Self-assembly processes in the prebiotic environment

On the role of α-alumina in the origin of life: Surface-driven assembly of amino acids

We investigate the hypothesis that mineral/water interfaces played a crucial catalytic role in peptide formation by promoting the self-assembly of amino acids. Using classical molecular dynamics simulations, we demonstrate that the α-alumina(0001) surface exhibits an affinity of 4 kBT for individual glycine or GG dipeptide molecules due to hydrogen bonds. In simulations with multiple glycine molecules, surface-bound glycine enhances further adsorption, leading to the formation of long chains connected by hydrogen bonds between the carboxyl and amine groups of glycine molecules. We find that the likelihood of observing chains longer than 10 glycine units increases by at least five orders of magnitude at the surface compared to the bulk. This surface-driven assembly is primarily due to local high density and alignment with the alumina surface pattern. Together, these results propose a model for how mineral surfaces can induce configuration-specific assembly of amino acids, thereby promoting condensation reactions.

Origin of the RNA World in Cold Hadean Geothermal Fields Enriched in Zinc and Potassium: Abiogenesis as a Positive Fallout from the Moon-Forming Impact?

The ubiquitous, evolutionarily oldest RNAs and proteins exclusively use rather rare zinc as transition metal cofactor and potassium as alkali metal cofactor, which implies their abundance in the habitats of the first organisms. Intriguingly, lunar rocks contain a hundred times less zinc and ten times less potassium than the Earth's crust; the Moon is also depleted in other moderately volatile elements (MVEs). Current theories of impact formation of the Moon attribute this depletion to the MVEs still being in a gaseous state when the hot post-impact disk contracted and separated from the nascent Moon. The MVEs then fell out onto juvenile Earth's protocrust; zinc, as the most volatile metal, precipitated last, just after potassium. According to our calculations, the top layer of the protocrust must have contained up to 1019 kg of metallic zinc, a powerful reductant. The venting of hot geothermal fluids through this MVE-fallout layer, rich in metallic zinc and radioactive potassium, both capable of reducing carbon dioxide and dinitrogen, must have yielded a plethora of organic molecules released with the geothermal vapor. In the pools of vapor condensate, the RNA-like molecules may have emerged through a pre-Darwinian selection for low-volatile, associative, mineral-affine, radiation-resistant, nitrogen-rich, and polymerizable molecules.

Prebiotic Nucleoside Phosphorylation in a Simulated Deep-Sea Supercritical Carbon Dioxide-Water Two-Phase Environment

Prebiotic synthesis of complex organic molecules in water-rich environments has been a long-standing challenge. In the modern deep sea, emission of liquid CO2 has been observed in multiple locations, which indicates the existence of benthic CO2 pools. Recently, a liquid/supercritical CO2 (ScCO2) hypothesis has been proposed that a two-phase ScCO2-water environment could lead to efficient dehydration and condensation of organics. To confirm this hypothesis, we conducted a nucleoside phosphorylation reaction in a hydrothermal reactor creating ScCO2-water two-phase environment. After 120 h of uridine, cytosine, guanosine, and adenosine phosphorylation at 68.9°C, various nucleoside monophosphates (NMPs), nucleotide diphosphates, and carbamoyl nucleosides were produced. The addition of urea enhanced the overall production of phosphorylated species with 5'-NMPs, the major products that reached over 10% yield. As predicted, phosphorylation did not proceed in the fully aqueous environment without ScCO2. Further, a glass window reactor was introduced for direct observation of the two-phase environment, where the escape of water into the ScCO2 phase was observed. These results are similar to those of a wet-dry cycle experiment simulating the terrestrial hot spring environment, indicating that the presence of ScCO2 can create a comparatively dry condition in the deep sea. In addition, the high acidity present in the aqueous phase further supports nucleotide synthesis by enabling the release of orthophosphate from the hydroxyapatite mineral solving the phosphate problem. Thus, the present study highlights the potential of the unique ScCO2-water two-phase environment to drive prebiotic nucleotide synthesis and likely induce condensation reactions of various organic and inorganic compounds in the deep-sea CO2 pool on Earth and potentially other ocean worlds.

Membrane Catalyzed Formation of Nucleotide Clusters and Their Role in the Origins of Life: Insights from Molecular Simulations and Lattice Modeling

One of the mysteries in studying the molecular "Origin of Life" is the emergence of RNA and RNA-based life forms, where nonenzymatic polymerization of nucleotides is a crucial hypothesis in formation of large RNA chains. The nonenzymatic polymerization can be mediated by various environmental settings, such as cycles of hydration and dehydration, temperature variations, and proximity to a variety of organizing matrices, such as clay, salt, fatty acids, lipid membrane, and mineral surface. In this work, we explore the influence of different phases of the lipid membrane toward nucleotide organization and polymerization in a simulated prebiotic setting. Our molecular simulations quantify the localization propensity of a mononucleotide, uridine monophosphate (UMP), in distinct membrane settings. We perform all-atom molecular dynamics (MD) simulations to estimate the role of the monophasic and biphasic membranes in modifying the behavior of UMPs localization and their clustering mechanism. Based on the interaction energy of mononucleotides with the membrane and their diffusion profile from our MD calculations, we developed a lattice-based model to explore the thermodynamic limits of the observations made from the MD simulations. The mathematical model substantiates our hypothesis that the lipid layers can act as unique substrates for "catalyzing" polymerization of mononucleotides due to the inherent spatiotemporal heterogeneity and phase change behavior.

Microfluidics-Based Drying-Wetting Cycles to Investigate Phase Transitions of Small Molecules Solutions

Drying-wetting cycles play a crucial role in the investigation of the origin of life as processes that both concentrate and induce the supramolecular assembly and polymerization of biomolecular building blocks, such as nucleotides and amino acids. Here, we test different microfluidic devices to study the dehydration-hydration cycles of the aqueous solutions of small molecules, and to observe, by optical microscopy, the insurgence of phase transitions driven by self-assembly, exploiting water pervaporation through polydimethylsiloxane (PDMS). As a testbed, we investigate solutions of the chromonic dye Sunset Yellow (SSY), which self-assembles into face-to-face columnar aggregates and produces nematic and columnar liquid crystal (LC) phases as a function of concentration. We show that the LC temperature-concentration phase diagram of SSY can be obtained with a fair agreement with previous reports, that droplet hydration-dehydration can be reversibly controlled and automated, and that the simultaneous incubation of samples with different final water contents, corresponding to different phases, can be implemented. These methods can be further extended to study the assembly of diverse prebiotically relevant small molecules and to characterize their phase transitions.

Chapter 4: A Geological and Chemical Context for the Origins of Life on Early Earth

Within the first billion years of Earth's history, the planet transformed from a hot, barren, and inhospitable landscape to an environment conducive to the emergence and persistence of life. This chapter will review the state of knowledge concerning early Earth's (Hadean/Eoarchean) geochemical environment, including the origin and composition of the planet's moon, crust, oceans, atmosphere, and organic content. It will also discuss abiotic geochemical cycling of the CHONPS elements and how these species could have been converted to biologically relevant building blocks, polymers, and chemical networks. Proposed environments for abiogenesis events are also described and evaluated. An understanding of the geochemical processes under which life may have emerged can better inform our assessment of the habitability of other worlds, the potential complexity that abiotic chemistry can achieve (which has implications for putative biosignatures), and the possibility for biochemistries that are vastly different from those on Earth.

Template-Directed Replication and Chiral Resolution during Wet-Dry Cycling in Hydrothermal Pools

The commonly supposed template-based format for RNA self-replication requires both duplex assembly and disassembly. This requisite binary provision presents a challenge to the development of a serviceable self-replication model since chemical reactions are thermochemically unidirectional. We submit that a solution to this problem lies in volcanic landmasses that engage in continuous cycles of wetting and drying and thus uniquely provide the twofold state required for self-replication. Moreover, they offer conditions that initiate chain branching, and thus furnish a path to autocatalytic self-replication. The foundations of this dual thermochemical landscape arise from the broad differences in the properties of the bulk water phase on the one hand, and the air/water interfacial regions that emerge in the evaporative stages on the other. With this reaction system as a basis and employing recognized thermochemical and kinetic parameters, we present simulations displaying the spontaneous and autocatalyzed conversion of racemic and unactivated RNA monomers to necessarily homochiral duplex structures over characteristic periods of years.

Proton Affinity in the Chemistry of Beta-Octamolybdate: HPLC-ICP-AES, NMR and Structural Studies

The affinity of [β-Mo8O26]4- toward different proton sources has been studied in various conditions. The proposed sites for proton coordination were highlighted with single crystal X-ray diffraction (SCXRD) analysis of (Bu4N)3[β-{Ag(py-NH2)Mo8O26]}] (1) and from analysis of reported structures. Structural rearrangement of [β-Mo8O26]4- as a direct response to protonation was studied in solution with 95Mo NMR and HPLC-ICP-AES techniques. A new type of proton transfer reaction between (Bu4N)4[β-Mo8O26] and (Bu4N)4H2[V10O28] in DMSO results in both polyoxometalates transformation into [V2Mo4O19]4-, which was confirmed by the 95Mo, 51V NMR and HPLC-ICP-AES techniques. The same type of reaction with [H4SiW12O40] in DMSO leads to metal redistribution with formation of [W2Mo4O19]2-.

Insights into the evolution of enzymatic specificity and catalysis: From Asgard archaea to human adenylate kinases

Enzymatic catalysis is critically dependent on selectivity, active site architecture, and dynamics. To contribute insights into the interplay of these properties, we established an approach with NMR, crystallography, and MD simulations focused on the ubiquitous phosphotransferase adenylate kinase (AK) isolated from Odinarchaeota (OdinAK). Odinarchaeota belongs to the Asgard archaeal phylum that is believed to be the closest known ancestor to eukaryotes. We show that OdinAK is a hyperthermophilic trimer that, contrary to other AK family members, can use all NTPs for its phosphorylation reaction. Crystallographic structures of OdinAK-NTP complexes revealed a universal NTP-binding motif, while 19F NMR experiments uncovered a conserved and rate-limiting dynamic signature. As a consequence of trimerization, the active site of OdinAK was found to be lacking a critical catalytic residue and is therefore considered to be "atypical." On the basis of discovered relationships with human monomeric homologs, our findings are discussed in terms of evolution of enzymatic substrate specificity and cold adaptation.

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.

Porphyrin in prebiotic catalysis: Ascertaining a route for the emergence of early metalloporphyrins

Metal ions are known to catalyze certain prebiotic reactions. However, the transition from metal ions to extant metalloenzymes remains unclear. Porphyrins are found ubiquitously in the catalytic core of many ancient metalloenzymes. In this study, we evaluated the influence of porphyrin-based organic scaffold, on the catalysis, emergence and putative molecular evolution of prebiotic metalloporphyrins. We studied the effect of porphyrins on the transition metal ion-mediated oxidation of hydroquinone (HQ). We report a change in the catalytic activity of the metal ions in the presence of porphyrin. This was observed to be facilitated by the coordination between metal ions and porphyrins or by the formation of non-coordinated complexes. The metal-porphyrin complexes also oxidized NADH, underscoring its versatility at oxidizing more than one substrate. Our study highlights the selective advantage that some of the metal ions would have had in the presence of porphyrin, underscoring their role in shaping the evolution of protometalloenzymes.

Harmonics, evolutionary generators, DANCE, and HEAR-functional dimensions

Evolution of the major kingdoms of life has spanned over the last 4 billion years on Earth. Studies of the process comprise different fields of study with alternative perspectives. This paper focuses on mathematic unification of the subject area; enriching an engineering based structure to advance our understanding of pathways which lead to distinct constructs in life, furthering geographic bordering processes with biological context. Application of logistic regression requires partitioning of variance within cellular and molecular systems; use of higher mathematic technique (multi-objective genetic algorithm) generates variance within the different scales of evolution, the result of which is analogous with the Fisher equation model of gene distribution within populations. Laboratory and field studies were integrated to illustrate emergence in evolutionary processes in the terrestrial/soil environment. Nematological field and laboratory trials validate the existence of triangular relationships within biological communities; further harmonic constants between interacting species may be found with emergent consequence. We distinguish different strategical groupings in the soil community, with the core groupings recognized with Meloidogyne spp. illustrating positive (emergent) growth; Radopholus similis (neutral growth), and Helicotylenchus pseudorobustus (negative growth). The patterns of emergent systems are shown in the extremes of Morocco's dynamic soil environment. Fuzzy classification methods: Mamdani, Takugi-Sugeno-Kang; additional novel DANCE (Differential Algorithmic Network Centered Emergence) and functional expressions HEAR (Harmonic Evolutionary Algorithmic Resilience), are recommended to give a basis for development of constructs covering different categories of life.

Universal features in the lifetime distribution of clusters in hydrogen-bonding liquids

Hydrogen-bonding liquids, typically water and alcohols, are known to form labile structures (network, chains, etc.); hence, the lifetime of these structures is an important microscopic parameter, which can be calculated via computer simulations. Since these cluster entities are mostly statistical in nature, one would expect that, in the short-timescale regime, their lifetime distribution would be a broad Gaussian-like function of time, with a single maximum representing their mean lifetime, and be weakly dependent on criteria such as the bonding distance and angle, much similar to non-hydrogen-bonding simple liquids, while the long-timescale regime is known to have some power law dependence. Unexpectedly, all the hydrogen-bonding liquids studied herein, namely water and alcohols, display three highly hierarchical specific lifetimes, in the sub-picosecond range 0-0.5 ps. The dominant lifetime depends very strongly on the bonding-distance criterion and is related to hydrogen-bonded pairs. This mode is absent in non-H-bonding simple liquids. The secondary and tertiary mean lifetimes are related to clusters and are nearly independent of the bonding criterion. Of these two lifetimes, only the first one can be related to that of simple liquids, which poses the question of the nature of the third lifetime. The study of alcohols reveals that this third lifetime is related to the topology of the H-bonded clusters and that its distribution may also be affected by the alkyl tail surrounding the "bath". This study shows that hydrogen-bonding liquids have a universal hierarchy of hydrogen-bonding lifetimes with a timescale regularity across very different types, and which depend on the topology of the cluster structures.

Plausible Emergence and Self Assembly of a Primitive Phospholipid from Reduced Phosphorus on the Primordial Earth

How life arose on the primitive Earth is one of the biggest questions in science. Biomolecular emergence scenarios have proliferated in the literature but accounting for the ubiquity of oxidized (+ 5) phosphate (PO43-) in extant biochemistries has been challenging due to the dearth of phosphate and molecular oxygen on the primordial Earth. A compelling body of work suggests that exogenous schreibersite ((Fe,Ni)3P) was delivered to Earth via meteorite impacts during the Heavy Bombardment (ca. 4.1-3.8 Gya) and there converted to reduced P oxyanions (e.g., phosphite (HPO32-) and hypophosphite (H2PO2-)) and phosphonates. Inspired by this idea, we review the relevant literature to deduce a plausible reduced phospholipid analog of modern phosphatidylcholines that could have emerged in a primordial hydrothermal setting. A shallow alkaline lacustrine basin underlain by active hydrothermal fissures and meteoritic schreibersite-, clay-, and metal-enriched sediments is envisioned. The water column is laden with known and putative primordial hydrothermal reagents. Small system dimensions and thermal- and UV-driven evaporation further concentrate chemical precursors. We hypothesize that a reduced phospholipid arises from Fischer-Tropsch-type (FTT) production of a C8 alkanoic acid, which condenses with an organophosphinate (derived from schreibersite corrosion to hypophosphite with subsequent methylation/oxidation), to yield a reduced protophospholipid. This then condenses with an α-amino nitrile (derived from Strecker-type reactions) to form the polar head. Preliminary modeling results indicate that reduced phospholipids do not aggregate rapidly; however, single layer micelles are stable up to aggregates with approximately 100 molecules.

Origin of Life on Mars: Suitability and Opportunities

Although the habitability of early Mars is now well established, its suitability for conditions favorable to an independent origin of life (OoL) has been less certain. With continued exploration, evidence has mounted for a widespread diversity of physical and chemical conditions on Mars that mimic those variously hypothesized as settings in which life first arose on Earth. Mars has also provided water, energy sources, CHNOPS elements, critical catalytic transition metal elements, as well as B, Mg, Ca, Na and K, all of which are elements associated with life as we know it. With its highly favorable sulfur abundance and land/ocean ratio, early wet Mars remains a prime candidate for its own OoL, in many respects superior to Earth. The relatively well-preserved ancient surface of planet Mars helps inform the range of possible analogous conditions during the now-obliterated history of early Earth. Continued exploration of Mars also contributes to the understanding of the opportunities for settings enabling an OoL on exoplanets. Favoring geochemical sediment samples for eventual return to Earth will enhance assessments of the likelihood of a Martian OoL.

The "Water Problem"(sic), the Illusory Pond and Life's Submarine Emergence-A Review

The assumption that there was a "water problem" at the emergence of life-that the Hadean Ocean was simply too wet and salty for life to have emerged in it-is here subjected to geological and experimental reality checks. The "warm little pond" that would take the place of the submarine alkaline vent theory (AVT), as recently extolled in the journal Nature, flies in the face of decades of geological, microbiological and evolutionary research and reasoning. To the present author, the evidence refuting the warm little pond scheme is overwhelming given the facts that (i) the early Earth was a water world, (ii) its all-enveloping ocean was never less than 4 km deep, (iii) there were no figurative "Icelands" or "Hawaiis", nor even an "Ontong Java" then because (iv) the solidifying magma ocean beneath was still too mushy to support such salient loadings on the oceanic crust. In place of the supposed warm little pond, we offer a well-protected mineral mound precipitated at a submarine alkaline vent as life's womb: in place of lipid membranes, we suggest peptides; we replace poisonous cyanide with ammonium and hydrazine; instead of deleterious radiation we have the appropriate life-giving redox and pH disequilibria; and in place of messy chemistry we offer the potential for life's emergence from the simplest of geochemically available molecules and ions focused at a submarine alkaline vent in the Hadean-specifically within the nano-confined flexible and redox active interlayer walls of the mixed-valent double layer oxyhydroxide mineral, fougerite/green rust comprising much of that mound.

Where Did Life Begin? Testing Ideas in Prebiotic Analogue Conditions

Publications related to the origin of life are mostly products of laboratory research and have the tacit assumption that the same reactions would have been possible on the early Earth some 4 billion years ago. Can this assumption be tested? We cannot go back in time, but we are able to venture out of the laboratory and perform experiments in natural conditions that are presumably analogous to the prebiotic environment. This brief review describes initial attempts to undertake such studies and some of the lessons we have learned.

Mechanical Energy before Chemical Energy at the Origins of Life?

Mechanical forces and mechanical energy are prevalent in living cells. This may be because mechanical forces and mechanical energy preceded chemical energy at life’s origins. Mechanical energy is more readily available in nonliving systems than the various forms of chemical energy used by living systems. Two possible prebiotic environments that might have provided mechanical energy are hot pools that experience wet/dry cycles and mica sheets as they move, open and shut, as heat pumps or in response to water movements.

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.

Geochemical influences on nonenzymatic oligomerization of prebiotically relevant cyclic nucleotides

The spontaneous emergence of long RNA molecules on the early Earth, a phenomenon central to the RNA World hypothesis, continues to remain an enigma in the field of origins of life. Few studies have looked at the nonenzymatic oligomerization of cyclic mononucleotides under neutral to alkaline conditions, albeit in fully dehydrated state. In this study, we systematically investigated the oligomerization of cyclic nucleotides under prebiotically relevant conditions, wherein starting reactants were subjected to repeated dehydration-rehydration (DH-RH) regimes. DH-RH conditions, a recurring geological theme that was prevalent on prebiotic Earth, are driven by naturally occurring processes including diurnal cycles and tidal pool activity. These conditions have been shown to facilitate uphill oligomerization reactions. The polymerization of 2'-3' and 3'-5' cyclic nucleotides of a purine (adenosine) and a pyrimidine (cytidine) was investigated. Additionally, the effect of amphiphiles was also evaluated. Furthermore, to discern the effect of "realistic" conditions on this process, the reactions were also performed using a hot spring water sample from a candidate early Earth environment. Our study showed that the oligomerization of cyclic nucleotides under DH-RH conditions resulted in intact informational oligomers. Amphiphiles increased the stability of both the starting monomers and the resultant oligomers in selected reactions. In the hot spring reactions, both the oligomerization of nucleotides and the back hydrolysis of the resultant oligomers were pronounced. Altogether, this study demonstrates how nonenzymatic oligomerization of cyclic nucleotides, under both laboratory-simulated prebiotic conditions and in a candidate early Earth environment, could have resulted in RNA oligomers of a putative RNA World.

Factoring Origin of Life Hypotheses into the Search for Life in the Solar System and Beyond

Two widely-cited alternative hypotheses propose geological localities and biochemical mechanisms for life's origins. The first states that chemical energy available in submarine hydrothermal vents supported the formation of organic compounds and initiated primitive metabolic pathways which became incorporated in the earliest cells; the second proposes that protocells self-assembled from exogenous and geothermally-delivered monomers in freshwater hot springs. These alternative hypotheses are relevant to the fossil record of early life on Earth, and can be factored into the search for life elsewhere in the Solar System. This review summarizes the evidence supporting and challenging these hypotheses, and considers their implications for the search for life on various habitable worlds. It will discuss the relative probability that life could have emerged in environments on early Mars, on the icy moons of Jupiter and Saturn, and also the degree to which prebiotic chemistry could have advanced on Titan. These environments will be compared to ancient and modern terrestrial analogs to assess their habitability and biopreservation potential. Origins of life approaches can guide the biosignature detection strategies of the next generation of planetary science missions, which could in turn advance one or both of the leading alternative abiogenesis hypotheses.

The Hot Spring Hypothesis for an Origin of Life

We present a testable hypothesis related to an origin of life on land in which fluctuating volcanic hot spring pools play a central role. The hypothesis is based on experimental evidence that lipid-encapsulated polymers can be synthesized by cycles of hydration and dehydration to form protocells. Drawing on metaphors from the bootstrapping of a simple computer operating system, we show how protocells cycling through wet, dry, and moist phases will subject polymers to combinatorial selection and draw structural and catalytic functions out of initially random sequences, including structural stabilization, pore formation, and primitive metabolic activity. We propose that protocells aggregating into a hydrogel in the intermediate moist phase of wet-dry cycles represent a primitive progenote system. Progenote populations can undergo selection and distribution, construct niches in new environments, and enable a sharing network effect that can collectively evolve them into the first microbial communities. Laboratory and field experiments testing the first steps of the scenario are summarized. The scenario is then placed in a geological setting on the early Earth to suggest a plausible pathway from life's origin in chemically optimal freshwater hot spring pools to the emergence of microbial communities tolerant to more extreme conditions in dilute lakes and salty conditions in marine environments. A continuity is observed for biogenesis beginning with simple protocell aggregates, through the transitional form of the progenote, to robust microbial mats that leave the fossil imprints of stromatolites so representative in the rock record. A roadmap to future testing of the hypothesis is presented. We compare the oceanic vent with land-based pool scenarios for an origin of life and explore their implications for subsequent evolution to multicellular life such as plants. We conclude by utilizing the hypothesis to posit where life might also have emerged in habitats such as Mars or Saturn's icy moon Enceladus. "To postulate one fortuitously catalyzed reaction, perhaps catalyzed by a metal ion, might be reasonable, but to postulate a suite of them is to appeal to magic." -Leslie Orgel.

Mechanical Energy before Chemical Energy at the Origins of Life?

Mechanical forces and mechanical energy are prevalent in living cells. This may be because mechanical forces and mechanical energy preceded chemical energy at life’s origins. Mechanical energy is more readily available in non-living systems than the various forms of chemical energy used by living systems. Two possible prebiotic environments that might have provided mechanical energy are hot pools that experience wet/dry cycles and mica sheets as they move, open and shut, as heat pumps or in response to water movements.

Mechanical Energy before Chemical Energy at the Origins of Life?

Mechanical forces and mechanical energy are prevalent in living cells. This may be because mechanical forces and mechanical energy preceded chemical energy at life’s origins. Mechanical energy is more readily available in non-living systems than the various forms of chemical energy used by living systems. Two possible prebiotic environments that might have provided mechanical energy are hot pools that experience wet/dry cycles and mica sheets as they move, open and shut, as heat pumps or in response to water movements.

Hydrothermal Chemistry and the Origin of Cellular Life

Two processes required for life's origin are condensation reactions that produce essential biopolymers by a nonenzymatic reaction, and self-assembly of membranous compartments that encapsulate the polymers into populations of protocells. Because life today thrives not just in the temperate ocean and lakes but also in extreme conditions of temperature, salinity, and pH, there is a general assumption that any form of liquid water would be sufficient to support the origin of life as long as there are sources of chemical energy and simple organic compounds. We argue here that the first forms of life would be physically and chemically fragile and would be strongly affected by ionic solutes and pH. A hypothesis emerges from this statement that hot springs associated with volcanic land masses have an ionic composition more conducive to self-assembly and polymerization than seawater. Here we have compared the ionic solutes of seawater with those of terrestrial hot springs. We then describe preliminary experimental results that show how the hypothesis can be tested in a prebiotic analog environment.

Mechanical Energy before Chemical Energy at the Origins of Life?

Forces and mechanical energy are prevalent in living cells. This may be because forces and mechanical energy preceded chemical energy at life’s origins. Mechanical energy is more readily available in non-living systems than the various other forms of energy used by living systems. Two possible prebiotic environments that might have provided mechanical energy are hot pools that experience wet/dry cycles and mica sheets as they move, open and shut, as heat pumps or in response to water movements.

Exploring the Kamchatka Geothermal Region in the Context of Life's Beginning

This article is a brief review of research in the Kamchatka geothermal region initiated by David Deamer and the author in 1999. Results obtained over the last 20 years are described, including a seminal experiment in which biologically important organic compounds were dispersed in a hot spring to determine their fate. Other investigations include ionic and organic composition of hydrothermal water, the source of hydrothermally generated oil, and pressure-temperature oscillations in hydrothermal systems. The relation of these results to research on the origin of life is discussed.

Origin of Life's Building Blocks in Carbon- and Nitrogen-Rich Surface Hydrothermal Vents

There are two dominant and contrasting classes of origin of life scenarios: those predicting that life emerged in submarine hydrothermal systems, where chemical disequilibrium can provide an energy source for nascent life; and those predicting that life emerged within subaerial environments, where UV catalysis of reactions may occur to form the building blocks of life. Here, we describe a prebiotically plausible environment that draws on the strengths of both scenarios: surface hydrothermal vents. We show how key feedstock molecules for prebiotic chemistry can be produced in abundance in shallow and surficial hydrothermal systems. We calculate the chemistry of volcanic gases feeding these vents over a range of pressures and basalt C/N/O contents. If ultra-reducing carbon-rich nitrogen-rich gases interact with subsurface water at a volcanic vent they result in 10 - 3 ⁻ 1 M concentrations of diacetylene (C₄H₂), acetylene (C₂H₂), cyanoacetylene (HC₃N), hydrogen cyanide (HCN), bisulfite (likely in the form of salts containing HSO₃-), hydrogen sulfide (HS-) and soluble iron in vent water. One key feedstock molecule, cyanamide (CH₂N₂), is not formed in significant quantities within this scenario, suggesting that it may need to be delivered exogenously, or formed from hydrogen cyanide either via organometallic compounds, or by some as yet-unknown chemical synthesis. Given the likely ubiquity of surface hydrothermal vents on young, hot, terrestrial planets, these results identify a prebiotically plausible local geochemical environment, which is also amenable to future lab-based simulation.

Determinism and boundedness of self-assembling structures

Self-assembly processes are widespread in nature and lie at the heart of many biological and physical phenomena. The characteristics of self-assembly building blocks determine the structures that they form. Two crucial properties are the determinism and boundedness of the self-assembly. The former tells us whether the same set of building blocks always generates the same structure, and the latter whether it grows indefinitely. These properties are highly relevant in the context of protein structures, as the difference between deterministic protein self-assembly and nondeterministic protein aggregation is central to a number of diseases. Here we introduce a graph theoretical approach that can determine the determinism and boundedness for several geometries and dimensionalities of self-assembly more accurately and quickly than conventional methods. We apply this methodology to a previously studied lattice self-assembly model and discuss generalizations to a wide range of other self-assembling systems.

Primitive Photosynthetic Architectures Based on Self-Organization and Chemical Evolution of Amino Acids and Metal Ions

The emergence of light-energy-utilizing metabolism is likely to be a critical milestone in prebiotic chemistry and the origin of life. However, how the primitive pigment is spontaneously generated still remains unknown. Herein, a primitive pigment model based on adaptive self-organization of amino acids (Cystine, Cys) and metal ions (zinc ion, Zn2+) followed by chemical evolution under hydrothermal conditions is developed. The resulting hybrid microspheres are composed of radially aligned cystine/zinc (Cys/Zn) assembly decorated with carbonate-doped zinc sulfide (C-ZnS) nanocrystals. The part of C-ZnS can work as a light-harvesting antenna to capture ultraviolet and visible light, and use it in various photochemical reactions, including hydrogen (H2) evolution, carbon dioxide (CO2) photoreduction, and reduction of nicotinamide adenine dinucleotide (NAD+) to nicotinamide adenine dinucleotide hydride (NADH). Additionally, guest molecules (e.g., glutamate dehydrogenase, GDH) can be encapsulated within the hierarchical Cys/Zn framework, which facilitates sustainable photoenzymatic synthesis of glutamate. This study helps deepen insight into the emergent functionality (conversion of light energy) and complexity (hierarchical architecture) from interaction and reaction of prebiotic molecules. The primitive pigment model is also promising to work as an artificial photosynthetic microreactor.

Amphiphilic Compounds Assemble into Membranous Vesicles in Hydrothermal Hot Spring Water but Not in Seawater

There is a general assumption that amphiphilic compounds, such as fatty acids, readily form membranous vesicles when dispersed in aqueous phases. However, from earlier studies, it is known that vesicle stability depends strongly on pH, temperature, chain length, ionic concentration and the presence or absence of divalent cations. To test how robust simple amphiphilic compounds are in terms of their ability to assemble into stable vesicles, we chose to study 10- and 12-carbon monocarboxylic acids and a mixture of the latter with its monoglyceride. These were dispersed in hydrothermal water samples drawn directly from hot springs in Yellowstone National Park at two pH ranges, and the results were compared with sea water under the same conditions. We found that the pure acids could form membranous vesicles in hydrothermal pool water, but that a mixture of dodecanoic acid and glycerol monododecanoate was less temperature-sensitive and assembled into relatively stable membranes at both acidic and alkaline pH ranges. Furthermore, the vesicles were able to encapsulate nucleic acids and pyranine, a fluorescent anionic dye. None of the amphiphiles that were tested formed stable vesicles in sea water because the high ionic concentrations disrupted membrane stability.

Wet-dry cycles enable the parallel origin of canonical and non-canonical nucleosides by continuous synthesis

The molecules of life were created by a continuous physicochemical process on an early Earth. In this hadean environment, chemical transformations were driven by fluctuations of the naturally given physical parameters established for example by wet-dry cycles. These conditions might have allowed for the formation of (self)-replicating RNA as the fundamental biopolymer during chemical evolution. The question of how a complex multistep chemical synthesis of RNA building blocks was possible in such an environment remains unanswered. Here we report that geothermal fields could provide the right setup for establishing wet-dry cycles that allow for the synthesis of RNA nucleosides by continuous synthesis. Our model provides both the canonical and many ubiquitous non-canonical purine nucleosides in parallel by simple changes of physical parameters such as temperature, pH and concentration. The data show that modified nucleosides were potentially formed as competitor molecules. They could in this sense be considered as molecular fossils.

Emergence of cytochrome bc complexes in the context of photosynthesis

The cytochrome bc (cyt bc) complexes are involved in Q-cycling; they oxidize membrane quinols by high-potential electron acceptors, such as cytochromes or plastocyanin, and generate transmembrane proton gradient. In several prokaryotic lineages, and also in plant chloroplasts, the catalytic core of the cyt bc complexes is built of a four-helical cytochrome b (cyt b) that contains three hemes, a three-helical subunit IV, and an iron-sulfur Rieske protein (cytochrome b₆ f-type complexes). In other prokaryotic lineages, and also in mitochondria, the cyt b subunit is fused with subunit IV, yielding a seven- or eight-helical cyt b with only two hemes (cyt bc₁ -type complexes). Here we present an updated phylogenomic analysis of the cyt b subunits of cyt bc complexes. This analysis provides further support to our earlier suggestion that (1) the ancestral version of cyt bc complex contained a small four-helical cyt b with three hemes similar to the plant cytochrome b₆ and (2) independent fusion events led to the formation of large cyts b in several lineages. In the search for a primordial function for the ancestral cyt bc complex, we address the intimate connection between the cyt bc complexes and photosynthesis. Indeed, the Q-cycle turnover in the cyt bc complexes demands high-potential electron acceptors. Before the Great Oxygenation Event, the biosphere had been highly reduced, so high-potential electron acceptors could only be generated upon light-driven charge separation. It appears that an ancestral cyt bc complex capable of Q-cycling has emerged in conjunction with the (bacterio)chlorophyll-based photosynthetic systems that continuously generated electron vacancies at the oxidized (bacterio)chlorophyll molecules.

The Role of Lipid Membranes in Life's Origin

At some point in early evolution, life became cellular. Assuming that this step was required for the origin of life, there would necessarily be a pre-existing source of amphihilic compounds capable of assembling into membranous compartments. It is possible to make informed guesses about the properties of such compounds and the conditions most conducive to their self-assembly into boundary structures. The membranes were likely to incorporate mixtures of hydrocarbon derivatives between 10 and 20 carbons in length with carboxylate or hydroxyl head groups. Such compounds can be synthesized by chemical reactions and small amounts were almost certainly present in the prebiotic environment. Membrane assembly occurs most readily in low ionic strength solutions with minimal content of salt and divalent cations, which suggests that cellular life began in fresh water pools associated with volcanic islands rather than submarine hydrothermal vents.

Review on the Role of Planetary Factors on Habitability

In this work various factors on the habitability were considered, focusing on conditions irrespective of the central star's radiation, to see the role of specific planetary body related effects. These so called planetary factors were evaluated to identify those trans-domain issues where important information is missing but good chance exit to be filled by new knowledge that might be gained in the next decade(s). Among these strategic knowledge gaps, specific issues are listed, like occurrence of radioactive nucleides in star forming regions, models to estimate the existence of subsurface liquid water from bulk parameters plus evolutionary context of the given system, estimation on the existence of redox gradient depending on the environment type etc. These issues require substantial improvement of modelling and statistical handling of various cases, as "planetary environment types". Based on our current knowledge it is probable that subsurface habitability is at least as frequent, or more frequent than surface habitability. Unfortunately it is more difficult from observations to infer conditions for subsurface habitability, but specific argumentation might help with indirect ways, which might result in new methods to approach habitability in general.

The RNA World as a Model System to Study the Origin of Life

Understanding how life arose is a fundamental problem of biology. Much progress has been made by adopting a synthetic and mechanistic perspective on originating life. We present a current view of the biochemistry of the origin of life, focusing on issues surrounding the emergence of an RNA World in which RNA dominated informational and functional roles. There is cause for optimism on this difficult problem: the prebiotic chemical inventory may not have been as nightmarishly complex as previously thought; the catalytic repertoire of ribozymes continues to expand, approaching the goal of self-replicating RNA; encapsulation in protocells provides evolutionary and biophysical advantages. Nevertheless, major issues remain unsolved, such as the origin of a genetic code. Attention to this field is particularly timely given the accelerating discovery and characterization of exoplanets.

A Field Trip to the Archaean in Search of Darwin's Warm Little Pond

Charles Darwin’s original intuition that life began in a “warm little pond” has for the last three decades been eclipsed by a focus on marine hydrothermal vents as a venue for abiogenesis. However, thermodynamic barriers to polymerization of key molecular building blocks and the difficulty of forming stable membranous compartments in seawater suggest that Darwin’s original insight should be reconsidered. I will introduce the terrestrial origin of life hypothesis, which combines field observations and laboratory results to provide a novel and testable model in which life begins as protocells assembling in inland fresh water hydrothermal fields. Hydrothermal fields are associated with volcanic landmasses resembling Hawaii and Iceland today and could plausibly have existed on similar land masses rising out of Earth’s first oceans. I will report on a field trip to the living and ancient stromatolite fossil localities of Western Australia, which provided key insights into how life may have emerged in Archaean, fluctuating fresh water hydrothermal pools, geological evidence for which has recently been discovered. Laboratory experimentation and fieldwork are providing mounting evidence that such sites have properties that are conducive to polymerization reactions and generation of membrane-bounded protocells. I will build on the previously developed coupled phases scenario, unifying the chemical and geological frameworks and proposing that a hydrogel of stable, communally supported protocells will emerge as a candidate Woese progenote, the distant common ancestor of microbial communities so abundant in the earliest fossil record.

Emergent Catalytic Behavior of Self-Assembled Low Molecular Weight Peptide-Based Aggregates and Hydrogels

We report a series of short peptides possessing the sequence (FE)n or (EF)n and bearing l-proline at their N-terminus that self-assemble into high aspect ratio aggregates and hydrogels. We show that these aggregates are able to catalyze the aldol reaction, whereas non-aggregated analogues are catalytically inactive. We have undertaken an analysis of the results, considering the accessibility of catalytic sites, pKa value shifts, and the presence of hydrophobic pockets. We conclude that the presence of hydrophobic regions is indeed relevant for substrate solubilization, but that the active site accessibility is the key factor for the observed differences in reaction rates. The results presented here provide an example of the emergence of a new chemical property caused by self-assembly, and support the relevant role played by self-assembled peptides in prebiotic scenarios. In this sense, the reported systems can be seen as primitive aldolase I mimics, and have been successfully tested for the synthesis of simple carbohydrate precursors.

Hydrothermal Conditions and the Origin of Cellular Life

The conditions and properties of hydrothermal vents and hydrothermal fields are compared in terms of their ability to support processes related to the origin of life. The two sites can be considered as alternative hypotheses, and from this comparison we propose a series of experimental tests to distinguish between them, focusing on those that involve concentration of solutes, self-assembly of membranous compartments, and synthesis of polymers. Key Word: Hydrothermal systems.

Faceted fatty acid vesicles formed from single-tailed perfluorinated surfactants

The aggregation behavior and rheological properties of two mixtures of perfluorononanoic acid (PFNA)/NaOH and perfluorodecanoic acid (PFDA)/NaOH were investigated in aqueous solutions. Interestingly, pH-sensitive polyhedral fatty acid vesicles were spontaneously formed in both systems, which were determined by freeze-fracture transmission electron microscopy (FF-TEM) measurements. Especially, a phase transition from faceted vesicles to the L3 phase with the increase of pH was observed in the PFNA/NaOH system while it was not observed in the PFDA/NaOH system. Differential scanning calorimetry (DSC) and wide angle X-ray scattering (WAXS) measurements confirmed that the bilayers of the faceted vesicles were in the crystalline station indicating that the crystallization of fluorocarbon chains was the main driving force for their formation. Besides, the two systems of faceted perfluorofatty acid vesicles exhibit interesting rheological properties, for instance, they showed high viscoelasticity and shear-thinning behaviour, and the elastic modulus (G') and viscous modulus (G'') of PFDA/NaOH vesicles were much higher than those of PFNA/NaOH vesicles. Conversely, the solution of the L3 phase with fluid bilayers did not present viscoelastic properties. Therefore, the viscoelastic properties of vesicles resulted from the crystalline fluorinated alkyl chains with high rigidity at room temperature and the dense packing of vesicles. As far as we know, such faceted fatty acid vesicles formed from single-tailed perfluorinated surfactants have been rarely reported. Our work successfully constructs polyhedral fatty acid vesicles and proposes their formation mechanism, which should be a great advance in the fundamental research of fatty acid vesicles.

Hydrothermal Systems of Kamchatka are Models of the Prebiotic Environment

The composition of organic matter and fluctuations of thermodynamic parameters were investigated in the hydrothermal systems of the Kamchatka peninsula in the context of the origin of life. Organics were analyzed by gas-chromatography/mass spectrometry, and 111 organic compounds belonging to 14 homologous series (aromatic hydrocarbons, alkanes and isoalkanes, halogenated aromatic hydrocarbons, carboxylic acids, esters, etc.) were found in hot springs inhabited by Archaeal and Bacterial thermophiles. The organics detected in the sterile condensate of water-steam mixture taken from deep boreholes (temperature 108-175 °C) consisted of 69 compounds of 11 homologous series, with aromatic hydrocarbons and alkanes being prevalent. The organic material included important prebiotic components such as nitrogen-containing compounds and lipid precursors. A separate organic phase (oil) was discovered in the Uzon Caldera. A biogenic origin is supported by the presence of sterane and hopane biomarkers and the δ(13)C value of the bulk oil; its age determined by (14)C measurements was 1030 ± 40 years. Multilevel fluctuations of thermodynamic parameters proposed to be required for the origin of life were determined in the Mutnovsky and Pauzhetsky hydrothermal systems. The low-frequency component of the hydrothermal fluid pressure varied by up to 2 bars over periods of hours to days, while mid-frequency variations had regular micro-oscillations with periods of about 20 min; the high-frequency component displayed sharp changes of pressure and microfluctuations with periods less than 5 min. The correlation coefficient between pressure and temperature ranges from 0.89 to 0.99 (average 0.96). The natural regimes of pressure and temperature fluctuations in Kamchatka hydrothermal systems can guide future experiments on prebiotic chemistry under oscillating conditions.

Coupled phases and combinatorial selection in fluctuating hydrothermal pools: a scenario to guide experimental approaches to the origin of cellular life

Hydrothermal fields on the prebiotic Earth are candidate environments for biogenesis. We propose a model in which molecular systems driven by cycles of hydration and dehydration in such sites undergo chemical evolution in dehydrated films on mineral surfaces followed by encapsulation and combinatorial selection in a hydrated bulk phase. The dehydrated phase can consist of concentrated eutectic mixtures or multilamellar liquid crystalline matrices. Both conditions organize and concentrate potential monomers and thereby promote polymerization reactions that are driven by reduced water activity in the dehydrated phase. In the case of multilamellar lipid matrices, polymers that have been synthesized are captured in lipid vesicles upon rehydration to produce a variety of molecular systems. Each vesicle represents a protocell, an “experiment” in a natural version of combinatorial chemistry. Two kinds of selective processes can then occur. The first is a physical process in which relatively stable molecular systems will be preferentially selected. The second is a chemical process in which rare combinations of encapsulated polymers form systems capable of capturing energy and nutrients to undergo growth by catalyzed polymerization. Given continued cycling over extended time spans, such combinatorial processes will give rise to molecular systems having the fundamental properties of life.

The dynamics of the RNA world: insights and challenges

The RNA world hypothesis of the origin of life, in which RNA emerged as both enzyme and information carrier, is receiving solid experimental support. The prebiotic synthesis of biomolecules, the catalytic aid offered by mineral surfaces, and the vast enzymatic repertoire of ribozymes are only pieces of the origin of life puzzle; the full picture can only emerge if the pieces fit together by either following from one another or coexisting with each other. Here, we review the theory of the origin, maintenance, and enhancement of the RNA world as an evolving population of dynamical systems. The dynamical view of the origin of life allows us to pinpoint the missing and the not fitting pieces: (1) How can the first self-replicating ribozyme emerge in the absence of template-directed information replication? (2) How can nucleotide replicators avoid competitive exclusion despite utilizing the very same resources (nucleobases)? (3) How can the information catastrophe be avoided? (4) How can enough genes integrate into a cohesive system in order to transition to a cellular stage? (5) How can the way information is stored and metabolic complexity coevolve to pave to road leading out of the RNA world to the present protein-DNA world?

Characterization of RNA-Like Oligomers from Lipid-Assisted Nonenzymatic Synthesis: Implications for Origin of Informational Molecules on Early Earth

Prebiotic polymerization had to be a nonenzymatic, chemically driven process. These processes would have been particularly favored in scenarios which push reaction regimes far from equilibrium. Dehydration-rehydration (DH-RH) cycles are one such regime thought to have been prevalent on prebiotic Earth in niches like volcanic geothermal pools. The present study defines the optimum DH-RH reaction conditions for lipid-assisted polymerization of nucleotides. The resultant products were characterized to understand their chemical makeup. Primarily, our study demonstrates that the resultant RNA-like oligomers have abasic sites, which means these oligomers lack information-carrying capability because of losing most of their bases during the reaction process. This results from low pH and high temperature conditions, which, importantly, also allows the formation of sugar-phosphate oligomers when ribose 5'-monophosphates are used as the starting monomers instead. Formation of such oligomers would have permitted sampling of a large variety of bases on a preformed polymer backbone, resulting in “prebiotic phosphodiester polymers” prior to the emergence of modern RNA-like molecules. This suggests that primitive genetic polymers could have utilized bases that conferred greater N-glycosyl bond stability, a feature crucial for information propagation in low pH and high temperature regimes of early Earth.

Salt-promoted synthesis of RNA-like molecules in simulated hydrothermal conditions

A fundamental problem in origins of life research is how the first polymers with the properties of nucleic acids were synthesized and incorporated into living systems on the prebiotic Earth. Here, we show that RNA-like polymers can be synthesized non-enzymatically from 5'-phosphate mononucleosides in salty environments. The polymers were identified and analyzed by gel electrophoresis, nanopore analysis, UV spectra, and action of RNases. The synthesis of phosphodiester bonds is driven by the chemical potential made available in the fluctuating hydrated and anhydrous conditions of hydrothermal fields associated with volcanic land masses.

NMR studies of the chiral selectivity of self-assembled guanosinemonophosphate

Among nucleobases in RNA and DNA, only guanine exhibits reversible self-assembly through Hoogsteen hydrogen bonding. Resulting "G-tetrads" are building blocks of higher-order structures of guanosine compounds, including GMP. These can further associate to form chiral, columnar assemblies, stabilized by a centrally located cation such as K(+). Here, we detail chiral selectivity of GMP under conditions for assembly, as previously used to separate enantiomeric solutes by capillary electrophoresis (CE). Using (1)H NMR, we track multisite chemical-shift responses vs the concentration of various chiral solutes with GMP. Shift changes in both GMP and the solutes are consistent with a structural model in which grooves of transiently assembled GMP are templates for chiral selection. This can also explain a previously noted superiority of selection for solutes with extended ring systems projecting from the chiral center. Here, site-by-site NMR shift changes (and their enantiomeric differential) are strongest at the ring extremities in d- vs l-tryptophan and R- vs S-BNPA. This is consistent with the fact that, for one enantiomer of each pair, steric hindrance prevents closest approach into assembled GMP. For smaller solutes (d/l-Trp and d/l-Phe), NMR reveals only slight (Tyr) or no (Phe) chiral discrimination, consistent with their failure to resolve in CE through GMP media. We present molecular models to visualize and evaluate a proposed mode of selection.

Guanine-centric self-assembly of nucleotides in water: an important consideration in prebiotic chemistry

Investigations of plausible prebiotic chemistry on early Earth must consider not only chemical reactions to form more complex products such as proto-biopolymers but also reversible, molecular self-assembly that would influence the availability, organization, and sequestration of reactant molecules. The self-assembly of guanosine compounds into higher-order structures and lyotropic liquid crystalline "gel" phases through formation of hydrogen-bonded guanine tetrads (G-tetrads) is one such consideration that is particularly relevant to an RNA-world scenario. G-tetrad-based gelation has been well studied for individual guanosine compounds and was recently observed in mixtures of guanosine with 5'-guanosine monophosphate (GMP) as well. The present work investigates the self-assembly of GMP in the presence of the other RNA nucleotides. Effects of the total concentration and relative proportion of the nucleotides in the mixtures, the form (disodium salt vs. free acid) of the nucleotides, temperature, pH, and salt concentration were determined by visual observations and circular dichroism (CD) spectroscopy. The results show that formation of cholesteric G-tetrad phases is influenced by interactions with other nucleotides, likely through association (e.g., intercalation) of the nucleotides with the G-tetrad structures. These interactions affect the structure and stability of the G-tetrad gel phase, as well as the formation of alternate self-assembled GMP structures such as a continuous, hydrogen-bonded GMP helix or dimers and aggregates of GMP. These interactions and multiple equilibria are influenced by the presence of cations, especially in the presence of K(+). This work could have important implications for the emergence of an RNA or proto-RNA world, which would require mixtures of nucleotides at sufficiently high, local concentrations for abiotic polymerization to occur.