How do Nucleotides Adsorb Onto Clays?

Effect of montmorillonite K10 clay on RNA structure and function

One of the earliest living systems was likely based on RNA ("the RNA world"). Mineral surfaces have been postulated to be an important environment for the prebiotic chemistry of RNA. In addition to adsorbing RNA and thus potentially reducing the chance of parasitic takeover through limited diffusion, minerals have been shown to promote a range of processes related to the emergence of life, including RNA polymerization, peptide bond formation, and self-assembly of vesicles. In addition, self-cleaving ribozymes have been shown to retain activity when adsorbed to the clay mineral montmorillonite. However, simulation studies suggest that adsorption to minerals is likely to interfere with RNA folding and, thus, function. To further evaluate the plausibility of a mineral-adsorbed RNA world, here we studied the effect of the synthetic clay montmorillonite K10 on the malachite green RNA aptamer, including binding of the clay to malachite green and RNA, as well as on the formation of secondary structures in model RNA and DNA oligonucleotides. We evaluated the fluorescence of the aptamer complex, adsorption to the mineral, melting curves, Förster resonance energy transfer interactions, and 1H-NMR signals to study the folding and functionality of these nucleic acids. Our results indicate that while some base pairings are unperturbed, the overall folding and binding of the malachite green aptamer are substantially disrupted by montmorillonite. These findings suggest that minerals would constrain the structures, and possibly the functions, available to an adsorbed RNA world.

Features of DNA-Montmorillonite Binding Visualized by Atomic Force Microscopy

In the present work, complexes of DNA with nano-clay montmorillonite (Mt) were investigated by means of atomic force microscopy (AFM) under various conditions. In contrast to the integral methods of analysis of the sorption of DNA on clay, AFM allowed us to study this process at the molecular level in detail. DNA molecules in the deionized water were shown to form a 2D fiber network weakly bound to both Mt and mica. The binding sites are mostly along Mt edges. The addition of Mg²⁺ cations led to the separation of DNA fibers into separate molecules, which bound mainly to the edge joints of the Mt particles according to our reactivity estimations. After the incubation of DNA with Mg²⁺, the DNA fibers were capable of wrapping around the Mt particles and were weakly bound to the Mt edge surfaces. The reversible sorption of nucleic acids onto the Mt surface allows it to be used for both RNA and DNA isolation for further reverse transcription and polymerase chain reaction (PCR). Our results show that the strongest binding sites for DNA are the edge joints of Mt particles.

Differential Surface Interactions and Surface Templating of Nucleotides (dGMP, dCMP, dAMP, and dTMP) on Oxide Particle Surfaces

The fate of biomolecules in the environment depends in part on understanding the surface chemistry occurring at the biological-geochemical (bio-geo) interface. Little is known about how environmental DNA (eDNA) or smaller components, like nucleotides and oligonucleotides, persist in aquatic environments and the role of surface interactions. This study aims to probe surface interactions and adsorption behavior of nucleotides on oxide surfaces. We have investigated the interactions of individual nucleotides (dGMP, dCMP, dAMP, and dTMP) on TiO₂ particle surfaces as a function of pH and in the presence of complementary and noncomplementary base pairs. Using attenuated total reflectance-Fourier transform infrared spectroscopy, there is an increased number of adsorbed nucleotides at lower pH with a preferential interaction of the phosphate group with the oxide surface. Additionally, differential adsorption behavior is seen where purine nucleotides are preferentially adsorbed, with higher surface saturation coverage, over their pyrimidine derivatives. These differences may be a result of intermolecular interactions between coadsorbed nucleotides. When the TiO₂ surface was exposed to two-component solutions of nucleotides, there was preferential adsorption of dGMP compared to dCMP and dTMP, and dAMP compared to dTMP and dCMP. Complementary nucleotide base pairs showed hydrogen-bond interactions between a strongly adsorbed purine nucleotide layer and a weaker interacting hydrogen-bonded pyrimidine second layer. Noncomplementary base pairs did not form a second layer. These results highlight several important findings: (i) there is differential adsorption of nucleotides; (ii) complementary coadsorbed nucleotides show base pairing with a second layer, and the stability depends on the strength of the hydrogen bonding interactions and; (iii) the first layer coverage strongly depends on pH. Overall, the importance of surface interactions in the adsorption of nucleotides and the templating of specific interactions between nucleotides are discussed.

A Physicochemical Consideration of Prebiotic Microenvironments for Self-Assembly and Prebiotic Chemistry

The origin of life on Earth required myriads of chemical and physical processes. These include the formation of the planet and its geological structures, the formation of the first primitive chemicals, reaction, and assembly of these primitive chemicals to form more complex or functional products and assemblies, and finally the formation of the first cells (or protocells) on early Earth, which eventually evolved into modern cells. Each of these processes presumably occurred within specific prebiotic reaction environments, which could have been diverse in physical and chemical properties. While there are resources that describe prebiotically plausible environments or nutrient availability, here, we attempt to aggregate the literature for the various physicochemical properties of different prebiotic reaction microenvironments on early Earth. We introduce a handful of properties that can be quantified through physical or chemical techniques. The values for these physicochemical properties, if they are known, are then presented for each reaction environment, giving the reader a sense of the environmental variability of such properties. Such a resource may be useful for prebiotic chemists to understand the range of conditions in each reaction environment, or to select the medium most applicable for their targeted reaction of interest for exploratory studies.

Protocells: Milestones and Recent Advances

The origin of life is still one of humankind's great mysteries. At the transition between nonliving and living matter, protocells, initially featureless aggregates of abiotic matter, gain the structure and functions necessary to fulfill the criteria of life. Research addressing protocells as a central element in this transition is diverse and increasingly interdisciplinary. The authors review current protocell concepts and research directions, address milestones, challenges and existing hypotheses in the context of conditions on the early Earth, and provide a concise overview of current protocell research methods.

Clays as Vehicles for Drug Photostability

Clay minerals are often used due to their high adsorption capacity, which has sparked interest in their biological applications to stabilize drugs and pharmaceutical products. This research aims to summarize information about the stability of drugs, cosmetics, dermocosmetics, and pharmaceutical compounds incorporated in the structure of different clay minerals. The databases used to search the articles were Web of Science, Scopus, PubMed, and Science Direct. Photostabilization of these compounds is reviewed and its importance demonstrated. For biological applications, the increase in solubility and bioavailability of clay minerals has proven useful for them as drug carriers. While their natural abundance, low toxicity, and accessible cost have contributed to classical applications of clay minerals, a wide range of interesting new applications may be facilitated, mainly through incorporating different organic molecules. The search for new functional materials is promising to challenge research on clay minerals in biological or biotechnological approaches.

Catalytic Prebiotic Formation of Glycerol Phosphate Esters and an Estimation of Their Steady State Abundance under Plausible Early Earth Conditions

The emergence of biological phosphate esters of glycerol could have been a crucial step in the origin and evolution of life on the early Earth as glycerol phosphates today play a central role in biochemistry. We investigate here the formation of the glycerol phosphates by employing various rock samples, salts, and minerals as potential catalysts to aid the phosphorylation process. We report the synthesis of various phosphate esters of glycerol including glycerol-1-phosphate, glycerol-2-phosphate, cyclic glycerol-monophosphate as well as various diphosphate esters. Furthermore, the decomposition rates of glycerol phosphate under mild heating were also studied while keeping the pH constant. It was observed that glycerol phosphate starts decomposing quickly under mild heating conditions into inorganic orthophosphate and pyrophosphate, and a steady state concentration of ~0.5 M of glycerol phosphate may have been reasonable in ponds with abundant glycerol, phosphate, urea, and catalytic minerals.

Molecular Fingerprints of Hydrophobicity at Aqueous Interfaces from Theory and Vibrational Spectroscopies

Hydrophobicity/hydrophilicity of aqueous interfaces at the molecular level results from a subtle balance in the water-water and water-surface interactions. This is characterized here via density functional theory-molecular dynamics (DFT-MD) coupled with vibrational sum frequency generation (SFG) and THz-IR absorption spectroscopies. We show that water at the interface with a series of weakly interacting materials is organized into a two-dimensional hydrogen-bonded network (2D-HB-network), which is also found above some macroscopically hydrophilic silica and alumina surfaces. These results are rationalized through a descriptor that measures the number of "vertical" and "horizontal" hydrogen bonds formed by interfacial water, quantifying the competition between water-surface and water-water interactions. The 2D-HB-network is directly revealed by THz-IR absorption spectroscopy, while the competition of water-water and water-surface interactions is quantified from SFG markers. The combination of SFG and THz-IR spectroscopies is thus found to be a compelling tool to characterize the finest details of molecular hydrophobicity at aqueous interfaces.

The Role of Minerals in Events That Led to the Origin of Life

The role of minerals in the events that led to the origin of life is discussed with regard to (1) their catalytic role for the formation of RNA-like oligomers from their monomers and (2) their protective role for organic molecules formed in space that were delivered to planetary surfaces. Results obtained in the laboratory demonstrate that minerals do catalyze the oligomerization of ribonucleic acid (RNA) monomers to produce short RNA chains. Furthermore, and more importantly, these synthetic RNA chains formed by mineral catalysis serve as a template for the formation of complementary RNA chains, which is a significant finding that demonstrates the role of minerals in the origin of life. Simulation experiments run under Mars-like conditions have also shown that Mars analog minerals can shield the precursors of RNA and proteins against the harmful effects of UV and gamma radiation at the martian surface and 5 cm below the surface.

Urea-Assisted Synthesis and Characterization of Saponite with Different Octahedral (Mg, Zn, Ni, Co) and Tetrahedral Metals (Al, Ga, B), a Review

Clay minerals surfaces potentially play a role in prebiotic synthesis through adsorption of organic monomers that give rise to highly concentrated systems; facilitate condensation and polymerization reactions, protection of early biomolecules from hydrolysis and photolysis, and surface-templating for specific adsorption and synthesis of organic molecules. This review presents processes of clay formation using saponite as a model clay mineral, since it has been shown to catalyze organic reactions, is easy to synthesize in large and pure form, and has tunable properties. In particular, a method involving urea is presented as a reasonable analog of natural processes. The method involves a two-step process: (1) formation of the precursor aluminosilicate gel and (2) hydrolysis of a divalent metal (Mg, Ni, Co, and Zn) by the slow release of ammonia from urea decomposition. The aluminosilicate gels in the first step forms a 4-fold-coordinated Al³⁺ similar to what is found in nature such as in volcanic glass. The use of urea, a compound figuring in many prebiotic model reactions, circumvents the formation of undesirable brucite, Mg(OH)₂, in the final product, by slowly releasing ammonia thereby controlling the hydrolysis of magnesium. In addition, the substitution of B and Ga for Si and Al in saponite is also described. The saponite products from this urea-assisted synthesis were tested as catalysts for several organic reactions, including Friedel–Crafts alkylation, cracking, and isomerization reactions.

Analysis of RNA Interference (RNAi) Biopesticides: Double-Stranded RNA (dsRNA) Extraction from Agricultural Soils and Quantification by RT-qPCR

Double-stranded RNA (dsRNA) molecules are used as a novel class of biopesticides. To enable assessments of the ecological risk associated with their release to receiving environments, we developed an approach to quantify dsRNA in agricultural soils using quantitative reverse transcription-polymerase chain reaction (RT-qPCR). To allow quantification of dsRNA adsorbed to particles, we also developed a protocol to transfer dsRNA from particles to the extraction buffer by changing particle surface charge and adding constituents to compete with dsRNA for adsorption sites. Our approach could quantify dsRNA amounts as low as 0.003 ng_dsRNA/g_soil. This approach is the first available field-applicable approach able to quantify dsRNA biopesticides down to environmentally relevant concentrations. We applied this approach to investigate dsRNA dissipation (including dilution, degradation, and adsorption) in two agricultural soils. When we applied a low amount of dsRNA (1 ng_dsRNA/g_soil) to the soils, we observed that a greater fraction of dsRNA was adsorbed to and extractable from soil particles in a silty clay loam soil than in a fine sandy loam soil. In both soils, dsRNA dissipated on the timescale of hours. Overall, these results demonstrate that our approach can be applied to assess the environmental fate of dsRNA biopesticides at concentrations relevant to their release to soils.

Preliminary evidences of the presence of extracellular DNA single stranded forms in soil

The relevance of extracellular DNA (eDNA) in the soil ecosystem is becoming more and more evident to the scientific community by the progressive discovery of functions accompanying to natural gene transformation. However, despite the increased number of published articles dedicated to eDNA in soil, so far only few are focused on its single stranded form (eDNAss). The present paper is the first to investigate the quantitative relevance of eDNAss in the total soil eDNA pool, discriminating between its linear (eDNAssl) and circular (eDNAssc) forms and the respective weakly (wa) and tightly (ta) adsorbed fractions. The results showed the prevalence of eDNAss and its linear form in both the total soil eDNA pool and its wa and ta fractions. Both of the eDNAss fractions (linear and circular) were characterized by small fragments.