NUCLEOTIDE SYNTHESIS UNDER POSSIBLE PRIMITIVE EARTH CONDITIONS

(Photoredox) Organocatalysis in the Emergence of Life: Discovery, Applications, and Molecular Evolution

ConspectusLife as we know it is built on complex and perfectly interlocking processes that have evolved over millions of years through evolutionary optimization processes. The emergence of life from nonliving matter and the evolution of such highly efficient systems therefore constitute an enormous synthetic and systems chemistry challenge. Advances in supramolecular and systems chemistry are opening new perspectives that provide insights into living and self-sustaining reaction networks as precursors for life. However, the ab initio synthesis of such a system requires the possibility of autonomous optimization of catalytic properties and, consequently, of an evolutionary system at the molecular level. In this Account, we present our discovery of the formation of substituted imidazolidine-4-thiones (photoredox) organocatalysts from simple prebiotic building blocks such as aldehydes and ketones under Strecker reaction conditions with ammonia and cyanides in the presence of hydrogen sulfide. The necessary aldehydes are formed from CO2 and hydrogen under prebiotically plausible meteoritic or volcanic iron-particle catalysis in the atmosphere of the early Earth. Remarkably, the investigated imidazolidine-4-thiones undergo spontaneous resolution by conglomerate crystallization, opening a pathway for symmetry breaking, chiral amplification, and enantioselective organocatalysis. These imidazolidine-4-thiones enable α-alkylations of aldehydes and ketones by photoredox organocatalysis. Therefore, these photoredox organocatalysts are able to modify their aldehyde building blocks, which leads in an evolutionary process to mutated second-generation and third-generation catalysts. In our experimental studies, we found that this mutation can occur not only by new formation of the imidazolidine core structure of the catalyst from modified aldehyde building blocks or by continuous supply from a pool of available building blocks but also by a dynamic exchange of the carbonyl moiety in ring position 2 of the imidazolidine moiety. Remarkably, it can be shown that by incorporating aldehyde building blocks from their environment, the imidazolidine-4-thiones are able to change and adapt to altering environmental conditions without undergoing the entire formation process. The selection of the mutated catalysts is then based on the different catalytic activities in the modification of the aldehyde building blocks and on the catalysis of subsequent processes that can lead to the formation of molecular reaction networks as progenitors for cellular processes. We were able to show that these imidazolidine-4-thiones not only enable α-alkylations but also facilitate other important transformations, such as the selective phosphorylation of nucleosides to nucleotides as a key step leading to the oligomerization to RNA and DNA. It can therefore be expected that evolutionary processes have already taken place on a small molecular level and have thus developed chemical tools that change over time, representing a hidden layer on the path to enzymatically catalyzed biochemical processes.

Prebiotic chemistry: a review of nucleoside phosphorylation and polymerization

The phosphorylation of nucleosides and their polymerization are crucial issues concerning the origin of life. The question of how these plausible chemical processes took place in the prebiotic Earth is still perplexing, despite several studies that have attempted to explain these prebiotic processes. The purpose of this article is to review these chemical reactions with respect to chemical evolution in the primeval Earth. Meanwhile, from our perspective, the chiral properties and selection of biomolecules should be considered in the prebiotic chemical origin of life, which may contribute to further research in this field to some extent.

Phosphorylation in liquid sulfur dioxide under prebiotically plausible conditions

In nature, organophosphates provide key functions such as information storage and transport, structural tasks, and energy transfer. Since condensations are unfavourable in water and nucleophilic attack at phosphate is kinetically inhibited, various abiogenesis hypotheses for the formation of organophosphate are discussed. Recently, the application of phosphites as phosphorylation agent showed promising results. However, elevated temperatures and additional reaction steps are required to obtain organophosphates. Here we show that in liquid sulfur dioxide, which acts as solvent and oxidant, efficient organophosphate formation is enabled. Phosphorous acid yields up to 32.6% 5' nucleoside monophosphate, 3.6% 5' nucleoside diphosphate, and the formation of nucleoside triphosphates and dinucleotides in a single reaction step at room temperature. In addition to the phosphorylation of organic compounds, we observed diserine formation. Thus, we suggest volcanic environments as reaction sites for biopolymer formation on Early Earth. Because of the simple recyclability of sulfur dioxide, the reaction is also interesting for synthesis chemistry.

Prebiotic Chemistry: The Role of Trimetaphosphate in Prebiotic Chemical Evolution

Life’s origins have always been a scientific puzzle. Understanding the production of biomolecules is crucial for understanding the evolution of life on Earth. Numerous studies on trimetaphosphate have been conducted in the field of prebiotic chemistry. However, its role in prebiotic chemistry has been documented infrequently in the review literature. The goal of this thesis is to review the role of trimetaphosphate in the early Earth’s biomolecule synthesis and phosphorylation. Additionally, various trimetaphosphate-mediated reaction pathways are discussed, as well as the role of trimetaphosphate in prebiotic chemistry. Finally, in our opinion, interactions between biomolecules should be considered in prebiotic synthesis scenarios since this may result in some advances in subsequent research on this subject. The research establishes an essential and opportune foundation for an in-depth examination of the “mystery of life".

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 (PO₄^3-) 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 (HPO₃^2-) 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.

Silicate-, Magnesium Ion-, and Urea-Induced Prebiotic Phosphorylation of Uridine via Pyrophosphate; Revisiting the Hot Drying Water Pool Scenario

The availability of nucleotides on the early Earth is of great significance for the origin of a self-replicating system capable of undergoing evolution. We hereby report the successful phosphorylation reactions of the nucleoside uridine under heating in the "drying pool" prebiotic model at temperatures ranging from 60-75 °C, and by using pyrophosphate as a phosphorylation agent. Uridine monophosphates (UMP) such as uridine-5'-monophosphate (5'-UMP), 2'-UMP, and 3'-UMP, as well as cyclic 2'-3'-UMP, were identified by ³¹P-NMR. In addition to the above-mentioned products, a dimer of uridine-phosphate-uridine (U-P-U) was also observed. The reactions were promoted by white quartz sand, Mg²⁺, and by using urea as a condensation agent. The reactions also proceeded without this mixture; however, the yields increased remarkably with the presence of the above-mentioned materials. The results suggest that a hot/evaporating-drying pool of water containing organics, salts, and reactive phosphorus could be sufficient to form significant phosphate esters.

The Prebiotic Provenance of Semi-Aqueous Solvents

The numerous and varied roles of phosphorylated organic molecules in biochemistry suggest they may have been important to the origin of life. The prominence of phosphorylated molecules presents a conundrum given that phosphorylation is a thermodynamically unfavorable, endergonic process in water, and most natural sources of phosphate are poorly soluble. We recently demonstrated that a semi-aqueous solvent consisting of urea, ammonium formate, and water (UAFW) supports the dissolution of phosphate and the phosphorylation of nucleosides. However, the prebiotic feasibility and robustness of the UAFW system are unclear. Here, we study the UAFW system as a medium in which phosphate minerals are potentially solubilized. Specifically, we conduct a series of chemical experiments alongside thermodynamic models that simulate the formation of ammonium formate from the hydrolysis of hydrogen cyanide, and demonstrate the stability of formamide in such solvents (as an aqueous mixture). The dissolution of hydroxylapatite requires a liquid medium, and we investigate whether a UAFW system is solid or liquid over varied conditions, finding that this characteristic is controlled by the molar ratios of the three components. For liquid UAFW mixtures, we also find the solubility of phosphate is higher when the quantity of ammonium formate is greater than urea. We suggest the urea within the system can lower the activity of water, help create a stable and persistent solution, and may act as a condensing agent/catalyst to improve nucleoside phosphorylation yields.

Synthesis of ribonucleotides from the corresponding ribonucleosides under plausible prebiotic conditions within self-assembled supramolecular structures

Abiotic synthesis of ribonucleotides, mainly at the 5′ position, from the corresponding ribonucleosides within guanosine:borate hydrogels in the temperature range of 70–90 °C, using urea and a phosphate source (K₂HPO₄ or hydroxyapatite).

A role for phosphorus redox in emerging and modern biochemistry

Phosphorus is a major biogeochemical element controlling growth in many ecosystems. It has presumably been an important element since the onset of life. In most chemical and biochemical considerations, phosphorus is synonymous with phosphates, a pentavalent oxidation state that includes the phosphate backbone of DNA and RNA, as well as major metabolites such as ATP. However, redox processing of phosphates to phosphites and phosphonates, and to even lower oxidation states provides a work-around to many of the problems of prebiotic chemistry, including phosphorus's low solubility and poor reactivity. In addition, modern phosphorus cycling has increasingly identified reduced P compounds as playing a role, sometimes significant, in biogeochemical processes. This suggests that phosphorus is not redox-insensitive and reduced P compounds should be considered as part of the phosphorus biogeochemical cycle.

A Chemist's Perspective on the Role of Phosphorus at the Origins of Life

The central role that phosphates play in biological systems, suggests they also played an important role in the emergence of life on Earth. In recent years, numerous important advances have been made towards understanding the influence that phosphates may have had on prebiotic chemistry, and here, we highlight two important aspects of prebiotic phosphate chemistry. Firstly, we discuss prebiotic phosphorylation reactions; we specifically contrast aqueous electrophilic phosphorylation, and aqueous nucleophilic phosphorylation strategies, with dry-state phosphorylations that are mediated by dissociative phosphoryl-transfer. Secondly, we discuss the non-structural roles that phosphates can play in prebiotic chemistry. Here, we focus on the mechanisms by which phosphate has guided prebiotic reactivity through catalysis or buffering effects, to facilitating selective transformations in neutral water. Several prebiotic routes towards the synthesis of nucleotides, amino acids, and core metabolites, that have been facilitated or controlled by phosphate acting as a general acid-base catalyst, pH buffer, or a chemical buffer, are outlined. These facile and subtle mechanisms for incorporation and exploitation of phosphates to orchestrate selective, robust prebiotic chemistry, coupled with the central and universally conserved roles of phosphates in biochemistry, provide an increasingly clear message that understanding phosphate chemistry will be a key element in elucidating the origins of life on Earth.

Has Inositol Played Any Role in the Origin of Life?

Phosphorus, as phosphate, plays a paramount role in biology. Since phosphate transfer reactions are an integral part of contemporary life, phosphate may have been incorporated into the initial molecules at the very beginning. To facilitate the studies into early phosphate utilization, we should look retrospectively to phosphate-rich molecules present in today’s cells. Overlooked by origin of life studies until now, inositol and the inositol phosphates, of which some species possess more phosphate groups that carbon atoms, represent ideal molecules to consider in this context. The current sophisticated association of inositol with phosphate, and the roles that some inositol phosphates play in regulating cellular phosphate homeostasis, intriguingly suggest that inositol might have played some role in the prebiotic process of phosphate exploitation. Inositol can be synthesized abiotically and, unlike glucose or ribose, is chemically stable. This stability makes inositol the ideal candidate for the earliest organophosphate molecules, as primitive inositol phosphates. I also present arguments suggesting roles for some inositol phosphates in early chemical evolution events. Finally, the possible prebiotic synthesis of inositol pyrophosphates could have generated high-energy molecules to be utilized in primitive trans-phosphorylating processes.

Spontaneous formation and base pairing of plausible prebiotic nucleotides in water

The RNA World hypothesis presupposes that abiotic reactions originally produced nucleotides, the monomers of RNA and universal constituents of metabolism. However, compatible prebiotic reactions for the synthesis of complementary (that is, base pairing) nucleotides and mechanisms for their mutual selection within a complex chemical environment have not been reported. Here we show that two plausible prebiotic heterocycles, melamine and barbituric acid, form glycosidic linkages with ribose and ribose-5-phosphate in water to produce nucleosides and nucleotides in good yields. Even without purification, these nucleotides base pair in aqueous solution to create linear supramolecular assemblies containing thousands of ordered nucleotides. Nucleotide anomerization and supramolecular assemblies favour the biologically relevant β-anomer form of these ribonucleotides, revealing abiotic mechanisms by which nucleotide structure and configuration could have been originally favoured. These findings indicate that nucleotide formation and selection may have been robust processes on the prebiotic Earth, if other nucleobases preceded those of extant life.

One of the questions for prebiotic chemistry is the formation of complementary base pairing systems. Here, the authors show that plausible two prebiotic heterocycles can form glycosidic bonds with ribose in water and that these spontaneously base-pair in aqueous solution.

The evolution of the surface of the mineral schreibersite in prebiotic chemistry

We demonstrate a synthesis of the meteoritic mineral schreibersite (Fe,Ni)₃P, study its surface chemistry, and show prebiotic phosphorylation.

Nucleoside phosphorylation by the mineral schreibersite

Phosphorylation of the nucleosides adenosine and uridine by the simple mixing and mild heating of aqueous solutions of the organic compounds with synthetic analogs of the meteoritic mineral schreibersite, (Fe,Ni)₃P under slightly basic conditions (pH ~9) is reported. These results suggest a potential role for meteoritic phosphorus in the origin and development of early life.

Drawbacks of the ancient RNA-based life-like system under primitive earth conditions

Following the discovery of ribozymes, the "RNA world" hypothesis has become the most accepted hypothesis concerning the origin of life and genetic information. However, this hypothesis has several drawbacks. Verification of the hypothesis from different viewpoints led us to proposals from the viewpoint of the hydrothermal origin of life, solubility of RNA and related biopolymers, and the possibility of creating an evolutionary system comparable to the in vitro selection technique for functional RNA molecules based on molecular biology.

Rethinking early Earth phosphorus geochemistry

Phosphorus is a key biologic element, and a prebiotic pathway leading to its incorporation into biomolecules has been difficult to ascertain. Most potentially prebiotic phosphorylation reactions have relied on orthophosphate as the source of phosphorus. It is suggested here that the geochemistry of phosphorus on the early Earth was instead controlled by reduced oxidation state phosphorus compounds such as phosphite (HPO(3)(2-)), which are more soluble and reactive than orthophosphates. This reduced oxidation state phosphorus originated from extraterrestrial material that fell during the heavy bombardment period or was produced during impacts, and persisted in the mildly reducing atmosphere. This alternate view of early Earth phosphorus geochemistry provides an unexplored route to the formation of pertinent prebiotic phosphorus compounds, suggests a facile reaction pathway to condensed phosphates, and is consistent with the biochemical usage of reduced oxidation state phosphorus compounds in life today. Possible studies are suggested that may detect reduced oxidation state phosphorus compounds in ancient Archean rocks.

Thermal synthesis of nucleoside H-phosphonates under mild conditions

Nucleosides react rapidly with ammonium phosphite ((NH4)2HPO3) at 60 degrees C to produce good yields of nucleoside-5'-phosphite monoesters within 24 h. Under the same conditions, ammonium phosphate is unreactive, producing low yields of nucleotide only after extended reactions. These results confirm earlier suggestions that nucleoside H-phosphonates and their possible condensation products may have been produced on the primitive earth more easily than nucleotides.

pH profile of the adsorption of nucleotides onto montmorillonite. I. Selected homoionic clays

The effect of adsorbed ions and pH on the adsorption of several purine and pyrimidine nucleotides on montmorillonite was studied. The cations used to prepare homoionic montmorillonite was Na+, Mn2+, Fe3+, Co2+, Ni+, Cu2+, and Zn2+. The nucleotides studied were 5'-,3'-, and 2'-AMP, and 5'-CMP in the pH range 2 through 12. The results show that preferential adsorption amongst nucleotides and similar molecules is dependent upon pH and the nature of the substituted metal cation in the clay. At neutral pH, it was observed that 5'-AMP was more strongly adsorbed than 2'AMP, 3'-AMP, and 5'-CMP. Cu2+ and Zn2+ clays showed enhanced adsorption of 5'-AMP compared to the other cation clays studied in the pH range 4-8. Below pH 4, the adsorption is attributed to cation and anion exchange adsorption mechanisms: above pH 4, anion exchange may also occur, but the adsorption (when it occurs) likely depends on a complexation mechanism occurring between metal cation in the clay exchange site the biomolecule. It is thus proposed that homoionic clays may have played a significant role in the concentration mechanism of biomonomers in the prebiotic environment, a prerequisite step necessary for the formation of biopolymers in the remaining steps leading to the origin of life.

Modulation of adenosine 5'-monophosphate adsorption onto aqueous resident pyrite: potential mechanisms for prebiotic reactions

The adsorption of adenosine 5'-monophosphate (5'-AMP) onto pyrite (FeS2) and its modulation by acetate, an organic precursor of complex metabolic pathways, was studied in aqueous media that simulate primitive environments. 5'-AMP adsorption requires divalent cations, indicating that a cationic bridge mediates its attachment to negatively charged sites of the mineral surface. The isotherm of 5'-AMP adsorption exhibits a strong cooperative effect at low nucleotide concentrations in acetate-rich medium, whereas high levels of adsorption were only found at high nucleotide concentrations in a model of primitive seawater (acetate free). The modulating role of acetate is also evidenced in the presence of high dipolar moment molecules: dimethyl sulfoxide (Me2SO) and dimethyl formamide (DMF) strongly inhibit 5'-AMP adsorption in acetate-rich media, whereas no effect of DMF was found in artificial seawater. The observation that exogenous divalent cations are not needed for acetate attachment onto FeS2 reveals that organic acids can interact with the Fe2+ atoms in the mineral surface. All considered, the results show that complex and flexible ironsulfide/biomonomers interactions can be modulated by molecules that accumulate in the interface layer.

Prebiotic formation of ADP and ATP from AMP, calcium phosphates and cyanate in aqueous solution

Adenosine-5'-triphosphate was synthesized by the phosphorylation of adenosine-5'-diphosphate in aqueous solution containing cyanate as a condensing reagent and insoluble calcium phosphate produced from phosphate and calcium chloride. In a similar manner, adenosine-5'-diphosphate was synthesized from adenosine-5'-monophosphate. When the experiment was carried out in the conditions of 4 degrees C and pH 5.75, the formation of adenosine-5'-diphosphate and adenosine-5'-triphosphate from adenosine-5'-monophosphate was observed in the yields of 19 and 7%, respectively. The other nucleoside-5'-triphosphates were also produced from their respective diphosphates.

Are polyphosphates or phosphate esters prebiotic reagents?

It is widely held that there was a phosphate compound in prebiotic chemistry that played the role of adenosine triphosphate and that the first living organisms had ribose-phosphate in the backbone of their genetic material. However, there are no known efficient prebiotic synthesis of high-energy phosphates or phosphate esters. We review the occurrence of phosphates in Nature, the efficiency of the volcanic synthesis of P4O10, the efficiency of polyphosphate synthesis by heating phosphate minerals under geological conditions, and the use of high-energy organic compounds such as cyanamide or hydrogen cyanide. These are shown to be inefficient processes especially when the hydrolysis of the polyphosphates is taken into account. For example, if a whole atmosphere of methane or carbon monoxide were converted to cyanide which somehow synthesized polyphosphates quantitatively, the polyphosphate concentration in the ocean would still have been insignificant. We also attempted to find more efficient high-energy polymerizing agents by spark discharge syntheses, but without success. There may still be undiscovered robust prebiotic syntheses of polyphosphates, or mechanisms for concentrating them, but we conclude that phosphate esters may not have been constituents of the first genetic material. Phosphoanhydrides are also unlikely as prebiotic energy sources.

Adsorption of 5'-AMP and catalytic synthesis of 5'-ADP onto phosphate surfaces: correlation to solid matrix structures

A non-enzymatic formation of 5'-ADP starting from phosphorylation of 5'-AMP in the presence of either calcium phosphate or calcium pyrophosphate precipitates is reported. This reaction is taken as a model for the study of heterogeneous catalysis of transphosphorylation in prebiotic conditions. Experiments were performed in completely aqueous media and in media containing dimethyl sulfoxide (Me2SO), to simulate periods of dehydration in primitive aquatic environments. It has been observed that the nucleotide is adsorbed onto both calcium phosphate and calcium pyrophosphate in accordance with Langmuir isotherms. Adsorptive capacity and affinity of the precipitates for nucleotide are changed by the presence of Me2SO, suggesting that the interaction between biomonomers and surfaces can be modulated by the degree of hydration of the anionic components of these compounds. In completely aqueous environments, formation of 5'-ADP from 5'-AMP adsorbed on precipitates of calcium phosphate and calcium pyrophosphate is very small. However, in the presence of 60% Me2SO this synthesis increases by factors of 3 and 6 for surfaces of calcium phosphate and calcium pyrophosphate, respectively, and follows first-order kinetics. Determinations of free energy changes show that phosphorylation of 5'-AMP adsorbed to these precipitates is thermodynamically favorable. Depending on the precipitation time of the samples and the composition of the medium, structural analysis of these precipitates by electron and X-ray diffraction shows changes in their cristallinity grade. It is proposed that these changes are responsible for the modulation of the quantity of adsorbed nucleotides to the surface of solid matrices as well as the catalytic activity of the precipitates.

Radiation and thermal stabilities of adenine nucleotides

We have investigated in detail radiation and thermal stabilities and transformations of adenosine mono- and triphosphates in liquid and frozen solid aqueous solutions within a wide range of absorbed radiation dose (up to 75 kGy) and temperature (up to 160 degrees C). Dephosphorylation is the main pathway of high temperature hydrolysis of adenine nucleotides. Basic thermodynamic and kinetic parameters of this process have been determined. Radiolysis of investigated compounds at room temperature results in scission of N-glycosidic bond with a radiation yield about of 1 mol/100 eV. Solution freezing significantly enhances radiation stability of nucleotides as well as other biomolecules. This circumstance is essential in the discussion of panspermia concepts.

Volcanic production of polyphosphates and its relevance to prebiotic evolution

Phosphates would probably have been essential compounds for prebiotic evolution on the primitive Earth. In this context, there have been several studies of condensation of water-soluble phosphates to polyphosphates and phosphorylation and condensation or polymerization of biomolecules with polyphosphates. But most of the phosphorus on the early Earth would have been in the form of water-insoluble apatite, and the origin of the water-soluble polyphosphates required for prebiotic evolution has therefore been a mystery. Here we show, both from experiments that simulate magmatic conditions and from analysis of volatile condensates in volcanic gas, that volcanic activity can produce water-soluble polyphosphates through partial hydrolysis of P4O10. This mechanism seems to be the only viable route identified so far for the production of these species on the primitive Earth.

Nucleoside and deoxynucleoside phosphorylation in formamide solutions

Nucleosides or deoxynucleosides were converted to a number of phosphorylated nucleotide and deoxynucleotide derivatives by ammonium of alkali dihydrogen phosphates in formamide. Conversions were smaller and slower at room temperature and greater and faster at elevated temperatures. Nucleotides afforded product mixtures to those obtained for nucleosides under the same conditions, indicating the occurrence of transphosphorylation processes. Products of the reaction at elevated temperatures were cyclic nucleotides, nucleoside monophosphates, nucleoside diphosphates and cyclic nucleotide phosphates. The relative amounts of products formed were quite temperature dependent. Cyclic nucleotides were found to be in greatest abundance for reactions run at 125 degree or above. Relative yields of 2',3' and 5' nucleotides and 3' and 5' deoxynucleotides from several experiments are reported. 5'Monophosphates were generally found to be present in larger quantities than 2' or 3' monophosphates. 2'-Deoxyadenosine showed a preference for phosphorylation at the 3' position. Conclusion reached from mechanistic studies are that the phosphorylations are a series of equilibrium reactions, with cyclic nucleotides being formed irreversibly.

A neutral theory of biogenesis

The selective Darwinian theory of chemical evolution is critically reviewed and the tentative conclusion is reached that neither the theoretical analyses nor the experiments with phages can really prove it. An alternative proposal is put forth which considers the possibility that the biogenetic process has been driven by stochastic forces, e.g. it took place in the absence of Darwinian selection which, in turn, started only when the first protocells came into existence. The dynamics of the early self-organization of living structures should be understood in terms of self-assembly. The complexification of living matter is thus not represented as a gradual phenomenon but as a series of abrupt and relatively fast transitions consisting in the aggregation of pre-systems which had evolved by their own. The shift towards new and variegated states proposed by the bifurcation theory are not considered particularly relevant for reasons reported in the test, nor is it believed that dissipation can entirely account for the order observed in living cells.

A conformational rationale for the origin of the mechanism of nucleicacid-directed protein synthesis of 'living' organisms

The physical basis for the natural evolution of a primitive decoding system is presented using the concepts of molecular interactions. Oligoribonucleotides of five residues having U at the 5'-end, a purine at the 3'-end and any combination of three bases in the middle is taken as a primitive tRNA (PIT). From conformational considerations PIT is expected to have U-turn conformation wherein, N3-H3 of base U hydrogen-bonds with phosphate, three residues ahead leaving triplet bases called primitive anticodons (PAC) into a helical conformation, and this creates a cleft between U and PAC. An amino acid can be comfortably nestled into the cleft with the amide hydrogens and carboxyl oxygen hydrogen-bonded to the last purine and the first uridine, while the side-chain can interact with the cleft side of PAC. The other side of PAC is free to base-pair with triplet codons on a longer RNA. Also two PACs can 'recognize' consecutive triplet codons, and this leads to a dynamic interaction in which the amino and carboxyl ends are brought into proximity, making the formation of peptide bond feasible. The cleft formed by different anticodon triplets, broadly speaking, shows preferences for the corresponding amino acids of the presently known codon assignment. Thus the nucleicacid-directed protein synthesis, which is a unique feature of all 'living' organisms is shown to be a natural consequence of a particular way of favourable interaction between nucleic acids and amino acids, and our model provides the missing link between the chemical evolution of small organic molecules and biological evolution through the process of mutations in nucleicacids and nucleicacid-directed protein synthesis.

Ion-exchange separation of nucleic acid constituents by high-performance liquid chromatography

The high-performance liquid chromatographic separation of a large variety of nucleic acid constituents on a silica-based, weak-anion exchange column was accomplished. Using this technique it was possible to achieve some relatively difficult separations, such as the separation of 2'-, 3'-, and 5'-AMP, and the separation of a mixture of ribo- and deoxyribo-nucleosides and -nucleotides. A number of other separations are demonstrated by isocratic or gradient elution. These include the separation of a mixture of nucleoside monophosphates, the separation of a mixture of nucleoside mono-, di-, and triphosphates, the separation of a mixture of nucleosides and bases, and the separation of a mixture of nucleotide oligomers. These chromatographic separations were accomplished using relatively simple experimental procedures at ambient temperatures and involved relatively short analysis times. Excellent separations were obtained, in most cases, by adjustment of buffer concentration and pH, or by addition of an organic modifier. In some cases, it was necessary to use gradient elution to achieve optimum resolution.

Prebiotic phosphorylation of nucleosides in formamide

A possible prebiotic phosphorylation method has been investigated in which formamide served as the reaction medium. Nucleotides and nucleotide derivatives were formed when nucleosides were allowed to react with different orthophosphate, hydrogen phosphate or dihydrogen phosphate salts or with different condensed phosphate salts. The reaction products obtained from the phosphorylation of adenosine were 2'3' and 5'-AMPs, 2',5' and 3',5'-ADPs and 2',3'-cyclic AMP. The extent of phosphorylation in formamide exceeded 50% under favorable conditions after 15 days at 70 degrees. The acidic dihydrogen phosphates and condensed hydrogen phosphates proved to be the best phosphorylating agents. The presence of water in the medium decreased the yield of nucleotide derivatives, but some phosphorylation of adenosine was detected using dihydrogen phosphate in formamide containing water. The phosphorylation reactions were also observed for deoxynucleosides. Little decompression of the nucleosides was detected during the reaction time needed to form nucleotide derivatives. The facility with which phosphorylation takes place in formamide under very mild conditions may justify further studies both of prebiotic phosphorylation and synthetic phosphorylation using this solvent.

Models of prebiological phosphorylation

The hypothesis that contemporary metabolic pathways envolved from analogous chemical reaction sequences on the primitive Earth leads to a reexamination of models of prebiological phosphorylation. Present-day phosphate uptake by algae and bacteria seems to involve two transport systems: (a) A n active transport process occurring at low external phosphate concentrations (as in umpolluted natural waters), with a transport constant Ks of 10(-7) to 10(-6) M Pi. (b) Another (probably diffusive) process at higher phosphate concentrations (greater than 10-6 M)(as in the interstitial water of reducing sediments). Laboratory model experiments are described for the reation of reducing sugars with orthophosphate in the presence of cyanogen, producing glycosyl phosphates. These reactions proceed with appreciable yields only at high phosphate concentrations (greater than 10-3 M), and may thus possibly serve as simulations of prebiological phosphorylation with diffusive transport, as it may have occurred in the intestial water of reducing sediments.

Possible Prebiotic Condensation of Mononucleotides by Cyanamide

The condensation of mononucleotides has been carried out in aqueous solution at neutral pH in the presence of cyanamide. Oligodeoxyribonucleotides up to five units have been formed when montmorillonite was present.

Cyanovinyl phosphate: a prebiological phosphorylating agent?

Cyanovinyl phosphate may be prepared by the addition reaction of phosphate to cyanoacetylene. Kinetic studies have established that cyanovinyl phosphate undergoes a slow pseudo-first-order hydrolysis in aqueous solution. Cyanovinyl phosphate converts uridine to uridine monophosphate and phosphate to pyrophosphate.

Prebiotic synthesis: phosphorylation in aqueous solution

Formation of uridine-5'-phosphate from uridine and inorganic phosphate in aqueous solution is effected by the following condensing agents: cyanogen, cyanoformamide, cyanate, cyanamide, thioformate, ethylisocyanide, and a watersoluble carbodiimide. The yields are always small, even when a large excess of condensing agent is used. The cyclization of uridine-3'-(2')-phosphate occurs under the same conditions but in much greater yield.