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Nano- and microplastic analysis: Focus on their occurrence in freshwater ecosystems and remediation technologies
Laboratoire Sciences Analytiques Bioanalytiques et Miniaturisation - Yolanda Pico, Ahmed Alfarhan and Damia Barcelo
ELSEVIER - 113 409-425 - doi: 10.1016/j.trac.2019.02.016 - 2019
Plastic pollution is a global problem since 2016 when its production reached 322 million tonnes, excluding fibers. Daily discharges of microplastics (MPs, defined as <5 mm in size) are estimated in the range of 50,000 up to 15 million particles, whereas no information on nanoplastic (NP, <100 nm) release is available yet. Different processes further degraded these materials producing more MPs and NPs. This review attempts to fill the void of information on the state-of-art analysis of MPs and NPs (recently identified as emerging contaminants) and provides a critical overview on modern instrumentation, newly developed workflows, and promising techniques for their characterization (Raman and FT-IR spectroscopies and microscopies, pyrolysis and thermal desorption gas chromatography, imaging techniques, etc.). Available analytical methods, validation as well as applications with cells have been taken into account. MP and NP sampling, identification, and characterization are discussed. Finally, recent applications to establish their occurrence in freshwater ecosystems and the effectiveness of the proposed remediation technologies are considered.
Monitoring of the blend monoethanolamine/methyldiethanolamine/water for post-combustion CO2 capture
Laboratoire Sciences Analytiques Bioanalytiques et Miniaturisation - Lorena Cuccia, José Dugay, Bontemps Domitille, Myriam Louis-Louisy
International Journal of Greenhouse Gas Control - 80 43-53 - DOI: 10.1016/j.ijggc.2018.11.004 - 2019
The blend MEA/MDEA (5/25%wt.) was studied on the LEMEDES-CO2 lab-scale pilot plant, with representative conditions of post-combustion CO2 capture for power generation during 900 h. CO2 loadings were determined and showed average values of 0.12 and 0.40 respectively for the lean and rich solvents. Stability of the two amines, namely MEA and MDEA, was monitored using ionic chromatography; results did not show any significant degradation of MDEA during the campaign, in contrary to MEA which showed a significant degradation in the range of 0.03 points per day. Analytical methods involving GC–MS and IC were developed in order to identify potential degradation products in the liquid phase of the solvent. Study of the gaseous emissions’ composition was also realized using sampling on different solid sorbents followed by thermal desorption and GC–MS analysis. A total of 22 compounds were listed including amines, organic acids, and pyrazines derivatives. 12 degradation products were found in the solvent itself and 11 in the treated flue gas among which MDEA, the constituent amine of the blend. A quantitative monitoring was carried out for formic and oxalic acids. Results showed concentrations reaching 500 mg/L for oxalic acid and 1400 mg/L for formic acid.
Synthesis and Characterization of Molecularly Imprinted Polymers for the Selective Extraction of Carbamazepine and Analogs from Human Urine Samples
Laboratoire Sciences Analytiques Bioanalytiques et Miniaturisation - 287–295
Chromatographia - 82 287–295 - doi:10.1007/s10337-018-3680-4 - 2019
Two molecularly imprinted polymers (MIPs) were synthesized according to a previous work from our group dealing with the extraction of carbamazepine from environmental water. The potential of these MIPs, which differ in the nature of the monomer used for their synthesis, to selectively extract the drugs carbamazepine and oxcarbazepine and the metabolite 10,11-epoxycarbamazepine was first studied in spiked pure water, and high selectivity was obtained with both MIPs for the three target molecules in this pure medium. This selectivity was maintained when applying one of the MIPs to urine samples. Indeed, extraction recoveries were higher than 82% on the MIP and lower than 20% on the corresponding non-imprinted polymer used as a control. The repeatability of the extraction procedure applied to urine was also demonstrated, with relative standard deviation (RSD) below 20% for extraction recoveries of the three targets at a spiking level of 20 ng L−1. Limits of quantification between 1 and 7 ng L−1 were determined for urine samples using the MIP as extraction sorbent combined with LC–MS analysis. The potential of the MIP was compared to that of the Oasis HLB sorbent. This study shows that the MIP constitutes a powerful tool for avoiding matrix effects encountered in the quantification of the target molecules in urine samples extracted on Oasis HLB.
Investigation of serum proteome homeostasis during radiation therapy by a quantitative proteomics approach
Laboratoire Spectrométrie de masse biologique et protéomique - Amira Ouerhani ; Giovanni Chiappetta ; Oussema Souiai ; Halima Mahjoubi ; Joelle Vinh
Biosci Rep - 39 (7) BSR20182319 - doi.org/10.1042/BSR20182319 - 2019
The purpose of the present study is to analyze the serum proteome of patients receiving Radiation Therapy (RT) at different stages of their treatment to discovery candidate biomarkers of the radiation-induced skin lesions and the molecular pathways underlying the radiation signatures. Six stages of RT treatment were monitored from patients treated because of brain cancer: before starting the treatment, during the treatment (four time points), and at 4 weeks from the last RT dose. Serum samples were analyzed by a proteomics approach based on the Data Independent Acquisition (DIA) mass spectrometry (MS). RT induced clear changes in the expression levels of 36 serum proteins. Among these, 25 proteins were down- or up-regulated significantly before the emergence of skin lesions. Some of these were still deregulated after the completion of the treatment. Few days before the appearance of the skin lesions, the levels of some proteins involved in the wound healing processes were down-regulated. The pathway analysis indicated that after partial body irradiation, the expression levels of proteins functionally involved in the acute inflammatory and immune response, lipoprotein process and blood coagulation, were deregulated.
Contribution of proteases and cellulases produced by solid-state fermentation to the improvement of corn ethanol production
Laboratoire Spectrométrie de masse biologique et protéomique - Anaïs Guillaume, Aurore Thorigné, Yoann Carré, Joëlle Vinh and Loïc Levavasseur
Biosci Rep - 6 7 - doi.org/10.1186/s40643-019-0241-0 - 2019
By cultivating a strain of Aspergillus tubingensis on agro-industrial by-products using solid-state fermentation technology, a biocatalyst containing more than 130 different enzymes was obtained. The enzymatic complex was composed mainly of hydrolases, among which a protease, an aspergillopepsin, accounted for more than half of the total proteins. Cell-wall-degrading enzymes such as pectinases, cellulases and hemicellulases were also highly represented. Adding the biocatalyst to corn mash at 1 kg/T corn allowed to significantly improve ethanol production performances. The final ethanol concentration was increased by 6.8% and the kinetics was accelerated by 14 h. The aim of this study was to identify the enzymes implicated in the effect on corn ethanol production. By fractionating the biocatalyst, the particular effect of the major enzymes was investigated. Experiments revealed that, together, the protease and two cellulolytic enzymes (an endoglucanase and a β-glucosidase) were responsible for 80% of the overall effect of the biocatalyst. Nevertheless, the crude extract of the biocatalyst showed greater impact than the combination of up to seven purified enzymes, demonstrating the complementary enzymatic complex obtained by solid-state fermentation. This technology could, therefore, be a relevant natural alternative to the use of GMO-derived enzymes in the ethanol industry.
Benzoquinone, a leukemogenic metabolite of benzene, catalytically inhibits the protein tyrosine phosphatase PTPN2 and alters STAT1 signaling
Laboratoire Spectrométrie de masse biologique et protéomique - Romain Duval, Linh-Chi Bui, Cécile Mathieu, Qing Nian, Jérémy Berthelet, Ximing Xu, Iman Haddad, Joelle Vinh, Jean-Marie Dupret, Florent Busi, Fabien Guidez, Christine Chomienne, and Fernando Rodrigues-Lima
J Biol Chem - 294(33) 12483–12494 - doi: 10.1074/jbc.RA119.008666 - 2019
Protein tyrosine phosphatase, nonreceptor type 2 (PTPN2) is mainly expressed in hematopoietic cells, where it negatively regulates growth factor and cytokine signaling. PTPN2 is an important regulator of hematopoiesis and immune/inflammatory responses, as evidenced by loss-of-function mutations of PTPN2 in leukemia and lymphoma and knockout mice studies. Benzene is an environmental chemical that causes hematological malignancies, and its hematotoxicity arises from its bioactivation in the bone marrow to electrophilic metabolites, notably 1,4-benzoquinone, a major hematotoxic benzene metabolite. Although the molecular bases for benzene-induced leukemia are not well-understood, it has been suggested that benzene metabolites alter topoisomerases II function and thereby significantly contribute to leukemogenesis. However, several studies indicate that benzene and its hematotoxic metabolites may also promote the leukemogenic process by reacting with other targets and pathways. Interestingly, alterations of cell-signaling pathways, such as Janus kinase (JAK)/signal transducer and activator of transcription (STAT), have been proposed to contribute to benzene-induced malignant blood diseases. We show here that 1,4-benzoquinone directly impairs PTPN2 activity. Mechanistic and kinetic experiments with purified human PTPN2 indicated that this impairment results from the irreversible formation (kinact = 645 m−1·s−1) of a covalent 1,4-benzoquinone adduct at the catalytic cysteine residue of the enzyme. Accordingly, cell experiments revealed that 1,4-benzoquinone exposure irreversibly inhibits cellular PTPN2 and concomitantly increases tyrosine phosphorylation of STAT1 and expression of STAT1-regulated genes. Our results provide molecular and cellular evidence that 1,4-benzoquinone covalently modifies key signaling enzymes, implicating it in benzene-induced malignant blood diseases.

Investigation of serum proteome homeostasis during radiation therapy by a quantitative proteomics approach
Laboratoire Spectrométrie de masse biologique et protéomique - Amira Ouerhani, Giovanni Chiappetta, Oussema Souiai, Halima Mahjoubi, Joelle Vinh
Biosci Rep - 39(7) - doi: 10.1042/BSR20182319 - 2019
The purpose of the present study is to analyze the serum proteome of patients receiving Radiation Therapy (RT) at different stages of their treatment to discovery candidate biomarkers of the radiation-induced skin lesions and the molecular pathways underlying the radiation signatures. Six stages of RT treatment were monitored from patients treated because of brain cancer: before starting the treatment, during the treatment (four time points), and at 4 weeks from the last RT dose. Serum samples were analyzed by a proteomics approach based on the Data Independent Acquisition (DIA) mass spectrometry (MS). RT induced clear changes in the expression levels of 36 serum proteins. Among these, 25 proteins were down- or up-regulated significantly before the emergence of skin lesions. Some of these were still deregulated after the completion of the treatment. Few days before the appearance of the skin lesions, the levels of some proteins involved in the wound healing processes were down-regulated. The pathway analysis indicated that after partial body irradiation, the expression levels of proteins functionally involved in the acute inflammatory and immune response, lipoprotein process and blood coagulation, were deregulated.

Global host molecular perturbations upon in situ loss of bacterial endosymbionts in the deep-sea mussel Bathymodiolus azoricus assessed using proteomics and transcriptomics
Laboratoire Spectrométrie de masse biologique et protéomique - Camille Détrée, Iman Haddad, Emmanuelle Demey-Thomas, Joëlle Vinh, François H Lallier, Arnaud Tanguy, Jean Mary
BMC Genomics - 20(1) 109 - doi: 10.1186/s12864-019-5456-0 - 2019
Background: Colonization of deep-sea hydrothermal vents by most invertebrates was made efficient through their adaptation to a symbiotic lifestyle with chemosynthetic bacteria, the primary producers in these ecosystems. Anatomical adaptations such as the establishment of specialized cells or organs have been evidenced in numerous deep-sea invertebrates. However, very few studies detailed global inter-dependencies between host and symbionts in these ecosystems. In this study, we proposed to describe, using a proteo-transcriptomic approach, the effects of symbionts loss on the deep-sea mussel Bathymodiolus azoricus' molecular biology. We induced an in situ depletion of symbionts and compared the proteo-transcriptome of the gills of mussels in three conditions: symbiotic mussels (natural population), symbiont-depleted mussels and aposymbiotic mussels.

Results: Global proteomic and transcriptomic results evidenced a global disruption of host machinery in aposymbiotic organisms. We observed that the total number of proteins identified decreased from 1118 in symbiotic mussels to 790 in partially depleted mussels and 761 in aposymbiotic mussels. Using microarrays we identified 4300 transcripts differentially expressed between symbiont-depleted and symbiotic mussels. Among these transcripts, 799 were found differentially expressed in aposymbiotic mussels and almost twice as many in symbiont-depleted mussels as compared to symbiotic mussels. Regarding apoptotic and immune system processes - known to be largely involved in symbiotic interactions - an overall up-regulation of associated proteins and transcripts was observed in symbiont-depleted mussels.

Conclusion: Overall, our study showed a global impairment of host machinery and an activation of both the immune and apoptotic system following symbiont-depletion. One of the main assumptions is the involvement of symbiotic bacteria in the inhibition and regulation of immune and apoptotic systems. As such, symbiotic bacteria may increase their lifespan in gill cells while managing the defense of the holobiont against putative pathogens.

Keywords: Chemoautotrophic symbiosis; Hydrothermal vent; In situ experiment; Mutualism; Proteo-transcriptomics.
Physicochemical Characterization of Phthalocyanine-Functionalized Quantum Dots by Capillary Electrophoresis Coupled to a LED Fluorescence Detector
Laboratoire Synthèse Electrochimie Imagerie et Systèmes Analytiques - Ramírez-García G, d'Orlyé F, Nyokong T, Bedioui F, Varenne A
Methods in Molecular Biology (Clifton, N.J.) - 2000 373-385 - DOI: 10.1007/978-1-4939-9516-5_23 - 2019
Capillary zone electrophoresis (CZE) complemented with Taylor Dispersion Analysis-CE (TDA-CE) was developed to physicochemically characterize phthalocyanine-capped core/shell/shell quantum dots (QDs) at various pH and ionic strengths. An LED-induced fluorescence detector was used to specifically detect the QDs. The electropherograms and taylorgrams allowed calculating the phthalocyanine-QDs (Pc-QDs) ζ-potential and size, respectively, and determining the experimental conditions for colloidal stability. This methodology allowed evidencing either a colloidal stability or an aggregation state according to the background electrolytes nature. The calculated ζ-potential values of Pc-QDs decreased when ionic strength increased, being well correlated with the aggregation of the nanoconjugates at elevated salt concentrations. For the same reason, the hydrodynamic diameter of Pc-QDs increased with increasing background electrolyte ionic strength. The use of electrokinetic methodologies has provided insights into the colloidal stability of the photosensitizer-functionalized QDs in physiologically relevant solutions and, thereby, its usefulness for improving their design and applications for photodynamic therapy.
A Simple Efficient Click Synthesis of Novel Crown Ethers Containing 1,2,3-Triazole Moieties
Laboratoire Synthèse Electrochimie Imagerie et Systèmes Analytiques - H. Elamari, A. Ouerghui, F. Ammari & C. Girard
Russian Journal of Organic Chemistry - 55 1785-1790 - doi.org/10.1134/S1070428019110228 - 2019
Novel crown ether derivative containing 1,4-disubstituted-1,2,3-triazole moieties were synthesized. At the first step of the synthesis 4,13-diaza-18-crown-6 and 4-aminobenzo-15-crown-5 were converted into terminal alkynes, which were then subjected to copper(I)-catalyzed alkyne-azide coupling (CuAAC) in methylene chloride. This coupling reaction was performed according to the concept of click chemistry, using an Amberlyst A-21-supported copper(I) iodide catalyst
Surface functionalization of cyclic olefin copolymer by plasma‐enhanced chemical vapor deposition using atmospheric pressure plasma jet for microfluidic applications
Laboratoire Synthèse Electrochimie Imagerie et Systèmes Analytiques - Samantha Bourg Sophie Griveau Fanny d'Orlyé Michael Tatoulian Fethi Bedioui Cédric Guyon Anne Varenne
FULL PAPER - 16 6 - https://doi.org/10.1002/ppap.201800195 - 2019
Lab‐On‐A‐Chips promise solutions for high throughput and specific analysis for environmental and health applications, with the challenge to develop materials allowing fast, easy, and cheap microfabrication and efficient surface treatment. Cyclic olefin copolymer (COC) is a promising thermoplastic, easily microfabricated for both rapid prototyping and low‐cost mass production of microfluidic devices but still needing efficient surface modification strategies. This study reports for the first time the optimization of an easy COC silica coating process by plasma‐enhanced chemical vapor deposition at atmospheric pressure with plasma jet and tetraethylorthosilicate as precursor, leading to a 158 ± 7 nm thickness and a 14‐day‐stability of hydrophilic properties for a COC‐embedded microchannel (100 µm), paving the way for a simplified and controlled COC surface modification.

Synthesis of new polymers containing 1,2,3-triazole units from poly(vinylchloride) via "click” chemistry catalyzed by copper iodide and its application in extraction of nitrates and metals contained in wastewater
Laboratoire Synthèse Electrochimie Imagerie et Systèmes Analytiques - Ouerghui Abid , Dardouri Mokthar , Sleimi Noomene , Bel Hadj Amor Abir , Ammari Faycel , Girard Christian
Baztech - - DOI dx.doi.org/10.14314/polimery.2019.1.1 - 2019
New polymers with potential application in a waste water purification from inorganic contaminants were synthesized via a chemical modification of poly(vinyl chloride) by "click” method based on copper(I)-catalyzed Huisgen reaction. The structure of the resulting polymers containing 1,4-disubstituted triazole units was confirmed by infrared spectroscopy (ATR-FTIR), nitrogen elemental analysis and differential thermal analysis (DTA). The obtained polymers were subsequently used in the elimination of nitrate ions and metalions from the wastewater of Beja region (Tunisia). It was found that new polymers were most efficient in capturing of zinc ions, the average extraction percentage of Zn2+ was 28%, while the average extraction percentage of nitrates did not exceed 12.5%. The selectivity of the binding of investigated ions can be arranged in the following order: Zn2+> NO3–> Ca2+> Mg2+.
Chemical Modification of Polystyrene Merrifield: Extraction of Zinc and Magnesium Located in Wastewater
Laboratoire Synthèse Electrochimie Imagerie et Systèmes Analytiques - Mokhtar Dardouri Hichem Elamari Fayçel Ammari
ELSEVIER - 5(3) 73 - DOI: 10.11648/j.ajpst.20190503.11 - 2019
In order to remove metals (Zn & Mg) located in wastewater, a new series of clickable polystyrene Merrifield grafted with azide and alkynes were synthesized and implicated in this domain. In a first step, we transformed the polystyrene Merrifield into the known Azidomethyl polystyrene, in a second step, a coupling reaction between the Azidomethyl polystyrene and dipropargylamine was realized for the synthesis of a new terminated polystyrene alkyne containing one unit of (1,4)-triazole. To increase the length of the chain grafted on the polystyrene Merrifield, several coupling reactions are applied, the main idea of this work was to increase the number of (1,2,3) –triazole units of this grafted chain. The click chemistry based on the Huygens’s reaction catalyzed by copper (I) was used in this synthesis, the new polymers containing (1,4)-disubstituted triazole are tested for the extraction of Mg and Zn located in wastewater. The structure of new obtained polymers was confirmed by infrared spectroscopy (ATR-FTIR), UV-visible spectroscopy and elemental analysis for nitrogen. Differential Thermal Analysis (DTA) and Thermo Gravimetric Analysis (TGA) were used to study crosslinking behavior of these polymers. This study shows a low selectivity of studied polymers for the retention of magnesium, while for the Zinc, the percentage removal was average, it’s in the order of 30%
Synthesis of new polymers containing 1,2,3-triazole units from poly(vinylchloride) via "click” chemistry catalyzed by copper iodide and its application in extraction of nitrates and metals contained in wastewater
Laboratoire Synthèse Electrochimie Imagerie et Systèmes Analytiques - Ouerghui Abid , Dardouri Mokthar , Sleimi Noomene , Bel Hadj Amor Abir , Ammari Faycel , Girard Christian
Baztech - - DOI dx.doi.org/10.14314/polimery.2019.1.1 - 2019
New polymers with potential application in a waste water purification from inorganic contaminants were synthesized via a chemical modification of poly(vinyl chloride) by "click” method based on copper(I)-catalyzed Huisgen reaction. The structure of the resulting polymers containing 1,4-disubstituted triazole units was confirmed by infrared spectroscopy (ATR-FTIR), nitrogen elemental analysis and differential thermal analysis (DTA). The obtained polymers were subsequently used in the elimination of nitrate ions and metalions from the wastewater of Beja region (Tunisia). It was found that new polymers were most efficient in capturing of zinc ions, the average extraction percentage of Zn2+ was 28%, while the average extraction percentage of nitrates did not exceed 12.5%. The selectivity of the binding of investigated ions can be arranged in the following order: Zn2+> NO3–> Ca2+> Mg2+.
Cobalt-Salen Catalyzed Electroreductive Alkylation of Activated Olefins
Laboratoire Synthèse Electrochimie Imagerie et Systèmes Analytiques - Sylvie Condon , Céline Cannes , and Fethi Bedioui
Journal of Chemistry - - doi.org/10.1155/2019/9832639 - 2019
Cobalt-Salen mediated electroreductive and regioselective alkylation of electron deficient olefins is reported in one step in an undivided electrochemical cell, in the presence of an iron rod as sacrificial anode. Although the reactivity depends on the class of alkyl halides, the reported study offers a green and expeditious electrosynthetic route for Csp3-Csp3 bond formation in mild conditions. This study also confirms the possible formation of the heterobinuclear cobalt-Salen-iron complex previously reported as the effective catalyst.
Phase separations, liquid crystal ordering and molecular partitioning in mixtures of PEG and DNA oligomers
LABORATOIRE AUTO-ASSEMBLAGE MOLÉCULAIRE - Simone Di Leo, Marco Todisco, Tommaso Bellini, Tommaso P. Fraccia
Molecular Crystals and Liquid Crystals - - DOI: 10.1080/02678292.2018.1519123 - 2018
Liquid crystals (LCs) ordering of DNA and RNA oligomers relies on the presence of inter-duplex end-to-end attraction, driving the formation of linear aggregates. Such interactions are gauged, at a macroscopic level, by the osmotic pressure at the isotropic-nematic and nematic-columnar phase transitions. We studied aqueous solutions of PEG and DNA duplex-forming oligomers, finding that there is a wide range of concentrations in which these mixtures phase separate into coexisting PEG-rich and DNA-rich phases, the latter being either in the isotropic state or ordered as a nematic or columnar LC. We determined the phase diagram in mixtures of PEG and DNA duplexes with different terminal motifs – blunt ends, sticky overhangs, aggregation-preventing overhangs – and measured the partitioning of the species in the coexisting phases. On this basis, we determined the osmotic pressure as a function of the DNA concentration across the phase diagram. We compared the equation of state obtained in this way with both the Carnahan–Starling equation of state for hard spheres and with the pressure predicted by computer simulations of a system of aggregating cylinders. We obtain a good agreement between experiments and simulations, and end-to-end attraction energies of the order of 6 kcal/mol, a bit larger than expected, but still in agreement with the current models for DNA-DNA interactions.
Phase separations, liquid crystal ordering and molecular partitioning in mixtures of PEG and DNA oligomers
LABORATOIRE AUTO-ASSEMBLAGE MOLÉCULAIRE - Simone Di Leo, Marco Todisco, Tommaso Bellini, Tommaso P. Fraccia
Molecular Crystals and Liquid Crystals - - DOI: 10.1080/02678292.2018.1519123 - 2018
Liquid crystals (LCs) ordering of DNA and RNA oligomers relies on the presence of inter-duplex end-to-end attraction, driving the formation of linear aggregates. Such interactions are gauged, at a macroscopic level, by the osmotic pressure at the isotropic-nematic and nematic-columnar phase transitions. We studied aqueous solutions of PEG and DNA duplex-forming oligomers, finding that there is a wide range of concentrations in which these mixtures phase separate into coexisting PEG-rich and DNA-rich phases, the latter being either in the isotropic state or ordered as a nematic or columnar LC. We determined the phase diagram in mixtures of PEG and DNA duplexes with different terminal motifs – blunt ends, sticky overhangs, aggregation-preventing overhangs – and measured the partitioning of the species in the coexisting phases. On this basis, we determined the osmotic pressure as a function of the DNA concentration across the phase diagram. We compared the equation of state obtained in this way with both the Carnahan–Starling equation of state for hard spheres and with the pressure predicted by computer simulations of a system of aggregating cylinders. We obtain a good agreement between experiments and simulations, and end-to-end attraction energies of the order of 6 kcal/mol, a bit larger than expected, but still in agreement with the current models for DNA-DNA interactions.
Nonenzymatic Polymerization into Long Linear RNA Templated by Liquid Crystal Self-Assembly
LABORATOIRE AUTO-ASSEMBLAGE MOLÉCULAIRE - Marco Todisco Tommaso Pietro Fraccia Greg P. Smith Andrea Corno
ACS Nano - 12(10) - DOI: 10.1021/acsnano.8b05821 - 2018
Self-synthesizing materials, in which supramolecular structuring enhances the formation of new molecules that participate to the process, represent an intriguing notion to account for the first appearance of biomolecules in an abiotic Earth. We present here a study of the abiotic formation of interchain phosphodiester bonds in solutions of short RNA oligomers in various states of supramolecular arrangement and their reaction kinetics. We found a spectrum of conditions in which RNA oligomers self-assemble and phase separate into highly concentrated ordered fluid liquid crystal (LC) microdomains. We show that such supramolecular state provides a template guiding their ligation into hundred-bases long chains. The quantitative analysis presented here demonstrates that nucleic acid LC boosts the rate of end-to-end ligation and suppresses the formation of the otherwise dominant cyclic oligomers. These results strengthen the concept of supramolecular ordering as an efficient pathway toward the emergence of the RNA World in the primordial Earth.
Backbone-free duplex-stacked monomer nucleic acids exhibiting Watson-Crick selectivity
LABORATOIRE AUTO-ASSEMBLAGE MOLÉCULAIRE - Gregory P Smith , Tommaso P Fraccia , Marco Todisco , Giuliano Zanchetta , Chenhui Zhu , Emily Hayden , Tommaso Bellini , Noel A Clark
ACS Nano - 115(33) E7658-E7664 - DOI: 10.1073/pnas.1721369115 - 2018
We demonstrate that nucleic acid (NA) mononucleotide triphosphates (dNTPs and rNTPs), at sufficiently high concentration and low temperature in aqueous solution, can exhibit a phase transition in which chromonic columnar liquid crystal ordering spontaneously appears. Remarkably, this polymer-free state exhibits, in a self-assembly of NA monomers, the key structural elements of biological nucleic acids, including: long-ranged duplex stacking of base pairs, complementarity-dependent partitioning of molecules, and Watson-Crick selectivity, such that, among all solutions of adenosine, cytosine, guanine, and thymine NTPs and their binary mixtures, duplex columnar ordering is most stable in the A-T and C-G combinations.
Liquid Crystal Ordering of Four-Base-Long DNA Oligomers with Both G–C and A–T Pairing
LABORATOIRE AUTO-ASSEMBLAGE MOLÉCULAIRE - Tommaso P. Fraccia , Gregory P. Smith , Noel A. Clark and Tommaso Bellini
CRYSTALS - 8(1) 5 - doi.org/10.3390/cryst8010005 - 2018
We report the liquid crystal (LC) ordering in an aqueous solution of four-base-long DNA oligomers 50-GCTA-30. In such systems, the formation of the chiral nematic (N*) LC phase is the result of a continuous self-assembly process in which double helix stability is achieved only through linear chaining of multiple DNA strands. The thermal stability of the aggregates and their LC phase diagram have been experimentally investigated, quantitatively interpreted with theoretical models and compared with recent results on four-base sequences with only G–C or only A–T pairing motifs. N* phase is found at GCTA concentration, cDNA, between 240 and 480 mg/mL and at temperature T < 30 C. The twist of the nematic director is found to be left-handed with pitch (p) in the optical range, increasing with cDNA and decreasing with T.

638 publications.