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Lopez A, Vauchez A, Ajram G, Shvetsova A, Leveau G, Fiore M, Strazewski P. From the RNA-Peptide World: Prebiotic Reaction Conditions Compatible with Lipid Membranes for the Formation of Lipophilic Random Peptides in the Presence of Short Oligonucleotides, and More. Life (Basel) 2024; 14:108. [PMID: 38255723 PMCID: PMC10817532 DOI: 10.3390/life14010108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/25/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Deciphering the origins of life on a molecular level includes unravelling the numerous interactions that could occur between the most important biomolecules being the lipids, peptides and nucleotides. They were likely all present on the early Earth and all necessary for the emergence of cellular life. In this study, we intended to explore conditions that were at the same time conducive to chemical reactions critical for the origins of life (peptide-oligonucleotide couplings and templated ligation of oligonucleotides) and compatible with the presence of prebiotic lipid vesicles. For that, random peptides were generated from activated amino acids and analysed using NMR and MS, whereas short oligonucleotides were produced through solid-support synthesis, manually deprotected and purified using HPLC. After chemical activation in prebiotic conditions, the resulting mixtures were analysed using LC-MS. Vesicles could be produced through gentle hydration in similar conditions and observed using epifluorescence microscopy. Despite the absence of coupling or ligation, our results help to pave the way for future investigations on the origins of life that may gather all three types of biomolecules rather than studying them separately, as it is still too often the case.
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Affiliation(s)
- Augustin Lopez
- Laboratoire de Chimie Organique 2 (LCO2), Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS, UMR CNRS 5246), Bâtiment Edgar Lederer, Université Claude Bernard Lyon 1, Université de Lyon, 1 rue Victor Grignard, 69100 Villeurbanne, France (M.F.)
| | - Antoine Vauchez
- Centre Commun de la Spectrométrie de Masse (CCSM), ICBMS, Bâtiment Edgar Lederer, 1 rue Victor Grignard, 69100 Villeurbanne, France;
| | - Ghinwa Ajram
- Laboratoire de Chimie Organique 2 (LCO2), Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS, UMR CNRS 5246), Bâtiment Edgar Lederer, Université Claude Bernard Lyon 1, Université de Lyon, 1 rue Victor Grignard, 69100 Villeurbanne, France (M.F.)
| | - Anastasiia Shvetsova
- Laboratoire de Chimie Organique 2 (LCO2), Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS, UMR CNRS 5246), Bâtiment Edgar Lederer, Université Claude Bernard Lyon 1, Université de Lyon, 1 rue Victor Grignard, 69100 Villeurbanne, France (M.F.)
| | - Gabrielle Leveau
- Laboratoire de Chimie Organique 2 (LCO2), Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS, UMR CNRS 5246), Bâtiment Edgar Lederer, Université Claude Bernard Lyon 1, Université de Lyon, 1 rue Victor Grignard, 69100 Villeurbanne, France (M.F.)
| | - Michele Fiore
- Laboratoire de Chimie Organique 2 (LCO2), Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS, UMR CNRS 5246), Bâtiment Edgar Lederer, Université Claude Bernard Lyon 1, Université de Lyon, 1 rue Victor Grignard, 69100 Villeurbanne, France (M.F.)
| | - Peter Strazewski
- Laboratoire de Chimie Organique 2 (LCO2), Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS, UMR CNRS 5246), Bâtiment Edgar Lederer, Université Claude Bernard Lyon 1, Université de Lyon, 1 rue Victor Grignard, 69100 Villeurbanne, France (M.F.)
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Chieffo C, Altamura E, Pilet G, Mebarek S, Strazewski P, Fiore M. Microwave-Assisted Syntheses of Rhodamine, Rhodol, and Fluorescein Derivatives. Chempluschem 2023; 88:e202300189. [PMID: 37442786 DOI: 10.1002/cplu.202300189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/14/2023] [Indexed: 07/15/2023]
Abstract
A series of rhodol-; fluorescein- and rhodamines-based spirolactam compounds, bearing electron donor amines have been prepared. For this purpose we have redesigned the synthesis of the rhodol scaffold using 2-(2,4-dihydroxybenzoyl)benzoic acid obtaining one example rhodol methyl ester in good yields (25-30 %) Thus, one set of non-cytotoxic rhodamine-based compounds has been prepared using thermal and microwave assisted synthesis (40-78 %) and tested as high affinity ATP chemo-sensors.
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Affiliation(s)
- Carolina Chieffo
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS, UMR 5246), Université Claude Bernard Lyon 1, 1 Rue Victor Grignard, 69100, Villeurbanne, France
- Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Emiliano Altamura
- Chemistry Department, University of Bari "Aldo Moro", Via Orabona 4, 70121, Bari, Italy
| | - Guillaume Pilet
- Laboratoire des Multimatériaux et Interfaces (LMI, UMR 5615), Université Claude Bernard Lyon 1, 6 Rue Victor Grignard, 69100, Villeurbanne, France
| | - Saida Mebarek
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS, UMR 5246), Université Claude Bernard Lyon 1, 1 Rue Victor Grignard, 69100, Villeurbanne, France
| | - Peter Strazewski
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS, UMR 5246), Université Claude Bernard Lyon 1, 1 Rue Victor Grignard, 69100, Villeurbanne, France
| | - Michele Fiore
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS, UMR 5246), Université Claude Bernard Lyon 1, 1 Rue Victor Grignard, 69100, Villeurbanne, France
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3
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Chieffo C, Altamura E, Trad LB, Pilet G, Maniti O, Granjon T, Mebarek S, Strazewski P, Fiore M. Comprehensive Characterization of an "Off/On" Rhodol-Based Lysosomal Tracker for Orthogonal Cellular Analysis by Confocal Imaging. Chembiochem 2023; 24:e202200513. [PMID: 36420688 DOI: 10.1002/cbic.202200513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 11/25/2022]
Abstract
Two florescent xanthene-cyanamide lysosomal trackers emitting strongly at ∼525 nm were prepared from fluorescein and rhodol methyl esters in microwave-assisted reactions. Both forms named "off" (nonfluorescent lactam) and "on" (strongly fluorescent ring-opened amide) have been comprehensively characterized out by using a combination of NMR spectroscopy, X-ray analysis, fluorimetry and confocal microscopy. Known rhodamines bearing electron-withdrawing groups (EWGs) exhibit an equilibrium between non-fluorescent (off) and fluorescent (on) depending on the dielectric constant of the medium. Here, cyanamide was introduced as EWG amine into the fluorescein and rhodol framework. Unlike rhodamine-type dyes, the ring-opened forms of fluorescein- and rhodol-cyanamides are stable in protic solvents under circumneutral and basic pH conditions. The osteoblastic cell line MC3T3-E1 from C57BL/6 mouse calvaria was used for confocal imaging where the different organelles and nuclei were distinguished by using an orthogonal combination of fluorescent dyes.
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Affiliation(s)
- Carolina Chieffo
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, ICBMS, UMR 5246), Université de Lyon, Université Claude Bernard Lyon 1, Bâtiment Edgar Lederer, 1 Rue Victor Grignard, 69622, Lyon, France
| | - Emiliano Altamura
- Chemistry Department, Università degli studi di Bari "Aldo Moro", Via Orabona 4, 70125, Bari, Italy
| | - Layth Ben Trad
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, ICBMS, UMR 5246), Université de Lyon, Université Claude Bernard Lyon 1, Bâtiment Edgar Lederer, 1 Rue Victor Grignard, 69622, Lyon, France
| | - Guillaume Pilet
- Laboratoire des Multimatériaux et Interfaces (LMI, UMR 5615), Université de Lyon, Université Claude Bernard Lyon 1, Bâtiment Eugène Chevreul, 6 Rue Victor Grignard, 69622, Lyon, France
| | - Ofelia Maniti
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, ICBMS, UMR 5246), Université de Lyon, Université Claude Bernard Lyon 1, Bâtiment Edgar Lederer, 1 Rue Victor Grignard, 69622, Lyon, France
| | - Thierry Granjon
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, ICBMS, UMR 5246), Université de Lyon, Université Claude Bernard Lyon 1, Bâtiment Edgar Lederer, 1 Rue Victor Grignard, 69622, Lyon, France
| | - Saida Mebarek
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, ICBMS, UMR 5246), Université de Lyon, Université Claude Bernard Lyon 1, Bâtiment Edgar Lederer, 1 Rue Victor Grignard, 69622, Lyon, France
| | - Peter Strazewski
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, ICBMS, UMR 5246), Université de Lyon, Université Claude Bernard Lyon 1, Bâtiment Edgar Lederer, 1 Rue Victor Grignard, 69622, Lyon, France
| | - Michele Fiore
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, ICBMS, UMR 5246), Université de Lyon, Université Claude Bernard Lyon 1, Bâtiment Edgar Lederer, 1 Rue Victor Grignard, 69622, Lyon, France
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Lopez A, Fayolle D, Fiore M, Strazewski P. Chemical Analysis of Lipid Boundaries after Consecutive Growth and Division of Supported Giant Vesicles. iScience 2020; 23:101677. [PMID: 33163935 PMCID: PMC7609504 DOI: 10.1016/j.isci.2020.101677] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 09/21/2020] [Accepted: 10/09/2020] [Indexed: 11/17/2022] Open
Abstract
The reproduction of the shape of giant vesicles usually results in the increase of their "population" size. This may be achieved on giant vesicles by appropriately supplying "mother" vesicles with membranogenic amphiphiles. The next "generation" of "daughter" vesicles obtained from this "feeding" is inherently difficult to distinguish from the original mothers. Here we report on a method for the consecutive feeding with different fatty acids that each provoke membrane growth and detachment of daughter vesicles from glass microsphere-supported phospholipidic mother vesicles. We discovered that a saturated fatty acid was carried over to the next generation of mothers better than two unsaturated congeners. This has an important bearing on the growth and replication of primitive compartments at the early stages of life. Microsphere-supported vesicles are also a precise analytical tool.
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Affiliation(s)
- Augustin Lopez
- Université de Lyon, Université Claude Bernard Lyon 1, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Bâtiment Edgar Lederer, 1 Rue Victor Grignard, 69622 Villeurbanne Cedex, France
| | - Dimitri Fayolle
- Université de Lyon, Université Claude Bernard Lyon 1, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Bâtiment Edgar Lederer, 1 Rue Victor Grignard, 69622 Villeurbanne Cedex, France
| | - Michele Fiore
- Université de Lyon, Université Claude Bernard Lyon 1, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Bâtiment Edgar Lederer, 1 Rue Victor Grignard, 69622 Villeurbanne Cedex, France
| | - Peter Strazewski
- Université de Lyon, Université Claude Bernard Lyon 1, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Bâtiment Edgar Lederer, 1 Rue Victor Grignard, 69622 Villeurbanne Cedex, France
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Abstract
Systems Chemistry investigates the upkeep of specific interactions of an exceptionally broad choice of objects over longer periods of time than the average time of existence of the objects themselves. This maintenance of a dynamic state focuses on conditions where the objects are thermodynamically not very stable and should be rare or virtually inexistent. It does not matter whether they are homochirally enriched populations of chiral molecules, a specific composition of some sort of aggregate, supramolecules, or even a set of chemically relatively unstable molecules that constantly transform one into another. What does matter is that these specific interactions prevail in complex mixtures and eventually grow in numbers and frequency through the enhancing action of autocatalysis, which makes such systems ultimately resemble living cells and interacting living populations. Such chemical systems need to be correctly understood, but also intuitively described. They may be so complex that metaphors become practically more important, as a means of communication, than the precise and correct technical description of chemical models and complex molecular or supramolecular relations. This puts systems chemists on a tightrope walk of science communication, between the complex reality and an imaginative model world. This essay addresses, both, scientists who would like to read “A Brief History of Systems Chemistry”, that is, about its “essence”, and systems chemists who work with and communicate complex life-like chemical systems. I illustrate for the external reader a light mantra, that I call “to make more of it”, and I charily draw systems chemists to reflect upon the fact that chemists are not always good at drawing a clear line between a model and “the reality”: The real thing. We are in a constant danger of taking metaphors for real. Yet in real life, we do know very well that we cannot smoke with Magritte’s pipe, don’t we?
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Affiliation(s)
- Peter Strazewski
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (Unité Mixte de Recherche 5246), Université de Lyon, Claude Bernard Lyon 1, 43 bvd du 11 Novembre 1918, 69622 Villeurbanne CEDEX, France.
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Fayolle D, Berthet N, Doumeche B, Renaudet O, Strazewski P, Fiore M. Towards the preparation of synthetic outer membrane vesicle models with micromolar affinity to wheat germ agglutinin using a dialkyl thioglycoside. Beilstein J Org Chem 2019; 15:937-946. [PMID: 31164930 PMCID: PMC6541351 DOI: 10.3762/bjoc.15.90] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 04/02/2019] [Indexed: 12/15/2022] Open
Abstract
A series of alkyl thioglycosides and alkyl thiodiglycosides bearing glucose and N-acetylglucosamine residues were prepared by thiol-ene coupling in moderate to good yields (40-85%). Their binding ability towards wheat germ agglutinin was measured by competitive enzyme-linked lectin assays. One of the synthetic compounds presenting two GlcNAc units showed the highest inhibitory effect of this study with an IC50 of 11 µM corresponding to a 3182-fold improvement compared to GlcNAc. These synthetic molecules were used to produce giant vesicles, alone or in mixture with phospholipids, mimicking bacterial outer membrane vesicles (OMV) with potential antiadhesive properties.
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Affiliation(s)
- Dimitri Fayolle
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Université de Lyon, Claude Bernard Lyon 1, 43 blvd du 11 novembre 1918, 69622 Villeurbanne Cedex, France
| | - Nathalie Berthet
- Univ. Grenoble Alpes, CNRS, DCM UMR 5250, F-38000 Grenoble, France
| | - Bastien Doumeche
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Université de Lyon, Claude Bernard Lyon 1, 43 blvd du 11 novembre 1918, 69622 Villeurbanne Cedex, France
| | - Olivier Renaudet
- Univ. Grenoble Alpes, CNRS, DCM UMR 5250, F-38000 Grenoble, France
| | - Peter Strazewski
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Université de Lyon, Claude Bernard Lyon 1, 43 blvd du 11 novembre 1918, 69622 Villeurbanne Cedex, France
| | - Michele Fiore
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Université de Lyon, Claude Bernard Lyon 1, 43 blvd du 11 novembre 1918, 69622 Villeurbanne Cedex, France
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7
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Abstract
Extant life uses two kinds of linear biopolymers that mutually control their own production, as well as the cellular metabolism and the production and homeostatic maintenance of other biopolymers. Nucleic acids are linear polymers composed of a relatively low structural variety of monomeric residues, and thus a low diversity per accessed volume. Proteins are more compact linear polymers that dispose of a huge compositional diversity even at the monomeric level, and thus bear a much higher catalytic potential. The fine-grained diversity of proteins makes an unambiguous information transfer from protein templates too error-prone, so they need to be resynthesized in every generation. But proteins can catalyse both their own reproduction as well as the efficient and faithful replication of nucleic acids, which resolves in a most straightforward way an issue termed “Eigen’s paradox”. Here the importance of the existence of both kinds of linear biopolymers is discussed in the context of the emergence of cellular life, be it for the historic orgin of life on Earth, on some other habitable planet, or in the test tube. An immediate consequence of this analysis is the necessity for translation to appear early during the evolution of life.
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Affiliation(s)
- Peter Strazewski
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (Unité Mixte de Recherche 5246), Université de Lyon, Claude Bernard Lyon 1, 43 bvd du 11 Novembre 1918, 69622 Villeurbanne CEDEX, France.
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Abstract
Systems Chemistry has its roots in the research on the autocatalytic self-replication of biological macromolecules, first of all of synthetic deoxyribonucleic acids. A personal tour through the early works of the founder of Systems Chemistry, and of his first followers, recalls what's most important in this new era of chemistry: the growth and evolution of compartmented macromolecular populations, when provided with "food" and "fuel" and disposed of "waste".
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Affiliation(s)
- Peter Strazewski
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (Unité Mixte de Recherche 5246), Université de Lyon, Claude Bernard Lyon 1, 43 bvd du 11 Novembre 1918, 69622 Villeurbanne Cedex, France.
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9
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Fiore M, Madanamoothoo W, Berlioz-Barbier A, Maniti O, Girard-Egrot A, Buchet R, Strazewski P. Giant vesicles from rehydrated crude mixtures containing unexpected mixtures of amphiphiles formed under plausibly prebiotic conditions. Org Biomol Chem 2018; 15:4231-4240. [PMID: 28466946 DOI: 10.1039/c7ob00708f] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Giant lipid vesicles resemble compartments of biological cells, mimicking them in their dimension, membrane structure and partly in their membrane composition. The spontanenous appearance of closed membranes composed of bilayers of self-assembling amphiphiles was likely a prerequisite for Darwinian competitive behavior to set in at the molecular level. Such compartments should be dynamic in their membrane composition (evolvable), and sufficiently stable to harbor macromolecules (leak-free), yet semi-permeable for reactive small molecules to get across the membrane (stay away from chemical equilibrium). Here we describe bottom-up experiments simulating prebiotic environments that support the formation of simple amphiphilic molecules capable of self-assembling into vesicular objects on the micrometer scale. Long-chain alkyl phosphates, together with related amphiphilic compounds, were formed under simulated prebiotic phosphorylation conditions by using cyanamide, a recognized prebiotic chemical activator and a precursor for several compound classes. Crude dry material of the thus obtained prebiotic mixtures formed multilamellar giant vesicles once rehydrated at the appropriate pH and in the presence of plausibly prebiotic co-surfactants, as observed by optical microscopy. The size and the shape of lipid aggregates tentatively suggest that prebiotic lipid assemblies could encapsulate peptides or nucleic acids that could be formed under similar chemical prebiotic conditions. The formation of prebiotic amphiphiles was monitored by using TLC, IR, NMR and ESI-MS and UPLC-HRMS. In addition we provide a spectroscopic analysis of cyanamide under simulated prebiotic conditions in the presence of phosphate sources and spectroscopic analysis of O-phosphorylethanolamine as a plausible precursor for phosphoethanolamine lipids.
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Affiliation(s)
- Michele Fiore
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Université de Lyon, Claude Bernard Lyon 1, 43 bdv du 11 Novembre 1918, 69622 Villeurbanne Cedex, France.
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Abstract
Giant lipid vesicles (GVs) are emerging models for investigating the properties and reactivity of cell-like microcompartments, providing useful information about plausible protocellular structures in primitive times, as well as for the modern synthetic biology goal of constructing the first artificial cell from its reconstituted and partly modified components. Here we explore a novel methodology of GV purification by microfiltration under reduced pressure, operated by a simple apparatus. The method has been characterized in terms of flow rate, amount of lipid loss, quality of recovered GVs, and size distribution. A case study is reported to show the practicability of GV microfiltration. A clickable fluorescent probe was encapsulated inside GVs; more than 99.9% of the non-entrapped probe was easily and rapidly removed by multiple microfiltrations. This novel methodology is briefly discussed as a future tool for selection experiments on GV populations.
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Affiliation(s)
- Dimitri Fayolle
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Université de Lyon, Claude Bernard Lyon 1, Villeurbanne Cedex, France
| | - Michele Fiore
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Université de Lyon, Claude Bernard Lyon 1, Villeurbanne Cedex, France
| | - Pasquale Stano
- Department of Sciences, Roma Tre University, Rome, Italy
- * E-mail: (PSta); (PStr)
| | - Peter Strazewski
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Université de Lyon, Claude Bernard Lyon 1, Villeurbanne Cedex, France
- * E-mail: (PSta); (PStr)
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Fiore M, Maniti O, Girard-Egrot A, Monnard PA, Strazewski P. Glass Microsphere-Supported Giant Vesicles for the Observation of Self-Reproduction of Lipid Boundaries. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201710708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Michele Fiore
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires; Université de Lyon; Claude Bernard Lyon 1, 43 bvd du 11 Novembre 1918 69622 Villeurbanne Cedex France
| | - Ofelia Maniti
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires; Université de Lyon; Claude Bernard Lyon 1, 43 bvd du 11 Novembre 1918 69622 Villeurbanne Cedex France
| | - Agnes Girard-Egrot
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires; Université de Lyon; Claude Bernard Lyon 1, 43 bvd du 11 Novembre 1918 69622 Villeurbanne Cedex France
| | - Pierre-Alain Monnard
- Institute of Physics, Chemistry and Pharmacy; University of Southern Denmark; Campusvej 55 5230 Odense M Denmark
| | - Peter Strazewski
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires; Université de Lyon; Claude Bernard Lyon 1, 43 bvd du 11 Novembre 1918 69622 Villeurbanne Cedex France
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Fiore M, Maniti O, Girard-Egrot A, Monnard PA, Strazewski P. Glass Microsphere-Supported Giant Vesicles for the Observation of Self-Reproduction of Lipid Boundaries. Angew Chem Int Ed Engl 2017; 57:282-286. [PMID: 29105911 DOI: 10.1002/anie.201710708] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Indexed: 01/03/2023]
Abstract
Growth and division experiments on phospholipid boundaries were carried out using glass microsphere-supported phospholipid (DOPC) giant vesicles (GVs) fed with a fatty acid solution (oleic acid) at two distinct feeding rates. Both fast and slow feeding methods produced daughter GVs. Under slow feeding conditions the membrane growth process (evagination, buds, filaments) was observed in detail by fluorescence microscopy. The density difference between supported mother vesicles and newly formed daughter vesicles allowed their easy separation. Mass spectrometric analysis of the resulting mother and daughter GVs showed that the composition of both vesicle types was a mixture of original supported phospholipids and added fatty acids reflecting the total composition of amphiphiles after the feeding process. Thus, self-reproduction of phospholipid vesicles can take place under preservation of the lipid composition but different aggregate size.
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Affiliation(s)
- Michele Fiore
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Université de Lyon, Claude Bernard Lyon 1, 43 bvd du 11 Novembre 1918, 69622, Villeurbanne Cedex, France
| | - Ofelia Maniti
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Université de Lyon, Claude Bernard Lyon 1, 43 bvd du 11 Novembre 1918, 69622, Villeurbanne Cedex, France
| | - Agnes Girard-Egrot
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Université de Lyon, Claude Bernard Lyon 1, 43 bvd du 11 Novembre 1918, 69622, Villeurbanne Cedex, France
| | - Pierre-Alain Monnard
- Institute of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Peter Strazewski
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Université de Lyon, Claude Bernard Lyon 1, 43 bvd du 11 Novembre 1918, 69622, Villeurbanne Cedex, France
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13
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Fiore M, Madanamoothoo W, Berlioz-Barbier A, Maniti O, Girard-Egrot A, Buchet R, Strazewski P. Correction: Giant vesicles from rehydrated crude mixtures containing unexpected mixtures of amphiphiles formed under plausibly prebiotic conditions. Org Biomol Chem 2017; 15:5096. [PMID: 28561123 DOI: 10.1039/c7ob90082a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Correction for 'Giant vesicles from rehydrated crude mixtures containing unexpected mixtures of amphiphiles formed under plausibly prebiotic conditions' by Michele Fiore et al., Org. Biomol. Chem., 2017, 15, 4231-4240.
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Affiliation(s)
- Michele Fiore
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Université de Lyon, Claude Bernard Lyon 1, 43 bdv du 11 Novembre 1918, 69622 Villeurbanne Cedex, France.
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Fiore M, Strazewski P. Zur präbiotischen Synthese von Nukleosiden und Nukleotiden. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Michele Fiore
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires; Université de Lyon, Claude Bernard Lyon 1; 43 bdv du 11 novembre 1918 69622 Villeurbanne Cedex Frankreich
| | - Peter Strazewski
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires; Université de Lyon, Claude Bernard Lyon 1; 43 bdv du 11 novembre 1918 69622 Villeurbanne Cedex Frankreich
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15
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Abstract
There may be more than one way leading to RNA: Recent discoveries in the synthesis of nucleoside and nucleotide precursors are described and put into the wider context of prebiotic systems chemistry. Mixing Butlerow's carbohydrate precursors with Traube's 5-formylaminopyrimidines has led to the formation of prebiotic purine nucleosides whereas the mixing of 5-phosphoribose with barbituric acid and melamine gave supramolecular fibers from stacks of Whitesides' rosettas.
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Affiliation(s)
- Michele Fiore
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Université de Lyon, Claude Bernard Lyon 1, 43 bdv du 11 novembre 1918, 69622, Villeurbanne Cedex, France
| | - Peter Strazewski
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Université de Lyon, Claude Bernard Lyon 1, 43 bdv du 11 novembre 1918, 69622, Villeurbanne Cedex, France.
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16
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Le Chevalier Isaad A, Carrara P, Stano P, Krishnakumar KS, Lafont D, Zamboulis A, Buchet R, Bouchu D, Albrieux F, Strazewski P. A hydrophobic disordered peptide spontaneously anchors a covalently bound RNA hairpin to giant lipidic vesicles. Org Biomol Chem 2015; 12:6363-73. [PMID: 24915577 DOI: 10.1039/c4ob00721b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The attraction of nucleic acids to lipidic compartments is the first step for carriers of potentially inheritable information to self-organise in functionalised synthetic cells. Confocal fluorescence imaging shows that a synthetic amphiphilic peptidyl RNA molecule spontaneously accumulates at the outer bilayer membranes of phospho- and glycolipidic giant vesicles. Cooperatively attractive interactions of -3.4 to -4.0 kcal mol(-1) between a random coil hydrophobic peptide and lipid membranes can thus pilot lipophobic RNA to its compartmentation. The separation of mixed lipid phases in the membranes further enhances the local concentration of anchored RNA.
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Affiliation(s)
- Alexandra Le Chevalier Isaad
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (Unité Mixte de Recherche 5246), Université de Lyon, Claude Bernard Lyon 1, 69622 Villeurbanne Cedex, Lyon, France.
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17
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Strazewski P. Omne Vivum Ex Vivo … Omne? How to Feed an Inanimate Evolvable Chemical System so as to Let it Self-evolve into Increased Complexity and Life-like Behaviour. Isr J Chem 2015. [DOI: 10.1002/ijch.201400175] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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18
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Fung AWS, Ebhardt HA, Krishnakumar KS, Moore J, Xu Z, Strazewski P, Fahlman RP. Probing the leucyl/phenylalanyl tRNA protein transferase active site with tRNA substrate analogues. Protein Pept Lett 2015; 21:603-14. [PMID: 24521222 DOI: 10.2174/0929866521666140212110639] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 01/31/2014] [Accepted: 01/31/2014] [Indexed: 11/22/2022]
Abstract
Aminoacyl-tRNA protein transferases post-translationally conjugate an amino acid from an aminoacyl-tRNA onto the N-terminus of a target polypeptide. The eubacterial aminoacyl-tRNA protein transferase, L/F transferase, utilizes both leucyl-tRNA(Leu) and phenylalanyl-tRNA(Phe) as substrates. X-ray crystal structures with substrate analogues, the minimal substrate phenylalanyl adenosine (rA-Phe) and inhibitor puromycin, have been used to characterize tRNA recognition by L/F transferase. However analyses of these two X-ray crystal structures reveal significant differences in binding. Through structural analyses, mutagenesis, and enzymatic activity assays, we rationalize and demonstrate that the substrate analogues bind to L/F transferase with similar binding affinities using a series of different interactions by the various chemical groups of the analogues. Our data also demonstrates that enlarging the hydrophobic pocket of L/F transferase selectively enhances puromycin inhibition and may aid in the development of improved inhibitors for this class of enzymes.
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Affiliation(s)
| | | | | | | | | | | | - Richard P Fahlman
- 474 Medical Sciences Building. Department of Biochemistry. University of Alberta. Edmonton, Alberta, T6G 2H7, Canada.
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19
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Krishnakumar KS, Goudedranche S, Bouchu D, Strazewski P. The Shortest Synthetic Route to Puromycin Analogues Using a Modified Robins Approach. J Org Chem 2011; 76:2253-6. [DOI: 10.1021/jo102178h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kollappillil S. Krishnakumar
- Laboratoire de Synthèse de Biomolécules (UMR 5246, ICBMS), Université Claude Bernard Lyon 1, 43 boulevard du 11 novembre 1918, 69622 Villeurbanne Cedex, France
| | - Sébastien Goudedranche
- Laboratoire de Synthèse de Biomolécules (UMR 5246, ICBMS), Université Claude Bernard Lyon 1, 43 boulevard du 11 novembre 1918, 69622 Villeurbanne Cedex, France
| | - Denis Bouchu
- Laboratoire de Synthèse de Biomolécules (UMR 5246, ICBMS), Université Claude Bernard Lyon 1, 43 boulevard du 11 novembre 1918, 69622 Villeurbanne Cedex, France
| | - Peter Strazewski
- Laboratoire de Synthèse de Biomolécules (UMR 5246, ICBMS), Université Claude Bernard Lyon 1, 43 boulevard du 11 novembre 1918, 69622 Villeurbanne Cedex, France
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20
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Krishnakumar KS, Michel BY, Nguyen-Trung NQ, Fenet B, Strazewski P. Intrinsic pKa values of 3′-N-α-l-aminoacyl-3′-aminodeoxyadenosines determined by pH dependent 1H NMR in H2O. Chem Commun (Camb) 2011; 47:3290-2. [DOI: 10.1039/c0cc05136e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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21
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Abstract
Conformationally locked North and South versions of puromycin analogues built on a bicyclo[3.1.0]hexane pseudosugar template were synthesized. The final assembly of the products was accomplished by the Staudinger-Vilarrasa coupling of the corresponding North (2 and 3) and South (6 and 7) 3'-azidopurine carbanucleosides with the Fmoc-protected 1-hydroxybenzotriazole ester of 4-methoxy-L-tyrosine. North azides 2 and 3 were reported earlier. The 3'-azido intermediates 6 and 7 that are necessary for the synthesis of the South puromycin analogues are described herein for the first time.
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Affiliation(s)
- Hisao Saneyoshi
- Laboratory of Medicinal Chemistry, Center for Cancer Research, NCI-Frederick, Maryland 21702, USA
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Michel BY, Strazewski P. Total syntheses of a conformationally locked North-type methanocarba puromycin analogue and a dinucleotide derivative. Chemistry 2009; 15:6244-57. [PMID: 19441002 DOI: 10.1002/chem.200802629] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An original synthetic approach for the first synthesis of an enantiopure methanocarba puromycin (3'-alpha-aminoacylamino-3'-deoxyadenosine) analogue and its cytidine dinucleotide derivative is described. Each compound is conformationally locked in a North-type pucker and exhibits both a pseudoaxial hydroxy group and a pseudoequatorial aminoacyl group. The syntheses were accomplished from D-ribose in 18 and 19 steps, respectively, with key steps being a ring-closing metathesis, a Luche reduction, a Simmons-Smith cyclopropanation, a Mitsunobu coupling, a Mattocks bromoacetylation, a regioselective and a stereoselective nucleophilic substitution, a chemoselective phosphoramidite coupling and a Staudinger-Vilarrasa coupling. Both molecules are being tested for peptidyl transfer efficiency in ribosomes for comparison with the peptidyl transfer kinetics of natural puromycin and other natural and synthetic ribosomal A site substrates.
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Affiliation(s)
- Benoît Y Michel
- UMR 5246, CNRS, Laboratoire de Synthèse de Biomolécules, Université Claude Bernard Lyon 1, Villeurbanne, Université de Lyon, 69622 Lyon, France
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24
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Strazewski P. Adding to Hans Kuhn's thesis on the emergence of the genetic apparatus: of the Darwinian advantage to be neither too soluble, nor too insoluble, neither too solid, nor completely liquid. Colloids Surf B Biointerfaces 2009; 74:419-25. [PMID: 19651497 DOI: 10.1016/j.colsurfb.2009.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2009] [Revised: 06/28/2009] [Accepted: 07/02/2009] [Indexed: 10/20/2022]
Abstract
A scenario of the origin of the genetic apparatus is described where the surface and physico-chemical properties of lipid bilayers and multilayers of vesicles play a crucial role. Peptides, nucleic acids and lipids are 'collaborating' to bring about a first successful genetic apparatus. Lipidic vesicles acquire new properties through hosting nucleic acids that are transiently but covalently linked to lipophilic peptides. These peptides anchor the associated nucleic acids into the surface of lipidic vesicles. In the interior of such vesicles, within the lipidic bilayer, peptidyl transfers occur that are reminiscent of modern-day ribosomal peptidyl transfer reactions. One can expect that the growing peptides eventually acquire, stepwise and essentially arbitrarily, new functions different from anchoring nucleic acids, such as specific aminoacylation of nucleic acids, template-assisted nucleic acid synthesis, nucleotide deoxygenation and fatty acid synthesis.
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25
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Strazewski P, Michel B, Krishnakumar K. Synthesis of a xylo-Puromycin Analogue. Synlett 2008. [DOI: 10.1055/s-0028-1083437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Michel BY, Krishnakumar KS, Johansson M, Ehrenberg M, Strazewski P. Structural and functional prerequisites for ribosomal nascentpeptide acceptors: Attempts to decipher the nature of the ribosome's catalysis of peptide bond formation. ACTA ACUST UNITED AC 2008:33-4. [DOI: 10.1093/nass/nrn017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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28
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Lamy C, Lemoine J, Bouchu D, Goekjian P, Strazewski P. Glutamate–Glycine and Histidine–Glycine Co-oligopeptides: Batch Co-oligomerization versus Pulsed Addition ofN-Carboxyanhydrides. Chembiochem 2008; 9:710-3. [DOI: 10.1002/cbic.200700720] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Michel BY, Strazewski P. Total syntheses of a North methanocarba puromycin analog and its dinucleotide derivative. Nucleic Acids Symp Ser (Oxf) 2008; 52:559-560. [PMID: 18776502 DOI: 10.1093/nass/nrn283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
North methanocarba Puromycin analog 5 and its di-nucleotide derivative 6 were synthesized from D-ribose in respectively 18 and 19 steps, in order to be tested for peptidyl transfer efficiency in ribosomes.
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Affiliation(s)
- Benoît Y Michel
- Laboratoire de Synthèse de Biomolécules, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (UMR 5246), Université Claude Bernard Lyon 1, 69622, Villeurbanne, France.
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30
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Michel BY, Krishnakumar KS, Strazewski P. Total synthesis of a xylo-Puromycin analog. Nucleic Acids Symp Ser (Oxf) 2008; 52:575-576. [PMID: 18776510 DOI: 10.1093/nass/nrn291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
N(6)-bis-demethylated xylo-Puromycin analog 2 was synthesized in 56% over 6 steps from adenosine 3, involving a Mattocks bromo acetylation, a regio- and stereo-selective ribo-epoxide ring opening with sodium azide and an efficient Staudinger-Vilarrasa coupling reaction for which the conditions have been optimized.
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Affiliation(s)
- Benoît Y Michel
- Laboratoire de Synthèse de Biomolécules, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (UMR 5246), Université Claude Bernard Lyon 1, 69622, Villeurbanne, France.
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31
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Abstract
We have not yet reached a generally accepted view on how the genetic code might have originated. What has been proposed so far? The main part of the contribution to the panel discussion was devoted to recall to the audience the chronological order of publications the main aim of which it was, at least theoretically, to somehow connect physico-chemical properties of physically proximal 'universal adapters', usually some kind of nucleic acid polymer, with reactive forms of physically proximal amino acids that would subsequently polymerise into polypeptides.
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Affiliation(s)
- Peter Strazewski
- Laboratoire de Synthèse de Biomolécules (UMR 5246), Université Claude Bernard Lyon 1, 43 bvd du 11 novembre 1918, 69622 Villeurbanne Cedex, France.
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32
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Abstract
To study the ribosomal peptidyl transfer, puromycin analogues are of interest in which adenine has been replaced by hypoxanthine. We synthesized inosine puromycin analogues from 3'-azidodeoxyadenosine derivatives using adenylate deaminase for the quantitative transformation of the N-heterocycle. The amino acid coupling was carried out under Staudinger-Vilarrasa conditions in 94% yield starting from the protected and in 82% using the unprotected azide, thus, in the presence of two hydroxyls and a lactam function.
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Affiliation(s)
- Adib Charafeddine
- Laboratoire de Synthèse de Biomolécules, UMR 5246, ICBMS, Bâtiment Eugène Chevreul 5ième Etage, Université Claude Bernard Lyon 1, Villeurbanne Cedex, France
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33
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Charafeddine A, Dayoub W, Chapuis H, Strazewski P. First Synthesis of 2′-Deoxyfluoropuromycin Analogues: Experimental Insight into the Mechanism of the Staudinger Reaction. Chemistry 2007; 13:5566-84. [PMID: 17455187 DOI: 10.1002/chem.200700058] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The N(6),N(6)-dedimethyl-2'-deoxyfluoro analogue of puromycin (= 3'-deoxy-N(6),N(6)-dimethyl-3'-[O-methyltyrosylamido]adenosine), its 2',3'-regioisomer and a 3'-cytidyl-5'-(2'-deoxyfluoro)puromycyl dinucleotide analogue were synthesized following an approach involving i) the diastereospecific nitrite-assisted formation of a lyxo nucleosidic 2',3'-epoxide from an adenosine-2',3'-ditriflate derivative in a biphasic solvent mixture; ii) the regio- and stereoselective epoxide ring opening with sodium azide under mildly acidic aqueous conditions, iii) the stereospecific introduction of the fluor atom using DAST and iv) the reaction between the nucleosidyl or dinucleotidyl azide and an active ester of the N-protected amino acid using highly efficient solution conditions for the Staudinger-Vilarrasa coupling, to obtain the corresponding carboxamide directly from the in situ formed iminophosphorane. This coupling reaction furnished sterically quite demanding amides in 94 % isolated yields under very mild conditions and should therefore be of a more general value. Under certain reaction conditions we isolated (amino)acyltriazene derivatives from which dinitrogen was not eliminated. These secondary products are trapped and stabilized witnesses of the first intermediate of the Staudinger reaction, the phosphatriazenes (phosphazides, triazaphosphadienes) which usually eliminate dinitrogen in situ and rapidly rearrange into iminophosphoranes, unless they are derived from conjugated or sterically bulky azides and phosphines. The acyltriazenes could either be thermally decomposed or converted to the corresponding N-alkyl carboxamides through proton-assisted elimination of dinitrogen. All compounds were carefully characterized through MS spectrometry, (1)H, (19)F, (31)P and (13)C NMR spectroscopy.
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Affiliation(s)
- Adib Charafeddine
- Laboratoire de Synthèse des Biomolécules, Bâtiment Eugène Chevreul, UMR UCBL-CNRS 5246, ICBMS, Université Claude Bernard Lyon 1, Domaine Scientifique de la Doua, 43 bvd du 11 novembre 1918, 69622 Villeurbanne Cedex, France
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34
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Abstract
Amphiphilic peptidyl-RNA conjugates, molecules that mimic natural peptidyl-transfer RNA, are capable of self-assembling on glass substrates as vesicles and supported bilayers.
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Affiliation(s)
- Adina N Lazar
- Assemblages Moléculaires d'Intérêt Biologique (UMR CNRS 5086), Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, F-69367 Lyon, France
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35
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Amantea A, Walser M, Séquin U, Strazewski P. Synthesis and15N- and17O-NMR Spectra of 5-Methyl(15N2)[O2,O4-17O2]uridine (= (15N2)[O2,O4-17O2]Ribosylthymine). Helv Chim Acta 2004. [DOI: 10.1002/hlca.19950780507] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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36
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Niemann AC, Meyer M, Engeloch T, Botta O, Hädener A, Strazewski P. Biosynthetic Production of [N2,1,3,7,9-15N]Guanosine and [1,3,7,9-15N]inosine and conversion into [N6,1,3,7,9-15N]adenosine for structure elucidation of RNA by heteronuclear NMR. Helv Chim Acta 2004. [DOI: 10.1002/hlca.19950780213] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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37
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Nguyen-Trung NQ, Terenzi S, Scherer G, Strazewski P. High-yield immobilization of a puromycin analogue for the solid support synthesis of aminoacyl-tRNA fragments. Org Lett 2003; 5:2603-6. [PMID: 12868869 DOI: 10.1021/ol0346638] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] An efficient procedure for the immobilization of 3'-deoxy-3'-(O-methyltyrosyl)aminoadenosine was developed. A poly(ethylene glycol)-derived diacid linker/spacer was attached to aminomethyl polystyrene. Coupling of the 2'-hydroxy instead of the 2'-O-succinylated ribonucleoside resulted in high immobilization yields (over 80%) and allowed for the recovery of valuable unreacted material. This specific procedure should be applicable to other ribonucleosides containing a bulky modification at the 3'-position and can be used for the stepwise construction of 3'-aminoacyl- or 3'-peptidyl-RNA conjugates.
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Affiliation(s)
- Nhat Quang Nguyen-Trung
- Institute of Organic Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056 Basel, Switzerland
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38
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Affiliation(s)
- Silvia Terenzi
- Institute of Organic Chemistry, University Basel, St Johanns-Ring 19, 4056 Basel, Switzerland
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39
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40
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Abstract
3'-aminoacylamino-3'-deoxyadenosines, analogues of the antibiotic puromycin, have been synthesized from adenosine. They key 3'-azido derivative 10 was obtained through a 3'-oxidation/reduction/substitution procedure. A modified purification protocol on a larger scale was developed for the oxidation step using the Garegg reagent. The coupling reaction between an Fmoc-l-amino acid and the fully protected form of 3'-amino-3'-deoxyadenosine 11 furnished the aminoacylated compounds 12 in high yields. The puromycin analogues were obtained in 10 steps and up to 23% (14c) overall yield.
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Affiliation(s)
- Nhat Quang Nguyen-Trung
- Institute of Organic Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056 Basel, Switzerland
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41
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Abstract
The thermodynamic parameters DeltaH, DeltaS, T(m), and DeltaG of a total of 36 RNA strands, 22 tetralooped 22mers, and 14 heptalooped 25mers (same stem sequence) were analyzed with respect to enthalpy-entropy compensation (EEC). The EEC plots [DeltaH, DeltaS] were compared with collected literature data from protein and nucleic acid unfolding studies (3224 and 241 datapoints, respectively) which all proved to be remarkably linear. The similarity of the compensation slopes and intercepts for all compounds indicate that, irrespective of the chemical nature and stability of the folding solutes, the exothermicity DeltaH and entropic penalty T x DeltaS of folding are strongly dominated by the rearrangement and formation of hydration layers around the solutes, while it is well-known that the stability of folding results only from the difference (DeltaG) and ratio (T(m)) of both parameters. EEC plots [DeltaH, DeltaS] are presented in an extended context, as 3D plots [DeltaH, DeltaS, T(m)] allowing for a correct analytical description of the enthalpy-entropy relationship and for more practical interpretations of large amounts of thermodynamic data when replotted as [DeltaH, T(m)] or [DeltaG(T), T(m)]. The introduction of a variety of mismatches into nucleic acids, or limited irreguliarities into any supramolecular complex, and the analysis of the involved thermodynamics as shown in this study-i.e., scanning the "enthalpy-entropy space" of whole macromolecular subgroups-should permit to extract and quantify more "hidden information", such as hydration extent and sensitivity of macromolecular frameworks toward desolvation and structural perturbation, from thermodynamic analyses of large sample sizes.
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Affiliation(s)
- Peter Strazewski
- Institute of Organic Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056 Basel, Switzerland.
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42
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Biała E, Strazewski P. Internally mismatched RNA: pH and solvent dependence of the thermal unfolding of tRNA(Ala) acceptor stem microhairpins. J Am Chem Soc 2002; 124:3540-5. [PMID: 11929241 DOI: 10.1021/ja0161305] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The thermal unfolding of two RNA hairpin systems derived from the aminoacyl accepting arm of Escherichia coli tRNA(Ala) that included all possible single internal mismatches mostly in the third base pair position was measured spectroscopically in 0.1 M NaCl at pH 7.5 and, in part, 5.5. The thermodynamic parameters DeltaH(o), DeltaS(o), DeltaG(o), and T(m) of a total of 36 RNA strands were determined through nonlinear curve fitting of the melting profiles (22 tetralooped 22mers and 14 heptalooped 25mers, same stem sequence). Only three of the 22mers, the A.C-containing variants, were shown to be significantly more stable at pH 5.5. A number of remarkable differences-most likely of more general relevance-between the thermodynamics of certain structurally very similar hairpin variants (e.g., G.C versus A.U, G.U versus I.U) at pH 7.5 are discussed with respect to two possible ways of helix stabilization: pronounced hydration versus low entropic penalty. Four selected 22mers were additionally analyzed in 1 M NaCl and in solvent mixtures containing ethanol, ethylene glycol, and dimethylformamide. The wealth of thermodynamic data suggest that the exothermicity DeltaH(o) and entropic penalty T x DeltaS(o) of folding are strongly dominated by the rearrangement and formation of hydration layers around the solutes, while it is well-known that the stability of folding results only from the difference (DeltaG(o)) and ratio of both parameters (T(m) = DeltaH (o)/DeltaS(o)).
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Affiliation(s)
- Ewa Biała
- Institute of Organic Chemistry, University of Basel, St. Johanns-Ring 19, CH - 4056 Basel, Switzerland.
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43
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Abstract
[reaction: see text] A conformationally locked carbocyclic version of puromycin amino nucleoside was synthesized via Mitsunobu coupling of a 3-azido-substituted carbocyclic moiety with 6-chloropurine without interference from the azido group reacting with triphenylphosphine. The requisite 3-azido-substituted carbocyclic pseudosugar was prepared by a double inversion of configuration at C3' (nucleoside numbering) involving a nucleophilic displacement with azide.
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Affiliation(s)
- Yongseok Choi
- Laboratory of Medicinal Chemistry, Center for Cancer Research, NCI, Frederick, Maryland 21702, USA
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44
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Trung NQ, Strazewski P, Olsson M, Ehrenberg M. The conformational space of nascent peptide-accepting 3'-aminoacyl ribonucleos(t)ides: 1H NMR data and ab initio calculations of puromycin and some synthetic analogs. Nucleosides Nucleotides Nucleic Acids 2001; 20:383-4. [PMID: 11563051 DOI: 10.1081/ncn-100002310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- N Q Trung
- Institute of Organic Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056 Basel, Switzerland
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Strazewski P, Biala E, Gabriel K, McClain WH. The relationship of thermodynamic stability at a G x U recognition site to tRNA aminoacylation specificity. RNA 1999; 5:1490-4. [PMID: 10580477 PMCID: PMC1369870 DOI: 10.1017/s1355838299991586] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The G x U pair at the third position in the acceptor helix of Escherichia coli tRNA(Ala) is critical for aminoacylation. The features that allow G x U recognition are likely to include direct interaction of alanyl-tRNA synthetase with distinctive atomic groups and indirect recognition of the structural and stability information encoded in the sequence of G x U and its immediate context. The present work investigates the thermodynamic stability and acceptor activity for a comprehensive set of variant RNAs with substitutions of the G x U pair of E. coli tRNA(Ala). The four RNAs with Watson-Crick substitutions had a lower acceptor activity and a higher stability relative to the G x U RNA. On the other hand, the RNAs with mispair substitutions had a lower stability, but either a higher or a lower acceptor activity. Thus, the entire set of variant RNAs does not exhibit a correlation between thermodynamic stability of the free, unbound tRNA and its acceptor activity. The substantial acceptor activity of tRNAs with particular mispair substitutions may be explained by their ability to assume the conformational preferences of alanyl-tRNA synthetase. Moreover, the G x U pair may provide a point of deformability for the substrate tRNA to adapt to the enzyme's active site.
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Affiliation(s)
- P Strazewski
- Institute of Organic Chemistry, University of Basel, Switzerland.
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Abstract
Thermal denaturation studies were carried out on a set of site-specific variants of a 22mer RNA hairpin comprising the aminoacyl acceptor stem sequence of E. coli tRNA(Ala). The pairing thermodynamics were calculated from the melting profiles.
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Affiliation(s)
- E Biala
- Institute of Organic Chemistry, University of Basel, Switzerland
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