One Step up the Ladder of Prebiotic Complexity: Formation of Nonrandom Linear Polypeptides from Binary Systems of Amino Acids on Silica.

Evidence for the formation of linear oligopeptides with nonrandom sequences from mixtures of amino acids coadsorbed on silica and submitted to a simple thermal activation is presented. The amino acid couples (glutamic acid+leucine) and (aspartic acid+valine) were deposited on a fumed silica and submitted to a single heating step at moderate temperature. The evolution of the systems was characterized by X-ray diffraction, infrared spectroscopy, thermosgravimetric analysis, HPLC, and electrospray ionization mass spectrometry (ESI-MS). Evidence for the formation of amide bonds was found in all systems studied. While the products of single amino acids activation on silica could be considered as evolutionary dead ends, (glutamic acid+leucine) and, at to some extent, (aspartic acid+valine) gave rise to the high yield formation of linear peptides up to the hexamers. Oligopeptides of such length have not been observed before in surface polymerization scenarios (unless the amino acids had been deposited by chemical vapor deposition, which is not realistic in a prebiotic environment). Furthermore, not all possible amino acid sequences were present in the activation products, which is indicative of polymerization selectivity. These results are promising for origins of life studies because they suggest the emergence of nonrandom biopolymers in a simple prebiotic scenario.

Phosphoribosyl Pyrophosphate: A Molecular Vestige of the Origin of Life on Minerals.

In this contribution, we report the formation under prebiotic conditions of phosphoribosyl pyrophosphate (PRPP) as a molecular precursor in the one-pot synthesis of a canonical nucleotide, namely adenosine monophosphate (AMP) from its building blocks (KH2 PO4 or Pi , adenine, and d-ribose), on a fumed silica surface. The on-the-rocks approach has been successfully applied to the simultaneous phosphorylation and glycosylation of ribose. The one-pot formation mechanism of AMP involves a two-step pathway via an activated intermediate, namely PRPP, obtained by multiple ribose phosphorylations upon mild thermal activation.

Thermal Behavior of d-Ribose Adsorbed on Silica: Effect of Inorganic Salt Coadsorption and Significance for Prebiotic Chemistry.

Understanding ribose reactivity is a crucial step in the "RNA world" scenario because this molecule is a component of all extant nucleotides that make up RNA. In solution, ribose is unstable and susceptible to thermal destruction. We examined how ribose behaves upon thermal activation when adsorbed on silica, either alone or with the coadsorption of inorganic salts (MgCl2 , CaCl2 , SrCl2 , CuCl2 , FeCl2 , FeCl3 , ZnCl2 ). A combination of 13 C NMR, in situ IR, and TGA analyses revealed a variety of phenomena. When adsorbed alone, ribose remains stable up to 150 °C, at which point ring opening is observed, together with minor oxidation to a lactone. All the metal salts studied showed specific interactions with ribose after dehydration, resulting in the formation of polydentate metal ion complexes. Anomeric equilibria were affected, generally favoring ribofuranoses. Zn2+ stabilized ribose up to higher temperatures than bare silica (180 to 200 °C). Most other cations had an adverse effect on ribose stability, with ring opening already upon drying at 70 °C. In addition, alkaline earth cations catalyzed the dehydration of ribose to furfural and, to variable degrees, its further decarbonylation to furan. Transition-metal ions with open d-shells took part in redox reactions with ribose, either as reagents or as catalysts. These results allow the likelihood of prebiotic chemistry scenarios to be evaluated, and may also be of interest for the valorization of biomass-derived carbohydrates by heterogeneous catalysis.

Selective Uptake of Alkaline Earth Metals by Cyanobacteria Forming Intracellular Carbonates.

The uptakes of calcium (Ca), strontium (Sr), and barium (Ba) by two cyanobacterial strains, Cyanothece sp. PCC7425 and Gloeomargarita lithophora, both forming intracellular carbonates, were investigated in laboratory cultures. In the culture medium BG-11 amended with 250 µM Ca and 50 or 250 µM Sr and Ba, G. lithophora accumulated first Ba, then Sr, and finally Ca. Sr and Ba were completely accumulated by G. lithophora cells at rates between 0.02 and 0.10 fmol h-1 cell-1 and down to extracellular concentrations below the detection limits of inductively coupled plasma atomic emission spectroscopy. Accumulation of Sr and Ba did not affect the growth rate of the strain. This sequential accumulation occurred mostly intracellularly within polyphosphate and carbonate granules and resulted in the formation of core-shell structures in carbonates. In contrast, Cyanothece sp. PCC7425 showed neither a preferential accumulation of heavier alkaline earth metals nor core-shell structures in the carbonates. This indicated that fractionation between alkaline earth metals was not inherent to intracellularly calcifying cyanobacteria but was likely a genetically based trait of G. lithophora. Overall, the capability of G. lithophora to sequester preferentially Sr and Ba at high rates may be of considerable interest for designing new remediation strategies and better understanding the geochemical cycles of these elements.

Non-biological selectivity in amino acids polymerization on TiO2 nanoparticles.

For the first, time a strong selectivity is evidenced in inorganic peptide synthesis. When an equimolar mixture of Ala and Arg monomers is added to the synthesis medium of TiO2 nanoparticles from Ti(IV) isopropoxide in benzyl alcohol, the Ala-Arg dipeptide is observed by ¹³C NMR in the resulting solid, at the exclusion of other dipeptides or higher peptides.

A comparative study of the catalysis of peptide bond formation by oxide surfaces.

It is well-known that amino acids deposited on some inorganic oxides undergo peptidic condensation. It is seldom realised however that a large diversity of behaviours can be observed in such systems. Here we use the apparently simple case of glycine-non-porous silica as a reference system, in which glycine (Gly) dimerisation to diketopiperazine (DKP) is easy to evidence, especially when using TG in combination with NMR. We then proceed to compare it with other AA deposited on the same support on the one hand, with Gly deposited on other mineral surfaces on the other hand. In a final section, we provide more detailed mechanistic information on the glycine condensation process on silica, including kinetic data and a (13)C solid-state NMR follow up of the species at various stages of thermal condensation. The best mechanism to rationalise these data involves a crucial step of isomerisation from zwitterion to neutral glycine, and the participation of several distinct types of surface sites probably consisting of silanol ensembles.

Formation of activated biomolecules by condensation on mineral surfaces--a comparison of peptide bond formation and phosphate condensation.

Many studies have reported condensation reactions of prebiotic molecules, such as the formation of peptide bonds between amino acids, to occur to some degree on mineral surfaces. We have studied several such reactions on the same divided silica. When drying steps are applied, the equilibria of peptide formation from glycine, and polyphosphate formation from monophosphate, are displaced to the right because these reactions are dehydrating condensations, accompanied by the emission of water. In contrast, the equilibrium of AMP dismutation is not significantly favored by drying. The silica surface plays little role (if any) in the thermochemistry of the condensation reactions, but is does play a significant kinetic role by acting as a catalyst, lowering the condensation temperatures with respect to bulk solids. Of course, the surface also catalyzes the inverse hydrolysis reactions.

In Situ Raman Spectroscopy Monitoring of Material Changes During Proton Irradiation.

Organic molecules are prime targets in the search for life on other planetary bodies in the Solar System. Understanding their preservation potential and detectability after ionic irradiation, with fluences potentially representing those received for several millions to billions of years at Mars or in interplanetary space, is a crucial goal for astrobiology research. In order to be able to perform in situ characterization of such organic molecules under ionic irradiation in the near future, a feasibility experiment was performed with polymer test samples to validate the optical configuration and the irradiation chamber geometry. We present here a Raman in situ investigation of the evolution of a series of polymers during proton irradiation. To achieve this goal, a new type of Raman optical probe was designed, which documented that proton irradiation (with a final fluence of 3.1014 at·cm-2) leads to an increase in the background level of the signal, potentially explained by the scission of the polymeric chains and by atom displacements creating defects in the materials. To improve the setup further, a micro-Raman probe and a temperature-controlled sample holder are under development to provide higher spectral and spatial resolutions (by reducing the depth of field and laser spot size), to permit Raman mapping as well as to avoid any thermal effects.

Kinetic analyses and performance of a colloidal magnetic nanoparticle based immunoassay dedicated to allergy diagnosis.

In this paper, we demonstrate the possibility to use magnetic nanoparticles as immunosupports for allergy diagnosis. Most immunoassays used for immunosupports and clinical diagnosis are based on a heterogeneous solid-phase system and suffer from mass-transfer limitation. The nanoparticles' colloidal behavior and magnetic properties bring the advantages of homogeneous immunoassay, i.e., species diffusion, and of heterogeneous immunoassay, i.e., easy separation of the immunocomplex and free forms, as well as analyte preconcentration. We thus developed a colloidal, non-competitive, indirect immunoassay using magnetic core-shell nanoparticles (MCSNP) as immunosupports. The feasibility of such an immunoassay was first demonstrated with a model antibody and described by comparing the immunocapture kinetics using macro (standard microtiter plate), micro (microparticles) and nanosupports (MCSNP). The influence of the nanosupport properties (surface chemistry, antigen density) and of the medium (ionic strength, counter ion nature) on the immunocapture efficiency and specificity was then investigated. The performances of this original MCSNP-based immunoassay were compared with a gold standard enzyme-linked immunosorbent assay (ELISA) using a microtiter plate. The capture rate of target IgG was accelerated 200-fold and a tenfold lower limit of detection was achieved. Finally, the MCSNP-based immunoassay was successfully applied to the detection of specific IgE from milk-allergic patient's sera with a lower LOD and a good agreement (CV < 6%) with the microtiter plate, confirming the great potential of this analytical platform in the field of immunodiagnosis.

Equilibrium and non-equilibrium furanose selection in the ribose isomerisation network.

The exclusive presence of ß-D-ribofuranose in nucleic acids is still a conundrum in prebiotic chemistry, given that pyranose species are substantially more stable at equilibrium. However, a precise characterisation of the relative furanose/pyranose fraction at temperatures higher than about 50 °C is still lacking. Here, we employ a combination of NMR measurements and statistical mechanics modelling to predict a population inversion between furanose and pyranose at equilibrium at high temperatures. More importantly, we show that a steady temperature gradient may steer an open isomerisation network into a non-equilibrium steady state where furanose is boosted beyond the limits set by equilibrium thermodynamics. Moreover, we demonstrate that nonequilibrium selection of furanose is maximum at optimal dissipation, as gauged by the temperature gradient and energy barriers for isomerisation. The predicted optimum is compatible with temperature drops found in hydrothermal vents associated with extremely fresh lava flows on the seafloor.

Interactions between giant unilamellar vesicles and charged core-shell magnetic nanoparticles.

This work combined two tools, giant unilamellar vesicles (GUVs) and core-shell magnetic nanoparticles (CSMNs), to develop a simplified model for studying interactions between the cell membrane and nanoparticles. We focused on charged functionalized CSMNs that can be either cationic or anionic. Using optical, electron, and confocal microscopy, we found that giant vesicle-nanoparticle interactions did not result from a simple electrostatic phenomenon because cationic CSMNs tended to bind to positively charged bilayers, whereas anionic CSMNs remained inert.

Dimerization of Uracil in a Simulated Mars-like UV Radiation Environment.

The search for organic molecules at the surface of Mars is a key objective in astrobiology, given that many organic compounds are possible biosignatures and their presence is of interest with regard to the habitability of Mars. Current environmental conditions at the martian surface are harsh and affect the stability of organic molecules. For this reason, and because current and future Mars rovers collect samples from the upper surface layer, it is important to assess the fate of organic molecules under the conditions at the martian surface. Here, we present an experimental study of the evolution of uracil when exposed to UV radiation, pressure, and temperature conditions representative of the surface of Mars. Uracil was selected because it is a nucleobase that composes RNA, and it has been detected in interplanetary bodies that could be the exogenous source of this molecule by meteoritic delivery to the surface of Mars. Our results show that the experimental quantum efficiency of photodecomposition of uracil is 0.16 ± 0.14 molecule/photon. Although these results suggest that uracil is quickly photodegraded when directly exposed to UV light on Mars, such exposure produces dimers that are more stable over time than the monomer. The identified dimers could be targets of interest for current and future Mars space missions.

Metallomics in deep time and the influence of ocean chemistry on the metabolic landscapes of Earth's earliest ecosystems.

Modern biological dependency on trace elements is proposed to be a consequence of their enrichment in the habitats of early life together with Earth's evolving physicochemical conditions; the resulting metallic biological complement is termed the metallome. Herein, we detail a protocol for describing metallomes in deep time, with applications to the earliest fossil record. Our approach extends the metallome record by more than 3 Ga and provides a novel, non-destructive method of estimating biogenicity in the absence of cellular preservation. Using microbeam particle-induced X-ray emission (µPIXE), we spatially quantify transition metals and metalloids within organic material from 3.33 billion-year-old cherts of the Barberton greenstone belt, and demonstrate that elements key to anaerobic prokaryotic molecular nanomachines, including Fe, V, Ni, As and Co, are enriched within carbonaceous material. Moreover, Mo and Zn, likely incorporated into enzymes only after the Great Oxygenation Event, are either absent or present at concentrations below the limit of detection of µPIXE, suggesting minor biological utilisation in this environmental setting. Scanning and transmission electron microscopy demonstrates that metal enrichments do not arise from accumulation in nanomineral phases and thus unambiguously reflect the primary composition of the carbonaceous material. This carbonaceous material also has δ13C between -41.3‰ and 0.03‰, dominantly -21.0‰ to -11.5‰, consistent with biological fractionation and mostly within a restricted range inconsistent with abiotic processes. Considering spatially quantified trace metal enrichments and negative δ13C fractionations together, we propose that, although lacking cellular preservation, this organic material has biological origins and, moreover, that its precursor metabolism may be estimated from the fossilised "palaeo-metallome". Enriched Fe, V, Ni and Co, together with petrographic context, suggests that this kerogen reflects the remnants of a lithotrophic or organotrophic consortium cycling methane or nitrogen. Palaeo-metallome compositions could be used to deduce the metabolic networks of Earth's earliest ecosystems and, potentially, as a biosignature for evaluating the origin of preserved organic materials found on Mars.

Charge-based characterization of nanometric cationic bifunctional maghemite/silica core/shell particles by capillary zone electrophoresis.

In view of employing functionalized nanoparticles (NPs) in the context of an immunodiagnostic, aminated maghemite/silica core/shell particles were synthesized so as to be further coated with an antibody or an antigen via the amino groups at their surface. Different functionalization rates were obtained by coating these maghemite/silica core/shell particles with 3-(aminopropyl)triethoxysilane and 2-[methoxy(polyethyleneoxy)propyl]-trimethoxysilane at different molar ratios. Adequate analytical performances with CE coupled with UV-visible detection were obtained through semi-permanent capillary coating with didodecyldimethyl-ammonium bromide, thus preventing particle adsorption. First, the influence of experimental conditions such as electric field strength, injected particle amount as well as electrolyte ionic strength and pH, was evaluated. A charge-dependent electrophoretic mobility was evidenced and the separation selectivity was tuned according to electrolyte ionic strength and pH. The best resolutions were obtained at pH 8.0, high ionic strength (ca. 100 mM), and low total particle volume fraction (ca. 0.055%), thus eliminating interference effects between different particle populations in mixtures. A protocol derived from Kaiser's original description was performed for quantitation of the primary amino groups attached onto the NP surface. Thereafter a correlation between particle electrophoretic mobility and the density of amino groups at their surface was established. Eventually, CE proved to be an easy, fast, and reliable method for the determination of NP effective surface charge density.

The degradation of organic compounds impacts the crystallization of clay minerals and vice versa.

Expanding our capabilities to unambiguously identify ancient traces of life in ancient rocks requires laboratory experiments to better constrain the evolution of biomolecules during advanced fossilization processes. Here, we submitted RNA to hydrothermal conditions in the presence of a gel of Al-smectite stoichiometry at 200 °C for 20 days. NMR and STXM-XANES investigations revealed that the organic fraction of the residues is no longer RNA, nor the quite homogeneous aromatic-rich residue obtained in the absence of clays, but rather consists of particles of various chemical composition including amide-rich compounds. Rather than the pure clays obtained in the absence of RNA, electron microscopy (SEM and TEM) and diffraction (XRD) data showed that the mineralogy of the experimental residues includes amorphous silica and aluminosilicates mixed together with nanoscales phosphates and clay minerals. In addition to the influence of clay minerals on the degradation of organic compounds, these results evidence the influence of the presence of organic compounds on the nature of the mineral assemblage, highlighting the importance of fine-scale mineralogical investigations when discussing the nature/origin of organo-mineral microstructures found in ancient rocks.

Confinement and Time Immemorial: Prebiotic Synthesis of Nucleotides on a Porous Mineral Nanoreactor.

We report the successful one-pot synthesis of adenosine mono-, di-, and triphosphate in the confined space of a mordenite zeolite. This is also the first report of ATP synthesized onto a porous mineral surface. The results revealed a plausible prebiotic route to ribonucleotides and highlighted the contribution of microporous minerals in the origins of life.

Author Correction: Proton irradiation: a key to the challenge of N-glycosidic bond formation in a prebiotic context.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

Potential Role of Inorganic Confined Environments in Prebiotic Phosphorylation.

A concise outlook on the potential role of confinement in phosphorylation and phosphate condensation pertaining to prebiotic chemistry is presented. Inorganic confinement is a relatively uncharted domain in studies concerning prebiotic chemistry, and even more so in terms of experimentation. However, molecular crowding within confined dimensions is central to the functioning of contemporary biology. There are numerous advantages to confined environments and an attempt to highlight this fact, within this article, has been undertaken, keeping in context the limitations of aqueous phase chemistry in phosphorylation and, to a certain extent, traditional approaches in prebiotic chemistry.

Synthesis of RNA Nucleotides in Plausible Prebiotic Conditions from ab Initio Computer Simulations.

Understanding the mechanism of spontaneous formation of ribonucleotides under realistic prebiotic conditions is a key open issue of origins-of-life research. In cells, de novo and salvage nucleotide enzymatic synthesis combines 5-phospho-α-d-ribose-1-diphosphate (α-PRPP) and nucleobases. Interestingly, these reactants are also known as prebiotically plausible compounds. Combining ab initio molecular dynamics simulations with recently developed reaction exploration and enhanced sampling methods, we show that nucleobases and α-PRPP should spontaneously combine, under mild hydrothermal conditions, with an exothermic reaction and a facile mechanism, forming both purine and pyrimidine ribonucleotides. Surprisingly, this mechanism is very similar to the biological one and yields ribonucleotides with the same anomeric carbon chirality as in biological systems. Mass spectrometry experiments performed on solutions of adenine and PRPP in similar conditions support the formation of AMP. These results suggest that natural selection might have optimized, through enzymes, a pre-existing ribonucleotide formation mechanism, carrying it forward to modern life forms.

Going through the wine fining: Intimate dialogue between organics and clays.

Wine chemistry inspires and challenges with its complexity and intriguing composition. In this context, the composites based on the use of a model protein, a polyphenol of interest and montmorillonite in a model hydroalcoholic solution have been studied. A set of experimental characterization techniques highlighted the interactions between the organic and the inorganic parts in the composite. The amount of the organic part was determined by ultraviolet-visible (UV-VIS) and thermal analysis. X-ray diffraction (XRD) and transmission electronic microscopy (TEM) informed about the stacking/exfoliation of the layers in the composites. Vibrational and nuclear magnetic resonance spectroscopies methods stressed on the formation of a complex between the protein and the polyphenol before adsorption on the clay mineral. The mobility/rigidity of the organic parts were determined by fluorescence time resolved spectroscopy. Changes in the secondary structure of the protein occured upon complexation with polyphenol on clay mineral due to strong interactions. Although not representating faithfully enological conditions, these results highlight the range and nature of mechanisms possibly involved in wine fining.