Pierre-alain Monnard | University of Southern Denmark (original) (raw)

Papers by Pierre-alain Monnard

Research paper thumbnail of Glass Microsphere-Supported Giant Vesicles as Tools for Observation of Self-reproduction of Lipid Boundaries

Growth and division experiments on phospholipid boundaries were carried out using glass microsphe... more Growth and division experiments on phospholipid boundaries were carried out using glass microsphere-supported phospholipids (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 for 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.

Research paper thumbnail of Primordial Membranes: More than simple container boundaries.

Cellular membranes, which are self-assembled bilayer structures mainly composed of lipids, protei... more Cellular membranes, which are self-assembled bilayer structures mainly composed of lipids, proteins and conjugated polysaccharides, are the defining feature of cell physiology. It is likely that the complexity of contemporary cells was preceded by simpler chemical systems or protocells during the various evolutionary stages that led from inanimate to living matter. It is also likely that primitive membranes played a similar role in protocell “physiology”. The composition of such ancestral membranes has been proposed as mixtures of single hydrocarbon chain amphiphiles, which are simpler versions of modern lipids. In this review, we discuss the origins, self-assembly patterns, potential functions of these amphiphiles, and their possible roles in protocell activities, as well as their possible evolution towards modern lipids.
2017, Curr. Opin. Chem. Biol., 40, 78-86.

Research paper thumbnail of Chemical Systems, chemical contiguity and the emergence of life.

Charting the emergence of living cells from inanimate matter remains an intensely challenging sci... more Charting the emergence of living cells from inanimate matter remains an intensely challenging scientific problem. The complexity of cell biochemical machinery with its exquisite intricacies hints at cells being the products of a long evolutionary process. Research on the emergence of life has long been focusing on specific, well-defined problems related to one aspect of cellular make-up, such as the formation of membranes, the build-up of information/catalytic apparatus. This approach is being gradually replaced by a more “systemic” approach that privileges processes inherent to complex chemical systems over specific isolated functional apparatuses. We will summarize the recent advances in system chemistry and show that chemical systems in the geochemical context imply a form a chemical contiguity in the syntheses of the various molecules, that precede modern biomolecules.
2017, Beilstein J. Org. Chem., 13, 1551-1563.

Research paper thumbnail of Synthesis of Lipophilic Guanine N-9 Derivatives: Membrane Anchoring of Nucleobases Tailored to Fatty Acid Vesicles

Bioconj. Chem., 2017

Covalent or non-covalent surface functionalization of soft matter structures is an important tool... more Covalent or non-covalent surface functionalization of soft matter structures is an important tool for tailoring their function and stability. Functionalized surfaces and nanoparticles have found numerous applications in drug delivery and diagnostics and new functionalization chemistry is continuously being developed in the discipline of bottom-up systems chemistry. The association of polar functional molecules, e.g. molecular recognition agents, with soft matter structures can be achieved by derivatization with alkyl chains, allowing non-covalent anchoring into amphiphilic membranes. Here, we report the synthesis of five new guanine-N9-derivatives bearing alkyl chains with different attachment chemistries, exploiting a synthesis pathway that allows a flexible choice of hydrophobic anchor moiety. In this study, these guanine derivatives were functionalized with C10-chains for insertion into decanoic acid bilayer structures, where both alkyl chain-length and attachment chemistry determined their interaction with the membrane. Incubation of these guanine conjugates, as solids, with a decanoic acid vesicle suspension showed that ether- and triazole-linked C10-anchors yielded an increased partitioning of the guanine derivative into the membranous phase compared to directly N9-linked saturated alkyl anchors. Decanoic acid vesicle membranes could be loaded with up to 5.5 mol% guanine-derivative, a six-fold increase over previous limits. Thus, anchor chemistries exhibiting favorable interactions with a bilayer’s hydrophilic surface can significantly increase the degree of structure functionalization.
2017, Bioconj. Chem., 28, 1893-1905

Research paper thumbnail of Permeability-driven selection in a semi-empirical protocell model: the roots of prebiotic systems evolution.

The origin-of-life problem has been traditionally conceived as the chemical challenge to find the... more The origin-of-life problem has been traditionally conceived as the chemical challenge to find the type of molecule and free-solution reaction dynamics that could have started Darwinian evolution. Different autocatalytic and ‘self-replicative’ molecular species have been extensively investigated, together with plausible synthetic pathways that might have led, abiotically, to such a minimalist scenario. However, in addition to molecular kinetics or molecular evolutionary dynamics, other physical and chemical constraints (like compartmentalization, differential diffusion, selective transport, osmotic forces, energetic couplings) could have been crucial for the cohesion, functional integration, and intrinsic stability/robustness of intermediate systems between chemistry and biology. These less acknowledged mechanisms of interaction and molecular control might have made the initial pathways to prebiotic systems evolution more intricate, but were surely essential for sustaining far-from-equilibrium chemical dynamics, given their functional relevance in all modern cells. Here we explore a protocellular scenario in which some of those additional constraints/mechanisms are addressed, demonstrating their ‘system-level’ implications. In particular, an experimental study on the permeability of prebiotic vesicle membranes composed of binary lipid mixtures allows us to construct a semi-empirical model where protocells are able to reproduce and undergo an evolutionary process based on their coupling with an internal chemistry that supports lipid synthesis.
Scientific Reports 2017, 7 (1), 3141.

Research paper thumbnail of On the Emergence of a Proto- Metabolism and the Assembly of Early Protocells

P rotocells are envisaged as encapsulated networks of catalytic polymers, such as RNAs, which are... more P rotocells are envisaged as encapsulated networks of catalytic polymers, such as RNAs, which are thought to have existed on the prebiotic Earth as precursors to contemporary biological cells. Such protocells were not "alive" in the way this word would apply to a contemporary unicellular organism. Rather, protocells represent a necessary evolutionary step toward those first forms of cellular life. In this review, we explore how chemicals synthesized by minerals or delivered by meteorites could have contributed to the emergence of the first protocells and could have supported these protocell's evolution towards primitive cellular life.

Research paper thumbnail of Taming Prebiotic Chemistry: The Role of Heterogeneous and Interfacial Catalysis in the Emergence of a Prebiotic Catalytic/Information Polymer System

Cellular life is based on interacting polymer networks that serve as catalysts, genetic informati... more Cellular life is based on interacting polymer networks that serve as catalysts, genetic information and structural molecules. The complexity of the DNA, RNA and protein biochemistry suggests that it must have been preceded by simpler systems. The RNA world hypothesis proposes RNA as the prime candidate for such a primal system. Even though this proposition has gained currency, its investigations have highlighted several challenges with respect to bulk aqueous media: (1) the synthesis of RNA monomers is difficult; (2) efficient pathways for monomer polymerization into functional RNAs and their subsequent, sequence-specific replication remain elusive; and (3) the evolution of the RNA function towards cellular metabolism in isolation is questionable in view of the chemical mixtures expected on the early Earth. This review will address the question of the possible roles of heterogeneous media and catalysis as drivers for the emergence of RNA-based polymer networks. We will show that this approach to non-enzymatic polymerizations of RNA from monomers and RNA evolution cannot only solve some issues encountered during reactions in bulk aqueous solutions, but may also explain the co-emergence of the various polymers indispensable for life in complex mixtures and their organization into primitive networks.

Research paper thumbnail of The origin of life and the potential role of soaps

Keywords: Single hydrocarbon chain amphiphile / Fatty acids / Prebiotic compartmentalization / Pr... more Keywords: Single hydrocarbon chain amphiphile / Fatty acids / Prebiotic compartmentalization / Protocell / Origin of life Summary Single chain amphiphiles, such as fatty acids and alkyl sulfates, have found industrial uses as emulsifying agents, lubricants, detergents and soaps. Fatty acids are also used as excipients and, because of their biochemical activity, even as active ingredients in drug formulations. The applications are often linked to their amphipathic characters, i.e., their capacity to self-assemble into micelles or reverse-micelles. Their capacity to form bilayer structures with properties comparable to cellular membranes is less exploited in the industry. However, this property is central in the development of chemical model systems, so called protocells, aiming at understanding how cellular life emerged on the early Earth, at the time abiotic environment, and could evolve toward contemporary cells.

Research paper thumbnail of Current Ideas about Prebiological Compartmentalization

Contemporary biological cells are highly sophisticated dynamic compartment systems which separate... more Contemporary biological cells are highly sophisticated dynamic compartment systems which separate an internal volume from the external medium through a boundary, which controls, in complex ways, the exchange of matter and energy between the cell's interior and the environment. Since such compartmentalization is a fundamental principle of all forms of life, scenarios have been elaborated about the emergence of prebiological compartments on early Earth, in particular about their likely structural characteristics and dynamic features. Chemical systems that consist of potentially prebiological compartments and chemical reaction networks have been designed to model pre-cellular systems. These systems are often referred to as " protocells ". Past and current protocell model systems are presented and compared. Since the prebiotic formation of cell-like compartments is directly linked to the prebiotic availability of compartment building blocks, a few aspects on the likely chemical inventory on the early Earth are also summarized.

Research paper thumbnail of Dynamics of fatty acid vesicles in response to pH stimuli

Soft Matter, 2015

We investigate the dynamics of decanoic acid/decanoate (DA) vesicles in response to pH stimuli. T... more We investigate the dynamics of decanoic acid/decanoate (DA) vesicles in response to pH stimuli. Two types of dynamic processes induced by the micro-injection of NaOH solutions are sequentially observed: deformations and topological transitions. In the deformation stage, DA vesicles show a series of shape deformations, i.e., prolate-oblate-stomatocyte-sphere. In the topological transition stage, spherical DA vesicles follow either of the two pathways, pore formation and vesicle fusion. The pH stimuli modify a critical aggregation concentration of DA molecules, which causes the solubilization of DA molecules in the outer leaflet of the vesicle bilayers. This solubilization decreases the outer surface area of the vesicle, thereby increasing surface tension. A kinetic model based on area difference elasticity theory can accurately describe the dynamics of DA vesicles triggered by pH stimuli.

Research paper thumbnail of Transmission of photo-catalytic function in a self-replicating chemical system: in situ amphiphile production over two protocell generations

† Electronic supplementary information (ESI) available: It contains a description of experiments,... more † Electronic supplementary information (ESI) available: It contains a description of experiments, additional data supporting the construction of the microspheres supported decanoic acid bilayers, the interactions between the both ruthenium complex and the precursor lipid with the supported bilayers. There are additional figures and micrographs of the growth and division process of the system. See

Research paper thumbnail of Self-Assembly of Phosphate Amphiphiles in Mixtures of Prebiotically Plausible Surfactants

The spontaneous formation of closed bilayer structures from prebiotically plausible amphiphiles i... more The spontaneous formation of closed bilayer structures from prebiotically plausible amphiphiles is an essential requirement for the emergence of early cells on prebiotic Earth. The sources of amphiphiles could have been both endo-and exogenous (accretion of meteorite carbonaceous material or interstellar dust particles). Among all prebiotic possible amphiphile candidates, those containing phosphate are the least investigated species because their self-assembly occurs in a seemingly too narrow range of conditions. The self-assembly of simple phosphate amphiphiles should, however, be of great interest, as contemporary membranes predominantly contain phospholipids. In contrast to common expectations, we show that these amphiphiles can be easily synthesized under prebiotically plausible environmental conditions and can efficiently form bilayer structures in the presence of various co-surfactants across a large range of pH values. Vesiculation was even observed in crude reaction mixtures that contained 1-decanol as the amphiphile precursor. The two best co-surfactants promoted vesicle formation over the entire pH range in aqueous solutions. Expanding the pH range where bilayer membranes self-assemble and remain intact is a prerequisite for the emergence of early cell-like compartments and their preservation under fluctuating environmental conditions. These mixed bilayers also retained small charged solutes, such as dyes. These results demonstrate that alkyl phosphate amphiphiles might have played a significant role as early compartment building blocks.

Research paper thumbnail of Functionalization of Fatty Acid Vesicles through Newly Synthesized Bolaamphiphile–DNA Conjugates

Bioconjugate Chemistry, 2014

The surface functionalization of fatty acid vesicles will allow their use as nanoreactors for com... more The surface functionalization of fatty acid vesicles will allow their use as nanoreactors for complex chemistry. In this report, the tethering of several DNA conjugates to decanoic acid vesicles for molecular recognition and synthetic purposes was explored. Due to the highly dynamic nature of these structures, only one novel bola-amphiphile DNA conjugate could interact efficiently with or spontaneously pierce into the vesicle bilayers without jeopardizing their self-assembly or stability. This molecule was synthesized via a Cu(I)-catalyzed [3 + 2] azide− alkyne cycloaddition (click reaction), and consists of a single hydrocarbon chain of 20 carbons having on one end a triazole group linked to the 5′-phosphate of the nucleic acid and on the other side a hydroxyl-group. Its insertion was so effective that a fluorescent label on the DNA complementary to the conjugate could be used to visualize fatty acid structures.

Research paper thumbnail of Formation of RNA Phosphodiester Bond by Histidine- Containing Dipeptides

Research paper thumbnail of Sliding over the Blocks in Enzyme-Free RNA Copying – One-Pot Primer Extension in Ice

Template-directed polymerization of RNA in the absence of enzymes is the basis for an information... more Template-directed polymerization of RNA in the absence of enzymes is the basis for an information transfer in the 'RNA-world' hypothesis and in novel nucleic acid based technology. Previous investigations established that only cytidine rich strands are efficient templates in bulk aqueous solutions while a few specific sequences completely block the extension of hybridized primers. We show that a eutectic water/ice system can support Pb 2+ /Mg 2+-ion catalyzed extension of a primer across such sequences, i.e. AA, AU and AG, in a one-pot synthesis. Using mixtures of imidazole activated nucleotide 5′-monophosphates, the two first " blocking " residues could be passed during template-directed polymerization, i.e., formation of triply extended products containing a high fraction of faithful copies was demonstrated. Across the AG sequence, a mismatch sequence was formed in similar amounts to the correct product due to U·G wobble pairing. Thus, the template-directed extension occurs both across pyrimidine and purine rich sequences and insertions of pyrimidines did not inhibit the subsequent insertions. Products were mainly formed with 2′-5′-phosphodiester linkages, however, the abundance of 3′–5′-linkages was higher than previously reported for pyrimidine insertions. When enzyme-free, template-directed RNA polymerization is performed in a eutectic water ice environment, various intrinsic reaction limitations observed in bulk solution can then be overcome.

Research paper thumbnail of Viability Conditions for a Compartmentalized Protometabolic System: A Semi-Empirical Approach

In this work we attempt to find out the extent to which realistic prebiotic compartments, such as... more In this work we attempt to find out the extent to which realistic prebiotic compartments, such as fatty acid vesicles, would constrain the chemical network dynamics that could have sustained a minimal form of metabolism. We combine experimental and simulation results to establish the conditions under which a reaction network with a catalytically closed organization (more specifically, an (M,R)-system) would overcome the potential problem of self-suffocation that arises from the limited accessibility of nutrients to its internal reaction domain. The relationship between the permeability of the membrane, the lifetime of the key catalysts and their efficiency (reaction rate enhancement) turns out to be critical. In particular, we show how permeability values constrain the characteristic time scale of the bounded protometabolic processes. From this concrete and illustrative example we finally extend the discussion to a wider evolutionary context.

Research paper thumbnail of Phototriggered DNA Phosphoramidate Ligation in a Tandem 5′- Amine Deprotection/3′-Imidazole Activated Phosphate Coupling Reaction

We report the preparation and use of an N-methyl picolinium carbamate protecting group for applic... more We report the preparation and use of an N-methyl picolinium carbamate protecting group for applications in a phototriggered nonenzymatic DNA phosphoramidate ligation reaction. Selective 5′-amino protection of a modified 13-mer oligonucleotide is achieved in aqueous solution by reaction with an N-methyl-4-picolinium carbonyl imidazole triflate protecting group precursor. Deprotection is carried out by photoinduced electron transfer from Ru(bpy) 3 2+ using visible light photolysis and ascorbic acid as a sacrificial electron donor. Phototriggered 5′-amino oligonucleotide deprotection is used to initiate a nonenzymatic ligation of the 13-mer to an imidazole activated 3′-phospho-hairpin template to generate a ligated product with a phosphoramidate linkage. We demonstrate that this methodology offers a simple way to exert control over reaction initiation and rates in nonenzymatic DNA ligation for potential applications in the study of model protocellular systems and prebiotic nucleic acid synthesis.

Research paper thumbnail of Non-enzymatic Polymerization of Nucleic Acids from Monomers: Monomer Self- Condensation and Template-Directed Reactions

This review deals with the state-of-the-art techniques in non-enzymatic nucleic acid condensation... more This review deals with the state-of-the-art techniques in non-enzymatic nucleic acid condensation from monomers. In particular , the procedures called monomer self-condensation and template-directed monomer condensation are described, which have been developed to achieve efficient synthesis of long nucleic acid polymers or to sequence-specifically amplify nucleic acid polymers, respectively. Starting from molecular requirements, details of the polymerization mechanisms and strategies are first presented and then compared. Finally, we discuss the relevance of these strategies to the investigation of possible early molecular information systems on the prebiotic earth and the development of novel synthetic methodologies for nucleic acids.

Research paper thumbnail of Prebiotically relevant mixed fatty acid vesicles support anionic solute encapsulation and photochemically catalyzed trans-membrane charge transport

Chemical Science, 2011

The spontaneous assembly of amphiphile-based compartments in aqueous solution is widely viewed as... more The spontaneous assembly of amphiphile-based compartments in aqueous solution is widely viewed as a key step in models for the abiotic formation of primitive cell-like structures. Proposed organic components for such systems consist of mixed short chain fatty acids (FA) and polycyclic aromatic hydrocarbon (PAH) species, the composition of which have been modeled after organic extracts of carbonaceous meteorites. Self-assembly of amphiphiles from these extracts into aqueous suspensions of bilayer structures was long ago demonstrated, although little has since been reported concerning the stability and potential functionality of these complex mixtures. This work explores the thermodynamic and kinetic stability of vesicles prepared from complex mixtures of short chain FA species (CH 3 COOH-C 9 H 19 COOH) with membrane solubilized PAH species. Critical vesicle concentration measurements and ultrafiltration analyses of decanoic acid in the presence of other shorter chain FA species indicate the formation of mixed component vesicle phases composed mainly of C 10 -C 8 FA components. An electrostatic barrier to trans-membrane diffusion of negative charges allows observation of stably encapsulated poly-anionic solutes inside these vesicles. As a model for primitive energy transduction, trans-membrane electron transfer between EDTA and encapsulated ferricyanide was demonstrated, driven catalytically via PAH photochemistry without substantial decomposition of the chromophores or vesicles. These results indicate a plausible role for compartmentalization and catalysis by short chain fatty acids and PAH species in prebiotic vesicle-encapsulated systems.

Research paper thumbnail of Primitive Membrane Formation, Characteristics and Roles in the Emergent Properties of a Protocell

Entropy, 2011

All contemporary living cells are composed of a collection of self-assembled molecular elements t... more All contemporary living cells are composed of a collection of self-assembled molecular elements that by themselves are non-living but through the creation of a network exhibit the emergent properties of self-maintenance, self-reproduction, and evolution. This short review deals with the on-going research that aims at either understanding how life emerged on the early Earth or creating artificial cells assembled from a collection of small chemicals. In particular, this article focuses on the work carried out to investigate how self-assembled compartments, such as amphiphile and lipid vesicles, contribute to the emergent properties as part of a greater system.

Research paper thumbnail of Glass Microsphere-Supported Giant Vesicles as Tools for Observation of Self-reproduction of Lipid Boundaries

Growth and division experiments on phospholipid boundaries were carried out using glass microsphe... more Growth and division experiments on phospholipid boundaries were carried out using glass microsphere-supported phospholipids (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 for 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.

Research paper thumbnail of Primordial Membranes: More than simple container boundaries.

Cellular membranes, which are self-assembled bilayer structures mainly composed of lipids, protei... more Cellular membranes, which are self-assembled bilayer structures mainly composed of lipids, proteins and conjugated polysaccharides, are the defining feature of cell physiology. It is likely that the complexity of contemporary cells was preceded by simpler chemical systems or protocells during the various evolutionary stages that led from inanimate to living matter. It is also likely that primitive membranes played a similar role in protocell “physiology”. The composition of such ancestral membranes has been proposed as mixtures of single hydrocarbon chain amphiphiles, which are simpler versions of modern lipids. In this review, we discuss the origins, self-assembly patterns, potential functions of these amphiphiles, and their possible roles in protocell activities, as well as their possible evolution towards modern lipids.
2017, Curr. Opin. Chem. Biol., 40, 78-86.

Research paper thumbnail of Chemical Systems, chemical contiguity and the emergence of life.

Charting the emergence of living cells from inanimate matter remains an intensely challenging sci... more Charting the emergence of living cells from inanimate matter remains an intensely challenging scientific problem. The complexity of cell biochemical machinery with its exquisite intricacies hints at cells being the products of a long evolutionary process. Research on the emergence of life has long been focusing on specific, well-defined problems related to one aspect of cellular make-up, such as the formation of membranes, the build-up of information/catalytic apparatus. This approach is being gradually replaced by a more “systemic” approach that privileges processes inherent to complex chemical systems over specific isolated functional apparatuses. We will summarize the recent advances in system chemistry and show that chemical systems in the geochemical context imply a form a chemical contiguity in the syntheses of the various molecules, that precede modern biomolecules.
2017, Beilstein J. Org. Chem., 13, 1551-1563.

Research paper thumbnail of Synthesis of Lipophilic Guanine N-9 Derivatives: Membrane Anchoring of Nucleobases Tailored to Fatty Acid Vesicles

Bioconj. Chem., 2017

Covalent or non-covalent surface functionalization of soft matter structures is an important tool... more Covalent or non-covalent surface functionalization of soft matter structures is an important tool for tailoring their function and stability. Functionalized surfaces and nanoparticles have found numerous applications in drug delivery and diagnostics and new functionalization chemistry is continuously being developed in the discipline of bottom-up systems chemistry. The association of polar functional molecules, e.g. molecular recognition agents, with soft matter structures can be achieved by derivatization with alkyl chains, allowing non-covalent anchoring into amphiphilic membranes. Here, we report the synthesis of five new guanine-N9-derivatives bearing alkyl chains with different attachment chemistries, exploiting a synthesis pathway that allows a flexible choice of hydrophobic anchor moiety. In this study, these guanine derivatives were functionalized with C10-chains for insertion into decanoic acid bilayer structures, where both alkyl chain-length and attachment chemistry determined their interaction with the membrane. Incubation of these guanine conjugates, as solids, with a decanoic acid vesicle suspension showed that ether- and triazole-linked C10-anchors yielded an increased partitioning of the guanine derivative into the membranous phase compared to directly N9-linked saturated alkyl anchors. Decanoic acid vesicle membranes could be loaded with up to 5.5 mol% guanine-derivative, a six-fold increase over previous limits. Thus, anchor chemistries exhibiting favorable interactions with a bilayer’s hydrophilic surface can significantly increase the degree of structure functionalization.
2017, Bioconj. Chem., 28, 1893-1905

Research paper thumbnail of Permeability-driven selection in a semi-empirical protocell model: the roots of prebiotic systems evolution.

The origin-of-life problem has been traditionally conceived as the chemical challenge to find the... more The origin-of-life problem has been traditionally conceived as the chemical challenge to find the type of molecule and free-solution reaction dynamics that could have started Darwinian evolution. Different autocatalytic and ‘self-replicative’ molecular species have been extensively investigated, together with plausible synthetic pathways that might have led, abiotically, to such a minimalist scenario. However, in addition to molecular kinetics or molecular evolutionary dynamics, other physical and chemical constraints (like compartmentalization, differential diffusion, selective transport, osmotic forces, energetic couplings) could have been crucial for the cohesion, functional integration, and intrinsic stability/robustness of intermediate systems between chemistry and biology. These less acknowledged mechanisms of interaction and molecular control might have made the initial pathways to prebiotic systems evolution more intricate, but were surely essential for sustaining far-from-equilibrium chemical dynamics, given their functional relevance in all modern cells. Here we explore a protocellular scenario in which some of those additional constraints/mechanisms are addressed, demonstrating their ‘system-level’ implications. In particular, an experimental study on the permeability of prebiotic vesicle membranes composed of binary lipid mixtures allows us to construct a semi-empirical model where protocells are able to reproduce and undergo an evolutionary process based on their coupling with an internal chemistry that supports lipid synthesis.
Scientific Reports 2017, 7 (1), 3141.

Research paper thumbnail of On the Emergence of a Proto- Metabolism and the Assembly of Early Protocells

P rotocells are envisaged as encapsulated networks of catalytic polymers, such as RNAs, which are... more P rotocells are envisaged as encapsulated networks of catalytic polymers, such as RNAs, which are thought to have existed on the prebiotic Earth as precursors to contemporary biological cells. Such protocells were not "alive" in the way this word would apply to a contemporary unicellular organism. Rather, protocells represent a necessary evolutionary step toward those first forms of cellular life. In this review, we explore how chemicals synthesized by minerals or delivered by meteorites could have contributed to the emergence of the first protocells and could have supported these protocell's evolution towards primitive cellular life.

Research paper thumbnail of Taming Prebiotic Chemistry: The Role of Heterogeneous and Interfacial Catalysis in the Emergence of a Prebiotic Catalytic/Information Polymer System

Cellular life is based on interacting polymer networks that serve as catalysts, genetic informati... more Cellular life is based on interacting polymer networks that serve as catalysts, genetic information and structural molecules. The complexity of the DNA, RNA and protein biochemistry suggests that it must have been preceded by simpler systems. The RNA world hypothesis proposes RNA as the prime candidate for such a primal system. Even though this proposition has gained currency, its investigations have highlighted several challenges with respect to bulk aqueous media: (1) the synthesis of RNA monomers is difficult; (2) efficient pathways for monomer polymerization into functional RNAs and their subsequent, sequence-specific replication remain elusive; and (3) the evolution of the RNA function towards cellular metabolism in isolation is questionable in view of the chemical mixtures expected on the early Earth. This review will address the question of the possible roles of heterogeneous media and catalysis as drivers for the emergence of RNA-based polymer networks. We will show that this approach to non-enzymatic polymerizations of RNA from monomers and RNA evolution cannot only solve some issues encountered during reactions in bulk aqueous solutions, but may also explain the co-emergence of the various polymers indispensable for life in complex mixtures and their organization into primitive networks.

Research paper thumbnail of The origin of life and the potential role of soaps

Keywords: Single hydrocarbon chain amphiphile / Fatty acids / Prebiotic compartmentalization / Pr... more Keywords: Single hydrocarbon chain amphiphile / Fatty acids / Prebiotic compartmentalization / Protocell / Origin of life Summary Single chain amphiphiles, such as fatty acids and alkyl sulfates, have found industrial uses as emulsifying agents, lubricants, detergents and soaps. Fatty acids are also used as excipients and, because of their biochemical activity, even as active ingredients in drug formulations. The applications are often linked to their amphipathic characters, i.e., their capacity to self-assemble into micelles or reverse-micelles. Their capacity to form bilayer structures with properties comparable to cellular membranes is less exploited in the industry. However, this property is central in the development of chemical model systems, so called protocells, aiming at understanding how cellular life emerged on the early Earth, at the time abiotic environment, and could evolve toward contemporary cells.

Research paper thumbnail of Current Ideas about Prebiological Compartmentalization

Contemporary biological cells are highly sophisticated dynamic compartment systems which separate... more Contemporary biological cells are highly sophisticated dynamic compartment systems which separate an internal volume from the external medium through a boundary, which controls, in complex ways, the exchange of matter and energy between the cell's interior and the environment. Since such compartmentalization is a fundamental principle of all forms of life, scenarios have been elaborated about the emergence of prebiological compartments on early Earth, in particular about their likely structural characteristics and dynamic features. Chemical systems that consist of potentially prebiological compartments and chemical reaction networks have been designed to model pre-cellular systems. These systems are often referred to as " protocells ". Past and current protocell model systems are presented and compared. Since the prebiotic formation of cell-like compartments is directly linked to the prebiotic availability of compartment building blocks, a few aspects on the likely chemical inventory on the early Earth are also summarized.

Research paper thumbnail of Dynamics of fatty acid vesicles in response to pH stimuli

Soft Matter, 2015

We investigate the dynamics of decanoic acid/decanoate (DA) vesicles in response to pH stimuli. T... more We investigate the dynamics of decanoic acid/decanoate (DA) vesicles in response to pH stimuli. Two types of dynamic processes induced by the micro-injection of NaOH solutions are sequentially observed: deformations and topological transitions. In the deformation stage, DA vesicles show a series of shape deformations, i.e., prolate-oblate-stomatocyte-sphere. In the topological transition stage, spherical DA vesicles follow either of the two pathways, pore formation and vesicle fusion. The pH stimuli modify a critical aggregation concentration of DA molecules, which causes the solubilization of DA molecules in the outer leaflet of the vesicle bilayers. This solubilization decreases the outer surface area of the vesicle, thereby increasing surface tension. A kinetic model based on area difference elasticity theory can accurately describe the dynamics of DA vesicles triggered by pH stimuli.

Research paper thumbnail of Transmission of photo-catalytic function in a self-replicating chemical system: in situ amphiphile production over two protocell generations

† Electronic supplementary information (ESI) available: It contains a description of experiments,... more † Electronic supplementary information (ESI) available: It contains a description of experiments, additional data supporting the construction of the microspheres supported decanoic acid bilayers, the interactions between the both ruthenium complex and the precursor lipid with the supported bilayers. There are additional figures and micrographs of the growth and division process of the system. See

Research paper thumbnail of Self-Assembly of Phosphate Amphiphiles in Mixtures of Prebiotically Plausible Surfactants

The spontaneous formation of closed bilayer structures from prebiotically plausible amphiphiles i... more The spontaneous formation of closed bilayer structures from prebiotically plausible amphiphiles is an essential requirement for the emergence of early cells on prebiotic Earth. The sources of amphiphiles could have been both endo-and exogenous (accretion of meteorite carbonaceous material or interstellar dust particles). Among all prebiotic possible amphiphile candidates, those containing phosphate are the least investigated species because their self-assembly occurs in a seemingly too narrow range of conditions. The self-assembly of simple phosphate amphiphiles should, however, be of great interest, as contemporary membranes predominantly contain phospholipids. In contrast to common expectations, we show that these amphiphiles can be easily synthesized under prebiotically plausible environmental conditions and can efficiently form bilayer structures in the presence of various co-surfactants across a large range of pH values. Vesiculation was even observed in crude reaction mixtures that contained 1-decanol as the amphiphile precursor. The two best co-surfactants promoted vesicle formation over the entire pH range in aqueous solutions. Expanding the pH range where bilayer membranes self-assemble and remain intact is a prerequisite for the emergence of early cell-like compartments and their preservation under fluctuating environmental conditions. These mixed bilayers also retained small charged solutes, such as dyes. These results demonstrate that alkyl phosphate amphiphiles might have played a significant role as early compartment building blocks.

Research paper thumbnail of Functionalization of Fatty Acid Vesicles through Newly Synthesized Bolaamphiphile–DNA Conjugates

Bioconjugate Chemistry, 2014

The surface functionalization of fatty acid vesicles will allow their use as nanoreactors for com... more The surface functionalization of fatty acid vesicles will allow their use as nanoreactors for complex chemistry. In this report, the tethering of several DNA conjugates to decanoic acid vesicles for molecular recognition and synthetic purposes was explored. Due to the highly dynamic nature of these structures, only one novel bola-amphiphile DNA conjugate could interact efficiently with or spontaneously pierce into the vesicle bilayers without jeopardizing their self-assembly or stability. This molecule was synthesized via a Cu(I)-catalyzed [3 + 2] azide− alkyne cycloaddition (click reaction), and consists of a single hydrocarbon chain of 20 carbons having on one end a triazole group linked to the 5′-phosphate of the nucleic acid and on the other side a hydroxyl-group. Its insertion was so effective that a fluorescent label on the DNA complementary to the conjugate could be used to visualize fatty acid structures.

Research paper thumbnail of Formation of RNA Phosphodiester Bond by Histidine- Containing Dipeptides

Research paper thumbnail of Sliding over the Blocks in Enzyme-Free RNA Copying – One-Pot Primer Extension in Ice

Template-directed polymerization of RNA in the absence of enzymes is the basis for an information... more Template-directed polymerization of RNA in the absence of enzymes is the basis for an information transfer in the 'RNA-world' hypothesis and in novel nucleic acid based technology. Previous investigations established that only cytidine rich strands are efficient templates in bulk aqueous solutions while a few specific sequences completely block the extension of hybridized primers. We show that a eutectic water/ice system can support Pb 2+ /Mg 2+-ion catalyzed extension of a primer across such sequences, i.e. AA, AU and AG, in a one-pot synthesis. Using mixtures of imidazole activated nucleotide 5′-monophosphates, the two first " blocking " residues could be passed during template-directed polymerization, i.e., formation of triply extended products containing a high fraction of faithful copies was demonstrated. Across the AG sequence, a mismatch sequence was formed in similar amounts to the correct product due to U·G wobble pairing. Thus, the template-directed extension occurs both across pyrimidine and purine rich sequences and insertions of pyrimidines did not inhibit the subsequent insertions. Products were mainly formed with 2′-5′-phosphodiester linkages, however, the abundance of 3′–5′-linkages was higher than previously reported for pyrimidine insertions. When enzyme-free, template-directed RNA polymerization is performed in a eutectic water ice environment, various intrinsic reaction limitations observed in bulk solution can then be overcome.

Research paper thumbnail of Viability Conditions for a Compartmentalized Protometabolic System: A Semi-Empirical Approach

In this work we attempt to find out the extent to which realistic prebiotic compartments, such as... more In this work we attempt to find out the extent to which realistic prebiotic compartments, such as fatty acid vesicles, would constrain the chemical network dynamics that could have sustained a minimal form of metabolism. We combine experimental and simulation results to establish the conditions under which a reaction network with a catalytically closed organization (more specifically, an (M,R)-system) would overcome the potential problem of self-suffocation that arises from the limited accessibility of nutrients to its internal reaction domain. The relationship between the permeability of the membrane, the lifetime of the key catalysts and their efficiency (reaction rate enhancement) turns out to be critical. In particular, we show how permeability values constrain the characteristic time scale of the bounded protometabolic processes. From this concrete and illustrative example we finally extend the discussion to a wider evolutionary context.

Research paper thumbnail of Phototriggered DNA Phosphoramidate Ligation in a Tandem 5′- Amine Deprotection/3′-Imidazole Activated Phosphate Coupling Reaction

We report the preparation and use of an N-methyl picolinium carbamate protecting group for applic... more We report the preparation and use of an N-methyl picolinium carbamate protecting group for applications in a phototriggered nonenzymatic DNA phosphoramidate ligation reaction. Selective 5′-amino protection of a modified 13-mer oligonucleotide is achieved in aqueous solution by reaction with an N-methyl-4-picolinium carbonyl imidazole triflate protecting group precursor. Deprotection is carried out by photoinduced electron transfer from Ru(bpy) 3 2+ using visible light photolysis and ascorbic acid as a sacrificial electron donor. Phototriggered 5′-amino oligonucleotide deprotection is used to initiate a nonenzymatic ligation of the 13-mer to an imidazole activated 3′-phospho-hairpin template to generate a ligated product with a phosphoramidate linkage. We demonstrate that this methodology offers a simple way to exert control over reaction initiation and rates in nonenzymatic DNA ligation for potential applications in the study of model protocellular systems and prebiotic nucleic acid synthesis.

Research paper thumbnail of Non-enzymatic Polymerization of Nucleic Acids from Monomers: Monomer Self- Condensation and Template-Directed Reactions

This review deals with the state-of-the-art techniques in non-enzymatic nucleic acid condensation... more This review deals with the state-of-the-art techniques in non-enzymatic nucleic acid condensation from monomers. In particular , the procedures called monomer self-condensation and template-directed monomer condensation are described, which have been developed to achieve efficient synthesis of long nucleic acid polymers or to sequence-specifically amplify nucleic acid polymers, respectively. Starting from molecular requirements, details of the polymerization mechanisms and strategies are first presented and then compared. Finally, we discuss the relevance of these strategies to the investigation of possible early molecular information systems on the prebiotic earth and the development of novel synthetic methodologies for nucleic acids.

Research paper thumbnail of Prebiotically relevant mixed fatty acid vesicles support anionic solute encapsulation and photochemically catalyzed trans-membrane charge transport

Chemical Science, 2011

The spontaneous assembly of amphiphile-based compartments in aqueous solution is widely viewed as... more The spontaneous assembly of amphiphile-based compartments in aqueous solution is widely viewed as a key step in models for the abiotic formation of primitive cell-like structures. Proposed organic components for such systems consist of mixed short chain fatty acids (FA) and polycyclic aromatic hydrocarbon (PAH) species, the composition of which have been modeled after organic extracts of carbonaceous meteorites. Self-assembly of amphiphiles from these extracts into aqueous suspensions of bilayer structures was long ago demonstrated, although little has since been reported concerning the stability and potential functionality of these complex mixtures. This work explores the thermodynamic and kinetic stability of vesicles prepared from complex mixtures of short chain FA species (CH 3 COOH-C 9 H 19 COOH) with membrane solubilized PAH species. Critical vesicle concentration measurements and ultrafiltration analyses of decanoic acid in the presence of other shorter chain FA species indicate the formation of mixed component vesicle phases composed mainly of C 10 -C 8 FA components. An electrostatic barrier to trans-membrane diffusion of negative charges allows observation of stably encapsulated poly-anionic solutes inside these vesicles. As a model for primitive energy transduction, trans-membrane electron transfer between EDTA and encapsulated ferricyanide was demonstrated, driven catalytically via PAH photochemistry without substantial decomposition of the chromophores or vesicles. These results indicate a plausible role for compartmentalization and catalysis by short chain fatty acids and PAH species in prebiotic vesicle-encapsulated systems.

Research paper thumbnail of Primitive Membrane Formation, Characteristics and Roles in the Emergent Properties of a Protocell

Entropy, 2011

All contemporary living cells are composed of a collection of self-assembled molecular elements t... more All contemporary living cells are composed of a collection of self-assembled molecular elements that by themselves are non-living but through the creation of a network exhibit the emergent properties of self-maintenance, self-reproduction, and evolution. This short review deals with the on-going research that aims at either understanding how life emerged on the early Earth or creating artificial cells assembled from a collection of small chemicals. In particular, this article focuses on the work carried out to investigate how self-assembled compartments, such as amphiphile and lipid vesicles, contribute to the emergent properties as part of a greater system.