Cross references: In the Beginning The Origin of Life
Timeline of Evolution Last Universal (Common) Ancestor (LUCA)
Protobionts Viruses Prokaryotes Prokaryote Colonies
I've found some references which I feel go a long way toward describing an environmental niche which would have protected the newly evolving prebiotic chemistry from external disruption.
Montmorillonite - Wikipedia
"Montmorillonite is a very soft phyllosilicate group of minerals that typically form as microscopic crystals, known as clay. It is named after Montmorillon in France. Montmorillonite, a member of the smectite group, is a 2:1 clay, meaning that it has two tetrahedral sheets of silica sandwiching a central octahedral sheet of alumina. The particles are plate-shaped with an average diameter around 1 μm and a thickness of 9.6 nm. Members of this group include saponite.
Montmorillonite is a subclass of smectite, a 2:1 phyllosilicate mineral characterized as having greater than 50% octahedral charge; its cation exchange capacity is due to isomorphous substitution of Mg for Al in the central alumina plane. The substitution of lower valence cations in such instances leaves the nearby oxygen atoms with a net negative charge that can attract cations. In contrast, beidellite is smectite with greater than 50% tetrahedral charge originating from isomorphous substitution of Al for Si in the silica sheet.
The individual crystals of montmorillonite clay are not tightly bound hence water can intervene, causing the clay to swell. The water content of montmorillonite is variable and it increases greatly in volume when it absorbs water. Chemically, it is hydrated sodium calcium aluminium magnesium silicate hydroxide (Na,Ca)0.33(Al,Mg)2(Si4O10)(OH)2·nH2O. Potassium, iron, and other cations are common substitutes, and the exact ratio of cations varies with source. It often occurs intermixed with chlorite, muscovite, illite, cookeite, and kaolinite.
Prebiotic RNA synthesis by Montmorillonite catalysis.
"This review summarizes our recent findings on the role of mineral salts in prebiotic RNA synthesis, which is catalyzed by montmorillonite clay minerals (see below). The clay minerals not only catalyze the synthesis of RNA but also facilitate homochiral selection.
Preliminary data of these findings have been presented at the "Horizontal Gene Transfer and the Last Universal (Common) Ancestor (LUCA)" conference at the Open University, Milton Keynes, UK, 5-6 September 2013. The objective of this meeting was to recognize the significance of RNA in LUCA.
We believe that the prebiotic RNA synthesis from its monomers must have been a simple process. As a first step, it may have required activation of the 5'-end of the mononucleotide with a leaving group, e.g., imidazole in our model reaction (Figure 1). Wide ranges of activating groups are produced from HCN under plausible prebiotic Earth conditions.
The final step is clay mineral catalysis in the presence of mineral salts to facilitate selective production of functional RNA. Both the clay minerals and mineral salts would have been abundant on early Earth. We have demonstrated that while montmorillonite (pH 7) produced only dimers from its monomers in water, addition of sodium chloride (1 M) enhanced the chain length multifold, as detected by HPLC. The effect of monovalent cations on RNA synthesis was of the following order: Li+ > Na+ > K+. A similar effect was observed with the anions, enhancing catalysis in the following order: Cl- > Br- > I-. The montmorillonite-catalyzed RNA synthesis was not affected by hydrophobic or hydrophilic interactions. We thus show that prebiotic synthesis of RNA from its monomers was a simple process requiring only clay minerals and a small amount of salt. "
101 Similar articles:
Similar articles for PubMed (Select 25370375)
Note: The order in which I reviewed these references is not the same as the order in which PubMed found them. PubMed presents the references in what they call "Link" order, but I prefer to reorder them by "Publication Date" so that starting at the end with the oldest reference and moving forward allows me to read them in chronological order.
Simultaneous existence of different enviroments in aqueous clay systems and its possible role in prebiotic synthesis.
"The formation of packets of parallel oriented platelets and separating distances of several angstrom units in montmorillonite-water systems produces an intrinsic inhomogeneity with respect to the proton donating power of internal and external zones."
"Since these enviromental conditions are quite common in nature, both at present and in prebiotic times, it is proposed that the inhomogeneity of clay-water systems with respect to proton donating power should be taken into account in both theoretical and experimental efforts to demonstrate the catalytic activity of clays in prebiotic synthesis."
Clays as possible catalysts for peptide formation in the prebiotic era.
"From the point of view of prebiotic synthesis, clays might have performed functions of concentration, catalysis, and protection of molecules."
The effect of clays on the oligomerization of HCN.
Current status of the prebiotic synthesis of small molecules.
Prebiotic ribose synthesis: a critical analysis.
Montmorillonite: a multifunctional mineral catalyst for the prebiological formation of phosphate esters.
Mineral catalysis of the formation of dimers of 5'-AMP in aqueous solution: the possible role of montmorillonite clays in the prebiotic synthesis of RNA.
The adsorption of nucleotides and polynucleotides on montmorillonite clay.
Oligomerization reactions of deoxyribonucleotides on montmorillonite clay: the effect of mononucleotide structure on phosphodiester bond formation.
1989 87<101160630 - 1530
Mineral catalysis of the formation of the phosphodiester bond in aqueous solution: the possible role of montmorillonite clays.
Oligomerization reactions of deoxyribonucleotides on montmorillonite clay: the effect of mononucleotide structure, phosphate activation and montmorillonite composition on phosphodiester bond formation.
Oligomerization reactions of ribonucleotides: the reaction of the 5'-phosphorimidazolide of nucleosides on montmorillonite and other minerals.
Montmorillonite catalysis of RNA oligomer formation in aqueous solution. A model for the prebiotic formation of RNA.
Catalysis and prebiotic RNA synthesis.
Binding of adenine and adenine-related compounds to the clay montmorillonite and the mineral hydroxylapatite.
"The first living things may have consisted of no more than RNA or RNA-like molecules bound to the surfaces of mineral particles. A key aspect of this theory is that these mineral particles have binding sites for RNA and its prebiotic precursors. The object of this study is to explore the binding properties of two of the best studied minerals, montmorillonite and hydroxylapatite, for possible precursors of RNA."
Synthesis of RNA oligomers on heterogeneous templates.
Oligomerization of uridine phosphorimidazolides on montmorillonite: a model for the prebiotic synthesis of RNA on minerals.
Synthesis of long prebiotic oligomers on mineral surfaces.
"We find that whereas the reactions in solution produce only short oligomers (the longest typically being a 10-mer), the presence of mineral surfaces (montmorillonite for nucleotides, illite and hydroxylapatite for amino acids) induces the formation of oligomers up to 55 monomers long. These are formed by successive 'feedings' with the monomers; polymerization takes place on the mineral surfaces in a manner akin to solid-phase synthesis of biopolymers."
Template-directed synthesis using the heterogeneous templates produced by montmorillonite catalysis. A possible bridge between the prebiotic and RNA worlds.
"These findings support the postulate that origin of the RNA world was initiated by the RNA oligomers produced by polymerization of activated monomers formed by prebiotic processes."
Peptides and the origin of life.
"Considering the state-of-the-art views of the geochemical conditions of the primitive earth, it seems most likely that peptides were produced ahead of all other oligomer precursors of biomolecules. Among all the reactions proposed so far for the formation of peptides under primordial earth conditions, the salt-induced peptide formation reaction in connection with adsorption processes on clay minerals would appear to be the simplest and most universal mechanism known to date. The properties of this reaction greatly favor the formation of biologically relevant peptides within a wide variation of environmental conditions such as temperature, pH, and the presence of inorganic compounds. The reaction-inherent preferences of certain peptide linkages make the argument of 'statistical impossibility' of the evolutionary formation of the 'right' peptides and proteins rather insignificant. Indeed, the fact that these sequences are reflected in the preferential sequences of membrane proteins of archaebacteria and prokaryonta distinctly indicates the relevance of this reaction for chemical peptide evolution. On the basis of these results and the recent findings of self-replicating peptides, some ideas have been developed as to the first steps leading to life on earth."
1999 76<101 Free PMC Article
Surface geochemistry of the clay minerals.
The combination of salt induced peptide formation reaction and clay catalysis: a way to higher peptides under primitive earth conditions.
"Two reactions with suggested prebiotic relevance for peptide evolution, the salt induced peptide formation reaction and the peptide chain elongation/stabilization on clay minerals have been combined in experimental series starting from dipeptides and dipeptide/amino acid mixtures. The results show that both reactions can take place simultaneously in the same reaction environment and that the presence of mineral catalysts favours the formation of higher oligopeptides. These findings lend further support to the relevance of these reactions for peptide evolution on the primitive earth."
The interaction of biological molecules with clay minerals: a scanning force microscopy study.
Bridging the prebiotic and RNA worlds: prebiotic RNA synthesis on clay.
"Montmorillonite clay catalyzes the formation of RNAs containing 6-14 monomer units from the activated mononucleotides of A, C, G, I and U. The RNAs formed have 3', 5'- and 2', 5'-links, pyrophosphate links and have both linear and cyclic chains. ...
The dimer fraction formed in the reaction of a binary mixture of a purine and pyrimidine nucleotide shows sequence selectivity with about a 20 fold excess of the 5'-purine-pyrimidine dimer over that of the 5'-pyrimidine-purine dimer. RNAs as long as 50 mers are formed by the elongation of a decamer bound to montmorillonite by the daily addition of activated monomer to it over a 14-day time period."
Sequence- and regio-selectivity in the montmorillonite-catalyzed synthesis of RNA.
"The six binary montmorillonite clay-catalyzed reactions of the 5'-phosphorimidazolides of adenosine, cytidine, guanosine and uridine were performed and the eight dimers from each reaction were separated and analyzed by HPLC.
A 16-51-fold higher yield of the 5'-purine-pyrimidine dimers over that of the 5'-pyrimidine-purines was observed. The total yield of the 5'-purine-pyrimidine dimers was in the 50-70% range while that of the 5'-pyrimidine-purine dimers was 1.3-7.0%. Less sequence selectivity was observed in the homodimers formed.
Regioselectivity for the formation of 3', 5'-phosphodiester bonds over that found in the absence of clay was observed. The 5'-purine-pyrimidine, 5'-pyrimidine-pyrimidine and 5'-purine-purine dimers had 3', 5'-links in about half of their phosphodiester bonds. The percent phosphodiester links in the 5'-pyrimidine-pyrimidine dimers was 18%, a value close to that observed in the absence of the montmorillonite catalyst.
The montmorillonite-catalyzed reaction of all four activated nucleotides was performed and the 24 products were separated and analyzed. The trends observed in the binary reactions were confirmed and the results also showed that the relative reactivity of the activated monomers was A > G > C > U in the ratio 8.2:4.8:1.3:1 respectively. No 5'-pyrimidine-purines with a 5'-U and pG3' pU, pC3' pA and pC3' pG were detected.
These studies suggest that a limited population of RNAs would have formed in catalyzed prebiotic reactions."
Effect of inhibitors on the montmorillonite clay-catalyzed formation of RNA: studies on the reaction pathway.
Behavior of adenine in Na-montmorillonite exposed to gamma radiation: implications to chemical evolution studies.
"Adenine is an important compound in biological systems, such as genetic and energy utilization processes. Adenine is readily formed in prebiotic conditions. Its synthesis and stability in environmental conditions are of paramount importance in chemical evolution processes.
Clay minerals might have played an important role in the early Earth. Clays are known to have a high affinity for organic compounds, and they may provide protection to adsorbed molecules against high-energy radiation. The purpose of this work is to test these assumptions. We study the stability of adenine under irradiation, in aqueous solution and also adsorbed in a clay mineral.
The recovery of adenine after a gamma irradiation was higher in the system containing clay in relation to a system without clay. Results show that adenine is readily adsorbed in the clay, and that the clay act as surface protector toward the degradation of adenine by the radiation."
Montmorillonite catalysis of 30-50 mer oligonucleotides: laboratory demonstration of potential steps in the origin of the RNA world.
Cations as mediators of the adsorption of nucleic acids on clay surfaces in prebiotic environments.
Sequence- and regioselectivity in the montmorillonite-catalyzed synthesis of RNA.
"The possible role of catalysis in forming a limited number of RNAs from activated monomers is investigated by examining the sequence- and regioselectivity in the montmorillonite-catalyzed formation of RNA dimers and trimers. The reactivity of A was similar to that of G, and C was comparable in reactivity to U. Yet the reactivity of the purine nucleotides differed from that of the pyrimidines. ...
The reactivity of the dimers depended on the nucleotide attached to the 3'-end of the RNA and the regiochemistry of the phosphodiester bond. ...
This research establishes that the montmorillonite catalyst limits the number of RNA oligomer isomers formed. The potential significance of these findings to the origins of life is discussed "
Origin, persistence and biological activity of genetic material in prebiotic habitats.
"Molecules which store genetic information (i.e. RNA and DNA) are central to all life on Earth. The formation of these complex molecules, and ultimately life, required specific conditions, including the synthesis and concentration of precursors (nucleotides), the joining of these monomers into larger molecules (polynucleotides), their protection in critical conditions (like those probably existing in primeval habitats), and the expression of the biological potential of the informational molecule (its capacity to multiply and evolve). Determining how these steps occurred and how the earliest genetic molecules originated on Earth is a problem that is far from being resolved.
Recent observations on the polymerization of nucleotides on clay surfaces and on the resistance of clay-adsorbed nucleic acids to environmental degradation suggest that clay minerals could have acted as a resting place for the formation and preservation of prebiotic genetic molecules, whatever they were, and for the self-organization of the first auto-replicating systems. In the present work, the molecular characteristics and biological activity of different nucleic acids (DNA, RNAs) adsorbed/bound on clay minerals are discussed in the light of their possible role in ancestral environments."
Peptide synthesis through evolution.
Montmorillonite, oligonucleotides, RNA and origin of life.
A perspective on the role of minerals in prebiotic synthesis.
A surface-mediated origin of the RNA world: biogenic activities of clay-adsorbed RNA molecules.
Sites of adsorption of adenine, uracil, and their corresponding derivatives on sodium montmorillonite.
Catalysis and selectivity in prebiotic synthesis: initiation of the formation of oligo(U)s on montmorillonite clay by adenosine-5'-methylphosphate.
One-step, regioselective synthesis of up to 50-mers of RNA oligomers by montmorillonite catalysis.
Studies in the mineral and salt-catalyzed formation of RNA oligomers.
Mineral surface directed membrane assembly.
Selectivity of montmorillonite catalyzed prebiotic reactions of D, L-nucleotides.
2007 40<101 Free PMC Article
Montmorillonite protection of an UV-irradiated hairpin ribozyme: evolution of the RNA world in a mineral environment.
"These results provide a suggestion with which RNA, or RNA-like molecules, could have overcame the problem of protection from UV irradiation in the RNA world era, and suggest that a clay-rich environment could have favoured not only the formation of first genetic molecules, but also their evolution towards increasingly complex molecular organization."
Mechanism of montmorillonite catalysis in the formation of RNA oligomers.
"The montmorillonite clay-catalyzed reactions of nucleotides generate oligomers as long as 50-mers. The extent of catalysis depends on the magnitude of the negative charge on the montmorillonite lattice and the number of cations associated with it. When cations in raw montmorillonites are replaced by sodium ions, the resulting Na(+)-montmorillonite does not catalyze oligomer formation because they saturate the interlayers between the platelets of montmorillonites, which blocks the binding of the activated monomers. Treating the montmorillonite with dilute hydrochloric acid replaces the cations on the raw montmorillonite with protons. The protonated montmorillonite, titrated to pH 6-7, serves as a catalyst for the formation of RNA oligomers."
2010 30<101 Free PMC Article
Mineral surfaces, geochemical complexities, and the origins of life.
"Crystalline surfaces of common rock-forming minerals are likely to have played several important roles in life's geochemical origins. Transition metal sulfides and oxides promote a variety of organic reactions, including nitrogen reduction, hydroformylation, amination, and Fischer-Tropsch-type synthesis. Fine-grained clay minerals and hydroxides facilitate lipid self-organization and condensation polymerization reactions, notably of RNA monomers. Surfaces of common rock-forming oxides, silicates, and carbonates select and concentrate specific amino acids, sugars, and other molecular species, while potentially enhancing their thermal stabilities. Chiral surfaces of these minerals also have been shown to separate left- and right-handed molecules. Thus, mineral surfaces may have contributed centrally to the linked prebiotic problems of containment and organization by promoting the transition from a dilute prebiotic "soup" to highly ordered local domains of key biomolecules."
Clay minerals mediate folding and regioselective interactions of RNA: a large-scale atomistic simulation study.
"Since a mineral-mediated origin of life was first hypothesized over 60 years ago, clays have played a significant role in origins of life studies. Such studies have hitherto rarely used computer simulation to understand the possible chemical pathways to the formation of biomolecules. We use molecular dynamics techniques, performed on supercomputing grids, to carry out large-scale simulations of various 25-mer sequences of ribonucleic acid (RNA), in bulk water and with aqueous montmorillonite clay over many tens of nanoseconds. Hitherto, there has only been limited experimental data reported for these systems. Our simulations are found to be in agreement with various experimental observations pertaining to the relative adsorption of RNA on montmorillonite in the presence of charge balancing cations. Over time scales of only a few nanoseconds, specific RNA sequences fold to characteristic secondary structural motifs, which do not form in the corresponding bulk water simulations. Our simulations also show that, in aqueous Ca(2+) environments, RNA can tether to the clay surface through a nucleotide base, leaving the 3'-end of the strand exposed, providing a mechanism for the regiospecific adsorption and elongation of RNA oligomers on clay surfaces."
Homochiral selectivity in RNA synthesis: montmorillonite-catalyzed quaternary reactions of D, L-purine with D, L- pyrimidine nucleotides.
"Selective adsorption of D, L-ImpA with D, L-ImpU on the platelets of montmorillonite demonstrates an important reaction pathway for the origin of homochirality in RNA synthesis. Our earlier studies have shown that the individual reactions of D, L-ImpA or D, L-ImpU on montmorillonite catalyst produced oligomers which were only partially inhibited by the incorporation of both D- and L-enantiomers. Homochirality in these reactions was largely due to the formation of cyclic dimers that cannot elongate. We investigated the quaternary reactions of D, L-ImpA with D, L-ImpU on montmorillonite. The chain length of these oligomers increased from 9-mer to 11-mer as observed by HPLC, with a concomitant increase in the yield of linear dimers and higher oligomers in the reactions involving D, L-ImpA with D, L-ImpU as compared to the similar reactions carried out with D-enantiomers only. The formation of cyclic dimers of U was completely inhibited in the quaternary reactions. The yield of cyclic dimers of A was reduced from 60% to 10% within the dimer fraction. 12 linear dimers and 3 cyclic dimers were isolated and characterized from the quaternary reaction. The homochirality and regioselectivity of dimers were 64.1% and 71.7%, respectively. Their sequence selectivity was shown by the formation of purine-pyrimidine (54-59%) linkages, followed by purine-purine (29-32%) linkages and pyrimidine-pyrimidine (9-13%) linkages. Of the 16 trimers detected, 10 were homochiral with an overall homochirality of 73-76%. In view of the greater homochirality, sequence- and regio- selectivity, the quaternary reactions on montmorillonite demonstrate an unexpectedly favorable route for the prebiotic synthesis of homochiral RNA compared with the separate reactions of enantiomeric activated mononucleotides."
Progress in demonstrating total homochiral selection in montmorillonite-catalyzed RNA synthesis.
"The Na(+)-montmorillonite-catalyzed reactions of 5'-phosphorimidazolides of nucleosides generates RNA oligomers. The question arises as to how chiral selectivity was introduced into this biopolymer from a simple chemical system. We have demonstrated homochiral selection in quaternary reactions of a racemic mixture of D,L-ImpA and D,L-ImpU on Na(+)-montmorillonite. The dimer, trimer, tetramer and pentamer fractions were investigated for homochiral selection. The products were collected via ion exchange HPLC and their terminal 5'-phosphate was cleaved by alkaline phosphatase. These fractions were analyzed by reverse phase HPLC for the identification of homochiral and heterochiral isomers. Encouraged by favorable homochiral excesses of dimer (63.5 ± 0.8%) and trimer (74.3 ± 1.7%), the study was extended to the analysis of higher oligomers. The tetramer and pentamer of the quaternary reaction were separated into 26 and 22 isomers, respectively, on a reverse phase column. Their co-elution with those formed in the binary reactions of d-ImpA and D-ImpU on Na(+)-montmorillonite revealed 92.7 ± 2.0% and 97.2 ± 0.5% homochirality of the tetramer and pentamer, respectively. These results suggest that Na(+)-montmorillonite not only catalyzes the prebiotic synthesis of RNA but it also facilitates homochiral selection."
Progress in studies on the RNA world.
"The montmorillonite-catalyzed reactions of D, L-ImpA with D, L-ImpU generates RNA-like oligomers. The structures of the dimers to pentamers were investigated and homochiral products were identified in greater amounts than would be expected if theoretical amounts of each were formed. The homochirality increased from 64% to 97% as the chain length increased from dimers to pentamers. Investigation of the effect of pH, occupancy of the interlayer space and the influence of various cations in the reaction provided further insight into physical process in the mechanism of the catalysis. A detailed analysis of dimers was carried out in view of there being key intermediates towards formation of higher oligomers. The study was extended to the synthesis of non-standard dimers including those formed with deoxy-ribonucleotides."
Asphalt, water, and the prebiotic synthesis of ribose, ribonucleosides, and RNA.
"RNA has been called a "prebiotic chemist's nightmare" because of its combination of large size, carbohydrate building blocks, bonds that are thermodynamically unstable in water, and overall intrinsic instability. However, a discontinuous synthesis model is well-supported by experimental work that might produce RNA from atmospheric CO(2), H(2)O, and N(2). For example, electrical discharge in such atmospheres gives formaldehyde (HCHO) in large amounts and glycolaldehyde (HOCH(2)CHO) in small amounts. When rained into alkaline aquifers generated by serpentinizing rocks, these substances were undoubtedly converted to carbohydrates including ribose. Likewise, atmospherically generated HCN was undoubtedly converted in these aquifers to formamide and ammonium formate, precursors for RNA nucleobases. Finally, high reduction potentials maintained by mantle-derived rocks and minerals would allow phosphite to be present in equilibrium with phosphate, mobilizing otherwise insoluble phosphorus for the prebiotic synthesis of phosphite and phosphate esters after oxidation. So why does the community not view this discontinuous synthesis model as compelling evidence for the RNA-first hypothesis for the origin of life? In part, the model is deficient because no experiments have joined together those steps without human intervention. Further, many steps in the model have problems. Some are successful only if reactive compounds are presented in a specific order in large amounts. Failing controlled addition, the result produces complex mixtures that are inauspicious precursors for biology, a situation described as the "asphalt problem". Many bonds in RNA are thermodynamically unstable with respect to hydrolysis in water, creating a "water problem". Finally, some bonds in RNA appear to be "impossible" to form under any conditions considered plausible for early Earth. To get a community-acceptable "RNA first" model for the origin of life, the discontinuous synthesis model must be developed. In particular, the model must be refined so that it yields oligomeric RNA from CO(2), H(2)O, and N(2) without human intervention. This Account describes our efforts in this direction. Our hypothesis centers on a geological model that synthesizes RNA in a prebiotic intermountain dry valley (not in a marine environment). This valley receives high pH run-off from a watershed rich in serpentinizing olivines and eroding borate minerals. The runoff contains borate-stabilized carbohydrates, formamide, and ammonium formate. As atmospheric CO(2) dissolves in the subaerial aquifer, the pH of the aquifer is lowered. In the desert valley, evaporation of water, a solvent with a nucleophilic "background reactivity", leaves behind formamide, a solvent with an electrophilic "background reactivity". As a result, nucleobases, formylated nucleobases, and formylated carbohydrates, including formylated ribose, can form. Well-known chemistry transforms these structures into nucleosides, nucleotides, and partially formylated oligomeric RNA."
Significance of mineral salts in prebiotic RNA synthesis catalyzed by montmorillonite.
"The montmorillonite-catalyzed reactions of the 5'-phosphorimidazolide of adenosine used as a model generated RNA type oligomers. These reactions were found to be dependent on the presence of mineral salts. Whereas montmorillonite (pH 7) produced only dimers and traces of trimer in water, addition of sodium chloride (0.1-2.0 M) enhanced the chain length of oligomers to 10-mers as detected by HPLC. Maximum catalytic activity was observed with sodium chloride at a concentration between 0.8 and 1.2 M. This concentration of sodium chloride resembled its abundance in the ancient oceans (0.9-1.2 M). Magnesium chloride produced a similar effect but its joint action with sodium chloride did not produce any difference in the oligomer chain length. Therefore, Mg(2+) was not deemed necessary for generating longer oligomers. The effect of monovalent cations upon RNA chain length was: Li(+) > Na(+) > K(+). A similar effect was observed with the anions with enhanced oligomer length in the following order: Cl(-) > Br(-) > I(-). Thus, the smaller ions facilitated the formation of the longest oligomers. Inorganic salts that tend to salt out organic compounds from water and salts which show salt-in effects had no influence on the oligomerization process indicating that the montmorillonite-catalyzed RNA synthesis is not affected by either of these hydrophobic or hydrophilic interactions. A 2.3-fold decrease in the yield of cyclic dimer was observed upon increasing the sodium chloride concentration from 0.2 to 2.0 M. Inhibition of cyclic dimer formation is vital for increasing the yield of linear dimers and longer oligomers. In summary, sodium chloride is likely to have played an essential role in any clay mineral-catalyzed prebiotic RNA synthesis."
The role of fluoride in montmorillonite-catalyzed RNA synthesis.
2014 10<101 Free PMC Article
Prebiotic RNA synthesis by montmorillonite catalysis.
"This review summarizes our recent findings on the role of mineral salts in prebiotic RNA synthesis, which is catalyzed by montmorillonite clay minerals. The clay minerals not only catalyze the synthesis of RNA but also facilitate homochiral selection. Preliminary data of these findings have been presented at the "Horizontal Gene Transfer and the Last Universal Common Ancestor (LUCA)" conference at the Open University, Milton Keynes, UK, 5-6 September 2013. The objective of this meeting was to recognize the significance of RNA in LUCA. We believe that the prebiotic RNA synthesis from its monomers must have been a simple process. As a first step, it may have required activation of the 5'-end of the mononucleotide with a leaving group, e.g., imidazole in our model reaction (Figure 1). Wide ranges of activating groups are produced from HCN under plausible prebiotic Earth conditions. The final step is clay mineral catalysis in the presence of mineral salts to facilitate selective production of functional RNA. Both the clay minerals and mineral salts would have been abundant on early Earth. We have demonstrated that while montmorillonite (pH 7) produced only dimers from its monomers in water, addition of sodium chloride (1 M) enhanced the chain length multifold, as detected by HPLC. The effect of monovalent cations on RNA synthesis was of the following order: Li+ > Na+ > K+. A similar effect was observed with the anions, enhancing catalysis in the following order: Cl- > Br- > I-. The montmorillonite-catalyzed RNA synthesis was not affected by hydrophobic or hydrophilic interactions. We thus show that prebiotic synthesis of RNA from its monomers was a simple process requiring only clay minerals and a small amount of salt. "
2014 9<101 Free PMC Article
Synergism and mutualism in non-enzymatic RNA polymerization.
"The link between non-enzymatic RNA polymerization and RNA self-replication is a key step towards the "RNA world" and still far from being solved, despite extensive research. Clay minerals, lipids and, more recently, peptides were found to catalyze the non-enzymatic synthesis of RNA oligomers. Herein, a review of the main models for the formation of the first RNA polymers is presented in such a way as to emphasize the cooperation between life's building blocks in their emergence and evolution. A logical outcome of the previous results is a combination of these models, in which RNA polymerization might have been catalyzed cooperatively by clays, lipids and peptides in one multi-component prebiotic soup. The resulting RNAs and oligopeptides might have mutualistically evolved towards functional RNAs and catalytic peptides, preceding the first RNA replication, thus supporting an RNA-peptide world. The investigation of such a system is a formidable challenge, given its complexity deriving from a tremendously large number of reactants and innumerable products. A rudimentary experimental design is outlined, which could be used in an initial attempt to study a quaternary component system."
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."
2015 7<101 Free PMC Article
Adsorption of nucleic Acid bases, ribose, and phosphate by some clay minerals.
"Besides having a large capacity for taking up organic molecules, clay minerals can catalyze a variety of organic reactions. Derived from rock weathering, clay minerals would have been abundant in the early Earth. As such, they might be expected to play a role in chemical evolution. The interactions of clay minerals with biopolymers, including RNA, have been the subject of many investigations. The behavior of RNA components at clay mineral surfaces needs to be assessed if we are to appreciate how clays might catalyze the formation of nucleosides, nucleotides and polynucleotides in the "RNA world". The adsorption of purines, pyrimidines and nucleosides from aqueous solution to clay minerals is affected by suspension pH. With montmorillonite, adsorption is also influenced by the nature of the exchangeable cations. Here, we review the interactions of some clay minerals with RNA components."
In situ imidazole activation of ribonucleotides for abiotic RNA oligomerization reactions.
"The hypothesis that RNA played a significant role in the origin of life requires effective and efficient abiotic pathways to produce RNA oligomers. The most successful abiotic oligomerization reactions to date have utilized high-energy, modified, or pre-activated ribonucleotides to generate strands of RNA up to 50-mers in length. In spite of their success, these modifications and pre-activation reactions significantly alter the ribonucleotides in ways that are highly unlikely to have occurred on a prebiotic Earth. This research seeks to address this problem by exploring an aqueous based method for activating the canonical ribonucleotides in situ using 1-Ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC) and imidazole. The reactions were run with and without a montmorillonite clay catalyst and compared to reactions that used ribonucleotides that were pre-activated with imidazole. The effects of pH and ribonucleotide concentration were also investigated. The results demonstrate the ability of in situ activation of ribonucleotides to generate linear RNA oligomers in solution, providing an alternative route to produce RNA for use in prebiotic Earth scenarios."
2015 5<101 Free PMC Article
The Routes of Emergence of Life from LUCA during the RNA and Viral World: A Conspectus.
"How did life emerge on Earth? The aim of the Network of Researchers on Horizontal Gene Transfer and the Last Universal Cellular Ancestor (NoR HGT & LUCA) is to understand how the genetics of LUCAs were reorganised prior to the advent of the three domains of life. This paper reports the research of eminent scientists who have come together within the network and are making significant contributions to the wider knowledge base surrounding this, one of science's remaining mysteries. I also report on their relevance in relation to LUCAs and life's origins, as well as ask a question: what next?"
RNA Oligomerization in Laboratory Analogues of Alkaline Hydrothermal Vent Systems.
"Discovering pathways leading to long-chain RNA formation under feasible prebiotic conditions is an essential step toward demonstrating the viability of the RNA World hypothesis. Intensive research efforts have provided evidence of RNA oligomerization by using circular ribonucleotides, imidazole-activated ribonucleotides with montmorillonite catalyst, and ribonucleotides in the presence of lipids. Additionally, mineral surfaces such as borates, apatite, and calcite have been shown to catalyze the formation of small organic compounds from inorganic precursors (Cleaves, 2008 ), pointing to possible geological sites for the origins of life. Indeed, the catalytic properties of these particular minerals provide compelling evidence for alkaline hydrothermal vents as a potential site for the origins of life since, at these vents, large metal-rich chimney structures can form that have been shown to be energetically favorable to diverse forms of life. Here, we test the ability of iron- and sulfur-rich chimneys to support RNA oligomerization reactions using imidazole-activated and non-activated ribonucleotides. The chimneys were synthesized in the laboratory in aqueous "ocean" solutions under conditions consistent with current understanding of early Earth. Effects of elemental composition, pH, inclusion of catalytic montmorillonite clay, doping of chimneys with small organic compounds, and in situ ribonucleotide activation on RNA polymerization were investigated. These experiments, under certain conditions, showed successful dimerization by using unmodified ribonucleotides, with the generation of RNA oligomers up to 4 units in length when imidazole-activated ribonucleotides were used instead. Elemental analysis of the chimney precipitates and the reaction solutions showed that most of the metal cations that were determined were preferentially partitioned into the chimneys."
2016 2<101 Free PMC Article
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."