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Saha R, Kao WL, Malady B, Heng X, Chen IA. Effect of montmorillonite K10 clay on RNA structure and function. Biophys J 2024; 123:451-463. [PMID: 37924206 PMCID: PMC10912936 DOI: 10.1016/j.bpj.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 09/29/2023] [Accepted: 11/01/2023] [Indexed: 11/06/2023] Open
Abstract
One of the earliest living systems was likely based on RNA ("the RNA world"). Mineral surfaces have been postulated to be an important environment for the prebiotic chemistry of RNA. In addition to adsorbing RNA and thus potentially reducing the chance of parasitic takeover through limited diffusion, minerals have been shown to promote a range of processes related to the emergence of life, including RNA polymerization, peptide bond formation, and self-assembly of vesicles. In addition, self-cleaving ribozymes have been shown to retain activity when adsorbed to the clay mineral montmorillonite. However, simulation studies suggest that adsorption to minerals is likely to interfere with RNA folding and, thus, function. To further evaluate the plausibility of a mineral-adsorbed RNA world, here we studied the effect of the synthetic clay montmorillonite K10 on the malachite green RNA aptamer, including binding of the clay to malachite green and RNA, as well as on the formation of secondary structures in model RNA and DNA oligonucleotides. We evaluated the fluorescence of the aptamer complex, adsorption to the mineral, melting curves, Förster resonance energy transfer interactions, and 1H-NMR signals to study the folding and functionality of these nucleic acids. Our results indicate that while some base pairings are unperturbed, the overall folding and binding of the malachite green aptamer are substantially disrupted by montmorillonite. These findings suggest that minerals would constrain the structures, and possibly the functions, available to an adsorbed RNA world.
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Affiliation(s)
- Ranajay Saha
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, California; Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
| | - Wei-Ling Kao
- Department of Biochemistry, University of Missouri, Columbia, Missouri
| | - Brandon Malady
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
| | - Xiao Heng
- Department of Biochemistry, University of Missouri, Columbia, Missouri
| | - Irene A Chen
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, California; Department of Chemistry and Biochemistry, University of California, Santa Barbara, California.
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Ferreira GW, Samulewski RB, Ivashita FF, Paesano A, Urbano A, Zaia DAM. Did Salts in Seawater Play an Important Role in the Adsorption of Molecules on Minerals in the Prebiotic Earth? The Case of the Adsorption of Thiocyanate onto Forsterite-91. ORIGINS LIFE EVOL B 2023; 53:127-156. [PMID: 37676558 DOI: 10.1007/s11084-023-09640-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 08/09/2023] [Indexed: 09/08/2023]
Abstract
Thiocyanate may have played as important a role as cyanide in the synthesis of several molecules. However, its concentration in the seas of the prebiotic Earth could have been very low. Thiocyanate was dissolved in two different seawaters: a) a composition that comes close to the seawater of the prebiotic Earth (seawater-B, Ca2+ and Cl-) and b) a seawater (seawater-A, Mg2+ and SO42-) that could be related to the seas of Mars and other moons in the solar system. In addition, forsterite-91 was a very common mineral on the prebiotic Earth and Mars. Two important results are reported in this work: 1) thiocyanate adsorbed onto forsterite-91 and 2) the amount of thiocyanate adsorbed, adsorption thermodynamic, and adsorption kinetic depend on the composition of the artificial seawater. For all experiments, the adsorption was thermodynamically favorable (ΔG < 0). The adsorption data fitted well in the Freundlich and Langmuir-Freundlich models. When dissolving thiocyanate in seawater 4.0-A-Gy and seawater 4.0-B-Gy, the adsorption of thiocyanate onto forsterite-91 was ruled by enthalpy and entropy, respectively. As shown by n values, the thiocyanate/foraterite-91 system is heterogeneous. For all kinetic data, the pseudo-first-order model presented the best fit. The constant rate for thiocyanate dissolved in seawater 4.0-A-Gy was twice that compared to thiocyanate dissolved in seawater 4.0-B-Gy or ultrapure-water. The interaction between thiocyanate and Fe2+ of forsterite-91 was with the nitrogen atom of thiocyanate. In the presence of thiocyanate, sulfate interacts with forsterite-91 as an inner-sphere surface complex, and without thiocyanate as an outer-sphere surface complex.
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Affiliation(s)
- Giulio Wilgner Ferreira
- Laboratório de Química Prebiótica-LQP, Departamento de Química, Universidade Estadual de Londrina, CEP 86057-970, Londrina, PR, Brazil
| | - Rafael Block Samulewski
- COLIQ - Coordenação de Licenciatura em Química, Universidade Tecnológica Federal do Paraná UTFPR Campus Apucarana, CEP 86812-460, Apucarana, PR, Brazil.
| | | | - Andrea Paesano
- Departamento de Física-CCE, Universidade Estadual de Maringá, 87020-900, Maringá, PR, Brazil
- Departamento de Física Teórica e Experimental, UFRN, Av. Sen. Salgado Filho, 3000, Lagoa Nova, 59078-970, Natal, RN, Brazil
| | - Alexandre Urbano
- Departamento de Física-CCE, Universidade Estadual de Londrina, CEP 86057-970, Londrina, PR, Brazil
| | - Dimas Augusto Morozin Zaia
- Laboratório de Química Prebiótica-LQP, Departamento de Química, Universidade Estadual de Londrina, CEP 86057-970, Londrina, PR, Brazil.
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Šponer JE, Šponer J, Výravský J, Matyášek R, Kovařík A, Dudziak W, Ślepokura K. Crystallization as a selection force at the polymerization of nucleotides in a prebiotic context. iScience 2023; 26:107600. [PMID: 37664611 PMCID: PMC10470394 DOI: 10.1016/j.isci.2023.107600] [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: 03/29/2023] [Revised: 07/14/2023] [Accepted: 08/08/2023] [Indexed: 09/05/2023] Open
Abstract
Accumulation and selection of nucleotides is one of the most challenging problems surrounding the origin of the first RNA molecules on our planet. In the current work we propose that guanosine 3',5' cyclic monophosphate could selectively crystallize upon evaporation of an acidic prebiotic pool containing various other nucleotides. The conditions of the evaporative crystallization are fully compatible with the subsequent acid catalyzed polymerization of this cyclic nucleotide reported in earlier studies and may be relevant in a broad range of possible prebiotic environments. Albeit cytidine 3',5' cyclic monophosphate has the ability to selectively accumulate under the same conditions, its crystal structure is not likely to support polymer formation.
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Affiliation(s)
- Judit E. Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
| | - Jakub Výravský
- TESCAN Brno, s.r.o, Libušina třída 1, 62300 Brno, Czech Republic
- Department of Geological Sciences, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
| | - Roman Matyášek
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
| | - Aleš Kovařík
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
| | - Wojciech Dudziak
- University of Wrocław, Faculty of Chemistry, 14 F. Joliot-Curie, 50-383 Wrocław, Poland
| | - Katarzyna Ślepokura
- University of Wrocław, Faculty of Chemistry, 14 F. Joliot-Curie, 50-383 Wrocław, Poland
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Kristoffersen EL, Burman M, Noy A, Holliger P. Rolling circle RNA synthesis catalysed by RNA. eLife 2022; 11:75186. [PMID: 35108196 PMCID: PMC8937235 DOI: 10.7554/elife.75186] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/01/2022] [Indexed: 11/13/2022] Open
Abstract
RNA-catalyzed RNA replication is widely considered a key step in the emergence of life’s first genetic system. However, RNA replication can be impeded by the extraordinary stability of duplex RNA products, which must be dissociated for re-initiation of the next replication cycle. Here, we have explored rolling circle synthesis (RCS) as a potential solution to this strand separation problem. We observe sustained RCS by a triplet polymerase ribozyme beyond full-length circle synthesis with strand displacement yielding concatemeric RNA products. Furthermore, we show RCS of a circular Hammerhead ribozyme capable of self-cleavage and re-circularization. Thus, all steps of a viroid-like RNA replication pathway can be catalyzed by RNA alone. Finally, we explore potential RCS mechanisms by molecular dynamics simulations, which indicate a progressive build-up of conformational strain upon RCS with destabilization of nascent strand 5′- and 3′-ends. Our results have implications for the emergence of RNA replication and for understanding the potential of RNA to support complex genetic processes. Many organisms today rely on a trio of molecules for their survival: DNA, to store their genetic information; proteins, to conduct the biological processes required for growth or replication; and RNA, to mainly act as an intermediary between DNA and proteins. Yet, how these inanimate molecules first came together to form a living system remains unclear. Circumstantial evidence suggests that the first lifeforms relied to a much greater exrtent on RNA to conduct all necessary biological processes. There is no trace of this ‘RNA world’ today, but molecular ‘fossils’ may exist in current biology. Viroids, for example, are agents which can infect and replicate inside plant cells. They are formed of nothing but a circular strand of RNA that serves not only as genetic storage but also as ribozymes (RNA-based enzymes). Viroids need proteins from the host plant to replicate, but scientists have been able to engineer ribozymes that can copy complex RNA strands. This suggests that viroid-like replication could be achieved using only RNA. Kristoffersen et al. put this idea to the test and showed that it is possible to use RNA enzymatic activity alone to carry out all the steps of a viroid-like copying mechanism. This process included copying a viroid-like RNA circle with RNA, followed by trimming the copy to the right size and reforming the circle. These two latter steps could be carried out by a ribozyme that could itself be encoded on the RNA circle. A computer simulation indicated that RNA synthesis on the circle caused increasing tension that could ease some of the barriers to replication. These results increase our understanding of how RNA copying by RNA could be possible. This may lead to developing molecular models of a primordial RNA-based replication, which could be used to investigate early genetic systems and may have potential applications in synthetic biology.
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Affiliation(s)
| | - Matthew Burman
- Department of Physics, University of York, York, United Kingdom
| | - Agnes Noy
- Department of Physics, University of York, York, United Kingdom
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Šponer JE, Šponer J, Kovařík A, Šedo O, Zdráhal Z, Costanzo G, Di Mauro E. Questions and Answers Related to the Prebiotic Production of Oligonucleotide Sequences from 3',5' Cyclic Nucleotide Precursors. Life (Basel) 2021; 11:800. [PMID: 34440544 PMCID: PMC8400769 DOI: 10.3390/life11080800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 02/03/2023] Open
Abstract
Template-free nonenzymatic polymerization of 3',5' cyclic nucleotides is an emerging topic of the origin of life research. In the last ten years, a number of papers have been published addressing various aspects of this process. These works evoked a vivid discussion among scientists working in the field of prebiotic chemistry. The aim of the current review is to answer the most frequently raised questions related to the detection and characterization of oligomeric products as well as to the geological context of this chemistry.
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Affiliation(s)
- Judit E. Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265 Brno, Czech Republic; (J.Š.); (A.K.)
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265 Brno, Czech Republic; (J.Š.); (A.K.)
| | - Aleš Kovařík
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265 Brno, Czech Republic; (J.Š.); (A.K.)
| | - Ondrej Šedo
- Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (O.Š.); (Z.Z.)
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (O.Š.); (Z.Z.)
| | - Giovanna Costanzo
- Institute of Molecular Biology and Pathology, CNR, Piazzale A. Moro 5, 00185 Rome, Italy; (G.C.); (E.D.M.)
| | - Ernesto Di Mauro
- Institute of Molecular Biology and Pathology, CNR, Piazzale A. Moro 5, 00185 Rome, Italy; (G.C.); (E.D.M.)
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