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Shahabadi N, Moshtkoob A. In vitro interaction of nucleoside reverse transcriptase inhibitor, didanosine with calf-thymus DNA: Insights from spectroscopic studies. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2020; 39:1122-1133. [PMID: 32643522 DOI: 10.1080/15257770.2020.1780435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Many antivirals interact with DNA and alter their expression profile. Thus, it is necessary to understand the binding mode. Didanosine, a nucleoside reverse transcriptase inhibitor, is used to treat HIV infection in patients with or without acquired immunodeficiency syndrome. Understanding the mechanism of interaction of this nucleoside reverse transcriptase inhibitor with DNA can prove useful in the development of a rational drug designing system. In vitro studies (UV-vis, fluorescence, and viscometry techniques) under physiological conditions (Tris-HCl buffer solutions, pH 7.4) show that didanosine drug interacts with calf-thymus DNA (ct-DNA) via partial intercalative binding mode. UV-visible spectroscopy confirmed the formation didanosine-DNA complex with a binding strength of about 1.5 × 105 M-1 thus indicating their biological worth. Dye displace experiments and viscometry confirmed that didanosine partially intercalates toward DNA molecules. Negative value of Gibb's-free energy change revealed that the process is spontaneous. The thermodynamic parameters such as enthalpy change (ΔH) and entropy change (ΔS) showed that the acting forces between didanosine and ct-DNA mainly included hydrophobic interactions.
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Affiliation(s)
- Nahid Shahabadi
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran.,Medical Biology Research Center (MBRC), Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ayda Moshtkoob
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
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2
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Dalai P, Sahai N. A Model Protometabolic Pathway Across Protocell Membranes Assisted by Photocatalytic Minerals. J Phys Chem B 2019. [PMID: 31869230 DOI: 10.1021/acs.jpcb.9b10127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Protocell analogs (lipid vesicles) to modern cell membranes have been postulated as compartments that may have been involved in primordial metabolism during the transition from geochemistry to biochemistry on early Earth. The transduction of light energy into chemical energy for metabolism was a key step in the transition from the earliest metabolisms to phototrophy. Photocatalytic minerals may have served the role of enzymes during these transitional stages. Here, we demonstrate a simple photoheterotrophic protometabolism promoted by photocatalytic minerals across a model protocell (vesicle) membrane. These minerals in the extra-vesicular medium utilized light energy to drive a coupled, multi-step transmembrane electron transfer reaction (TMETR), while simultaneously generating a transmembrane pH gradient and reducing nicotinamide adenine dinucleotide (NAD+) to NADH within the vesicle. The proton gradient or chemiosmotic potential could have provided a basis for adenosine triphosphate (ATP) synthesis and NADH could potentially have driven further metabolic chemistry inside the protocells.
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Dalai P, Sahai N. Mineral–Lipid Interactions in the Origins of Life. Trends Biochem Sci 2019; 44:331-341. [DOI: 10.1016/j.tibs.2018.11.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/20/2018] [Accepted: 11/27/2018] [Indexed: 10/27/2022]
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Shahabadi N, Moradi Fili S. DNA-interaction studies of a copper(II) complex containing ceftobiprole drug using molecular modeling and multispectroscopic methods. J COORD CHEM 2018. [DOI: 10.1080/00958972.2018.1497165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Nahid Shahabadi
- Inorganic Chemistry Department, Faculty of Chemistry, Razi University, Kermanshah, Iran
- Medical Biology Research Center (MBRC), Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Soraya Moradi Fili
- Inorganic Chemistry Department, Faculty of Chemistry, Razi University, Kermanshah, Iran
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Shahabadi N, Mahdavi M, Taherpour A(A, Ghasemhezaveh F. Synthesis, characterization and in vitro DNA binding studies of a new copper(II) complex containing antioxidant ferulic acid. J COORD CHEM 2017. [DOI: 10.1080/00958972.2017.1363890] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Nahid Shahabadi
- Faculty of Chemistry, Department of Inorganic Chemistry, Razi University, Kermanshah, Iran
- Medical Biology Research Center (MBRC) Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Maryam Mahdavi
- Faculty of Chemistry, Department of Inorganic Chemistry, Razi University, Kermanshah, Iran
- Medical Biology Research Center (MBRC) Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Avat (Arman) Taherpour
- Medical Biology Research Center (MBRC) Kermanshah University of Medical Sciences, Kermanshah, Iran
- Faculty of Chemistry, Department of Organic Chemistry, Razi University, Kermanshah, Iran
| | - Fatemeh Ghasemhezaveh
- Faculty of Chemistry, Department of Organic Chemistry, Razi University, Kermanshah, Iran
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Deamer DW, Georgiou CD. Hydrothermal Conditions and the Origin of Cellular Life. ASTROBIOLOGY 2015; 15:1091-1095. [PMID: 26684507 DOI: 10.1089/ast.2015.1338] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The conditions and properties of hydrothermal vents and hydrothermal fields are compared in terms of their ability to support processes related to the origin of life. The two sites can be considered as alternative hypotheses, and from this comparison we propose a series of experimental tests to distinguish between them, focusing on those that involve concentration of solutes, self-assembly of membranous compartments, and synthesis of polymers. Key Word: Hydrothermal systems.
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Affiliation(s)
- David W Deamer
- 1 Department of Biomolecular Engineering, Baskin School of Engineering, University of California , Santa Cruz, California, USA
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Summers DP, Rodoni D. Vesicle encapsulation of a nonbiological photochemical system capable of reducing NAD(+) to NADH. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:10633-7. [PMID: 26177350 DOI: 10.1021/la502003j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
One of the fundamental structures of a cell is the membrane. Self-assembling lipid bilayer vesicles can form the membrane of an artificial cell and could also have plausibly assembled prebiotically for the origin of life. Such cell-like structures, that encapsulate some basic subset of the functions of living cells, are important for research to infer the minimum chemistry necessary for a cell, to help understand the origin of life, and to allow the production of useful species in microscopic containers. We show that the encapsulation of TiO2 particles has the potential to provide the basis for an energy transduction system inside vesicles which can be used to drive subsequent chemistry. TiO2 encapsulated in vesicles can be used to produce biochemical species such as NADH. The NADH is formed from NAD(+) reduction and is produced in a form that is able to drive further enzymatic chemistry. This allows us to link a mineral-based, nonbiological photosystem to biochemical reactions. This is a fundamental step toward being able to use this mineral photosystem in a protocell/artificial cell.
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Affiliation(s)
- David P Summers
- Carl Sagan Center, SETI Institute, c/o NASA Ames Research Center, Mail Stop 239-4, Moffett Field, California 94035, United States
| | - David Rodoni
- Foothill College , Los Altos, California 94022, United States
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de la Escosura A, Briones C, Ruiz-Mirazo K. The systems perspective at the crossroads between chemistry and biology. J Theor Biol 2015; 381:11-22. [DOI: 10.1016/j.jtbi.2015.04.036] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 04/26/2015] [Indexed: 01/21/2023]
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Manna A, Chakravorti S. Supramolecular effect of curcurbit[7]uril on the binding mode of 2-(4-(dimethylamino) styryl)-1-methylpyridinium iodide with Calf Thymus DNA: From minor groove to intercalative. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 150:120-126. [PMID: 26037496 DOI: 10.1016/j.saa.2015.05.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 05/08/2015] [Accepted: 05/12/2015] [Indexed: 06/04/2023]
Abstract
The effect of curcurbit[7]uril (CB[7]) in the binding mode of 2-(4-(dimethylamino) styryl)-1-methylpyridinium (DASPMI) with Calf Thymus DNA has been discussed in this paper. Red shift, intensity change in absorption and emission spectra and presence of isosbestic point with increasing concentration of CB[7] in groove bound DASPMI-DNA complex indicates a change in binding pattern. Appearance of a third slower component in lifetime decay in presence of CB[7] which gets more slow in high CB[7] concentration is indicative of a new type of binding. Major changes in ct-DNA bands in circular dichroism spectra with addition of CB[7] make a strong case for intercalative binding. Increased computed values of binding constant associated with diminishing quenching constant in presence of potassium iodide make a positive candidate for intercalative binding. Formation of big spherical condensate in DASPMI-DNA complex in presence of CB[7] which grows bigger in higher CB[7] concentration shows a morphological change. Molecular docking nicely portrays the intercalative nature of binding corroborating the experimental evidences.
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Affiliation(s)
- Anamika Manna
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Sankar Chakravorti
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India.
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Current Ideas about Prebiological Compartmentalization. Life (Basel) 2015; 5:1239-63. [PMID: 25867709 PMCID: PMC4500137 DOI: 10.3390/life5021239] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 04/01/2015] [Accepted: 04/02/2015] [Indexed: 01/17/2023] Open
Abstract
Contemporary biological cells are highly sophisticated dynamic compartment systems which separate an internal volume from the external medium through a boundary, which controls, in complex ways, the exchange of matter and energy between the cell's interior and the environment. Since such compartmentalization is a fundamental principle of all forms of life, scenarios have been elaborated about the emergence of prebiological compartments on early Earth, in particular about their likely structural characteristics and dynamic features. Chemical systems that consist of potentially prebiological compartments and chemical reaction networks have been designed to model pre-cellular systems. These systems are often referred to as "protocells". Past and current protocell model systems are presented and compared. Since the prebiotic formation of cell-like compartments is directly linked to the prebiotic availability of compartment building blocks, a few aspects on the likely chemical inventory on the early Earth are also summarized.
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Francis BR. The Hypothesis that the Genetic Code Originated in Coupled Synthesis of Proteins and the Evolutionary Predecessors of Nucleic Acids in Primitive Cells. Life (Basel) 2015; 5:467-505. [PMID: 25679748 PMCID: PMC4390864 DOI: 10.3390/life5010467] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 02/02/2015] [Indexed: 12/22/2022] Open
Abstract
Although analysis of the genetic code has allowed explanations for its evolution to be proposed, little evidence exists in biochemistry and molecular biology to offer an explanation for the origin of the genetic code. In particular, two features of biology make the origin of the genetic code difficult to understand. First, nucleic acids are highly complicated polymers requiring numerous enzymes for biosynthesis. Secondly, proteins have a simple backbone with a set of 20 different amino acid side chains synthesized by a highly complicated ribosomal process in which mRNA sequences are read in triplets. Apparently, both nucleic acid and protein syntheses have extensive evolutionary histories. Supporting these processes is a complex metabolism and at the hub of metabolism are the carboxylic acid cycles. This paper advances the hypothesis that the earliest predecessor of the nucleic acids was a β-linked polyester made from malic acid, a highly conserved metabolite in the carboxylic acid cycles. In the β-linked polyester, the side chains are carboxylic acid groups capable of forming interstrand double hydrogen bonds. Evolution of the nucleic acids involved changes to the backbone and side chain of poly(β-d-malic acid). Conversion of the side chain carboxylic acid into a carboxamide or a longer side chain bearing a carboxamide group, allowed information polymers to form amide pairs between polyester chains. Aminoacylation of the hydroxyl groups of malic acid and its derivatives with simple amino acids such as glycine and alanine allowed coupling of polyester synthesis and protein synthesis. Use of polypeptides containing glycine and l-alanine for activation of two different monomers with either glycine or l-alanine allowed simple coded autocatalytic synthesis of polyesters and polypeptides and established the first genetic code. A primitive cell capable of supporting electron transport, thioester synthesis, reduction reactions, and synthesis of polyesters and polypeptides is proposed. The cell consists of an iron-sulfide particle enclosed by tholin, a heterogeneous organic material that is produced by Miller-Urey type experiments that simulate conditions on the early Earth. As the synthesis of nucleic acids evolved from β-linked polyesters, the singlet coding system for replication evolved into a four nucleotide/four amino acid process (AMP = aspartic acid, GMP = glycine, UMP = valine, CMP = alanine) and then into the triplet ribosomal process that permitted multiple copies of protein to be synthesized independent of replication. This hypothesis reconciles the “genetics first” and “metabolism first” approaches to the origin of life and explains why there are four bases in the genetic alphabet.
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Affiliation(s)
- Brian R Francis
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA.
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Henderson IM, Paxton WF. Salt, Shake, Fuse-Giant Hybrid Polymer/Lipid Vesicles through Mechanically Activated Fusion. Angew Chem Int Ed Engl 2014; 53:3372-6. [DOI: 10.1002/anie.201309433] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Indexed: 11/09/2022]
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13
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Henderson IM, Paxton WF. Salt, Shake, Fuse-Giant Hybrid Polymer/Lipid Vesicles through Mechanically Activated Fusion. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201309433] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Ruiz-Mirazo K, Briones C, de la Escosura A. Prebiotic Systems Chemistry: New Perspectives for the Origins of Life. Chem Rev 2013; 114:285-366. [DOI: 10.1021/cr2004844] [Citation(s) in RCA: 563] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kepa Ruiz-Mirazo
- Biophysics
Unit (CSIC-UPV/EHU), Leioa, and Department of Logic and Philosophy
of Science, University of the Basque Country, Avenida de Tolosa 70, 20080 Donostia−San Sebastián, Spain
| | - Carlos Briones
- Department
of Molecular Evolution, Centro de Astrobiología (CSIC−INTA, associated to the NASA Astrobiology Institute), Carretera de Ajalvir, Km 4, 28850 Torrejón de Ardoz, Madrid, Spain
| | - Andrés de la Escosura
- Organic
Chemistry Department, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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Manna A, Chakravorti S. Modification of a Styryl Dye Binding Mode with Calf Thymus DNA in Vesicular Medium: From Minor Groove to Intercalative. J Phys Chem B 2012; 116:5226-33. [DOI: 10.1021/jp301211m] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Anamika Manna
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Sankar Chakravorti
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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Paleos CM, Tsiourvas D, Sideratou Z. Preparation of multicompartment lipid-based systems based on vesicle interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:2337-2346. [PMID: 21988476 DOI: 10.1021/la2027187] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Various strategies for constructing artificial multicompartment vesicular systems, which primitively mimic the structure of eukaryotic cells, are presented. These model systems are appropriate for addressing several issues such as the understanding of cell processes, the development of nanoreactors and novel multicompartment delivery systems for specific drug applications, the transport through bilayer membranes, and also hypothesizing on the evolution of eukaryotic cells as originating from the symbiotic association of prokaryotes.
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Alpermann T, Rüdel K, Rüger R, Steiniger F, Nietzsche S, Filiz V, Förster S, Fahr A, Weigand W. Polymersomes containing iron sulfide (FeS) as primordial cell model : for the investigation of energy providing redox reactions. ORIGINS LIFE EVOL B 2011; 41:103-19. [PMID: 20697814 DOI: 10.1007/s11084-010-9223-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Accepted: 06/03/2010] [Indexed: 10/19/2022]
Abstract
According to Wächtershäuser's "Iron-Sulfur-World" one major requirement for the development of life on the prebiotic Earth is compartmentalization. Vesicles spontaneously formed from amphiphilic components containing a specific set of molecules including sulfide minerals may have lead to the first autotrophic prebiotic units. The iron sulfide minerals may have been formed by geological conversions in the environment of deep-sea volcanos (black smokers), which can be observed even today. Wächtershäuser postulated the evolution of chemical pathways as fundamentals of the origin of life on earth. In contrast to the classical Miller-Urey experiment, depending on external energy sources, the "Iron-Sulfur-World" is based on the catalytic and energy reproducing redox system FeS+H2S-->FeS2+H2. The energy release out of this redox reaction (∆RG°=-38 kJ/mol, pH 0) could be the cause for the subsequent synthesis of complex organic molecules and the precondition for the development of more complex units similar to cells known today. Here we show the possibility for precipitating iron sulfide inside vesicles composed of amphiphilic block-copolymers as a model system for a first prebiotic unit. Our findings could be an indication for a chemoautotrophic FeS based origin of life.
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Affiliation(s)
- Theodor Alpermann
- Institut für Anorganische und Analytische Chemie, Friedrich-Schiller-Universität Jena, August-Bebel-Straße 2, 07743, Jena, Germany
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Cape JL, Monnard PA, Boncella JM. Prebiotically relevant mixed fatty acid vesicles support anionic solute encapsulation and photochemically catalyzed trans-membrane charge transport. Chem Sci 2011. [DOI: 10.1039/c0sc00575d] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Meierhenrich UJ, Filippi JJ, Meinert C, Vierling P, Dworkin JP. On the origin of primitive cells: from nutrient intake to elongation of encapsulated nucleotides. Angew Chem Int Ed Engl 2010; 49:3738-50. [PMID: 20437432 DOI: 10.1002/anie.200905465] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Recent major discoveries in membrane biophysics hold the key to a modern understanding of the origin of life on Earth. Membrane bilayer vesicles have been shown to provide a multifaceted microenvironment in which protometabolic reactions could have developed. Cell-membrane-like aggregates of amphiphilic molecules capable of retaining encapsulated oligonucleotides have been successfully created in the laboratory. Sophisticated laboratory studies on the origin of life now show that elongation of the DNA primer takes place inside fatty acid vesicles when activated nucleotide nutrients are added to the external medium. These studies demonstrate that cell-like vesicles can be sufficiently permeable to allow for the intake of charged molecules such as activated nucleotides, which can then take part in copying templates in the protocell interior. In this Review we summarize recent experiments in this area and describe a possible scenario for the origin of primitive cells, with an emphasis on the elongation of encapsulated nucleotides.
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Affiliation(s)
- Uwe J Meierhenrich
- LCMBA UMR 6001 CNRS, Institut de Chimie de Nice, Université de Nice-Sophia Antipolis, Faculté des Sciences, Parc Valrose, 06108 Nice, France.
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Meierhenrich U, Filippi JJ, Meinert C, Vierling P, Dworkin J. Die Entstehung erster Zellen - von der Nährstoffaufnahme hin zur Verlängerung eingeschlossener Nucleotide. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200905465] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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