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Göppel T, Rosenberger JH, Altaner B, Gerland U. Thermodynamic and Kinetic Sequence Selection in Enzyme-Free Polymer Self-Assembly Inside a Non-Equilibrium RNA Reactor. Life (Basel) 2022; 12:life12040567. [PMID: 35455058 PMCID: PMC9032526 DOI: 10.3390/life12040567] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/03/2022] [Accepted: 04/06/2022] [Indexed: 11/18/2022] Open
Abstract
The RNA world is one of the principal hypotheses to explain the emergence of living systems on the prebiotic Earth. It posits that RNA oligonucleotides acted as both carriers of information as well as catalytic molecules, promoting their own replication. However, it does not explain the origin of the catalytic RNA molecules. How could the transition from a pre-RNA to an RNA world occur? A starting point to answer this question is to analyze the dynamics in sequence space on the lowest level, where mononucleotide and short oligonucleotides come together and collectively evolve into larger molecules. To this end, we study the sequence-dependent self-assembly of polymers from a random initial pool of short building blocks via templated ligation. Templated ligation requires two strands that are hybridized adjacently on a third strand. The thermodynamic stability of such a configuration crucially depends on the sequence context and, therefore, significantly influences the ligation probability. However, the sequence context also has a kinetic effect, since non-complementary nucleotide pairs in the vicinity of the ligation site stall the ligation reaction. These sequence-dependent thermodynamic and kinetic effects are explicitly included in our stochastic model. Using this model, we investigate the system-level dynamics inside a non-equilibrium ‘RNA reactor’ enabling a fast chemical activation of the termini of interacting oligomers. Moreover, the RNA reactor subjects the oligomer pool to periodic temperature changes inducing the reshuffling of the system. The binding stability of strands typically grows with the number of complementary nucleotides forming the hybridization site. While shorter strands unbind spontaneously during the cold phase, larger complexes only disassemble during the temperature peaks. Inside the RNA reactor, strand growth is balanced by cleavage via hydrolysis, such that the oligomer pool eventually reaches a non-equilibrium stationary state characterized by its length and sequence distribution. How do motif-dependent energy and stalling parameters affect the sequence composition of the pool of long strands? As a critical factor for self-enhancing sequence selection, we identify kinetic stalling due to non-complementary base pairs at the ligation site. Kinetic stalling enables cascades of self-amplification that result in a strong reduction of occupied states in sequence space. Moreover, we discuss the significance of the symmetry breaking for the transition from a pre-RNA to an RNA world.
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Dass AV, Georgelin T, Westall F, Foucher F, De Los Rios P, Busiello DM, Liang S, Piazza F. Equilibrium and non-equilibrium furanose selection in the ribose isomerisation network. Nat Commun 2021; 12:2749. [PMID: 33980850 PMCID: PMC8115175 DOI: 10.1038/s41467-021-22818-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 03/19/2021] [Indexed: 11/08/2022] Open
Abstract
The exclusive presence of β-D-ribofuranose in nucleic acids is still a conundrum in prebiotic chemistry, given that pyranose species are substantially more stable at equilibrium. However, a precise characterisation of the relative furanose/pyranose fraction at temperatures higher than about 50 °C is still lacking. Here, we employ a combination of NMR measurements and statistical mechanics modelling to predict a population inversion between furanose and pyranose at equilibrium at high temperatures. More importantly, we show that a steady temperature gradient may steer an open isomerisation network into a non-equilibrium steady state where furanose is boosted beyond the limits set by equilibrium thermodynamics. Moreover, we demonstrate that nonequilibrium selection of furanose is maximum at optimal dissipation, as gauged by the temperature gradient and energy barriers for isomerisation. The predicted optimum is compatible with temperature drops found in hydrothermal vents associated with extremely fresh lava flows on the seafloor.
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Affiliation(s)
- Avinash Vicholous Dass
- Centre de Biophysique Moléculaire, CNRS-UPR4301, Rue C. Sadron, Orléans, France
- Department of Physics, Ludwig Maximilians University, München, Germany
| | - Thomas Georgelin
- Centre de Biophysique Moléculaire, CNRS-UPR4301, Rue C. Sadron, Orléans, France
- Laboratoire de Réactivité de Surface, UMR 7197, Sorbonne Université, Paris, France
| | - Frances Westall
- Centre de Biophysique Moléculaire, CNRS-UPR4301, Rue C. Sadron, Orléans, France
| | - Frédéric Foucher
- Centre de Biophysique Moléculaire, CNRS-UPR4301, Rue C. Sadron, Orléans, France
| | - Paolo De Los Rios
- Institute of Physics, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne-EPFL, Lausanne, Switzerland
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne-EPFL, Lausanne, Switzerland
| | - Daniel Maria Busiello
- Institute of Physics, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne-EPFL, Lausanne, Switzerland
| | - Shiling Liang
- Institute of Physics, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne-EPFL, Lausanne, Switzerland
| | - Francesco Piazza
- Centre de Biophysique Moléculaire, CNRS-UPR4301, Rue C. Sadron, Orléans, France.
- Université d'Orléans, UFR CoST Sciences et Techniques, Orléans, France.
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Ball R, Brindley J. Anomalous thermal fluctuation distribution sustains proto-metabolic cycles and biomolecule synthesis. Phys Chem Chem Phys 2020; 22:971-975. [PMID: 31854402 DOI: 10.1039/c9cp05756k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
An environment far from equilibrium is thought to be a necessary condition for the origin and persistence of life. In this context we report open-flow simulations of a non-enzymic proto-metabolic system, in which hydrogen peroxide acts both as oxidant and driver of thermochemical cycling. We find that a Gaussian perturbed input produces a non-Boltzmann output fluctuation distribution around the mean oscillation maximum. Our main result is that net biosynthesis can occur under fluctuating cyclical but not steady drive. Consequently we may revise the necessary condition to "dynamically far from equilibrium".
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Affiliation(s)
- Rowena Ball
- Mathematical Sciences Institute and Research School of Chemistry, Australian National University, Canberra, ACT 2602, Australia.
| | - John Brindley
- School of Mathematics, University of Leeds, Leeds LS2 9JT, UK
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Cassone G, Šponer J, Saija F, Di Mauro E, Marco Saitta A, Šponer JE. Stability of 2',3' and 3',5' cyclic nucleotides in formamide and in water: a theoretical insight into the factors controlling the accumulation of nucleic acid building blocks in a prebiotic pool. Phys Chem Chem Phys 2018; 19:1817-1825. [PMID: 28000820 DOI: 10.1039/c6cp07993h] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Synthesis of the first RNAs represents one of the cornerstones of the emergence of life. Recent studies demonstrated powerful scenarios of prebiotic synthesis of cyclic nucleotides in aqueous and formamide environments. This raised a question about their thermodynamic stability, a decisive factor determining their accumulation in a prebiotic pool. Here we performed ab initio molecular dynamics simulations at various temperatures in formamide and water to study the relative stabilities of the 2',3' and 3',5' isomers of cyclic nucleotides. The computations show that in an aqueous environment 2',3' cyclic nucleotides are more stable than their 3',5' counterparts at all temperatures up to the boiling point. In contrast, in formamide higher temperatures favor the accumulation of the 3',5' cyclic form, whereas below about 400 K the 2',3' cyclic form becomes more stable. The latter observation is consistent with a formamide-based origin scenario, suggesting that 3',5' cyclic nucleotides accumulated at higher temperatures subsequently allowed oligomerization reactions after fast cooling to lower temperatures. A statistical analysis of the geometrical parameters of the solutes indicates that thermodynamics of cyclic nucleotides in aqueous and formamide environments are dictated by the floppiness of the molecules rather than by the ring strain of the cyclic phosphodiester linkages.
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Affiliation(s)
- Giuseppe Cassone
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic.
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic. and Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17. Listopadu, 1192/12, 771 46 Olomouc, Czech Republic
| | - Franz Saija
- CNR-IPCF, Viale Ferdinando Stagno d'Alcontres 37, 98158 Messina, Italy
| | - Ernesto Di Mauro
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia, Via San Camillo De Lellis, 01100 Viterbo, Italy
| | - A Marco Saitta
- Sorbonne Universités, Université Pierre et Marie Curie Paris 6, CNRS, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d'Histoire Naturelle, Institut de Recherche pour le Développement, UMR 7590, F-75005 Paris, France
| | - Judit E Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic.
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