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Wunnava S, Dirscherl CF, Výravský J, Kovařík A, Matyášek R, Šponer J, Braun D, Šponer JE. Acid-Catalyzed RNA-Oligomerization from 3',5'-cGMP. Chemistry 2021; 27:17581-17585. [PMID: 34726799 PMCID: PMC9299008 DOI: 10.1002/chem.202103672] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Indexed: 11/28/2022]
Abstract
The assembly of ancient informational polymers from nucleotide precursors is the central challenge of life's origin on our planet. Among the possible solutions, dry polymerization of 3',5'-cyclic guanosine monophosphate (3',5'-cGMP) has been proposed as a candidate to create oligonucleotides of 15-20 units in length. However, the reported sensitivity of the reaction to the presence of cations raised questions of whether this chemistry could be relevant in a geological context. The experiments in this study show that the presence of cations is not restrictive as long as the reaction is conducted in an acidic environment, in contrast to previous reports that suggested optimal conditions at pH 9.
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Affiliation(s)
- Sreekar Wunnava
- Department of PhysicsNanoSystems Initiative Munich and Center for NanoscienceLudwig-Maximilians-Universität MünchenAmalienstrasse 5480799MunichGermany
| | - Christina F. Dirscherl
- Department of PhysicsNanoSystems Initiative Munich and Center for NanoscienceLudwig-Maximilians-Universität MünchenAmalienstrasse 5480799MunichGermany
| | - Jakub Výravský
- Tescan Brno s.r.o.Libušina třída 162300BrnoCzech Republic
- Department of Geological SciencesFaculty of ScienceMasaryk UniversityKotlářská 261137BrnoCzech Republic
| | - Aleš Kovařík
- Institute of Biophysics Academy of Sciences of the Czech RepublicKrálovopolská 13561265BrnoCzech Republic
| | - Roman Matyášek
- Institute of Biophysics Academy of Sciences of the Czech RepublicKrálovopolská 13561265BrnoCzech Republic
| | - Jiří Šponer
- Institute of Biophysics Academy of Sciences of the Czech RepublicKrálovopolská 13561265BrnoCzech Republic
| | - Dieter Braun
- Department of PhysicsNanoSystems Initiative Munich and Center for NanoscienceLudwig-Maximilians-Universität MünchenAmalienstrasse 5480799MunichGermany
| | - Judit E. Šponer
- Institute of Biophysics Academy of Sciences of the Czech RepublicKrálovopolská 13561265BrnoCzech Republic
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Hesko O, Fojta M, Špaček J. A simple electroanalysis of polyG RNA in mixtures with 3′,5′-cyclic guanosine monophosphate achieved by selective desorption of the monomers from the electrode surface. J Electroanal Chem (Lausanne) 2021. [DOI: 10.1016/j.jelechem.2021.115773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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3
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Šponer JE, Šponer J, Kovařík A, Šedo O, Zdráhal Z, Costanzo G, Di Mauro E. Questions and Answers Related to the Prebiotic Production of Oligonucleotide Sequences from 3',5' Cyclic Nucleotide Precursors. Life (Basel) 2021; 11:800. [PMID: 34440544 PMCID: PMC8400769 DOI: 10.3390/life11080800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 02/03/2023] Open
Abstract
Template-free nonenzymatic polymerization of 3',5' cyclic nucleotides is an emerging topic of the origin of life research. In the last ten years, a number of papers have been published addressing various aspects of this process. These works evoked a vivid discussion among scientists working in the field of prebiotic chemistry. The aim of the current review is to answer the most frequently raised questions related to the detection and characterization of oligomeric products as well as to the geological context of this chemistry.
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Affiliation(s)
- Judit E. Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265 Brno, Czech Republic; (J.Š.); (A.K.)
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265 Brno, Czech Republic; (J.Š.); (A.K.)
| | - Aleš Kovařík
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265 Brno, Czech Republic; (J.Š.); (A.K.)
| | - Ondrej Šedo
- Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (O.Š.); (Z.Z.)
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (O.Š.); (Z.Z.)
| | - Giovanna Costanzo
- Institute of Molecular Biology and Pathology, CNR, Piazzale A. Moro 5, 00185 Rome, Italy; (G.C.); (E.D.M.)
| | - Ernesto Di Mauro
- Institute of Molecular Biology and Pathology, CNR, Piazzale A. Moro 5, 00185 Rome, Italy; (G.C.); (E.D.M.)
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Šponer JE, Šponer J, Výravský J, Šedo O, Zdráhal Z, Costanzo G, Di Mauro E, Wunnava S, Braun D, Matyášek R, Kovařík A. Nonenzymatic, Template‐Free Polymerization of 3’,5’ Cyclic Guanosine Monophosphate on Mineral Surfaces. CHEMSYSTEMSCHEM 2021. [DOI: 10.1002/syst.202100017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Judit E. Šponer
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
| | - Jakub Výravský
- TESCAN Brno, s.r.o. Libušina třída 1 62300 Brno Czech Republic
- Department of Geological Sciences Faculty of Science Masaryk University Kotlářská 2 61137 Brno Czech Republic
| | - Ondrej Šedo
- Central European Institute of Technology Masaryk University Kamenice 5 62500 Brno Czech Republic
| | - Zbyněk Zdráhal
- Central European Institute of Technology Masaryk University Kamenice 5 62500 Brno Czech Republic
| | - Giovanna Costanzo
- Institute of Molecular Biology and Pathology, CNR Piazzale A. Moro 5 00185 Rome Italy
| | - Ernesto Di Mauro
- Institute of Molecular Biology and Pathology, CNR Piazzale A. Moro 5 00185 Rome Italy
| | - Sreekar Wunnava
- Physics Department Center for Nanoscience Ludwig-Maximilians-Universität München Amalienstrasse 54 80799 Munich Germany
| | - Dieter Braun
- Physics Department Center for Nanoscience Ludwig-Maximilians-Universität München Amalienstrasse 54 80799 Munich Germany
| | - Roman Matyášek
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
| | - Aleš Kovařík
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
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Dagar S, Sarkar S, Rajamani S. Geochemical influences on nonenzymatic oligomerization of prebiotically relevant cyclic nucleotides. RNA (NEW YORK, N.Y.) 2020; 26:756-769. [PMID: 32205323 PMCID: PMC7266160 DOI: 10.1261/rna.074302.119] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/19/2020] [Indexed: 06/01/2023]
Abstract
The spontaneous emergence of long RNA molecules on the early Earth, a phenomenon central to the RNA World hypothesis, continues to remain an enigma in the field of origins of life. Few studies have looked at the nonenzymatic oligomerization of cyclic mononucleotides under neutral to alkaline conditions, albeit in fully dehydrated state. In this study, we systematically investigated the oligomerization of cyclic nucleotides under prebiotically relevant conditions, wherein starting reactants were subjected to repeated dehydration-rehydration (DH-RH) regimes. DH-RH conditions, a recurring geological theme that was prevalent on prebiotic Earth, are driven by naturally occurring processes including diurnal cycles and tidal pool activity. These conditions have been shown to facilitate uphill oligomerization reactions. The polymerization of 2'-3' and 3'-5' cyclic nucleotides of a purine (adenosine) and a pyrimidine (cytidine) was investigated. Additionally, the effect of amphiphiles was also evaluated. Furthermore, to discern the effect of "realistic" conditions on this process, the reactions were also performed using a hot spring water sample from a candidate early Earth environment. Our study showed that the oligomerization of cyclic nucleotides under DH-RH conditions resulted in intact informational oligomers. Amphiphiles increased the stability of both the starting monomers and the resultant oligomers in selected reactions. In the hot spring reactions, both the oligomerization of nucleotides and the back hydrolysis of the resultant oligomers were pronounced. Altogether, this study demonstrates how nonenzymatic oligomerization of cyclic nucleotides, under both laboratory-simulated prebiotic conditions and in a candidate early Earth environment, could have resulted in RNA oligomers of a putative RNA World.
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Affiliation(s)
- Shikha Dagar
- Department of Biology, Indian Institute of Science Education and Research, Pune 411008, India
| | - Susovan Sarkar
- Department of Biology, Indian Institute of Science Education and Research, Pune 411008, India
| | - Sudha Rajamani
- Department of Biology, Indian Institute of Science Education and Research, Pune 411008, India
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Puzzarini C, Barone V. The challenging playground of astrochemistry: an integrated rotational spectroscopy - quantum chemistry strategy. Phys Chem Chem Phys 2020; 22:6507-6523. [PMID: 32163090 DOI: 10.1039/d0cp00561d] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
While it is now well demonstrated that the interstellar medium (ISM) is characterized by a diverse and complex chemistry, a significant number of features in radioastronomical spectra are still unassigned and call for new laboratory efforts, which are increasingly based on integrated experimental and computational strategies. In parallel, the identification of an increasing number of molecules containing more than five atoms and at least one carbon atom (the so-called "interstellar" complex organic molecules), which can play a relevant role in the chemistry of life, raises the additional issue of how these species can be produced in the typical harsh conditions of the ISM. On these grounds, this perspective aims to present an integrated rotational spectroscopy - quantum chemistry approach for supporting radioastronomical observations and a computational strategy for contributing to the elucidation of chemical reactivity in the interstellar space.
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Affiliation(s)
- Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", University of Bologna, via F. Selmi 2, I-40126 Bologna, Italy.
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, Pisa, I-56126, Italy
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Šponer JE, Šponer J, Di Mauro E. Structural and Energetic Compatibility: The Driving Principles of Molecular Evolution. ASTROBIOLOGY 2019; 19:1117-1122. [PMID: 31045430 DOI: 10.1089/ast.2018.1978] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In this work, we provide an answer to the question formulated by Albert Eschenmoser: "How would you envisage the bridge between potentially primordial geochemistry that had been disordered and one that gradually became self-organizing?" Analysis of the free-energy profiles of some of the key reactions leading to formation of nucleotides and their oligomers shows that, whereas the first part of the pathway, up to nucleotides, is energy-driven, in the second low-energy part entropic control in the form of structural compatibility becomes more important. We suggest that the birth of modern metabolism requires structural compatibility, which is enabled by the commensurability of the thermodynamics of the synthetic steps with the stabilizing effect of those intermolecular interactions that play a key role in dictating entropic control of these reactions.
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Affiliation(s)
- Judit E Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Ernesto Di Mauro
- Institute for Molecular Biology and Pathology, CNR, c/o Università Sapienza, Roma, Italy
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Prebiotic Soup Components Trapped in Montmorillonite Nanoclay Form New Molecules: Car-Parrinello Ab Initio Simulations. Life (Basel) 2019; 9:life9020046. [PMID: 31167366 PMCID: PMC6617125 DOI: 10.3390/life9020046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/30/2019] [Accepted: 05/30/2019] [Indexed: 01/08/2023] Open
Abstract
The catalytic effects of complex minerals or meteorites are often mentioned as important factors for the origins of life. To assess the possible role of nanoconfinement within a catalyst consisting of montmorillonite (MMT) and the impact of local electric field on the formation efficiency of the simple hypothetical precursors of nucleic acid bases or amino acids, we performed ab initio Car–Parrinello molecular dynamics simulations. We prepared four condensed-phase systems corresponding to previously suggested prototypes of a primordial soup. We monitored possible chemical reactions occurring within gas-like bulk and MMT-confined four simulation boxes on a 20-ps time scale at 1 atm and 300 K, 400 K, and 600 K. Elevated temperatures did not affect the reactivity of the elementary components of the gas-like boxes considerably; however, the presence of the MMT nanoclay substantially increased the formation probability of new molecules. Approximately 20 different new compounds were found in boxes containing carbon monoxide or formaldehyde molecules. This observation and an analysis of the atom–atom radial distribution functions indicated that the presence of Ca2+ ions at the surface of the internal MMT cavities may be an important factor in the initial steps of the formation of complex molecules at the early stages of the Earth’s history.
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Sleep NH. Geological and Geochemical Constraints on the Origin and Evolution of Life. ASTROBIOLOGY 2018; 18:1199-1219. [PMID: 30124324 DOI: 10.1089/ast.2017.1778] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The traditional tree of life from molecular biology with last universal common ancestor (LUCA) branching into bacteria and archaea (though fuzzy) is likely formally valid enough to be a basis for discussion of geological processes on the early Earth. Biologists infer likely properties of nodal organisms within the tree and, hence, the environment they inhabited. Geologists both vet tenuous trees and putative origin of life scenarios for geological and ecological reasonability and conversely infer geological information from trees. The latter approach is valuable as geologists have only weakly constrained the time when the Earth became habitable and the later time when life actually existed to the long interval between ∼4.5 and ∼3.85 Ga where no intact surface rocks are known. With regard to vetting, origin and early evolution hypotheses from molecular biology have recently centered on serpentinite settings in marine and alternatively land settings that are exposed to ultraviolet sunlight. The existence of these niches on the Hadean Earth is virtually certain. With regard to inferring geological environment from genomics, nodes on the tree of life can arise from true bottlenecks implied by the marine serpentinite origin scenario and by asteroid impact. Innovation of a very useful trait through a threshold allows the successful organism to quickly become very abundant and later root a large clade. The origin of life itself, that is, the initial Darwinian ancestor, the bacterial and archaeal roots as free-living cellular organisms that independently escaped hydrothermal chimneys above marine serpentinite or alternatively from shallow pore-water environments on land, the Selabacteria root with anoxygenic photosynthesis, and the Terrabacteria root colonizing land are attractive examples that predate the geological record. Conversely, geological reasoning presents likely events for appraisal by biologists. Asteroid impacts may have produced bottlenecks by decimating life. Thermophile roots of bacteria and archaea as well as a thermophile LUCA are attractive.
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Affiliation(s)
- Norman H Sleep
- Department of Geophysics, Stanford University , Stanford, California
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10
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Chemomimesis and Molecular Darwinism in Action: From Abiotic Generation of Nucleobases to Nucleosides and RNA. Life (Basel) 2018; 8:life8020024. [PMID: 29925796 PMCID: PMC6027154 DOI: 10.3390/life8020024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 06/14/2018] [Accepted: 06/19/2018] [Indexed: 01/26/2023] Open
Abstract
Molecular Darwinian evolution is an intrinsic property of reacting pools of molecules resulting in the adaptation of the system to changing conditions. It has no a priori aim. From the point of view of the origin of life, Darwinian selection behavior, when spontaneously emerging in the ensembles of molecules composing prebiotic pools, initiates subsequent evolution of increasingly complex and innovative chemical information. On the conservation side, it is a posteriori observed that numerous biological processes are based on prebiotically promptly made compounds, as proposed by the concept of Chemomimesis. Molecular Darwinian evolution and Chemomimesis are principles acting in balanced cooperation in the frame of Systems Chemistry. The one-pot synthesis of nucleosides in radical chemistry conditions is possibly a telling example of the operation of these principles. Other indications of similar cases of molecular evolution can be found among biogenic processes.
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Gimenez Molina A, Barvik I, Müller S, Vasseur JJ, Smietana M. RNA-based boronate internucleosidic linkages: an entry into reversible templated ligation and loop formation. Org Biomol Chem 2018; 16:8824-8830. [DOI: 10.1039/c8ob02182a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis of a 5′-boronoribonucleotidic phosphoramidite building block has been achieved and incorporated at the 5′ extremities of RNA sequences for the templated assembly of RNA shortmers.
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Affiliation(s)
- Alejandro Gimenez Molina
- Institut des Biomolecules Max Mousseron
- IBMM UMR 5247 CNRS
- Université de Montpellier
- ENSCM
- 34095 Montpellier
| | - Ivan Barvik
- Institute of Physics
- Faculty of Mathematics and Physics
- Charles University
- 121 16 Prague 2
- Czech Republic
| | - Sabine Müller
- Institut für Biochemie
- Ernst-Moritz-Arndt-Universität Greifswald
- D-17489 Greifswald
- Germany
| | - Jean-Jacques Vasseur
- Institut des Biomolecules Max Mousseron
- IBMM UMR 5247 CNRS
- Université de Montpellier
- ENSCM
- 34095 Montpellier
| | - Michael Smietana
- Institut des Biomolecules Max Mousseron
- IBMM UMR 5247 CNRS
- Université de Montpellier
- ENSCM
- 34095 Montpellier
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