-c]pyridine-1,3,6(2H,5H)-trione (HPPT).
Collapse
Affiliation(s)
- Wiktor Kasprzyk
- Department of Biotechnology and Physical Chemistry, Faculty of Chemical Engineering and Technology, Cracow University of Technology, 24 Warszawska St., 32-048 Krakow, Poland.
| | - Tomasz Swiergosz
- Department of Analytical Chemistry, Faculty of Chemical Engineering and Technology, Cracow University of Technology, 24 Warszawska St., 32-048 Krakow, Poland
| | - Szczepan Bednarz
- Department of Biotechnology and Physical Chemistry, Faculty of Chemical Engineering and Technology, Cracow University of Technology, 24 Warszawska St., 32-048 Krakow, Poland.
| | - Karolina Walas
- Department of Biotechnology and Physical Chemistry, Faculty of Chemical Engineering and Technology, Cracow University of Technology, 24 Warszawska St., 32-048 Krakow, Poland.
| | - Natalia V Bashmakova
- Department of Experimental Physics, Faculty of Physics, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Dariusz Bogdał
- Department of Biotechnology and Physical Chemistry, Faculty of Chemical Engineering and Technology, Cracow University of Technology, 24 Warszawska St., 32-048 Krakow, Poland.
| |
Collapse
|
27
|
Clark BC, Kolb VM. Comet Pond II: Synergistic Intersection of Concentrated Extraterrestrial Materials and Planetary Environments to Form Procreative Darwinian Ponds. Life (Basel) 2018; 8:E12. [PMID: 29751593 PMCID: PMC6027224 DOI: 10.3390/life8020012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/24/2018] [Accepted: 05/02/2018] [Indexed: 12/12/2022] Open
Abstract
In the “comet pond” model, a rare combination of circumstances enables the entry and landing of pristine organic material onto a planetary surface with the creation of a pond by a soft impact and melting of entrained ices. Formation of the constituents of the comet in the cold interstellar medium and our circumstellar disk results in multiple constituents at disequilibrium which undergo rapid chemical reactions in the warmer, liquid environment. The planetary surface also provides minerals and atmospheric gases which chemically interact with the pond’s organic- and trace-element-rich constituents. Pond physical morphology and the heterogeneities imposed by gravitational forces (bottom sludge; surface scum) and weather result in a highly heterogeneous variety of macro- and microenvironments. Wet/dry, freeze/thaw, and natural chromatography processes further promote certain reaction sequences. Evaporation concentrates organics less volatile than water. Freezing concentrates all soluble organics into a residual liquid phase, including CH₃OH, HCN, etc. The pond’s evolutionary processes culminate in the creation of a Macrobiont with the metabolically equivalent capabilities of energy transduction and replication of RNA (or its progenitor informational macromolecule), from which smaller organisms can emerge. Planet-wide dispersal of microorganisms is achieved through wind transport, groundwater, and/or spillover from the pond into surface hydrologic networks.
Collapse
Affiliation(s)
- Benton C Clark
- Research Branch, Space Science Institute, Boulder, CO 80201, USA.
| | - Vera M Kolb
- Department of Chemistry, University of Wisconsin⁻Parkside, Kenosha, WI 53141, USA.
| |
Collapse
|
28
|
Hao J, Giovenco E, Pedreira-Segade U, Montagnac G, Daniel I. Compatibility of Amino Acids in Ice Ih: Implications for the Origin of Life. ASTROBIOLOGY 2018; 18:381-392. [PMID: 29620923 DOI: 10.1089/ast.2017.1735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Icy environments may have been common on early Earth due to the faint young sun. Previous studies have proposed that the formation of large icy bodies in the early ocean could concentrate the building blocks of life in eutectic fluids and, therefore, facilitate the polymerization of monomers. This hypothesis is based on the untested assumption that organic molecules are virtually incompatible in ice Ih (hexagonal ice). In this study, we conducted freezing experiments to explore the partitioning behavior of selected amino acids (AAs; glycine, l-alanine, l-proline, and l-phenylalanine) between ice Ih and aqueous solutions analogous to seawater. We allowed ice crystals to grow slowly from a few seeds in equilibrium with the solution and used Raman spectroscopy to analyze in situ the relative concentrations of AAs in the ice and aqueous solution. During freezing, there was no precipitation of AA crystals, indicating that the concentrations in solution never reached their solubility limit, even when the droplet was mostly frozen. Analyses of the Raman spectra of the ice and eutectic solution suggested that considerable amounts of AAs existed in the ice phase with partition coefficients varying between 0.2 and 0.5. These observations imply little incompatibility of AAs in ice Ih during the freezing of the solutions, rendering the concentration hypothesis in a eutectic system unwarranted. However, incorporation into ice Ih could protect AAs from decomposition or racemization and significantly improve the efficiency of extraterrestrial transport of small organics. Therefore, this study supports the hypothesis of extraterrestrial delivery of organic molecules in icy comets and asteroids to the primitive Earth as suggested by an increasing number of independent observations. Key Words: Ice Ih-Partition coefficient-Amino acids-Polymerization-Extraterrestrial transport of organics. Astrobiology 18, 381-392.
Collapse
Affiliation(s)
- Jihua Hao
- Univ Lyon, Université Lyon 1 , Ens de Lyon, CNRS, UMR 5276 LGL-TPE, Villeurbanne, France
| | - Elena Giovenco
- Univ Lyon, Université Lyon 1 , Ens de Lyon, CNRS, UMR 5276 LGL-TPE, Villeurbanne, France
| | - Ulysse Pedreira-Segade
- Univ Lyon, Université Lyon 1 , Ens de Lyon, CNRS, UMR 5276 LGL-TPE, Villeurbanne, France
| | - Gilles Montagnac
- Univ Lyon, Université Lyon 1 , Ens de Lyon, CNRS, UMR 5276 LGL-TPE, Villeurbanne, France
| | - Isabelle Daniel
- Univ Lyon, Université Lyon 1 , Ens de Lyon, CNRS, UMR 5276 LGL-TPE, Villeurbanne, France
| |
Collapse
|
29
|
Marín-Yaseli MR, Moreno M, de la Fuente JL, Briones C, Ruiz-Bermejo M. Experimental conditions affecting the kinetics of aqueous HCN polymerization as revealed by UV-vis spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 191:389-397. [PMID: 29065330 DOI: 10.1016/j.saa.2017.10.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 09/27/2017] [Accepted: 10/01/2017] [Indexed: 05/26/2023]
Abstract
HCN polymerization is one of the most important and fascinating reactions in prebiotic chemistry, and interest in HCN polymers in the field of materials science is growing. However, little is known about the kinetics of the HCN polymerization process. In the present study, a first approach to the kinetics of two sets of aqueous HCN polymerizations, from NH4CN and NaCN, at middle temperatures between 4 and 38°C, has been carried out. For each series, the presence of air and salts in the reaction medium has been systematically explored. A previous kinetic analysis was conducted during the conversion of the insoluble black HCN polymers obtained as gel fractions in these precipitation polymerizations for a reaction of one month, where a limit conversion was achieved at the highest polymerization temperature. The kinetic description of the gravimetric data for this complex system shows a clear change in the linear dependence with the polymerization temperature for the reaction from NH4CN, besides a relevant catalytic effect of ammonium, in comparison with those data obtained from the NaCN series. These results also demonstrated the notable influence of air, oxygen, and the saline medium in HCN polymer formation. Similar conclusions were reached when the sol fractions were monitored by UV-vis spectroscopy, and a Hill type correlation was used to describe the polymerization profiles obtained. This technique was chosen because it provides an easy, prompt and fast method to follow the evolution of the liquid or continuous phase of the process under study.
Collapse
Affiliation(s)
- Margarita R Marín-Yaseli
- Centro de Astrobiología (INTA-CSIC), Dpto. Evolución Molecular, Ctra. Torrejón-Ajalvir, km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - Miguel Moreno
- Centro de Astrobiología (INTA-CSIC), Dpto. Evolución Molecular, Ctra. Torrejón-Ajalvir, km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - José L de la Fuente
- Instituto Nacional de Técnica Aeroespacial "Esteban Terradas" (INTA), Ctra. Torrejón-Ajalvir, km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - Carlos Briones
- Centro de Astrobiología (INTA-CSIC), Dpto. Evolución Molecular, Ctra. Torrejón-Ajalvir, km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - Marta Ruiz-Bermejo
- Centro de Astrobiología (INTA-CSIC), Dpto. Evolución Molecular, Ctra. Torrejón-Ajalvir, km 4, Torrejón de Ardoz, 28850 Madrid, Spain.
| |
Collapse
|
30
|
Mungi CV, Singh SK, Chugh J, Rajamani S. Synthesis of barbituric acid containing nucleotides and their implications for the origin of primitive informational polymers. Phys Chem Chem Phys 2018; 18:20144-52. [PMID: 27153469 DOI: 10.1039/c6cp00686h] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Given that all processes in modern biology are encoded and orchestrated by polymers, the origin of informational molecules had to be a crucial and significant step in the origin of life on Earth. An important molecule in this context is RNA that is thought to have allowed the transition from chemistry to biology. However, the RNA molecule is comprised of intramolecular bonds which are prone to hydrolysis, especially so under the harsh conditions of the early Earth. Furthermore, the formation of nucleotides with extant bases and their subsequent polymerization have both been problematic, to say the least. Alternate heterocycles, in contrast, have resulted in nucleosides in higher yields, suggesting a viable and prebiotically relevant solution to the longstanding "nucleoside problem". In the present study, we have synthesized a nucleotide using ribose 5'-monophosphate (rMP) and barbituric acid (BA), as the base analog, using dry-heating conditions that are thought to be prevalent in several regimes of the early Earth. Polymerization of the resultant monomers, i.e. BA-nucleotides, was also observed when dehydration-rehydration cycles were carried out at low pH and high temperature. The resulting RNA-like oligomers have intact bases unlike in reactions that were carried out with canonical nucleotides, which resulted in abasic sites under acidic conditions due to cleavage of the N-glycosidic linkages. Furthermore, the incorporation of BA directly into preformed sugar-phosphate backbones was also observed when rMP oligomers were subjected to heating with BA. The results from our aforementioned experiments provide preliminary evidence that BA could have been a putative precursor of modern nucleobases, which could have been incorporated into primitive informational polymers that predated the molecules of an RNA world. Moreover, they also highlight that the prebiotic soup, which would have been replete with alternate heterocycles, could have allowed the sampling of other such heterocycles, which would have had a selective advantage under pertinent selection pressures. Importantly, these kinds of processes have implications for shaping the prebiotic landscape that allowed for the emergence of primitive informational polymers of the pre-RNA world(s), prior to the emergence of a putative RNA world.
Collapse
Affiliation(s)
- Chaitanya V Mungi
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra 411008, India.
| | - Sachin Kumar Singh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra 411008, India.
| | - Jeetender Chugh
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra 411008, India. and Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra 411008, India.
| | - Sudha Rajamani
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra 411008, India.
| |
Collapse
|
31
|
Menor-Salván C. From the Dawn of Organic Chemistry to Astrobiology: Urea as a Foundational Component in the Origin of Nucleobases and Nucleotides. PREBIOTIC CHEMISTRY AND CHEMICAL EVOLUTION OF NUCLEIC ACIDS 2018. [DOI: 10.1007/978-3-319-93584-3_4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
|
32
|
Jamshidi MP, MacDonald MJ, Beauchemin AM. On the Ability of Formaldehyde to Act as a Tethering Catalyst in Water. ORIGINS LIFE EVOL B 2017; 47:405-412. [PMID: 28474281 DOI: 10.1007/s11084-017-9538-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 04/20/2017] [Indexed: 10/19/2022]
Abstract
The low concentration issue is a fundamental challenge when it comes to prebiotic chemistry, as macromolecular systems need to be assembled via intermolecular reactions, and this is inherently difficult in dilute solutions. This is especially true when the reactions are challenging, and reactions that proceeded more rapidly could have dictated chemical evolution. Herein we establish that formaldehyde is capable of catalyzing, via temporary intramolecularity, a challenging reaction in water at low concentrations, thus providing an alternative to other approaches that can either lead to higher concentrations or higher effective molarities.
Collapse
Affiliation(s)
- Mohammad P Jamshidi
- Center for Catalysis Research and Innovation, Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie, Ottawa, ON, K1N 6N5, Canada
| | - Melissa J MacDonald
- Center for Catalysis Research and Innovation, Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie, Ottawa, ON, K1N 6N5, Canada
| | - André M Beauchemin
- Center for Catalysis Research and Innovation, Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie, Ottawa, ON, K1N 6N5, Canada.
| |
Collapse
|
33
|
Kiss B, Fábián B, Idrissi A, Szőri M, Jedlovszky P. Miscibility and Thermodynamics of Mixing of Different Models of Formamide and Water in Computer Simulation. J Phys Chem B 2017; 121:7147-7155. [PMID: 28657740 DOI: 10.1021/acs.jpcb.7b04965] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The thermodynamic changes that occur upon mixing five models of formamide and three models of water, including the miscibility of these model combinations itself, is studied by performing Monte Carlo computer simulations using an appropriately chosen thermodynamic cycle and the method of thermodynamic integration. The results show that the mixing of these two components is close to the ideal mixing, as both the energy and entropy of mixing turn out to be rather close to the ideal term in the entire composition range. Concerning the energy of mixing, the OPLS/AA_mod model of formamide behaves in a qualitatively different way than the other models considered. Thus, this model results in negative, while the other ones in positive energy of mixing values in combination with all three water models considered. Experimental data supports this latter behavior. Although the Helmholtz free energy of mixing always turns out to be negative in the entire composition range, the majority of the model combinations tested either show limited miscibility, or, at least, approach the miscibility limit very closely in certain compositions. Concerning both the miscibility and the energy of mixing of these model combinations, we recommend the use of the combination of the CHARMM formamide and TIP4P water models in simulations of water-formamide mixtures.
Collapse
Affiliation(s)
- Bálint Kiss
- Institute of Chemistry, University of Miskolc , Egyetemváros A/2, H-3515 Miskolc, Hungary.,Laboratoire de Spectrochimie Infrarouge et Raman (UMR CNRS 8516), University of Lille Nord de France , 59655 Villeneuve d'Ascq Cedex, France
| | - Balázs Fábián
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics , Szt. Gellért tér 4, H-1111 Budapest, Hungary.,Institut UTINAM (CNRS UMR 6213), Université Bourgogne Franche-Comté , 16 route de Gray, F-25030 Besançon, France
| | - Abdenacer Idrissi
- Laboratoire de Spectrochimie Infrarouge et Raman (UMR CNRS 8516), University of Lille Nord de France , 59655 Villeneuve d'Ascq Cedex, France
| | - Milán Szőri
- Institute of Chemistry, University of Miskolc , Egyetemváros A/2, H-3515 Miskolc, Hungary
| | - Pál Jedlovszky
- Department of Chemistry, Eszterházy Károly University , Leányka utca 6, H-3300 Eger, Hungary
| |
Collapse
|
34
|
Cryosphere and Psychrophiles: Insights into a Cold Origin of Life? Life (Basel) 2017; 7:life7020025. [PMID: 28604605 PMCID: PMC5492147 DOI: 10.3390/life7020025] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 06/06/2017] [Accepted: 06/08/2017] [Indexed: 11/23/2022] Open
Abstract
Psychrophiles thrive permanently in the various cold environments on Earth. Their unsuspected ability to remain metabolically active in the most extreme low temperature conditions provides insights into a possible cold step in the origin of life. More specifically, metabolically active psychrophilic bacteria have been observed at −20 °C in the ice eutectic phase (i.e., the liquid veins between sea ice crystals). In the context of the RNA world hypothesis, this ice eutectic phase would have provided stability to the RNA molecules and confinement of the molecules in order to react and replicate. This aspect has been convincingly tested by laboratory experiments.
Collapse
|
35
|
Li BJ, EI-Nachef C, Beauchemin AM. Organocatalysis using aldehydes: the development and improvement of catalytic hydroaminations, hydrations and hydrolyses. Chem Commun (Camb) 2017; 53:13192-13204. [DOI: 10.1039/c7cc07352f] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Aldehydes as organocatalysts? Simple aldehydes achieve difficult intermolecular reactions by exploiting temporary intramolecularity and inducing electrophilic activation.
Collapse
Affiliation(s)
- Bin-Jie Li
- Centre for Catalysis Research and Innovation
- Department of Chemistry and Biomolecular Sciences
- University of Ottawa
- Ottawa
- Canada
| | - Claudia EI-Nachef
- Centre for Catalysis Research and Innovation
- Department of Chemistry and Biomolecular Sciences
- University of Ottawa
- Ottawa
- Canada
| | - André M. Beauchemin
- Centre for Catalysis Research and Innovation
- Department of Chemistry and Biomolecular Sciences
- University of Ottawa
- Ottawa
- Canada
| |
Collapse
|
36
|
Haji M. Multicomponent reactions: A simple and efficient route to heterocyclic phosphonates. Beilstein J Org Chem 2016; 12:1269-301. [PMID: 27559377 PMCID: PMC4979670 DOI: 10.3762/bjoc.12.121] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 05/23/2016] [Indexed: 12/22/2022] Open
Abstract
Multicomponent reactions (MCRs) are one of the most important processes for the preparation of highly functionalized organic compounds in modern synthetic chemistry. As shown in this review, they play an important role in organophosphorus chemistry where phosphorus reagents are used as substrates for the synthesis of a wide range of phosphorylated heterocycles. In this article, an overview about multicomponent reactions used for the synthesis of heterocyclic compounds bearing a phosphonate group on the ring is given.
Collapse
Affiliation(s)
- Mohammad Haji
- Chemistry Department, Science and Research Branch, Islamic Azad University, Tehran, Iran
| |
Collapse
|
37
|
Platt SP, Attah IK, El-Shall MS, Hilal R, Elroby SA, Aziz SG. Unconventional CH(δ+)···N hydrogen bonding interactions in the stepwise solvation of the naphthalene radical cation by hydrogen cyanide and acetonitrile molecules. Phys Chem Chem Phys 2016; 18:2580-90. [PMID: 26700190 DOI: 10.1039/c5cp06502j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Equilibrium thermochemical measurements using the mass-selected ion mobility (MSIM) technique have been utilized to investigate the binding energies and entropy changes of the stepwise association of hydrogen cyanide (HCN) and acetonitrile (CH3CN) molecules with the naphthalene radical cation (C10H8˙(+)) in the gas phase forming the C10H8˙(+)(HCN)n and C10H8˙(+)(CH3CN)n clusters with n = 1-3 and 1-5, respectively. The lowest energy structures of the C10H8˙(+)(HCN)n and C10H8˙(+)(CH3CN)n clusters for n = 1-2 have been calculated using the M062X and ω97XD methods within the 6-311+G** basis set, and for n = 1-6 using the B3LYP method within the 6-311++G** basis set. In both systems, the initial interaction occurs through unconventional CH(δ+)···N ionic hydrogen bonds between the hydrogen atoms of the naphthalene cation and the lone pair of electrons on the N atom of the HCN or the CH3CN molecule. The binding energy of CH3CN to the naphthalene cation (11 kcal mol(-1)) is larger than that of HCN (7 kcal mol(-1)) due to a stronger ion-dipole interaction resulting from the large dipole moment of CH3CN (3.9 D). On the other hand, HCN can form both unconventional hydrogen bonds with the hydrogen atoms of the naphthalene cation (CH(δ+)···NCH), and conventional linear hydrogen bonding chains involving HCN···HCN interactions among the associated HCN molecules. HCN molecules tend to form "externally solvated" structures with the naphthalene cation where the naphthalene ion is hydrogen bonded to the exterior of an HCN···HCN chain. For the C10H8˙(+)(CH3CN)n clusters, "internally solvated" structures are favored where the acetonitrile molecules are directly interacting with the naphthalene cation through CH(δ+)···N unconventional ionic hydrogen bonds. In both the C10H8˙(+)(HCN)n and C10H8˙(+)(CH3CN)n clusters, the sequential binding energy decreases stepwise to about 6-7 kcal mol(-1) by three HCN or CH3CN molecules, approaching the macroscopic enthalpy of vaporization of liquid HCN (6.0 kcal mol(-1)).
Collapse
Affiliation(s)
- Sean P Platt
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284-2006, USA.
| | - Isaac K Attah
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284-2006, USA.
| | - M S El-Shall
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284-2006, USA.
| | - Rifaat Hilal
- Department of Chemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia and Department of Chemistry, Faculty of Science, Cairo University, Giza, Egypt
| | - Shaaban A Elroby
- Department of Chemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia and Department of Chemistry, Faculty of Science, Beni-Seif University, Beni-Suef, Egypt
| | - Saadullah G Aziz
- Department of Chemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| |
Collapse
|
38
|
Maccario L, Sanguino L, Vogel TM, Larose C. Snow and ice ecosystems: not so extreme. Res Microbiol 2015; 166:782-95. [PMID: 26408452 DOI: 10.1016/j.resmic.2015.09.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 09/02/2015] [Accepted: 09/11/2015] [Indexed: 11/18/2022]
Abstract
Snow and ice environments cover up to 21% of the Earth's surface. They have been regarded as extreme environments because of their low temperatures, high UV irradiation, low nutrients and low water availability, and thus, their microbial activity has not been considered relevant from a global microbial ecology viewpoint. In this review, we focus on why snow and ice habitats might not be extreme from a microbiological perspective. Microorganisms interact closely with the abiotic conditions imposed by snow and ice habitats by having diverse adaptations, that include genetic resistance mechanisms, to different types of stresses in addition to inhabiting various niches where these potential stresses might be reduced. The microbial communities inhabiting snow and ice are not only abundant and taxonomically diverse, but complex in terms of their interactions. Altogether, snow and ice seem to be true ecosystems with a role in global biogeochemical cycles that has likely been underestimated. Future work should expand past resistance studies to understanding the function of these ecosystems.
Collapse
Affiliation(s)
- Lorrie Maccario
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Université de Lyon, Ecole Centrale de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France
| | - Laura Sanguino
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Université de Lyon, Ecole Centrale de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France
| | - Timothy M Vogel
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Université de Lyon, Ecole Centrale de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France
| | - Catherine Larose
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Université de Lyon, Ecole Centrale de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France.
| |
Collapse
|
39
|
Mungi CV, Rajamani S. Characterization of RNA-Like Oligomers from Lipid-Assisted Nonenzymatic Synthesis: Implications for Origin of Informational Molecules on Early Earth. Life (Basel) 2015; 5:65-84. [PMID: 25569237 PMCID: PMC4390841 DOI: 10.3390/life5010065] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 12/23/2014] [Indexed: 11/16/2022] Open
Abstract
Prebiotic polymerization had to be a nonenzymatic, chemically driven process. These processes would have been particularly favored in scenarios which push reaction regimes far from equilibrium. Dehydration-rehydration (DH-RH) cycles are one such regime thought to have been prevalent on prebiotic Earth in niches like volcanic geothermal pools. The present study defines the optimum DH-RH reaction conditions for lipid-assisted polymerization of nucleotides. The resultant products were characterized to understand their chemical makeup. Primarily, our study demonstrates that the resultant RNA-like oligomers have abasic sites, which means these oligomers lack information-carrying capability because of losing most of their bases during the reaction process. This results from low pH and high temperature conditions, which, importantly, also allows the formation of sugar-phosphate oligomers when ribose 5'-monophosphates are used as the starting monomers instead. Formation of such oligomers would have permitted sampling of a large variety of bases on a preformed polymer backbone, resulting in “prebiotic phosphodiester polymers” prior to the emergence of modern RNA-like molecules. This suggests that primitive genetic polymers could have utilized bases that conferred greater N-glycosyl bond stability, a feature crucial for information propagation in low pH and high temperature regimes of early Earth.
Collapse
Affiliation(s)
- Chaitanya V Mungi
- Indian Institute of Science Education and Research (IISER), Pune, Maharashtra 411008, India.
| | - Sudha Rajamani
- Indian Institute of Science Education and Research (IISER), Pune, Maharashtra 411008, India.
| |
Collapse
|
40
|
Sun YY, Liu FS, Xu LH, Liu QJ, Ma XJ, Cai LC. Vibrational spectrum of condensed H 2O in hydrogen-bonding environment: an ab initiosimulation study. Mol Phys 2015. [DOI: 10.1080/00268976.2014.944237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
41
|
Shaw JW, Grayson DH, Rozas I. Synthesis of Guanidines and Some of Their Biological Applications. TOPICS IN HETEROCYCLIC CHEMISTRY 2015. [DOI: 10.1007/7081_2015_174] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
42
|
Hamid AM, Bera PP, Lee TJ, Aziz SG, Alyoubi AO, El-Shall MS. Evidence for the Formation of Pyrimidine Cations from the Sequential Reactions of Hydrogen Cyanide with the Acetylene Radical Cation. J Phys Chem Lett 2014; 5:3392-3398. [PMID: 26278451 DOI: 10.1021/jz501648q] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Herein, we report the first direct evidence for the formation of pyrimidine ion isomers by sequential reactions of HCN with the acetylene radical cation in the gas phase at ambient temperature using the mass-selected variable temperature and pressure ion mobility technique. The formation and structures of the pyrimidine ion isomers are theoretically predicted via coupled cluster and density functional theory calculations. This ion-molecule synthesis may indicate that pyrimidine is produced in the gas phase in space environments before being incorporated into condensed-phase ices and transformed into nucleic acid bases such as uracil.
Collapse
Affiliation(s)
- Ahmed M Hamid
- †Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, United States
| | - Partha P Bera
- ‡NASA Ames Research Center, Moffett Field, California 94035, United States
- #Bay Area Environmental Research Institute, Petaluma, California 94952, United States
| | - Timothy J Lee
- ‡NASA Ames Research Center, Moffett Field, California 94035, United States
| | - Saadullah G Aziz
- §Department of Chemistry, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | | | - M Samy El-Shall
- †Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, United States
| |
Collapse
|
43
|
Hamid AM, El-Shall MS, Hilal R, Elroby S, Aziz SG. Unconventional hydrogen bonding to organic ions in the gas phase: Stepwise association of hydrogen cyanide with the pyridine and pyrimidine radical cations and protonated pyridine. J Chem Phys 2014; 141:054305. [DOI: 10.1063/1.4890372] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
|
44
|
Mutschler H, Holliger P. Non-canonical 3'-5' extension of RNA with prebiotically plausible ribonucleoside 2',3'-cyclic phosphates. J Am Chem Soc 2014; 136:5193-6. [PMID: 24660752 PMCID: PMC4333585 DOI: 10.1021/ja4127714] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
![]()
Ribonucleoside
2′,3′-cyclic phosphates (N>p’s)
are generated by multiple prebiotically plausible processes and are
credible building blocks for the assembly of early RNA oligomers.
While N>p’s can be polymerized into short RNAs by non-enzymatic
processes with variable efficiency and regioselectivity, no enzymatic
route for RNA synthesis had been described. Here we report such a
non-canonical 3′-5′ nucleotidyl transferase activity.
We engineered a variant of the hairpin ribozyme to catalyze addition
of all four N>p’s (2′,3′-cyclic A-, G-, U-,
and
CMP) to the 5′-hydroxyl termini of RNA strands with 5′
nucleotide addition enhanced in all cases by eutectic ice phase formation
at −7 °C. We also observed 5′ addition of 2′,3′-cyclic
phosphate-activated β-nicotinamide adenine dinucleotide (NAD>p)
and ACA>p RNA trinucleotide, and multiple additions of GUCCA>p
RNA
pentamers. Our results establish a new mode of RNA 3′-5′
extension with implications for RNA oligomer synthesis from prebiotic
nucleotide pools.
Collapse
Affiliation(s)
- Hannes Mutschler
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus , Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | | |
Collapse
|
45
|
Ruiz-Mirazo K, Briones C, de la Escosura A. Prebiotic Systems Chemistry: New Perspectives for the Origins of Life. Chem Rev 2013; 114:285-366. [DOI: 10.1021/cr2004844] [Citation(s) in RCA: 563] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kepa Ruiz-Mirazo
- Biophysics
Unit (CSIC-UPV/EHU), Leioa, and Department of Logic and Philosophy
of Science, University of the Basque Country, Avenida de Tolosa 70, 20080 Donostia−San Sebastián, Spain
| | - Carlos Briones
- Department
of Molecular Evolution, Centro de Astrobiología (CSIC−INTA, associated to the NASA Astrobiology Institute), Carretera de Ajalvir, Km 4, 28850 Torrejón de Ardoz, Madrid, Spain
| | - Andrés de la Escosura
- Organic
Chemistry Department, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| |
Collapse
|
46
|
Attah IK, Hamid AM, Meot-Ner (Mautner) M, El-Shall MS, Aziz SG, Alyoubi AO. Substituent Effects on Noncovalent Bonds: Complexes of Ionized Benzene Derivatives with Hydrogen Cyanide. J Phys Chem A 2013; 117:10588-97. [DOI: 10.1021/jp4069202] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Isaac K. Attah
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, United States
| | - Ahmed M. Hamid
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, United States
| | | | - M. S. El-Shall
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, United States
| | - Saadullah G. Aziz
- Department of Chemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Abdulrahman O. Alyoubi
- Department of Chemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| |
Collapse
|
47
|
Hamid AM, Sharma P, Samy El-Shall M, Hilal R, Elroby S, Aziz SG, Alyoubi AO. Hydration of the pyrimidine radical cation and stepwise solvation of protonated pyrimidine with water, methanol, and acetonitrile. J Chem Phys 2013; 139:084304. [DOI: 10.1063/1.4817327] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
|
48
|
Rios AC, Tor Y. On the Origin of the Canonical Nucleobases: An Assessment of Selection Pressures across Chemical and Early Biological Evolution. Isr J Chem 2013; 53:469-483. [PMID: 25284884 PMCID: PMC4181368 DOI: 10.1002/ijch.201300009] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The native bases of RNA and DNA are prominent examples of the narrow selection of organic molecules upon which life is based. How did nature "decide" upon these specific heterocycles? Evidence suggests that many types of heterocycles could have been present on the early Earth. It is therefore likely that the contemporary composition of nucleobases is a result of multiple selection pressures that operated during early chemical and biological evolution. The persistence of the fittest heterocycles in the prebiotic environment towards, for example, hydrolytic and photochemical assaults, may have given some nucleobases a selective advantage for incorporation into the first informational polymers. The prebiotic formation of polymeric nucleic acids employing the native bases remains, however, a challenging problem to reconcile. Hypotheses have proposed that the emerging RNA world may have included many types of nucleobases. This is supported by the extensive utilization of non-canonical nucleobases in extant RNA and the resemblance of many of the modified bases to heterocycles generated in simulated prebiotic chemistry experiments. Selection pressures in the RNA world could have therefore narrowed the composition of the nucleic acid bases. Two such selection pressures may have been related to genetic fidelity and duplex stability. Considering these possible selection criteria, the native bases along with other related heterocycles seem to exhibit a certain level of fitness. We end by discussing the strength of the N-glycosidic bond as a potential fitness parameter in the early DNA world, which may have played a part in the refinement of the alphabetic bases.
Collapse
Affiliation(s)
- Andro C. Rios
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358 (USA), phone: (+1) 8585346401, fax: (+1) 858534 0202
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358 (USA), phone: (+1) 8585346401, fax: (+1) 858534 0202
| |
Collapse
|
49
|
Singh P, Singh A. Formation of adenine from CH3COONH4/NH4HCO3—the probable prebiotic route for adenine. Tetrahedron Lett 2013. [DOI: 10.1016/j.tetlet.2013.03.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
50
|
Menor-Salván C, Marín-Yaseli MR. A New Route for the Prebiotic Synthesis of Nucleobases and Hydantoins in Water/Ice Solutions Involving the Photochemistry of Acetylene. Chemistry 2013; 19:6488-97. [DOI: 10.1002/chem.201204313] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 02/15/2013] [Indexed: 11/11/2022]
|