1
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Matreux T, Aikkila P, Scheu B, Braun D, Mast CB. Heat flows enrich prebiotic building blocks and enhance their reactivity. Nature 2024; 628:110-116. [PMID: 38570715 PMCID: PMC10990939 DOI: 10.1038/s41586-024-07193-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/09/2024] [Indexed: 04/05/2024]
Abstract
The emergence of biopolymer building blocks is a crucial step during the origins of life1-6. However, all known formation pathways rely on rare pure feedstocks and demand successive purification and mixing steps to suppress unwanted side reactions and enable high product yields. Here we show that heat flows through thin, crack-like geo-compartments could have provided a widely available yet selective mechanism that separates more than 50 prebiotically relevant building blocks from complex mixtures of amino acids, nucleobases, nucleotides, polyphosphates and 2-aminoazoles. Using measured thermophoretic properties7,8, we numerically model and experimentally prove the advantageous effect of geological networks of interconnected cracks9,10 that purify the previously mixed compounds, boosting their concentration ratios by up to three orders of magnitude. The importance for prebiotic chemistry is shown by the dimerization of glycine11,12, in which the selective purification of trimetaphosphate (TMP)13,14 increased reaction yields by five orders of magnitude. The observed effect is robust under various crack sizes, pH values, solvents and temperatures. Our results demonstrate how geologically driven non-equilibria could have explored highly parallelized reaction conditions to foster prebiotic chemistry.
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Affiliation(s)
- Thomas Matreux
- Systems Biophysics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Paula Aikkila
- Systems Biophysics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Bettina Scheu
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Dieter Braun
- Systems Biophysics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Christof B Mast
- Systems Biophysics, Ludwig-Maximilians-Universität München, Munich, Germany.
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2
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Haugerud IS, Jaiswal P, Weber CA. Nonequilibrium Wet-Dry Cycling Acts as a Catalyst for Chemical Reactions. J Phys Chem B 2024; 128:1724-1736. [PMID: 38335971 PMCID: PMC10895654 DOI: 10.1021/acs.jpcb.3c05824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
Recent experimental studies suggest that wet-dry cycles and coexisting phases can each strongly alter chemical processes. The mechanisms of why and to what degree chemical processes are altered when subjected to evaporation and condensation are unclear. To close this gap, we developed a theoretical framework for nondilute chemical reactions subject to nonequilibrium conditions of evaporation and condensation. We find that such conditions can change the half-time of the product's yield by more than an order of magnitude, depending on the substrate-solvent interaction. We show that the cycle frequency strongly affects the chemical turnover when the system is maintained out of equilibrium by wet-dry cycles. There exists a resonance behavior in the cycle frequency where the turnover is maximal. This resonance behavior enables wet-dry cycles to select specific chemical reactions, suggesting a potential mechanism for chemical evolution in prebiotic soups at early Earth.
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Affiliation(s)
- Ivar Svalheim Haugerud
- Faculty of Mathematics, Natural Sciences, and Materials Engineering: Institute of Physics, University of Augsburg, Universitätsstraße 1, Augsburg 86159, Germany
| | - Pranay Jaiswal
- Faculty of Mathematics, Natural Sciences, and Materials Engineering: Institute of Physics, University of Augsburg, Universitätsstraße 1, Augsburg 86159, Germany
| | - Christoph A Weber
- Faculty of Mathematics, Natural Sciences, and Materials Engineering: Institute of Physics, University of Augsburg, Universitätsstraße 1, Augsburg 86159, Germany
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3
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Agmon I. Three Biopolymers and Origin of Life Scenarios. Life (Basel) 2024; 14:277. [PMID: 38398786 PMCID: PMC10890401 DOI: 10.3390/life14020277] [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: 12/28/2023] [Revised: 02/08/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024] Open
Abstract
To track down the possible roots of life, various models for the initial living system composed of different combinations of the three extant biopolymers, RNA, DNA, and proteins, are presented. The suitability of each molecular set is assessed according to its ability to emerge autonomously, sustain, and evolve continuously towards life as we know it. The analysis incorporates current biological knowledge gained from high-resolution structural data and large sequence datasets, together with experimental results concerned with RNA replication and with the activity demonstrated by standalone constructs of the ribosomal Peptidyl Transferase Center region. The scrutiny excludes the DNA-protein combination and assigns negligible likelihood to the existence of an RNA-DNA world, as well as to an RNA world that contained a replicase made of RNA. It points to the precedence of an RNA-protein system, whose model of emergence suggests specific processes whereby a coded proto-ribosome ribozyme, specifically aminoacylated proto-tRNAs and a proto-polymerase enzyme, could have autonomously emerged, cross-catalyzing the formation of each other. This molecular set constitutes a feasible starting point for a continuous evolutionary path, proceeding via natural processes from the inanimate matter towards life as we know it.
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Affiliation(s)
- Ilana Agmon
- Institute for Advanced Studies in Theoretical Chemistry, Schulich Faculty of Chemistry, Technion—Israel Institute of Technology, Haifa 3200003, Israel;
- Fritz Haber Research Center for Molecular Dynamics, Hebrew University, Jerusalem 9190401, Israel
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4
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Bartolucci G, Calaça Serrão A, Schwintek P, Kühnlein A, Rana Y, Janto P, Hofer D, Mast CB, Braun D, Weber CA. Sequence self-selection by cyclic phase separation. Proc Natl Acad Sci U S A 2023; 120:e2218876120. [PMID: 37847736 PMCID: PMC10614837 DOI: 10.1073/pnas.2218876120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 09/06/2023] [Indexed: 10/19/2023] Open
Abstract
The emergence of functional oligonucleotides on early Earth required a molecular selection mechanism to screen for specific sequences with prebiotic functions. Cyclic processes such as daily temperature oscillations were ubiquitous in this environment and could trigger oligonucleotide phase separation. Here, we propose sequence selection based on phase separation cycles realized through sedimentation in a system subjected to the feeding of oligonucleotides. Using theory and experiments with DNA, we show sequence-specific enrichment in the sedimented dense phase, in particular of short 22-mer DNA sequences. The underlying mechanism selects for complementarity, as it enriches sequences that tightly interact in the dense phase through base-pairing. Our mechanism also enables initially weakly biased pools to enhance their sequence bias or to replace the previously most abundant sequences as the cycles progress. Our findings provide an example of a selection mechanism that may have eased screening for auto-catalytic self-replicating oligonucleotides.
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Affiliation(s)
- Giacomo Bartolucci
- Division Biological Physics, Max Planck Institute for the Physics of Complex Systems, Dresden01187, Germany
- Center for Systems Biology Dresden, Dresden01307, Germany
| | - Adriana Calaça Serrão
- Ludwigs-Maximilian-Universität München and Center for NanoScience, Munich80799, Germany
| | - Philipp Schwintek
- Ludwigs-Maximilian-Universität München and Center for NanoScience, Munich80799, Germany
| | - Alexandra Kühnlein
- Ludwigs-Maximilian-Universität München and Center for NanoScience, Munich80799, Germany
| | - Yash Rana
- Division Biological Physics, Max Planck Institute for the Physics of Complex Systems, Dresden01187, Germany
- Center for Systems Biology Dresden, Dresden01307, Germany
| | - Philipp Janto
- Ludwigs-Maximilian-Universität München and Center for NanoScience, Munich80799, Germany
| | - Dorothea Hofer
- Ludwigs-Maximilian-Universität München and Center for NanoScience, Munich80799, Germany
| | - Christof B. Mast
- Ludwigs-Maximilian-Universität München and Center for NanoScience, Munich80799, Germany
| | - Dieter Braun
- Ludwigs-Maximilian-Universität München and Center for NanoScience, Munich80799, Germany
| | - Christoph A. Weber
- Faculty of Mathematics, Natural Sciences, and Materials Engineering: Institute of Physics, University of Augsburg, Augsburg86159, Germany
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5
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Weingart M, Chen S, Donat C, Helmbrecht V, Orsi WD, Braun D, Alim K. Alkaline vents recreated in two dimensions to study pH gradients, precipitation morphology, and molecule accumulation. SCIENCE ADVANCES 2023; 9:eadi1884. [PMID: 37774032 PMCID: PMC10541008 DOI: 10.1126/sciadv.adi1884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/30/2023] [Indexed: 10/01/2023]
Abstract
Alkaline vents (AVs) are hypothesized to have been a setting for the emergence of life, by creating strong gradients across inorganic membranes within chimney structures. In the past, three-dimensional chimney structures were formed under laboratory conditions; however, no in situ visualization or testing of the gradients was possible. We develop a quasi-two-dimensional microfluidic model of AVs that allows spatiotemporal visualization of mineral precipitation in low-volume experiments. Upon injection of an alkaline fluid into an acidic, iron-rich solution, we observe a diverse set of precipitation morphologies, mainly controlled by flow rate and ion concentration. Using microscope imaging and pH-dependent dyes, we show that finger-like precipitates can facilitate formation and maintenance of microscale pH gradients and accumulation of dispersed particles in confined geometries. Our findings establish a model to investigate the potential of gradients across a semipermeable boundary for early compartmentalization, accumulation, and chemical reactions at the origins of life.
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Affiliation(s)
- Maximilian Weingart
- Systems Biophysics and Center for NanoScience (CeNS), Ludwig-Maximilians University Munich, Amalienstraße 54, 80799 München, Germany
| | - Siyu Chen
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany
| | - Clara Donat
- TUM School of Natural Sciences, Department of Bioscience; Center for Protein Assemblies (CPA), Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748 Garching b. München, Germany
| | - Vanessa Helmbrecht
- Department of Earth and Environmental Sciences, Ludwig-Maximilians University Munich, Richard-Wagner Straße 10, 80333 München, Germany
| | - William D. Orsi
- Department of Earth and Environmental Sciences, Ludwig-Maximilians University Munich, Richard-Wagner Straße 10, 80333 München, Germany
- GeoBio-CenterLMU, Ludwig-Maximilians University Munich, Richard-Wagner Straße 10, 80333 München, Germany
| | - Dieter Braun
- Systems Biophysics and Center for NanoScience (CeNS), Ludwig-Maximilians University Munich, Amalienstraße 54, 80799 München, Germany
| | - Karen Alim
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany
- TUM School of Natural Sciences, Department of Bioscience; Center for Protein Assemblies (CPA), Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748 Garching b. München, Germany
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6
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Ashwood B, Jones MS, Radakovic A, Khanna S, Lee Y, Sachleben JR, Szostak JW, Ferguson AL, Tokmakoff A. Thermodynamics and kinetics of DNA and RNA dinucleotide hybridization to gaps and overhangs. Biophys J 2023; 122:3323-3339. [PMID: 37469144 PMCID: PMC10465710 DOI: 10.1016/j.bpj.2023.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/27/2023] [Accepted: 07/17/2023] [Indexed: 07/21/2023] Open
Abstract
Hybridization of short nucleic acid segments (<4 nt) to single-strand templates occurs as a critical intermediate in processes such as nonenzymatic nucleic acid replication and toehold-mediated strand displacement. These templates often contain adjacent duplex segments that stabilize base pairing with single-strand gaps or overhangs, but the thermodynamics and kinetics of hybridization in such contexts are poorly understood because of the experimental challenges of probing weak binding and rapid structural dynamics. Here we develop an approach to directly measure the thermodynamics and kinetics of DNA and RNA dinucleotide dehybridization using steady-state and temperature-jump infrared spectroscopy. Our results suggest that dinucleotide binding is stabilized through coaxial stacking interactions with the adjacent duplex segments as well as from potential noncanonical base-pairing configurations and structural dynamics of gap and overhang templates revealed using molecular dynamics simulations. We measure timescales for dissociation ranging from 0.2-40 μs depending on the template and temperature. Dinucleotide hybridization and dehybridization involve a significant free energy barrier with characteristics resembling that of canonical oligonucleotides. Together, our work provides an initial step for predicting the stability and kinetics of hybridization between short nucleic acid segments and various templates.
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Affiliation(s)
- Brennan Ashwood
- Department of Chemistry, The University of Chicago, Chicago, Illinois; The James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois
| | - Michael S Jones
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois
| | | | - Smayan Khanna
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois
| | - Yumin Lee
- Department of Chemistry, The University of Chicago, Chicago, Illinois; The James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois
| | - Joseph R Sachleben
- Biomolecular NMR Core Facility, Biological Sciences Division, The University of Chicago, Chicago, Illinois
| | - Jack W Szostak
- Department of Chemistry, The University of Chicago, Chicago, Illinois
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois
| | - Andrei Tokmakoff
- Department of Chemistry, The University of Chicago, Chicago, Illinois; The James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois.
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7
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Fraccia TP, Martin N. Non-enzymatic oligonucleotide ligation in coacervate protocells sustains compartment-content coupling. Nat Commun 2023; 14:2606. [PMID: 37160869 PMCID: PMC10169843 DOI: 10.1038/s41467-023-38163-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 04/18/2023] [Indexed: 05/11/2023] Open
Abstract
Modern cells are complex chemical compartments tightly regulated by an underlying DNA-encoded program. Achieving a form of coupling between molecular content, chemical reactions, and chassis in synthetic compartments represents a key step to the assembly of evolvable protocells but remains challenging. Here, we design coacervate droplets that promote non-enzymatic oligonucleotide polymerization and that restructure as a result of the reaction dynamics. More specifically, we rationally exploit complexation between end-reactive oligonucleotides able to stack into long physical polymers and a cationic azobenzene photoswitch to produce three different phases-soft solids, liquid crystalline or isotropic coacervates droplets-each of them having a different impact on the reaction efficiency. Dynamical modulation of coacervate assembly and dissolution via trans-cis azobenzene photo-isomerization is used to demonstrate cycles of light-actuated oligonucleotide ligation. Remarkably, changes in the population of polynucleotides during polymerization induce phase transitions due to length-based DNA self-sorting to produce multiphase coacervates. Overall, by combining a tight reaction-structure coupling and environmental responsiveness, our reactive coacervates provide a general route to the non-enzymatic synthesis of polynucleotides and pave the way to the emergence of a primitive compartment-content coupling in membrane-free protocells.
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Affiliation(s)
- Tommaso P Fraccia
- Institut Pierre-Gilles de Gennes, Chimie Biologie et Innovation, UMR 8231, ESPCI Paris, PSL University, CNRS, 6 rue Jean Calvin, 75005, Paris, France.
- Department of Pharmacological and Biomolecular Sciences, University of Milano, 20133, Milano, Italy.
| | - Nicolas Martin
- Univ. Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR 5031, 115 avenue du Dr. Schweitzer, 33600, Pessac, France.
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8
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Mayer DB, Franosch T, Mast C, Braun D. Thermophoresis beyond Local Thermodynamic Equilibrium. PHYSICAL REVIEW LETTERS 2023; 130:168202. [PMID: 37154655 DOI: 10.1103/physrevlett.130.168202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 03/08/2023] [Indexed: 05/10/2023]
Abstract
We measure the thermophoresis of polysterene beads over a wide range of temperature gradients and find a pronounced nonlinear phoretic characteristic. The transition to the nonlinear behavior is marked by a drastic slowing down of thermophoretic motion and is characterized by a Péclet number of order unity as corroborated for different particle sizes and salt concentrations. The data follow a single master curve covering the entire nonlinear regime for all system parameters upon proper rescaling of the temperature gradients with the Péclet number. For low thermal gradients, the thermal drift velocity follows a theoretical linear model relying on the local-equilibrium assumption, while linear theoretical approaches based on hydrodynamic stresses, ignoring fluctuations, predict significantly slower thermophoretic motion for steeper thermal gradients. Our findings suggest that thermophoresis is fluctuation dominated for small gradients and crosses over to a drift-dominated regime for larger Péclet numbers in striking contrast to electrophoresis.
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Affiliation(s)
- Daniel B Mayer
- Institut für Theoretische Physik, Universität Innsbruck, Technikerstraße 21A, A-6020 Innsbruck, Austria
| | - Thomas Franosch
- Institut für Theoretische Physik, Universität Innsbruck, Technikerstraße 21A, A-6020 Innsbruck, Austria
| | - Christof Mast
- Systems Biophysics, Physics Department, Nanosystems Initiative Munich and Center for NanoScience, Ludwig-Maximilians-Universität München, Amalienstrasse 54, D-80799 München, Germany
| | - Dieter Braun
- Systems Biophysics, Physics Department, Nanosystems Initiative Munich and Center for NanoScience, Ludwig-Maximilians-Universität München, Amalienstrasse 54, D-80799 München, Germany
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9
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Ashwood B, Jones MS, Radakovic A, Khanna S, Lee Y, Sachleben JR, Szostak JW, Ferguson AL, Tokmakoff A. Direct monitoring of the thermodynamics and kinetics of DNA and RNA dinucleotide dehybridization from gaps and overhangs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.10.536266. [PMID: 37090657 PMCID: PMC10120721 DOI: 10.1101/2023.04.10.536266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Hybridization of short nucleic acid segments (<4 nucleotides) to single-strand templates occurs as a critical intermediate in processes such as non-enzymatic nucleic acid replication and toehold-mediated strand displacement. These templates often contain adjacent duplex segments that stabilize base pairing with single-strand gaps or overhangs, but the thermodynamics and kinetics of hybridization in such contexts are poorly understood due to experimental challenges of probing weak binding and rapid structural dynamics. Here we develop an approach to directly measure the thermodynamics and kinetics of DNA and RNA dinucleotide dehybridization using steady-state and temperature-jump infrared spectroscopy. Our results suggest that dinucleotide binding is stabilized through coaxial stacking interactions with the adjacent duplex segments as well as from potential non-canonical base pairing configurations and structural dynamics of gap and overhang templates revealed using molecular dynamics simulations. We measure timescales for dissociation ranging from 0.2 to 40 µs depending on the template and temperature. Dinucleotide hybridization and dehybridization involves a significant free energy barrier with characteristics resembling that of canonical oligonucleotides. Together, our work provides an initial step for predicting the stability and kinetics of hybridization between short nucleic acid segments and various templates.
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Affiliation(s)
- Brennan Ashwood
- Department of Chemistry, The University of Chicago, 5735 S. Ellis Avenue, Chicago, IL 60637
- The James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57 Street, Chicago, Illinois 60637, United States
| | - Michael S Jones
- Pritzker School of Molecular Engineering, The University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United States
| | | | - Smayan Khanna
- Pritzker School of Molecular Engineering, The University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Yumin Lee
- Department of Chemistry, The University of Chicago, 5735 S. Ellis Avenue, Chicago, IL 60637
| | - Joseph R Sachleben
- Biomolecular NMR Core Facility, Biological Sciences Division, The University of Chicago, Chicago, IL 60637, United States
| | - Jack W Szostak
- Department of Chemistry, The University of Chicago, 5735 S. Ellis Avenue, Chicago, IL 60637
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, The University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Andrei Tokmakoff
- Department of Chemistry, The University of Chicago, 5735 S. Ellis Avenue, Chicago, IL 60637
- The James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57 Street, Chicago, Illinois 60637, United States
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10
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Dirscherl CF, Ianeselli A, Tetiker D, Matreux T, Queener RM, Mast CB, Braun D. A heated rock crack captures and polymerizes primordial DNA and RNA. Phys Chem Chem Phys 2023; 25:3375-3386. [PMID: 36633199 DOI: 10.1039/d2cp04538a] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Life is based on informational polymers such as DNA or RNA. For their polymerization, high concentrations of complex monomer building blocks are required. Therefore, the dilution by diffusion poses a major problem before early life could establish a non-equilibrium of compartmentalization. Here, we explored a natural non-equilibrium habitat to polymerize RNA and DNA. A heat flux across thin rock cracks is shown to accumulate and maintain nucleotides. This boosts the polymerization to RNA and DNA inside the crack. Moreover, the polymers remain localized, aiding both the creation of longer polymers and fostering downstream evolutionary steps. In a closed system, we found single nucleotides concentrate 104-fold at the bottom of the crack compared to the top after 24 hours. We detected enhanced polymerization for 2 different activation chemistries: aminoimidazole-activated DNA nucleotides and 2',3'-cyclic RNA nucleotides. The copolymerization of 2',3'-cGMP and 2',3'-cCMP in the thermal pore showed an increased heterogeneity in sequence composition compared to isothermal drying. Finite element models unravelled the combined polymerization and accumulation kinetics and indicated that the escape of the nucleotides from such a crack is negligible over a time span of years. The thermal non-equilibrium habitat establishes a cell-like compartment that actively accumulates nucleotides for polymerization and traps the resulting oligomers. We argue that the setting creates a pre-cellular non-equilibrium steady state for the first steps of molecular evolution.
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Affiliation(s)
- Christina F Dirscherl
- Systems Biophysics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80799 Munich, Germany.
| | - Alan Ianeselli
- Systems Biophysics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80799 Munich, Germany.
| | - Damla Tetiker
- Systems Biophysics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80799 Munich, Germany.
| | - Thomas Matreux
- Systems Biophysics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80799 Munich, Germany.
| | - Robbin M Queener
- Systems Biophysics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80799 Munich, Germany.
| | - Christof B Mast
- Systems Biophysics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80799 Munich, Germany.
| | - Dieter Braun
- Systems Biophysics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80799 Munich, Germany.
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11
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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.
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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
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12
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A liquid crystal world for the origins of life. Emerg Top Life Sci 2022; 6:557-569. [PMID: 36373852 DOI: 10.1042/etls20220081] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/23/2022] [Accepted: 10/27/2022] [Indexed: 11/16/2022]
Abstract
Nucleic acids (NAs) in modern biology accomplish a variety of tasks, and the emergence of primitive nucleic acids is broadly recognized as a crucial step for the emergence of life. While modern NAs have been optimized by evolution to accomplish various biological functions, such as catalysis or transmission of genetic information, primitive NAs could have emerged and been selected based on more rudimental chemical-physical properties, such as their propensity to self-assemble into supramolecular structures. One such supramolecular structure available to primitive NAs are liquid crystal (LC) phases, which are the outcome of the collective behavior of short DNA or RNA oligomers or monomers that self-assemble into linear aggregates by combinations of pairing and stacking. Formation of NA LCs could have provided many essential advantages for a primitive evolving system, including the selection of potential genetic polymers based on structure, protection by compartmentalization, elongation, and recombination by enhanced abiotic ligation. Here, we review recent studies on NA LC assembly, structure, and functions with potential prebiotic relevance. Finally, we discuss environmental or geological conditions on early Earth that could have promoted (or inhibited) primitive NA LC formation and highlight future investigation axes essential to further understanding of how LCs could have contributed to the emergence of life.
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13
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Prebiotic Assembly of Cloverleaf tRNA, Its Aminoacylation and the Origin of Coding, Inferred from Acceptor Stem Coding-Triplets. Int J Mol Sci 2022; 23:ijms232415756. [PMID: 36555394 PMCID: PMC9778954 DOI: 10.3390/ijms232415756] [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: 10/25/2022] [Revised: 11/25/2022] [Accepted: 12/03/2022] [Indexed: 12/14/2022] Open
Abstract
tRNA is a key component in life's most fundamental process, the translation of the instructions contained in mRNA into proteins. Its role had to be executed as soon as the earliest translation emerged, but the questions of the prebiotic tRNA materialization, aminoacylation, and the origin of the coding triplets it carries are still open. Here, these questions are addressed by utilizing a distinct pattern of coding triplets highly conserved in the acceptor stems from the modern bacterial tRNAs of five early-emerging amino acids. Self-assembly of several copies of a short RNA oligonucleotide that carries a related pattern of coding triplets, via a simple and statistically feasible process, is suggested to result in a proto-tRNA model highly compatible with the cloverleaf secondary structure of the modern tRNA. Furthermore, these stem coding triplets evoke the possibility that they were involved in self-aminoacylation of proto-tRNAs prior to the emergence of the earliest synthetases, a process proposed to underlie the formation of the genetic code. Being capable of autonomous materialization and of self-aminoacylation, this verifiable model of the proto-tRNA advent adds principal components to an initial set of molecules and processes that may have led, exclusively through natural means, to the emergence of life.
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Lerin-Morales KM, Olguín LF, Mateo-Martí E, Colín-García M. Prebiotic Chemistry Experiments Using Microfluidic Devices. Life (Basel) 2022; 12:life12101665. [PMID: 36295100 PMCID: PMC9605377 DOI: 10.3390/life12101665] [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: 09/30/2022] [Revised: 10/15/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
Microfluidic devices are small tools mostly consisting of one or more channels, with dimensions between one and hundreds of microns, where small volumes of fluids are manipulated. They have extensive use in the biomedical and chemical fields; however, in prebiotic chemistry, they only have been employed recently. In prebiotic chemistry, just three types of microfluidic devices have been used: the first ones are Y-form devices with laminar co-flow, used to study the precipitation of minerals in hydrothermal vents systems; the second ones are microdroplet devices that can form small droplets capable of mimic cellular compartmentalization; and the last ones are devices with microchambers that recreate the microenvironment inside rock pores under hydrothermal conditions. In this review, we summarized the experiments in the field of prebiotic chemistry that employed microfluidic devices. The main idea is to incentivize their use and discuss their potential to perform novel experiments that could contribute to unraveling some prebiotic chemistry questions.
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Affiliation(s)
- Karen Melissa Lerin-Morales
- Posgrado en Ciencias de la Tierra, Universidad Nacional Autónoma de México, Ciudad de Mexico 04510, Mexico
- Correspondence: (K.M.L.-M.); (M.C.-G.); Tel.: +52-(55)-5622-4300 (ext. 164) (M.C.-G.)
| | - Luis F. Olguín
- Laboratorio de Biofisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de Mexico 04510, Mexico
| | - Eva Mateo-Martí
- Centro de Astrobiología (CAB), CSIC-INTA, Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - María Colín-García
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad de Mexico 04510, Mexico
- Correspondence: (K.M.L.-M.); (M.C.-G.); Tel.: +52-(55)-5622-4300 (ext. 164) (M.C.-G.)
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15
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Saha A, Yi R, Fahrenbach AC, Wang A, Jia TZ. A Physicochemical Consideration of Prebiotic Microenvironments for Self-Assembly and Prebiotic Chemistry. LIFE (BASEL, SWITZERLAND) 2022; 12:life12101595. [PMID: 36295030 PMCID: PMC9604842 DOI: 10.3390/life12101595] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/07/2022] [Accepted: 10/08/2022] [Indexed: 11/06/2022]
Abstract
The origin of life on Earth required myriads of chemical and physical processes. These include the formation of the planet and its geological structures, the formation of the first primitive chemicals, reaction, and assembly of these primitive chemicals to form more complex or functional products and assemblies, and finally the formation of the first cells (or protocells) on early Earth, which eventually evolved into modern cells. Each of these processes presumably occurred within specific prebiotic reaction environments, which could have been diverse in physical and chemical properties. While there are resources that describe prebiotically plausible environments or nutrient availability, here, we attempt to aggregate the literature for the various physicochemical properties of different prebiotic reaction microenvironments on early Earth. We introduce a handful of properties that can be quantified through physical or chemical techniques. The values for these physicochemical properties, if they are known, are then presented for each reaction environment, giving the reader a sense of the environmental variability of such properties. Such a resource may be useful for prebiotic chemists to understand the range of conditions in each reaction environment, or to select the medium most applicable for their targeted reaction of interest for exploratory studies.
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Affiliation(s)
- Arpita Saha
- Blue Marble Space Institute of Science, 600 1st Ave, Floor 1, Seattle, WA 98104, USA
- Amity Institute of Applied Sciences, Amity University, Kolkata 700135, India
| | - Ruiqin Yi
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Albert C. Fahrenbach
- School of Chemistry, UNSW Sydney, Sydney, NSW 2052, Australia
- Australian Centre for Astrobiology, UNSW Sydney, Sydney, NSW 2052, Australia
- UNSW RNA Institute, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Anna Wang
- School of Chemistry, UNSW Sydney, Sydney, NSW 2052, Australia
- Australian Centre for Astrobiology, UNSW Sydney, Sydney, NSW 2052, Australia
- UNSW RNA Institute, UNSW Sydney, Sydney, NSW 2052, Australia
- Correspondence: (A.W.); (T.Z.J.)
| | - Tony Z. Jia
- Blue Marble Space Institute of Science, 600 1st Ave, Floor 1, Seattle, WA 98104, USA
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Correspondence: (A.W.); (T.Z.J.)
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16
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Roy S, Sengupta S. The Effect of Environment on the Evolution and Proliferation of Protocells of Increasing Complexity. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081227. [PMID: 36013406 PMCID: PMC9410160 DOI: 10.3390/life12081227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/01/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022]
Abstract
The formation, growth, division and proliferation of protocells containing RNA strands is an important step in ensuring the viability of a mixed RNA-lipid world. Experiments and computer simulations indicate that RNA encapsulated inside protocells can favor the protocell, promoting its growth while protecting the system from being over-run by selfish RNA sequences. Recent work has also shown that the rolling-circle replication mechanism can be harnessed to ensure the rapid growth of RNA strands and the probabilistic emergence and proliferation of protocells with functionally diverse ribozymes. Despite these advances in our understanding of a primordial RNA-lipid world, key questions remain about the ideal environment for the formation of protocells and its role in regulating the proliferation of functionally complex protocells. The hot spring hypothesis suggests that mineral-rich regions near hot springs, subject to dry-wet cycles, provide an ideal environment for the origin of primitive protocells. We develop a computational model to study protocellular evolution in such environments that are distinguished by the occurrence of three distinct phases, a wet phase, followed by a gel phase, and subsequently by a dry phase. We determine the conditions under which protocells containing multiple types of ribozymes can evolve and proliferate in such regions. We find that diffusion in the gel phase can inhibit the proliferation of complex protocells with the extent of inhibition being most significant when a small fraction of protocells is eliminated during environmental cycling. Our work clarifies how the environment can shape the evolution and proliferation of complex protocells.
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17
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Englert A, Vogel JF, Bergner T, Loske J, von Delius M. A Ribonucleotide ↔ Phosphoramidate Reaction Network Optimized by Computer-Aided Design. J Am Chem Soc 2022; 144:15266-15274. [PMID: 35953065 PMCID: PMC9413217 DOI: 10.1021/jacs.2c05861] [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] [Indexed: 12/02/2022]
Abstract
![]()
A growing number of out-of-equilibrium systems have been
created
and investigated in chemical laboratories over the past decade. One
way to achieve this is to create a reaction cycle, in which the forward
reaction is driven by a chemical fuel and the backward reaction follows
a different pathway. Such dissipative reaction networks are still
relatively rare, however, and most non-enzymatic examples are based
on the carbodiimide-driven generation of carboxylic acid anhydrides.
In this work, we describe a dissipative reaction network that comprises
the chemically fueled formation of phosphoramidates from natural ribonucleotides
(e.g., GMP or AMP) and phosphoramidate hydrolysis as a mild backward
reaction. Because the individual reactions are subject to a multitude
of interconnected parameters, the software-assisted tool “Design
of Experiments” (DoE) was a great asset for optimizing and
understanding the network. One notable insight was the stark effect
of the nucleophilic catalyst 1-ethylimidazole (EtIm) on the hydrolysis
rate, which is reminiscent of the action of the histidine group in
phosphoramidase enzymes (e.g., HINT1). We were also able to use the
reaction cycle to generate transient self-assemblies, which were characterized
by dynamic light scattering (DLS), confocal microscopy (CLSM), and
cryogenic transmission electron microscopy (cryo-TEM). Because these
compartments are based on prebiotically plausible building blocks,
our findings may have relevance for origin-of-life scenarios.
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Affiliation(s)
- Andreas Englert
- Institute of Organic Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Julian F Vogel
- Institute of Organic Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Tim Bergner
- Central Facility for Electron Microscopy, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Jessica Loske
- Institute of Organic Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Max von Delius
- Institute of Organic Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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18
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Kobayashi I, Sasa SI. Characterizing the Asymmetry in Hardness between Synthesis and Destruction of Heteropolymers. PHYSICAL REVIEW LETTERS 2022; 128:247801. [PMID: 35776448 DOI: 10.1103/physrevlett.128.247801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 05/11/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
We present a simple model describing the assembly and disassembly of heteropolymers consisting of two types of monomers A and B. We prove that no matter how we manipulate the concentrations of A and B, it takes longer than the exponential function of d to synthesize a fixed amount of the desired heteropolymer, where d is the number of A-B connections. We also prove the decomposition time is linear for chain length n. When d is proportional to n, synthesis and destruction have an exponential asymmetry. Our findings may facilitate research on the more general asymmetry of operational hardness.
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Affiliation(s)
- Ikumi Kobayashi
- Department of Physics, Kyoto University, Kyoto 606-8502, Japan
| | - Shin-Ichi Sasa
- Department of Physics, Kyoto University, Kyoto 606-8502, Japan
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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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20
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Jia TZ, Nishikawa S, Fujishima K. Sequencing the Origins of Life. BBA ADVANCES 2022; 2:100049. [PMID: 37082609 PMCID: PMC10074849 DOI: 10.1016/j.bbadva.2022.100049] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/27/2022] [Accepted: 03/02/2022] [Indexed: 01/10/2023] Open
Abstract
One goal of origins of life research is to understand how primitive informational and catalytic biopolymers emerged and evolved. Recently, a number of sequencing techniques have been applied to analysis of replicating and evolving primitive biopolymer systems, providing a sequence-specific and high-resolution view of primitive chemical processes. Here, we review application of sequencing techniques to analysis of synthetic and primitive nucleic acids and polypeptides. This includes next-generation sequencing of primitive polymerization and evolution processes, followed by discussion of other novel biochemical techniques that could contribute to sequence analysis of primitive biopolymer driven chemical systems. Further application of sequencing to origins of life research, perhaps as a life detection technology, could provide insight into the origin and evolution of informational and catalytic biopolymers on early Earth or elsewhere.
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Affiliation(s)
- Tony Z. Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Blue Marble Space Institute of Science, 600 1st Ave, Floor 1, Seattle, WA 98104, USA
- Corresponding author
| | - Shota Nishikawa
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa-shi, Kanagawa 252-0882, Japan
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21
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Juritz J, Poulton JM, Ouldridge TE. Minimal mechanism for cyclic templating of length-controlled copolymers under isothermal conditions. J Chem Phys 2022; 156:074103. [DOI: 10.1063/5.0077865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Jordan Juritz
- Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jenny M. Poulton
- Foundation for Fundamental Research on Matter (FOM), Institute for Atomic and Molecular Physics (AMOLF), 1098 XE Amsterdam, The Netherlands
| | - Thomas E. Ouldridge
- Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
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22
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Hansma HG. Potassium at the Origins of Life: Did Biology Emerge from Biotite in Micaceous Clay? Life (Basel) 2022; 12:life12020301. [PMID: 35207588 PMCID: PMC8880093 DOI: 10.3390/life12020301] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/31/2022] [Accepted: 01/31/2022] [Indexed: 12/15/2022] Open
Abstract
Intracellular potassium concentrations, [K+], are high in all types of living cells, but the origins of this K+ are unknown. The simplest hypothesis is that life emerged in an environment that was high in K+. One such environment is the spaces between the sheets of the clay mineral mica. The best mica for life’s origins is the black mica, biotite, because it has a high content of Mg++ and because it has iron in various oxidation states. Life also has many of the characteristics of the environment between mica sheets, giving further support for the possibility that mica was the substrate on and within which life emerged. Here, a scenario for life’s origins is presented, in which the necessary processes and components for life arise in niches between mica sheets; vesicle membranes encapsulate these processes and components; the resulting vesicles fuse, forming protocells; and eventually, all of the necessary components and processes are encapsulated within individual cells, some of which survive to seed the early Earth with life. This paper presents three new foci for the hypothesis of life’s origins between mica sheets: (1) that potassium is essential for life’s origins on Earth; (2) that biotite mica has advantages over muscovite mica; and (3) that micaceous clay is a better environment than isolated mica for life’s origins.
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23
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Sithamparam M, Satthiyasilan N, Chen C, Jia TZ, Chandru K. A material-based panspermia hypothesis: The potential of polymer gels and membraneless droplets. Biopolymers 2022; 113:e23486. [PMID: 35148427 DOI: 10.1002/bip.23486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 01/08/2023]
Abstract
The Panspermia hypothesis posits that either life's building blocks (molecular Panspermia) or life itself (organism-based Panspermia) may have been interplanetarily transferred to facilitate the origins of life (OoL) on a given planet, complementing several current OoL frameworks. Although many spaceflight experiments were performed in the past to test for potential terrestrial organisms as Panspermia seeds, it is uncertain whether such organisms will likely "seed" a new planet even if they are able to survive spaceflight. Therefore, rather than using organisms, using abiotic chemicals as seeds has been proposed as part of the molecular Panspermia hypothesis. Here, as an extension of this hypothesis, we introduce and review the plausibility of a polymeric material-based Panspermia seed (M-BPS) as a theoretical concept, where the type of polymeric material that can function as a M-BPS must be able to: (1) survive spaceflight and (2) "function", i.e., contingently drive chemical evolution toward some form of abiogenesis once arriving on a foreign planet. We use polymeric gels as a model example of a potential M-BPS. Polymeric gels that can be prebiotically synthesized on one planet (such as polyester gels) could be transferred to another planet via meteoritic transfer, where upon landing on a liquid bearing planet, can assemble into structures containing cellular-like characteristics and functionalities. Such features presupposed that these gels can assemble into compartments through phase separation to accomplish relevant functions such as encapsulation of primitive metabolic, genetic and catalytic materials, exchange of these materials, motion, coalescence, and evolution. All of these functions can result in the gels' capability to alter local geochemical niches on other planets, thereby allowing chemical evolution to lead to OoL events.
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Affiliation(s)
- Mahendran Sithamparam
- Space Science Center (ANGKASA), Institute of Climate Change, National University of Malaysia (UKM), Bangi, Selangor, Malaysia
| | - Nirmell Satthiyasilan
- Space Science Center (ANGKASA), Institute of Climate Change, National University of Malaysia (UKM), Bangi, Selangor, Malaysia
| | - Chen Chen
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - Tony Z Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,Blue Marble Space Institute of Science, Seattle, Washington, USA
| | - Kuhan Chandru
- Space Science Center (ANGKASA), Institute of Climate Change, National University of Malaysia (UKM), Bangi, Selangor, Malaysia
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24
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Luo D, Zhao C, Xue G, Cao Z, Oztekin A, Cheng X. Label-free focusing of viral particles under a temperature gradient coupled with continuous swirling flow. RSC Adv 2022; 12:4263-4275. [PMID: 35425424 PMCID: PMC8981173 DOI: 10.1039/d1ra09462a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 01/14/2022] [Indexed: 11/21/2022] Open
Abstract
The advances of biomedicine and biotechnology demand new approaches to enrich biological nanoparticles, such as viruses, viral vectors and nanovesicles, in an easy-to-operate fashion. Conventional methods, such as ultracentrifugation and ultrafiltration, require bulky instruments and extensive manual operation. Inspired by recent research of thermophoresis of biomolecules and bio-nanoparticles in aqueous solutions, we present a microfluidic design that directly focuses nanoparticles in a label-free and flow-through process by coupling an engineered swirling flow and a moderate, one-dimensional temperature gradient. Enrichment of polystyrene particles, HIV and bacteriophage samples was quantitatively determined, indicating the compatibility of the microfluidic approach with synthetic and biological samples. The focusing results are well predicted using a numerical model. As thermophoresis is ubiquitous, the microfluidic approach can be applied broadly to bio-nanoparticle enrichment without the necessity of labeling, buffer exchange, or sheath fluids, permitting continuous retrieval of concentrated species in a simple, controlled flow with little infrastructure needs.
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Affiliation(s)
- Danli Luo
- Department of Materials Science and Engineering, Lehigh University Bethlehem PA 18015 USA
| | - Chao Zhao
- Department of Materials Science and Engineering, Lehigh University Bethlehem PA 18015 USA
| | - Guanyang Xue
- Department of Mechanical Engineering and Mechanics, Lehigh University Bethlehem PA 18015 USA
| | - Zhibo Cao
- Department of Materials Science and Engineering, Lehigh University Bethlehem PA 18015 USA
| | - Alparslan Oztekin
- Department of Mechanical Engineering and Mechanics, Lehigh University Bethlehem PA 18015 USA
| | - Xuanhong Cheng
- Department of Materials Science and Engineering, Lehigh University Bethlehem PA 18015 USA
- Department of Bioengineering, Lehigh University Bethlehem PA 18015 USA
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25
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Liu C, Tian F, Deng J, Sun J. Thermomicrofluidic Biosensing Systems ※. ACTA CHIMICA SINICA 2022. [DOI: 10.6023/a21120610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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26
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Diaz-Marquez A, Stirnemann G. In silico all-atom approach to thermodiffusion in dilute aqueous solutions. J Chem Phys 2021; 155:174503. [PMID: 34742198 DOI: 10.1063/5.0067756] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Thermodiffusion (or thermophoresis) is the phenomenon by which the spatial distributions of constituents of liquid or gas phases become inhomogeneous in response to a temperature gradient. It has been evidenced in a variety of systems and has many practical applications as well as implications in the context of the origins of life. A complete molecular picture of thermophoresis is still missing, and phenomenological approaches are often employed to account for the experimental observations. In particular, the amplitude of the resulting concentration-gradients (quantified by the Soret coefficient) depends on many factors that are not straightforwardly rationalized. All-atom molecular dynamics simulations appear as an exquisite tool to shed light on the molecular origins for this phenomenon in molecular systems, but the practical implementation of thermophoretic settings in silico poses significant challenges. Here, we propose a robust approach to tackle thermophoresis in dilute realistic solutions at the molecular level. We rely on a recent enhanced heat-exchange algorithm to generate temperature-gradients. We carefully assess the convergence of thermophoretic simulations in dilute aqueous solutions. We show that simulations typically need to be propagated on long timescales (hundreds of nanoseconds). We find that the magnitude of the temperature gradient and the box sizes have little effect on the measured Soret coefficients. Practical guidelines are derived from such observations. Provided with this reliable setup, we discuss the results of thermophoretic simulations on several examples of molecular, neutral solutes, which we find in very good agreement with experimental measurements regarding the concentration-, mass-, and temperature-dependence of the Soret coefficient.
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Affiliation(s)
- Alejandro Diaz-Marquez
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, PSL University, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, PSL University, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France
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27
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Wang W, Cherstvy AG, Kantz H, Metzler R, Sokolov IM. Time averaging and emerging nonergodicity upon resetting of fractional Brownian motion and heterogeneous diffusion processes. Phys Rev E 2021; 104:024105. [PMID: 34525678 DOI: 10.1103/physreve.104.024105] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/14/2021] [Indexed: 12/12/2022]
Abstract
How different are the results of constant-rate resetting of anomalous-diffusion processes in terms of their ensemble-averaged versus time-averaged mean-squared displacements (MSDs versus TAMSDs) and how does stochastic resetting impact nonergodicity? We examine, both analytically and by simulations, the implications of resetting on the MSD- and TAMSD-based spreading dynamics of particles executing fractional Brownian motion (FBM) with a long-time memory, heterogeneous diffusion processes (HDPs) with a power-law space-dependent diffusivity D(x)=D_{0}|x|^{γ} and their "combined" process of HDP-FBM. We find, inter alia, that the resetting dynamics of originally ergodic FBM for superdiffusive Hurst exponents develops disparities in scaling and magnitudes of the MSDs and mean TAMSDs indicating weak ergodicity breaking. For subdiffusive HDPs we also quantify the nonequivalence of the MSD and TAMSD and observe a new trimodal form of the probability density function. For reset FBM, HDPs and HDP-FBM we compute analytically and verify by simulations the short-time MSD and TAMSD asymptotes and long-time plateaus reminiscent of those for processes under confinement. We show that certain characteristics of these reset processes are functionally similar despite a different stochastic nature of their nonreset variants. Importantly, we discover nonmonotonicity of the ergodicity-breaking parameter EB as a function of the resetting rate r. For all reset processes studied we unveil a pronounced resetting-induced nonergodicity with a maximum of EB at intermediate r and EB∼(1/r)-decay at large r. Alongside the emerging MSD-versus-TAMSD disparity, this r-dependence of EB can be an experimentally testable prediction. We conclude by discussing some implications to experimental systems featuring resetting dynamics.
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Affiliation(s)
- Wei Wang
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Straße 38, 01187 Dresden, Germany
| | - Andrey G Cherstvy
- Institute for Physics & Astronomy University of Potsdam, Karl-Liebknecht-Straße 24/25, 14476 Potsdam-Golm, Germany.,Institut für Physik, Humboldt-Universität zu Berlin, Newtonstraße 15, 12489 Berlin, Germany
| | - Holger Kantz
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Straße 38, 01187 Dresden, Germany
| | - Ralf Metzler
- Institute for Physics & Astronomy University of Potsdam, Karl-Liebknecht-Straße 24/25, 14476 Potsdam-Golm, Germany
| | - Igor M Sokolov
- Institut für Physik, Humboldt-Universität zu Berlin, Newtonstraße 15, 12489 Berlin, Germany.,IRIS Adlershof, Zum Großen Windkanal 6, 12489 Berlin, Germany
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29
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Lingam M. Theoretical Constraints Imposed by Gradient Detection and Dispersal on Microbial Size in Astrobiological Environments. ASTROBIOLOGY 2021; 21:813-830. [PMID: 33902321 DOI: 10.1089/ast.2020.2392] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The capacity to sense gradients efficiently and acquire information about the ambient environment confers many advantages such as facilitating movement toward nutrient sources or away from toxic chemicals. The amplified dispersal evinced by organisms endowed with motility is possibly beneficial in related contexts. Hence, the connections between information acquisition, motility, and microbial size are explored from an explicitly astrobiological standpoint. By using prior theoretical models, the constraints on organism size imposed by gradient detection and motility are elucidated in the form of simple heuristic scaling relations. It is argued that environments such as alkaline hydrothermal vents, which are distinguished by the presence of steep gradients, might be conducive to the existence of "small" microbes (with radii of ≳0.1 μm) in principle, when only the above two factors are considered; other biological functions (e.g., metabolism and genetic exchange) could, however, regulate the lower bound on microbial size and elevate it. The derived expressions are potentially applicable to a diverse array of settings, including those entailing solvents other than water; for example, the lakes and seas of Titan. The article concludes with a brief exposition of how this formalism may be of practical and theoretical value to astrobiology.
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Affiliation(s)
- Manasvi Lingam
- Department of Aerospace, Physics and Space Science, Florida Institute of Technology, Melbourne, Florida, USA
- Institute for Theory and Computation, Harvard University, Cambridge, Massachusetts, USA
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30
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Affiliation(s)
- Fei Tian
- Beijing Engineering Research Center for BioNanotechnology CAS Key Laboratory of Standardization and Measurement for Nanotechnology CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing P. R. China
- School of Future Technology University of Chinese Academy of Sciences Beijing P. R. China
| | - Ziwei Han
- Beijing Engineering Research Center for BioNanotechnology CAS Key Laboratory of Standardization and Measurement for Nanotechnology CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing P. R. China
- School of Future Technology University of Chinese Academy of Sciences Beijing P. R. China
| | - Jinqi Deng
- Beijing Engineering Research Center for BioNanotechnology CAS Key Laboratory of Standardization and Measurement for Nanotechnology CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing P. R. China
- School of Future Technology University of Chinese Academy of Sciences Beijing P. R. China
| | - Chao Liu
- Beijing Engineering Research Center for BioNanotechnology CAS Key Laboratory of Standardization and Measurement for Nanotechnology CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing P. R. China
- School of Future Technology University of Chinese Academy of Sciences Beijing P. R. China
| | - Jiashu Sun
- Beijing Engineering Research Center for BioNanotechnology CAS Key Laboratory of Standardization and Measurement for Nanotechnology CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing P. R. China
- School of Future Technology University of Chinese Academy of Sciences Beijing P. R. China
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31
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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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Kazakevičius R, Kononovicius A. Anomalous diffusion in nonlinear transformations of the noisy voter model. Phys Rev E 2021; 103:032154. [PMID: 33862826 DOI: 10.1103/physreve.103.032154] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/04/2021] [Indexed: 11/07/2022]
Abstract
Voter models are well known in the interdisciplinary community, yet they have not been studied from the perspective of anomalous diffusion. In this paper, we show that the original voter model exhibits a ballistic regime. Nonlinear transformations of the observation variable and time scale allow us to observe other regimes of anomalous diffusion as well as normal diffusion. We show that numerical simulation results coincide with derived analytical approximations describing the temporal evolution of the raw moments.
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Affiliation(s)
- Rytis Kazakevičius
- Institute of Theoretical Physics and Astronomy, Vilnius University, Saulėtekio 3, LT-10257 Vilnius, Lithuania
| | - Aleksejus Kononovicius
- Institute of Theoretical Physics and Astronomy, Vilnius University, Saulėtekio 3, LT-10257 Vilnius, Lithuania
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33
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Ameta S, Matsubara YJ, Chakraborty N, Krishna S, Thutupalli S. Self-Reproduction and Darwinian Evolution in Autocatalytic Chemical Reaction Systems. Life (Basel) 2021; 11:308. [PMID: 33916135 PMCID: PMC8066523 DOI: 10.3390/life11040308] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/25/2021] [Accepted: 03/27/2021] [Indexed: 11/18/2022] Open
Abstract
Understanding the emergence of life from (primitive) abiotic components has arguably been one of the deepest and yet one of the most elusive scientific questions. Notwithstanding the lack of a clear definition for a living system, it is widely argued that heredity (involving self-reproduction) along with compartmentalization and metabolism are key features that contrast living systems from their non-living counterparts. A minimal living system may be viewed as "a self-sustaining chemical system capable of Darwinian evolution". It has been proposed that autocatalytic sets of chemical reactions (ACSs) could serve as a mechanism to establish chemical compositional identity, heritable self-reproduction, and evolution in a minimal chemical system. Following years of theoretical work, autocatalytic chemical systems have been constructed experimentally using a wide variety of substrates, and most studies, thus far, have focused on the demonstration of chemical self-reproduction under specific conditions. While several recent experimental studies have raised the possibility of carrying out some aspects of experimental evolution using autocatalytic reaction networks, there remain many open challenges. In this review, we start by evaluating theoretical studies of ACSs specifically with a view to establish the conditions required for such chemical systems to exhibit self-reproduction and Darwinian evolution. Then, we follow with an extensive overview of experimental ACS systems and use the theoretically established conditions to critically evaluate these empirical systems for their potential to exhibit Darwinian evolution. We identify various technical and conceptual challenges limiting experimental progress and, finally, conclude with some remarks about open questions.
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Affiliation(s)
- Sandeep Ameta
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Yoshiya J. Matsubara
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Nayan Chakraborty
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Sandeep Krishna
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Shashi Thutupalli
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
- International Centre for Theoretical Sciences, Tata Institute of Fundamental Research, Bangalore 560089, India
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Abstract
Using light to manipulate fluids has been a long-sought-after goal for lab-on-a-chip applications to address the size mismatch between bulky external fluid controllers and microfluidic devices. Yet, this goal has remained elusive due to the complexity of thermally driven fluid dynamic phenomena, and the lack of approaches that allow comprehensive multiscale and multiparameter studies. Here, we report an innovative optofluidic platform that fulfills this need by combining digital holographic microscopy with state-of-the-art thermoplasmonics, allowing us to identify the different contributions from thermophoresis, thermo-osmosis, convection, and radiation pressure. In our experiments, we demonstrate that a local thermal perturbation at the microscale can lead to mm-scale changes in both the particle and fluid dynamics, thus achieving long-range transport. Furthermore, thanks to a comprehensive parameter study involving sample geometry, temperature increase, light fluence, and size of the heat source, we showcase an integrated and reconfigurable all-optical control strategy for microfluidic devices, thereby opening new frontiers in fluid actuation technology.
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Lu T, Nakashima KK, Spruijt E. Temperature-Responsive Peptide-Nucleotide Coacervates. J Phys Chem B 2021; 125:3080-3091. [PMID: 33757284 PMCID: PMC8020381 DOI: 10.1021/acs.jpcb.0c10839] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Coacervates are a
type of liquid–liquid phase separated
(LLPS) droplets that can serve as models of membraneless organelles
(MLOs) in living cells. Peptide–nucleotide coacervates have
been widely used to mimic properties of ribonucleoprotein (RNP) granules,
but the thermal stability and the role of base stacking is still poorly
understood. Here, we report a systematic investigation of coacervates
formed by five different nucleoside triphosphates (NTPs) with poly-l-lysine and poly-l-arginine as a function of temperature.
All studied combinations exhibit an upper critical solution temperature
(UCST), and a temperature-dependent critical salt concentration, originating
from a significant nonelectrostatic contribution to the mixing free
energy. Both the enthalpic and entropic parts of this nonelectrostatic
interaction decrease in the order G/A/U/C/T, in accordance with nucleobase
stacking free energies. Partitioning of two dyes proves that the local
hydrophobicity inside the peptide–nucleotide coacervates is
different for every nucleoside triphosphate. We derive a simple relation
between the temperature and salt concentration at the critical point
based on a mean-field model of phase separation. Finally, when different
NTPs are mixed with one common oppositely charged peptide, hybrid
coacervates were formed, characterized by a single intermediate UCST
and critical salt concentration. NTPs with lower critical salt concentrations
can remain condensed in mixed coacervates far beyond their original
critical salt concentration. Our results show that NTP-based coacervates
have a strong temperature sensitivity due to base stacking interactions
and that mixing NTPs can significantly influence the stability of
condensates and, by extension, their bioavailability.
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Affiliation(s)
- Tiemei Lu
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Karina K Nakashima
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Evan Spruijt
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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Farajpour N, Lastra LS, Sharma V, Freedman KJ. Measuring trapped DNA at the liquid-air interface for enhanced single molecule sensing. NANOSCALE 2021; 13:5780-5790. [PMID: 33704302 DOI: 10.1039/d0nr07759c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Nanopore sensing is a promising tool with widespread application in single-molecule detection. Borosilicate glass nanopores are a viable alternative to other solid-state nanopores due to low noise and cost-efficient fabrication. For dielectric materials, including borosilicate glass, the capacitive noise is one of the major contributors to noise, which depends on the wall thickness and the surface area submerged in an ionic solution. Here, we investigated the root mean square (IRMS) noise and ionic conductance for borosilicate nanopores in different depths (i.e., tip submersion depth) ranging from the solution surface (assumed to be zero) to 5000 μm. Our findings demonstrate a decrease in IRMS noise as the pipette moves toward the surface. We further demonstrate that borosilicate nanopores can detect single lambda DNA (λ-DNA) molecules with a high signal-to noise ratio close to the liquid-air interface. Specifically, our results indicate a higher signal to noise ratio as the submersion depth is reduced owing to the reduced surface area and thus capacitive noise. Further, our experimental results show higher DNA capture frequency at the air-water interface due to a combined effect of evaporation and an evaporation-induced thermal gradient at the surface. Therefore, our findings demonstrate that borosilicate glass nanopores are suitable for studying interfacial concentration gradients of molecules, specifically DNA, with a higher signal to noise.
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Affiliation(s)
- Nasim Farajpour
- Department of Bioengineering, University of California Riverside, Riverside, CA 92521, USA.
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37
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Kühnlein A, Lanzmich SA, Braun D. tRNA sequences can assemble into a replicator. eLife 2021; 10:e63431. [PMID: 33648631 PMCID: PMC7924937 DOI: 10.7554/elife.63431] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/28/2021] [Indexed: 11/29/2022] Open
Abstract
Can replication and translation emerge in a single mechanism via self-assembly? The key molecule, transfer RNA (tRNA), is one of the most ancient molecules and contains the genetic code. Our experiments show how a pool of oligonucleotides, adapted with minor mutations from tRNA, spontaneously formed molecular assemblies and replicated information autonomously using only reversible hybridization under thermal oscillations. The pool of cross-complementary hairpins self-selected by agglomeration and sedimentation. The metastable DNA hairpins bound to a template and then interconnected by hybridization. Thermal oscillations separated replicates from their templates and drove an exponential, cross-catalytic replication. The molecular assembly could encode and replicate binary sequences with a replication fidelity corresponding to 85-90 % per nucleotide. The replication by a self-assembly of tRNA-like sequences suggests that early forms of tRNA could have been involved in molecular replication. This would link the evolution of translation to a mechanism of molecular replication.
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Affiliation(s)
- Alexandra Kühnlein
- Systems Biophysics, Physics Department, Center for NanoScience, Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Simon A Lanzmich
- Systems Biophysics, Physics Department, Center for NanoScience, Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Dieter Braun
- Systems Biophysics, Physics Department, Center for NanoScience, Ludwig-Maximilians-Universität MünchenMunichGermany
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38
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Mizuuchi R, Ichihashi N. Primitive Compartmentalization for the Sustainable Replication of Genetic Molecules. Life (Basel) 2021; 11:life11030191. [PMID: 33670881 PMCID: PMC7997230 DOI: 10.3390/life11030191] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/21/2021] [Accepted: 02/25/2021] [Indexed: 01/03/2023] Open
Abstract
Sustainable replication and evolution of genetic molecules such as RNA are likely requisites for the emergence of life; however, these processes are easily affected by the appearance of parasitic molecules that replicate by relying on the function of other molecules, while not contributing to their replication. A possible mechanism to repress parasite amplification is compartmentalization that segregates parasitic molecules and limits their access to functional genetic molecules. Although extent cells encapsulate genomes within lipid-based membranes, more primitive materials or simple geological processes could have provided compartmentalization on early Earth. In this review, we summarize the current understanding of the types and roles of primitive compartmentalization regarding sustainable replication of genetic molecules, especially from the perspective of the prevention of parasite replication. In addition, we also describe the ability of several environments to selectively accumulate longer genetic molecules, which could also have helped select functional genetic molecules rather than fast-replicating short parasitic molecules.
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Affiliation(s)
- Ryo Mizuuchi
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
- JST, PRESTO, Kawaguchi, Saitama 332-0012, Japan
- Correspondence: (R.M.); (N.I.)
| | - Norikazu Ichihashi
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
- Universal Biology Institute, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
- Correspondence: (R.M.); (N.I.)
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39
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Zhang D, Ouyang Q. Nonequilibrium Thermodynamics in Biochemical Systems and Its Application. ENTROPY (BASEL, SWITZERLAND) 2021; 23:271. [PMID: 33668768 PMCID: PMC7996154 DOI: 10.3390/e23030271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 12/05/2022]
Abstract
Living systems are open systems, where the laws of nonequilibrium thermodynamics play the important role. Therefore, studying living systems from a nonequilibrium thermodynamic aspect is interesting and useful. In this review, we briefly introduce the history and current development of nonequilibrium thermodynamics, especially that in biochemical systems. We first introduce historically how people realized the importance to study biological systems in the thermodynamic point of view. We then introduce the development of stochastic thermodynamics, especially three landmarks: Jarzynski equality, Crooks' fluctuation theorem and thermodynamic uncertainty relation. We also summarize the current theoretical framework for stochastic thermodynamics in biochemical reaction networks, especially the thermodynamic concepts and instruments at nonequilibrium steady state. Finally, we show two applications and research paradigms for thermodynamic study in biological systems.
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Affiliation(s)
- Dongliang Zhang
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China;
| | - Qi Ouyang
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China;
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, AAIC, Peking University, Beijing 100871, China
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40
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Busiello DM, Liang S, Piazza F, De Los Rios P. Dissipation-driven selection of states in non-equilibrium chemical networks. Commun Chem 2021; 4:16. [PMID: 36697543 PMCID: PMC9814615 DOI: 10.1038/s42004-021-00454-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/15/2021] [Indexed: 01/28/2023] Open
Abstract
Life has most likely originated as a consequence of processes taking place in non-equilibrium conditions (e.g. in the proximity of deep-sea thermal vents) selecting states of matter that would have been otherwise unfavorable at equilibrium. Here we present a simple chemical network in which the selection of states is driven by the thermodynamic necessity of dissipating heat as rapidly as possible in the presence of a thermal gradient: states participating to faster reactions contribute the most to the dissipation rate, and are the most populated ones in non-equilibrium steady-state conditions. Building upon these results, we show that, as the complexity of the chemical network increases, the velocity of the reaction path leading to a given state determines its selection, giving rise to non-trivial localization phenomena in state space. A byproduct of our studies is that, in the presence of a temperature gradient, thermophoresis-like behavior inevitably appears depending on the transport properties of each individual state, thus hinting at a possible microscopic explanation of this intriguing yet still not fully understood phenomenon.
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Affiliation(s)
- Daniel Maria Busiello
- grid.5333.60000000121839049Institute of Physics, École Polytechnique Fédérale de Lausanne - EPFL, Lausanne, Switzerland
| | - Shiling Liang
- grid.5333.60000000121839049Institute of Physics, École Polytechnique Fédérale de Lausanne - EPFL, Lausanne, Switzerland
| | - Francesco Piazza
- grid.417870.d0000 0004 0614 8532Centre de Biophysique Moléculaire (CBM), CNRS-UPR 4301, Rue C. Sadron, Orléans, 45071 France ,grid.112485.b0000 0001 0217 6921Université d’Orléans, UFR CoST Sciences et Techniques, 1 rue de Chartres, Orléans, 45100 France
| | - Paolo De Los Rios
- grid.5333.60000000121839049Institute of Physics, École Polytechnique Fédérale de Lausanne - EPFL, Lausanne, Switzerland ,grid.5333.60000000121839049Institute of Bioengineering, École Polytechnique Fédérale de Lausanne - EPFL, Lausanne, Switzerland
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41
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Jia TZ, Wang PH, Niwa T, Mamajanov I. Connecting primitive phase separation to biotechnology, synthetic biology, and engineering. J Biosci 2021; 46:79. [PMID: 34373367 PMCID: PMC8342986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
One aspect of the study of the origins of life focuses on how primitive chemistries assembled into the first cells on Earth and how these primitive cells evolved into modern cells. Membraneless droplets generated from liquid-liquid phase separation (LLPS) are one potential primitive cell-like compartment; current research in origins of life includes study of the structure, function, and evolution of such systems. However, the goal of primitive LLPS research is not simply curiosity or striving to understand one of life's biggest unanswered questions, but also the possibility to discover functions or structures useful for application in the modern day. Many applicational fields, including biotechnology, synthetic biology, and engineering, utilize similar phaseseparated structures to accomplish specific functions afforded by LLPS. Here, we briefly review LLPS applied to primitive compartment research and then present some examples of LLPS applied to biomolecule purification, drug delivery, artificial cell construction, waste and pollution management, and flavor encapsulation. Due to a significant focus on similar functions and structures, there appears to be much for origins of life researchers to learn from those working on LLPS in applicational fields, and vice versa, and we hope that such researchers can start meaningful cross-disciplinary collaborations in the future.
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Affiliation(s)
- Tony Z Jia
- grid.32197.3e0000 0001 2179 2105Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550 Japan ,grid.482804.2Blue Marble Space Institute of Science, 1001 4th Ave., Suite 3201, Seattle, Washington 98154 USA
| | - Po-Hsiang Wang
- grid.32197.3e0000 0001 2179 2105Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550 Japan ,grid.37589.300000 0004 0532 3167Graduate Institute of Environmental Engineering, National Central University, Zhongli Dist, 300 Zhongda Rd, Taoyuan City, 32001 Taiwan
| | - Tatsuya Niwa
- grid.32197.3e0000 0001 2179 2105Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, 226-8503 Japan
| | - Irena Mamajanov
- grid.32197.3e0000 0001 2179 2105Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550 Japan
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Sustainability and Chaos in the Abiotic Polymerization of 3′,5′ Cyclic Guanosine Monophosphate: The Role of Aggregation. CHEMSYSTEMSCHEM 2020. [DOI: 10.1002/syst.202000011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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43
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Thermophoretic Micron-Scale Devices: Practical Approach and Review. ENTROPY 2020; 22:e22090950. [PMID: 33286719 PMCID: PMC7597233 DOI: 10.3390/e22090950] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/18/2020] [Accepted: 08/25/2020] [Indexed: 12/15/2022]
Abstract
In recent years, there has been increasing interest in the development of micron-scale devices utilizing thermal gradients to manipulate molecules and colloids, and to measure their thermophoretic properties quantitatively. Various devices have been realized, such as on-chip implements, micro-thermogravitational columns and other micron-scale thermophoretic cells. The advantage of the miniaturized devices lies in the reduced sample volume. Often, a direct observation of particles using various microscopic techniques is possible. On the other hand, the small dimensions lead to some technical problems, such as a precise temperature measurement on small length scale with high spatial resolution. In this review, we will focus on the "state of the art" thermophoretic micron-scale devices, covering various aspects such as generating temperature gradients, temperature measurement, and the analysis of the current micron-scale devices. We want to give researchers an orientation for their development of thermophoretic micron-scale devices for biological, chemical, analytical, and medical applications.
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44
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Roy S, Bapat NV, Derr J, Rajamani S, Sengupta S. Emergence of ribozyme and tRNA-like structures from mineral-rich muddy pools on prebiotic earth. J Theor Biol 2020; 506:110446. [PMID: 32798505 DOI: 10.1016/j.jtbi.2020.110446] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 07/21/2020] [Accepted: 08/06/2020] [Indexed: 10/23/2022]
Abstract
The RNA world hypothesis, although a viable one regarding the origin of life on earth, has so far failed to provide a compelling explanation for the synthesis of RNA enzymes from free nucleotides via abiotic processes. To tackle this long-standing problem, we develop a realistic model for the onset of the RNA world, using experimentally determined rates for polymerization reactions. We start with minimal assumptions about the initial state that only requires the presence of short oligomers or just free nucleotides and consider the effects of environmental cycling by dividing a day into a dry, semi-wet and wet phases that are distinguished by the nature of reactions they support. Long polymers, with maximum lengths sometimes exceeding 100 nucleotides, spontaneously emerge due to a combination of non-enzymatic, non-templated polymer extension and template-directed primer extension processes. The former helps in increasing the lengths of RNA strands, whereas the later helps in producing complementary copies of the strands. Strands also undergo hydrolysis in a structure-dependent manner that favour breaking of bonds connecting unpaired nucleotides. We identify the most favourable conditions needed for the emergence of ribozyme and tRNA-like structures and double stranded RNA molecules, classify all RNA strands on the basis of their secondary structures and determine their abundance in the population. Our results indicate that under suitable environmental conditions, non-enzymatic processes would have been sufficient to lead to the emergence of a variety of ribozyme-like molecules with complex secondary structures and potential catalytic functions.
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Affiliation(s)
- Suvam Roy
- Department of Physical Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur 741246, India
| | - Niraja V Bapat
- Department of Biology, Indian Institute of Science Education and Research, Pune; Dr. Homi-Bhabha Road, Pune 411008, India
| | - Julien Derr
- Laboratoire Matière et Systèmes Complexes, Université Paris Diderot, 5 Rue Thomas Mann, 75013 Paris, France.
| | - Sudha Rajamani
- Department of Biology, Indian Institute of Science Education and Research, Pune; Dr. Homi-Bhabha Road, Pune 411008, India
| | - Supratim Sengupta
- Department of Physical Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur 741246, India.
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Salditt A, Keil LMR, Horning DP, Mast CB, Joyce GF, Braun D. Thermal Habitat for RNA Amplification and Accumulation. PHYSICAL REVIEW LETTERS 2020; 125:048104. [PMID: 32794805 DOI: 10.1103/physrevlett.125.048104] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 07/02/2020] [Indexed: 05/07/2023]
Abstract
The RNA world scenario posits replication by RNA polymerases. On early Earth, a geophysical setting is required to separate hybridized strands after their replication and to localize them against diffusion. We present a pointed heat source that drives exponential, RNA-catalyzed amplification of short RNA with high efficiency in a confined chamber. While shorter strands were periodically melted by laminar convection, the temperature gradient caused aggregated polymerase molecules to accumulate, protecting them from degradation in hot regions of the chamber. These findings demonstrate a size-selective pathway for autonomous RNA-based replication in natural nonequilibrium conditions.
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Affiliation(s)
- Annalena Salditt
- Systems Biophysics, Physics Department, Center for Nanoscience, Ludwig-Maximilians-Universität München, Amalienstraße 54, 80799 Munich, Germany
| | - Lorenz M R Keil
- Systems Biophysics, Physics Department, Center for Nanoscience, Ludwig-Maximilians-Universität München, Amalienstraße 54, 80799 Munich, Germany
| | - David P Horning
- The Salk Institute, 10010 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Christof B Mast
- Systems Biophysics, Physics Department, Center for Nanoscience, Ludwig-Maximilians-Universität München, Amalienstraße 54, 80799 Munich, Germany
| | - Gerald F Joyce
- The Salk Institute, 10010 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Dieter Braun
- Systems Biophysics, Physics Department, Center for Nanoscience, Ludwig-Maximilians-Universität München, Amalienstraße 54, 80799 Munich, Germany
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46
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From self-replication to replicator systems en route to de novo life. Nat Rev Chem 2020; 4:386-403. [PMID: 37127968 DOI: 10.1038/s41570-020-0196-x] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/14/2020] [Indexed: 01/01/2023]
Abstract
The process by which chemistry can give rise to biology remains one of the biggest mysteries in contemporary science. The de novo synthesis and origin of life both require the functional integration of three key characteristics - replication, metabolism and compartmentalization - into a system that is maintained out of equilibrium and is capable of open-ended Darwinian evolution. This Review takes systems of self-replicating molecules as starting points and describes the steps necessary to integrate additional characteristics of life. We analyse how far experimental self-replicators have come in terms of Darwinian evolution. We also cover models of replicator communities that attempt to solve Eigen's paradox, whereby accurate replication needs complex machinery yet obtaining such complex self-replicators through evolution requires accurate replication. Successful models rely on a collective metabolism and a way of (transient) compartmentalization, suggesting that the invention and integration of these two characteristics is driven by evolution. Despite our growing knowledge, there remain numerous key challenges that may be addressed by a combined theoretical and experimental approach.
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47
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Opto-thermal diffusiophoresis of soft biological matter: from physical principle to molecular manipulation. Biophys Rev 2020; 12:309-315. [PMID: 32300983 DOI: 10.1007/s12551-020-00692-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 03/16/2020] [Indexed: 10/24/2022] Open
Abstract
Transport of ions and molecules under external field gradients is fundamental phenomena relevant to many biological systems including molecular motors in nature. As inspired from such biological transport, novel optical manipulation by using local solute gradient and the creation of self-propulsive particles are being developed using this technology. In this review article, we describe the basic principles behind those transport phenomena under a temperature and a solute concentration gradient and discuss novel manipulation tools for soft biological materials. The control of such micron-scale transport will bring new insight in design principles of functional materials showing autonomous motion as seen in molecular motors.
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Morasch M, Liu J, Dirscherl CF, Ianeselli A, Kühnlein A, Le Vay K, Schwintek P, Islam S, Corpinot MK, Scheu B, Dingwell DB, Schwille P, Mutschler H, Powner MW, Mast CB, Braun D. Heated gas bubbles enrich, crystallize, dry, phosphorylate and encapsulate prebiotic molecules. Nat Chem 2019; 11:779-788. [PMID: 31358919 DOI: 10.1038/s41557-019-0299-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 06/21/2019] [Indexed: 12/19/2022]
Abstract
Non-equilibrium conditions must have been crucial for the assembly of the first informational polymers of early life, by supporting their formation and continuous enrichment in a long-lasting environment. Here, we explore how gas bubbles in water subjected to a thermal gradient, a likely scenario within crustal mafic rocks on the early Earth, drive a complex, continuous enrichment of prebiotic molecules. RNA precursors, monomers, active ribozymes, oligonucleotides and lipids are shown to (1) cycle between dry and wet states, enabling the central step of RNA phosphorylation, (2) accumulate at the gas-water interface to drastically increase ribozymatic activity, (3) condense into hydrogels, (4) form pure crystals and (5) encapsulate into protecting vesicle aggregates that subsequently undergo fission. These effects occur within less than 30 min. The findings unite, in one location, the physical conditions that were crucial for the chemical emergence of biopolymers. They suggest that heated microbubbles could have hosted the first cycles of molecular evolution.
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Affiliation(s)
- Matthias Morasch
- Physics Department, Center for Nanoscience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jonathan Liu
- Physics Department, Center for Nanoscience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Christina F Dirscherl
- Physics Department, Center for Nanoscience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Alan Ianeselli
- Physics Department, Center for Nanoscience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Alexandra Kühnlein
- Physics Department, Center for Nanoscience, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Philipp Schwintek
- Physics Department, Center for Nanoscience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Saidul Islam
- Department of Chemistry, University College London, London, UK
| | | | - Bettina Scheu
- Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Donald B Dingwell
- Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Petra Schwille
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | | | - Christof B Mast
- Physics Department, Center for Nanoscience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Dieter Braun
- Physics Department, Center for Nanoscience, Ludwig-Maximilians-Universität München, Munich, Germany.
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49
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Stopnitzky E, Still S. Nonequilibrium abundances for the building blocks of life. Phys Rev E 2019; 99:052101. [PMID: 31212495 DOI: 10.1103/physreve.99.052101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Indexed: 11/07/2022]
Abstract
The difficulty of obtaining appreciable quantities of biologically important molecules in thermodynamic equilibrium has long been identified as an obstacle to life's emergence, and determining the specific nonequilibrium conditions that might have given rise to life is challenging. To address these issues, we investigate how the concentrations of life's building blocks change as a function of the distance from equilibrium on average, in two example settings: (i) the synthesis of heavy amino acids and (ii) their polymerization into peptides. We find that relative concentrations of the heaviest amino acids can be boosted by four orders of magnitude, and concentrations of the longest peptide chains can be increased by hundreds of orders of magnitude. The average nonequilibrium distribution does not depend on the details of how the system was driven from equilibrium, indicating that environments might not have to be fine-tuned to support life.
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Affiliation(s)
- Elan Stopnitzky
- Department of Physics and Astronomy, University of Hawai'i at Mānoa, Honolulu, Hawai'i 96822, USA
| | - Susanne Still
- Department of Physics and Astronomy, University of Hawai'i at Mānoa, Honolulu, Hawai'i 96822, USA.,Department of Information and Computer Sciences, University of Hawai'i at Mānoa, Honolulu, Hawai'i 96822, USA
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50
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Edeleva E, Salditt A, Stamp J, Schwintek P, Boekhoven J, Braun D. Continuous nonenzymatic cross-replication of DNA strands with in situ activated DNA oligonucleotides. Chem Sci 2019; 10:5807-5814. [PMID: 31293769 PMCID: PMC6568275 DOI: 10.1039/c9sc00770a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/28/2019] [Indexed: 12/28/2022] Open
Abstract
A nonenzymatic DNA cross-replicator uses temperature cycling to overcome product inhibition and thus survives exponential dilution conditions.
Continuous enzyme-free replication of oligonucleotides is central for open-ended evolution experiments that mimic the origin of life. Here, we studied a reaction system, whereby two 24mer DNA templates cross-catalyzed each other's synthesis from four 12mer DNA fragments, two of which were in situ activated with the condensing agent 1-ethyl-3-(3-dimethylamino-propyl)carbodiimide (EDC). We circumvented the problem of product inhibition by melting the stable product duplexes for their reuse as templates in the following ligation step. The system reproduced itself through ligation/melting cycles and survived exponential dilution. We quantified EDC-induced side reactions in a detailed kinetic model. The model allowed us to analyze the effects of various reaction rates on the system's kinetics and confirmed maximal replication under the chosen conditions. The presented system enables us to study nonenzymatic open-ended evolution experiments starting from diverse sequence pools.
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Affiliation(s)
- Evgeniia Edeleva
- Systems Biophysics , Physics Department , Ludwig-Maximilians-Universität München , Amalienstraße 54 , 80799 München , Germany .
| | - Annalena Salditt
- Systems Biophysics , Physics Department , Ludwig-Maximilians-Universität München , Amalienstraße 54 , 80799 München , Germany .
| | - Julian Stamp
- Systems Biophysics , Physics Department , Ludwig-Maximilians-Universität München , Amalienstraße 54 , 80799 München , Germany .
| | - Philipp Schwintek
- Systems Biophysics , Physics Department , Ludwig-Maximilians-Universität München , Amalienstraße 54 , 80799 München , Germany .
| | - Job Boekhoven
- Chemistry Department and Institute for Advanced Study , Technical University of Munich , Lichtenbergstraße 4 , 80895 Garching , Germany
| | - Dieter Braun
- Systems Biophysics , Physics Department , Ludwig-Maximilians-Universität München , Amalienstraße 54 , 80799 München , Germany .
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