1
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Bastian CD, Rabitz H. Hitting Times of Some Critical Events in RNA Origins of Life. Life (Basel) 2021; 11:life11121419. [PMID: 34947949 PMCID: PMC8705503 DOI: 10.3390/life11121419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/09/2021] [Accepted: 12/11/2021] [Indexed: 11/24/2022] Open
Abstract
Can a replicase be found in the vast sequence space by random drift? We partially answer this question through a proof-of-concept study of the times of occurrence (hitting times) of some critical events in the origins of life for low-dimensional RNA sequences using a mathematical model and stochastic simulation studies from Python software. We parameterize fitness and similarity landscapes for polymerases and study a replicating population of sequences (randomly) participating in template-directed polymerization. Under the ansatz of localization where sequence proximity correlates with spatial proximity of sequences, we find that, for a replicating population of sequences, the hitting and establishment of a high-fidelity replicator depends critically on the polymerase fitness and sequence (spatial) similarity landscapes and on sequence dimension. Probability of hitting is dominated by landscape curvature, whereas hitting time is dominated by sequence dimension. Surface chemistries, compartmentalization, and decay increase hitting times. Compartmentalization by vesicles reveals a trade-off between vesicle formation rate and replicative mass, suggesting that compartmentalization is necessary to ensure sufficient concentration of precursors. Metabolism is thought to be necessary to replication by supplying precursors of nucleobase synthesis. We suggest that the dynamics of the search for a high-fidelity replicase evolved mostly during the final period and, upon hitting, would have been followed by genomic adaptation of genes and to compartmentalization and metabolism, effecting degree-of-freedom gains of replication channel control over domain and state to ensure the fidelity and safe operations of the primordial genetic communication system of life.
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Affiliation(s)
- Caleb Deen Bastian
- Program in Applied and Computational Mathematics, Princeton University, Princeton, NJ 08544, USA;
- Correspondence:
| | - Hershel Rabitz
- Program in Applied and Computational Mathematics, Princeton University, Princeton, NJ 08544, USA;
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
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2
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Factors in Protobiomonomer Selection for the Origin of the Standard Genetic Code. Acta Biotheor 2021; 69:745-767. [PMID: 34283307 DOI: 10.1007/s10441-021-09420-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 07/01/2021] [Indexed: 10/20/2022]
Abstract
Natural selection of specific protobiomonomers during abiogenic development of the prototype genetic code is hindered by the diversity of structural, spatial, and rotational isomers that have identical elemental composition and molecular mass (M), but can vary significantly in their physicochemical characteristics, such as the melting temperature Tm, the Tm:M ratio, and the solubility in water, due to different positions of atoms in the molecule. These parameters differ between cis- and trans-isomers of dicarboxylic acids, spatial monosaccharide isomers, and structural isomers of α-, β-, and γ-amino acids. The stable planar heterocyclic molecules of the major nucleobases comprise four (C, H, N, O) or three (C, H, N) elements and contain a single -C=C bond and two nitrogen atoms in each heterocycle involved in C-N and C=N bonds. They exist as isomeric resonance hybrids of single and double bonds and as a mixture of tautomer forms due to the presence of -C=O and/or -NH2 side groups. They are thermostable, insoluble in water, and exhibit solid-state stability, which is of central importance for DNA molecules as carriers of genetic information. In M-Tm diagrams, proteinogenic amino acids and the corresponding codons are distributed fairly regularly relative to the distinct clusters of purine and pyrimidine bases, reflecting the correspondence between codons and amino acids that was established in different periods of genetic code development. The body of data on the evolution of the genetic code system indicates that the elemental composition and molecular structure of protobiomonomers, and their M, Tm, photostability, and aqueous solubility determined their selection in the emergence of the standard genetic code.
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3
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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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4
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Chance and Necessity in the Evolution of Matter to Life: A Comprehensive Hypothesis. Symmetry (Basel) 2021. [DOI: 10.3390/sym13101918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Specialists in several branches of life sciences are trying to solve, piece by piece, the immensely complex puzzle of the origin of life. Some parts of the puzzle seem to appear with a rather high degree of clarity, while others remain totally obscure. We cannot be sure that life emerged only on our Earth, but we believe that the presence of large amounts of water in its liquid state is absolutely essential for the emergence and evolution of living matter. We can also assume that the latter exploits everywhere the same light elements, mainly C, H, O, N, S, and P, and somehow manipulates the same simple monomeric and polymeric organic compounds, such as alpha-amino acids, carbohydrates, nucleic bases, and surface-active carboxylic acids. The author contributes to the field by stating that all fundamental particles of our matter are “homochiral” and predominantly produce in an absolute asymmetric synthesis amino acids of L-configuration and carbohydrates of D-series. Another important point is that free atmospheric oxygen mainly stems from the photolysis of water molecules by cosmic irradiation and is not necessarily bound to living organisms on the planet.
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5
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Thripati S, Ramabhadran RO. Pathways for the Formation of Formamide, a Prebiotic Biomonomer: Metal-Ions in Interstellar Gas-Phase Chemistry. J Phys Chem A 2021; 125:3457-3472. [PMID: 33861935 DOI: 10.1021/acs.jpca.1c02132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The chemistry occurring in the interstellar medium (ISM) is an active area of contemporary research. New aspects of interstellar chemistry are getting unraveled regularly. In this context, the role of metal-ions in the chemistry occurring in the ISM is not well-studied so far. Herein, we highlight the role of metal-ions in interstellar chemistry. For this purpose, we choose the problem of gas-phase formamide formation in interstellar molecular clouds. Formamide is a key biomonomer and contains the simplest peptide [-(C═O)-NH-] linkage. With its two electronegative atoms ("O" and "N"), it provides an excellent platform to probe the role of the metal-ions. The metal-ions chosen are Na+, K+, Al+, Mg+, and Mg2+-all of them present in the ISM. The metal-ions are studied in three different forms as bare positively charged ions, as hydrated metal-ions co-ordinated with a molecule of water, and when the metal-ions are part of a neutral covalent molecule. With the aid of electronic structure calculations [CCSD(T) and DFT methods], we study different gas-phase pathways which result in the generation of interstellar formamide. Throughout our study, we find that metal-ions lower the barriers (with Mg+, Mg++, and Al+ offering maximal stabilization of the transition states) and facilitate the reactions. The chemical factors influencing the reactions, how we consider the putative conditions in the ISM, the astrochemical implications of this study, and its connection with terrestrial prebiotic chemistry and refractory astrochemistry are subsequently presented. Based on our results, we also recommend the detection of two new closed-shell molecules, NH2CH2OH (aminomethanol) and CH2NH2+ (iminium ion), and two open-shell molecules, CONH2 (carbamyl radical) and HCONH (an isomer of carbamyl radical), in the ISM.
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Affiliation(s)
- Sorakayala Thripati
- Department of Chemistry, Indian Institute of Science Education and Research, Tirupati Andhra Pradesh 517507, India.,Center for Atomic, Molecular, and Optical Sciences and Technologies (CAMOST), Tirupati, Andhra Pradesh 517507, India
| | - Raghunath O Ramabhadran
- Department of Chemistry, Indian Institute of Science Education and Research, Tirupati Andhra Pradesh 517507, India.,Center for Atomic, Molecular, and Optical Sciences and Technologies (CAMOST), Tirupati, Andhra Pradesh 517507, India
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6
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Rankine CD. Ultrafast excited-state dynamics of promising nucleobase ancestor 2,4,6-triaminopyrimidine. Phys Chem Chem Phys 2021; 23:4007-4017. [PMID: 33554987 DOI: 10.1039/d0cp05609j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ultrafast excited-state dynamics of 2,4,6-triaminopyrimidine - thought to be a promising candidate for a proto-RNA nucleobase - have been investigated via static multireference quantum-chemical calculations and mixed-quantum-classical/trajectory surface-hopping dynamics with a focus on the lowest-lying electronic states of the singlet manifold and with a view towards understanding the UV(C)/UV(B) photostability of the molecule. Ultrafast internal conversion channels have been identified that connect the lowest-lying ππ* electronically-excited state of 2,4,6-triaminopyrimidine with the ground electronic state, and non-radiative decay has been observed to take place on the picosecond timescale via a ππ* out-of-plane NH2 ("oop-NH2") minimum-energy crossing point. The short excited-state lifetime is competitive with the excited-state lifetimes of the canonical pyrimidine nucleobases, affirming the promise of 2,4,6-triaminopyrimidine as an ancestor. Evidence for energy-dependent excited-state dynamics is presented, and the open question of intersystem crossing is discussed speculatively.
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Affiliation(s)
- Conor D Rankine
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK.
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7
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Pastorek A, Ferus M, Čuba V, Šrámek O, Ivanek O, Civiš S. Primordial Radioactivity and Prebiotic Chemical Evolution: Effect of γ Radiation on Formamide-Based Synthesis. J Phys Chem B 2020; 124:8951-8959. [PMID: 32970439 DOI: 10.1021/acs.jpcb.0c05233] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although the effect of ionizing radiation on prebiotic chemistry is often overlooked, primordial natural radioactivity might have been an important source of energy for various chemical transformations. Estimates of the abundances of short-lived radionuclides on early Earth suggest that the primordial intensity of endogenous terrestrial radioactivity was up to 4 × 103 times higher than it is today. Therefore, we assume that chemical substances in contact with radioactive rocks should therefore undergo radiolysis. The calculations are followed by research investigating the influence of ionizing γ radiation on basic prebiotic substances, including formamide mixed with various clays, which might have played the role of a catalyst and an agent that partially blocked radiation that was potentially destructive for the products. Our explorations of this effect have shown that the irradiation of formamide-clay mixtures at doses of ∼6 kGy produces significant amounts of urea (up to the maximal concentration of approximately 250 mg L-1), which plays a role in HCN-based prebiotic chemistry.
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Affiliation(s)
- Adam Pastorek
- J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 2155/3, 18200 Prague, Prague 8, Czech Republic.,Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Břehová 78/7, 11519 Prague, Prague 1, Czech Republic
| | - Martin Ferus
- J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 2155/3, 18200 Prague, Prague 8, Czech Republic
| | - Václav Čuba
- Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Břehová 78/7, 11519 Prague, Prague 1, Czech Republic
| | - Ondřej Šrámek
- Department of Geophysics, Faculty of Mathematics and Physics, Charles University, V Holešovičkách 2, 18000 Prague, Prague 8, Czech Republic
| | - Ondřej Ivanek
- J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 2155/3, 18200 Prague, Prague 8, Czech Republic
| | - Svatopluk Civiš
- J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 2155/3, 18200 Prague, Prague 8, Czech Republic
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8
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Gospodinov A, Kunnev D. Universal Codons with Enrichment from GC to AU Nucleotide Composition Reveal a Chronological Assignment from Early to Late Along with LUCA Formation. Life (Basel) 2020; 10:life10060081. [PMID: 32516985 PMCID: PMC7345086 DOI: 10.3390/life10060081] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 05/30/2020] [Accepted: 06/03/2020] [Indexed: 12/14/2022] Open
Abstract
The emergence of a primitive genetic code should be considered the most essential event during the origin of life. Almost a complete set of codons (as we know them) should have been established relatively early during the evolution of the last universal common ancestor (LUCA) from which all known organisms descended. Many hypotheses have been proposed to explain the driving forces and chronology of the evolution of the genetic code; however, none is commonly accepted. In the current paper, we explore the features of the genetic code that, in our view, reflect the mechanism and the chronological order of the origin of the genetic code. Our hypothesis postulates that the primordial RNA was mostly GC-rich, and this bias was reflected in the order of amino acid codon assignment. If we arrange the codons and their corresponding amino acids from GC-rich to AU-rich, we find that: 1. The amino acids encoded by GC-rich codons (Ala, Gly, Arg, and Pro) are those that contribute the most to the interactions with RNA (if incorporated into short peptides). 2. This order correlates with the addition of novel functions necessary for the evolution from simple to longer folded peptides. 3. The overlay of aminoacyl-tRNA synthetases (aaRS) to the amino acid order produces a distinctive zonal distribution for class I and class II suggesting an interdependent origin. These correlations could be explained by the active role of the bridge peptide (BP), which we proposed earlier in the evolution of the genetic code.
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Affiliation(s)
- Anastas Gospodinov
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. 21, Sofia 1113, Bulgaria;
| | - Dimiter Kunnev
- Department of Molecular & Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
- Correspondence:
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9
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Kunnev D, Gospodinov A. Possible Emergence of Sequence Specific RNA Aminoacylation via Peptide Intermediary to Initiate Darwinian Evolution and Code Through Origin of Life. Life (Basel) 2018; 8:E44. [PMID: 30279401 PMCID: PMC6316189 DOI: 10.3390/life8040044] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 09/30/2018] [Accepted: 09/30/2018] [Indexed: 12/12/2022] Open
Abstract
One of the most intriguing questions in biological science is how life originated on Earth. A large number of hypotheses have been proposed to explain it, each putting an emphasis on different events leading to functional translation and self-sustained system. Here, we propose a set of interactions that could have taken place in the prebiotic environment. According to our hypothesis, hybridization-induced proximity of short aminoacylated RNAs led to the synthesis of peptides of random sequence. We postulate that among these emerged a type of peptide(s) capable of stimulating the interaction between specific RNAs and specific amino acids, which we call "bridge peptide" (BP). We conclude that translation should have emerged at the same time when the standard genetic code begun to evolve due to the stabilizing effect on RNA-peptide complexes with the help of BPs. Ribosomes, ribozymes, and the enzyme-directed RNA replication could co-evolve within the same period, as logical outcome of RNA-peptide world without the need of RNA only self-sustained step.
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Affiliation(s)
- Dimiter Kunnev
- Roswell Park Cancer Institute, Department of Molecular & Cellular Biology, Buffalo, NY 14263, USA.
| | - Anastas Gospodinov
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. 21, Sofia 1113, Bulgaria.
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10
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Wojciechowska M, Dudek M, Trylska J. Thermodynamics of the pseudo-knot in helix 18 of 16S ribosomal RNA. Biopolymers 2018; 109:e23116. [PMID: 29570767 DOI: 10.1002/bip.23116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 02/24/2018] [Accepted: 02/27/2018] [Indexed: 01/13/2023]
Abstract
A fragment of E. coli 16S rRNA formed by nucleotides 500 to 545 is termed helix 18. Nucleotides 505-507 and 524-526 form a pseudo-knot and its distortion affects ribosome function. Helix 18 isolated from the ribosome context is thus an interesting fragment to investigate the structural properties and folding of RNA with pseudo-knots. With all-atom molecular dynamics simulations, spectroscopic and gel electrophoresis experiments, we investigated thermodynamics of helix 18, with a focus on its pseudo-knot. In solution studies at ambient conditions we observed dimerization of helix 18. We proposed that the loop, containing nucleotides forming the pseudo-knot, interacts with another monomer of helix 18. The native dimer is difficult to break but introducing mutations in the pseudo-knot indeed assured a monomeric form of helix 18. Molecular dynamics simulations at 310 K confirmed the stability of the pseudo-knot but at elevated temperatures this pseudo-knot was the first part of helix 18 to lose the hydrogen bond pattern. To further determine helix 18 stability, we analyzed the interactions of helix 18 with short oligomers complementary to a nucleotide stretch containing the pseudo-knot. The formation of higher-order structures by helix 18 impacts hybridization efficiency of peptide nucleic acid and 2'-O methyl RNA oligomers.
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Affiliation(s)
- Monika Wojciechowska
- Centre of New Technologies, University of Warsaw, Banacha 2C, Warsaw, 02-09, Poland
| | - Marta Dudek
- Centre of New Technologies, University of Warsaw, Banacha 2C, Warsaw, 02-09, Poland.,School of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw, 02-106, Poland.,First Faculty of Medicine, Department of Hematology, Oncology and Internal Diseases, Medical University of Warsaw, Al. Żwirki i Wigury 61, Warsaw, 02-091, Poland
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Banacha 2C, Warsaw, 02-09, Poland
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11
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Szabla R, Góra RW, Šponer J. Ultrafast excited-state dynamics of isocytosine. Phys Chem Chem Phys 2018; 18:20208-18. [PMID: 27346684 DOI: 10.1039/c6cp01391k] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The alternative nucleobase isocytosine has long been considered as a plausible component of hypothetical primordial informational polymers. To examine this hypothesis we investigated the excited-state dynamics of the two most abundant forms of isocytosine in the gas phase (keto and enol). Our surface-hopping nonadiabatic molecular dynamics simulations employing the algebraic diagrammatic construction to the second order [ADC(2)] method for the electronic structure calculations suggest that both tautomers undergo efficient radiationless deactivation to the electronic ground state with time constants which amount to τketo = 182 fs and τenol = 533 fs. The dominant photorelaxation pathways correspond to ring-puckering (ππ* surface) and C[double bond, length as m-dash]O stretching/N-H tilting (nπ* surface) for the enol and keto forms respectively. Based on these findings, we infer that isocytosine is a relatively photostable compound in the gas phase and in these terms resembles biologically relevant nucleobases. The estimated S1 [radiolysis arrow - arrow with voltage kink] T1 intersystem crossing rate constant of 8.02 × 10(10) s(-1) suggests that triplet states might also play an important role in the overall excited-state dynamics of the keto tautomer. The reliability of ADC(2)-based surface-hopping molecular dynamics simulations was tested against multireference quantum-chemical calculations and the potential limitations of the employed ADC(2) approach are briefly discussed.
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Affiliation(s)
- Rafał Szabla
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic.
| | - Robert W Góra
- Department of Physical and Quantum Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic. and CEITEC-Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, CZ-62500 Brno, Czech Republic
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12
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Pesce D, Lehman N, de Visser JAGM. Sex in a test tube: testing the benefits of in vitro recombination. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0529. [PMID: 27619693 DOI: 10.1098/rstb.2015.0529] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2016] [Indexed: 01/06/2023] Open
Abstract
The origin and evolution of sex, and the associated role of recombination, present a major problem in biology. Sex typically involves recombination of closely related DNA or RNA sequences, which is fundamentally a random process that creates but also breaks up beneficial allele combinations. Directed evolution experiments, which combine in vitro mutation and recombination protocols with in vitro or in vivo selection, have proved to be an effective approach for improving functionality of nucleic acids and enzymes. As this approach allows extreme control over evolutionary conditions and parameters, it also facilitates the detection of small or position-specific recombination benefits and benefits associated with recombination between highly divergent genotypes. Yet, in vitro approaches have been largely exploratory and motivated by obtaining improved end products rather than testing hypotheses of recombination benefits. Here, we review the various experimental systems and approaches used by in vitro studies of recombination, discuss what they say about the evolutionary role of recombination, and sketch their potential for addressing extant questions about the evolutionary role of sex and recombination, in particular on complex fitness landscapes. We also review recent insights into the role of 'extracellular recombination' during the origin of life.This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'.
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Affiliation(s)
- Diego Pesce
- Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands
| | - Niles Lehman
- Department of Chemistry, Portland State University, Portland, OR 97207, USA
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13
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Costanzo G, Giorgi A, Scipioni A, Timperio AM, Mancone C, Tripodi M, Kapralov M, Krasavin E, Kruse H, Šponer J, Šponer JE, Ranc V, Otyepka M, Pino S, Di Mauro E. Nonenzymatic Oligomerization of 3',5'-Cyclic CMP Induced by Proton and UV Irradiation Hints at a Nonfastidious Origin of RNA. Chembiochem 2017; 18:1535-1543. [PMID: 28471098 DOI: 10.1002/cbic.201700122] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Indexed: 12/25/2022]
Abstract
We report that 3',5'-cyclic CMP undergoes nonenzymatic di- and trimerization at 20 °C under dry conditions upon proton or UV irradiation. The reaction involves stacking of the cyclic monomers and subsequent polymerization through serial transphosphorylations between the stacked monomers. Proton- and UV-induced oligomerization of 3',5'-cyclic CMP demonstrates that pyrimidines-similar to purines-might also have taken part in the spontaneous generation of RNA under plausible prebiotic conditions as well as in an extraterrestrial context. The observed polymerization of naturally occurring 3',5'-cyclic nucleotides supports the possibility that the extant genetic nucleic acids might have originated by way of a straight Occamian path, starting from simple reactions between plausibly preactivated monomers.
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Affiliation(s)
- Giovanna Costanzo
- Istituto di Biologia e Patologia Molecolari, CNR, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Alessandra Giorgi
- Dipartimento di Scienze Biochimiche, "Sapienza" Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Anita Scipioni
- Dipartimento di Chimica, "Sapienza" Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Anna Maria Timperio
- Department of Ecology and Biology, "La Tuscia" University, Viale dell'Università snc, 01100, Viterbo, Italy
| | - Carmine Mancone
- Department of Cellular Biotechnologies and Hematology, Sapienza University of Rome, Via Regina Elena 324, 00161, Roma, Italy.,National Institute for Infectious Diseases "L. Spallanzani", IRCCS, Via Portuense 292, 00149, Rome, Italy
| | - Marco Tripodi
- Department of Cellular Biotechnologies and Hematology, Sapienza University of Rome, Via Regina Elena 324, 00161, Roma, Italy.,National Institute for Infectious Diseases "L. Spallanzani", IRCCS, Via Portuense 292, 00149, Rome, Italy
| | - Michail Kapralov
- Joint Institute for Nuclear Research, Laboratory of Radiation Biology, 141980, Dubna, Russia
| | - Eugene Krasavin
- Joint Institute for Nuclear Research, Laboratory of Radiation Biology, 141980, Dubna, Russia
| | - Holger Kruse
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17. Listopadu, 771 46, Olomouc, Czech Republic
| | - Judit E Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic
| | - Václav Ranc
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17. Listopadu, 771 46, Olomouc, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17. Listopadu, 771 46, Olomouc, Czech Republic
| | - Samanta Pino
- Department of Biology and Biotechnology, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Ernesto Di Mauro
- Department of Biology and Biotechnology, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
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14
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Ferus M, Pietrucci F, Saitta AM, Knížek A, Kubelík P, Ivanek O, Shestivska V, Civiš S. Formation of nucleobases in a Miller-Urey reducing atmosphere. Proc Natl Acad Sci U S A 2017; 114:4306-4311. [PMID: 28396441 PMCID: PMC5410828 DOI: 10.1073/pnas.1700010114] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Miller-Urey experiments pioneered modern research on the molecular origins of life, but their actual relevance in this field was later questioned because the gas mixture used in their research is considered too reducing with respect to the most accepted hypotheses for the conditions on primordial Earth. In particular, the production of only amino acids has been taken as evidence of the limited relevance of the results. Here, we report an experimental work, combined with state-of-the-art computational methods, in which both electric discharge and laser-driven plasma impact simulations were carried out in a reducing atmosphere containing NH3 + CO. We show that RNA nucleobases are synthesized in these experiments, strongly supporting the possibility of the emergence of biologically relevant molecules in a reducing atmosphere. The reconstructed synthetic pathways indicate that small radicals and formamide play a crucial role, in agreement with a number of recent experimental and theoretical results.
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Affiliation(s)
- Martin Ferus
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, CZ18223 Prague 8, Czech Republic
| | - Fabio Pietrucci
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Université Pierre et Marie Curie, Sorbonne Universités, CNRS, Muséum National d'Histoire Naturelle, Institut de Recherche pour le Développement, UMR 7590, F-75005 Paris, France
| | - Antonino Marco Saitta
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Université Pierre et Marie Curie, Sorbonne Universités, CNRS, Muséum National d'Histoire Naturelle, Institut de Recherche pour le Développement, UMR 7590, F-75005 Paris, France
| | - Antonín Knížek
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, CZ18223 Prague 8, Czech Republic
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, CZ12840 Prague 2, Czech Republic
| | - Petr Kubelík
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, CZ18223 Prague 8, Czech Republic
| | - Ondřej Ivanek
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, CZ18223 Prague 8, Czech Republic
| | - Violetta Shestivska
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, CZ18223 Prague 8, Czech Republic
| | - Svatopluk Civiš
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, CZ18223 Prague 8, Czech Republic;
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15
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Heuristic Approach to Understanding the Accumulation Process in Hydrothermal Pores. ENTROPY 2017. [DOI: 10.3390/e19010033] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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16
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Urso RG, Scirè C, Baratta GA, Brucato JR, Compagnini G, Kaňuchová Z, Palumbo ME, Strazzulla G. Infrared study on the thermal evolution of solid state formamide. Phys Chem Chem Phys 2017; 19:21759-21768. [DOI: 10.1039/c7cp03959j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Formamide synthesized in interstellar ice analogues after energetic processing remains trapped in the refractory residue simultaneously produced.
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Affiliation(s)
- Riccardo Giovanni Urso
- Dipartimento di Scienze Chimiche
- Università degli Studi di Catania
- 95125 Catania
- Italy
- INAF-Osservatorio Astrofisico di Catania
| | - Carlotta Scirè
- INAF-Osservatorio Astrofisico di Catania
- 95123 Catania
- Italy
| | | | | | - Giuseppe Compagnini
- Dipartimento di Scienze Chimiche
- Università degli Studi di Catania
- 95125 Catania
- Italy
| | - Zuzana Kaňuchová
- INAF-Osservatorio Astrofisico di Catania
- 95123 Catania
- Italy
- Astronomical Institute of Slovak Academy of Sciences
- 05960 Tatranská Lomnica
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17
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Vazart F, Calderini D, Puzzarini C, Skouteris D, Barone V. State-of-the-Art Thermochemical and Kinetic Computations for Astrochemical Complex Organic Molecules: Formamide Formation in Cold Interstellar Clouds as a Case Study. J Chem Theory Comput 2016; 12:5385-5397. [PMID: 27689448 PMCID: PMC5856337 DOI: 10.1021/acs.jctc.6b00379] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe an integrated computational strategy aimed at providing reliable thermochemical and kinetic information on the formation processes of astrochemical complex organic molecules. The approach involves state-of-the-art quantum-mechanical computations, second-order vibrational perturbation theory, and kinetic models based on capture and transition state theory together with the master equation approach. Notably, tunneling, quantum reflection, and leading anharmonic contributions are accounted for in our model. Formamide has been selected as a case study in view of its interest as a precursor in the abiotic amino acid synthesis. After validation of the level of theory chosen for describing the potential energy surface, we have investigated several pathways of the OH + CH2NH and NH2 + H2CO reaction channels. Our results show that both reaction channels are essentially barrierless (in the sense that all relevant transition states lie below or only marginally above the reactants) and once tunneling is taken into the proper account indicate that the reaction can occur under the low temperature conditions of interstellar environments.
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Affiliation(s)
- Fanny Vazart
- Scuola Normale Superiore, piazza dei Cavalieri 7, 56125 Pisa, Italy
| | - Danilo Calderini
- Scuola Normale Superiore, piazza dei Cavalieri 7, 56125 Pisa, Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", Via F. Selmi 2, 40126 Bologna, Italy
| | | | - Vincenzo Barone
- Scuola Normale Superiore, piazza dei Cavalieri 7, 56125 Pisa, Italy
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18
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Taming Prebiotic Chemistry: The Role of Heterogeneous and Interfacial Catalysis in the Emergence of a Prebiotic Catalytic/Information Polymer System. Life (Basel) 2016; 6:life6040040. [PMID: 27827919 PMCID: PMC5198075 DOI: 10.3390/life6040040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/31/2016] [Accepted: 11/01/2016] [Indexed: 01/10/2023] Open
Abstract
Cellular life is based on interacting polymer networks that serve as catalysts, genetic information and structural molecules. The complexity of the DNA, RNA and protein biochemistry suggests that it must have been preceded by simpler systems. The RNA world hypothesis proposes RNA as the prime candidate for such a primal system. Even though this proposition has gained currency, its investigations have highlighted several challenges with respect to bulk aqueous media: (1) the synthesis of RNA monomers is difficult; (2) efficient pathways for monomer polymerization into functional RNAs and their subsequent, sequence-specific replication remain elusive; and (3) the evolution of the RNA function towards cellular metabolism in isolation is questionable in view of the chemical mixtures expected on the early Earth. This review will address the question of the possible roles of heterogeneous media and catalysis as drivers for the emergence of RNA-based polymer networks. We will show that this approach to non-enzymatic polymerizations of RNA from monomers and RNA evolution cannot only solve some issues encountered during reactions in bulk aqueous solutions, but may also explain the co-emergence of the various polymers indispensable for life in complex mixtures and their organization into primitive networks.
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19
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Fiore M, Strazewski P. Zur präbiotischen Synthese von Nukleosiden und Nukleotiden. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Michele Fiore
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires; Université de Lyon, Claude Bernard Lyon 1; 43 bdv du 11 novembre 1918 69622 Villeurbanne Cedex Frankreich
| | - Peter Strazewski
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires; Université de Lyon, Claude Bernard Lyon 1; 43 bdv du 11 novembre 1918 69622 Villeurbanne Cedex Frankreich
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20
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Fiore M, Strazewski P. Bringing Prebiotic Nucleosides and Nucleotides Down to Earth. Angew Chem Int Ed Engl 2016; 55:13930-13933. [PMID: 27629398 DOI: 10.1002/anie.201606232] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Indexed: 12/20/2022]
Abstract
There may be more than one way leading to RNA: Recent discoveries in the synthesis of nucleoside and nucleotide precursors are described and put into the wider context of prebiotic systems chemistry. Mixing Butlerow's carbohydrate precursors with Traube's 5-formylaminopyrimidines has led to the formation of prebiotic purine nucleosides whereas the mixing of 5-phosphoribose with barbituric acid and melamine gave supramolecular fibers from stacks of Whitesides' rosettas.
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Affiliation(s)
- Michele Fiore
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Université de Lyon, Claude Bernard Lyon 1, 43 bdv du 11 novembre 1918, 69622, Villeurbanne Cedex, France
| | - Peter Strazewski
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Université de Lyon, Claude Bernard Lyon 1, 43 bdv du 11 novembre 1918, 69622, Villeurbanne Cedex, France.
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21
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Accumulation of formamide in hydrothermal pores to form prebiotic nucleobases. Proc Natl Acad Sci U S A 2016; 113:4272-7. [PMID: 27044100 DOI: 10.1073/pnas.1600275113] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Formamide is one of the important compounds from which prebiotic molecules can be synthesized, provided that its concentration is sufficiently high. For nucleotides and short DNA strands, it has been shown that a high degree of accumulation in hydrothermal pores occurs, so that temperature gradients might play a role in the origin of life [Baaske P, et al. (2007)Proc Natl Acad Sci USA104(22):9346-9351]. We show that the same combination of thermophoresis and convection in hydrothermal pores leads to accumulation of formamide up to concentrations where nucleobases are formed. The thermophoretic properties of aqueous formamide solutions are studied by means of Infrared Thermal Diffusion Forced Rayleigh Scattering. These data are used in numerical finite element calculations in hydrothermal pores for various initial concentrations, ambient temperatures, and pore sizes. The high degree of formamide accumulation is due to an unusual temperature and concentration dependence of the thermophoretic behavior of formamide. The accumulation fold in part of the pores increases strongly with increasing aspect ratio of the pores, and saturates to highly concentrated aqueous formamide solutions of ∼85 wt% at large aspect ratios. Time-dependent studies show that these high concentrations are reached after 45-90 d, starting with an initial formamide weight fraction of[Formula: see text]wt % that is typical for concentrations in shallow lakes on early Earth.
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22
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Bada JL, Chalmers JH, Cleaves HJ. Is formamide a geochemically plausible prebiotic solvent? Phys Chem Chem Phys 2016; 18:20085-90. [DOI: 10.1039/c6cp03290g] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
From a geochemical perspective, significant amounts of pure formamide (HCONH2) would have likely been rare on the early Earth.
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Affiliation(s)
- Jeffrey L. Bada
- Scripps Institution of Oceanography
- University of California at San Diego
- La Jolla
- USA
| | - John H. Chalmers
- Scripps Institution of Oceanography
- University of California at San Diego
- La Jolla
- USA
| | - H. James Cleaves
- Earth-Life Science Institute
- Tokyo Institute of Technology
- Tokyo
- Japan
- Institute for Advanced Study
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23
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The RNA World: 4,000,000,050 years old. Life (Basel) 2015; 5:1583-6. [PMID: 26791312 PMCID: PMC4695837 DOI: 10.3390/life5041583] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 10/13/2015] [Indexed: 12/26/2022] Open
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