The adsorption of nucleotides and polynucleotides on montmorillonite clay

RNA Hydrolysis at Mineral-Water Interfaces

As an essential biomolecule for life, RNA is ubiquitous across environmental systems where it plays a central role in biogeochemical processes and emerging technologies. The persistence of RNA in soils and sediments is thought to be limited by enzymatic or microbial degradation, which occurs on timescales that are orders of magnitude faster than known abiotic pathways. Herein, we unveil a previously unreported abiotic pathway by which RNA rapidly hydrolyzes on the timescale of hours upon adsorption to iron (oxyhydr)oxide minerals such as goethite (α-FeOOH). The hydrolysis products were consistent with iron present in the minerals acting as a Lewis acid to accelerate sequence-independent hydrolysis of phosphodiester bonds comprising the RNA backbone. In contrast to acid- or base-catalyzed RNA hydrolysis in solution, mineral-catalyzed hydrolysis was fastest at circumneutral pH, which allowed for both sufficient RNA adsorption and hydroxide concentration. In addition to goethite, we observed that RNA hydrolysis was also catalyzed by hematite (α-Fe₂O₃) but not by aluminum-containing minerals (e.g., montmorillonite). Given the extensive adsorption of nucleic acids to environmental surfaces, we anticipate previously overlooked mineral-catalyzed hydrolysis of RNA may be prevalent particularly in iron-rich soils and sediments, which must be considered across biogeochemical applications of nucleic acid analysis in environmental systems.

The Formation of RNA Pre-Polymers in the Presence of Different Prebiotic Mineral Surfaces Studied by Molecular Dynamics Simulations

We used all-atom Molecular Dynamics (MD) computer simulations to study the formation of pre-polymers between the four nucleotides in RNA (AMP, UMP, CMP, GMP) in the presence of different substrates that could have been present in a prebiotic environment. Pre-polymers are C3'-C5' hydrogen-bonded nucleotides that have been suggested to be the precursors of phosphodiester-bonded RNA polymers. We simulated wet-dry cycles by successively removing water molecules from the simulations, from ~60 to 3 water molecules per nucleotide. The nine substrates in this study include three clay minerals, one mica, one phosphate mineral, one silica, and two metal oxides. The substrates differ in their surface charge and ability to form hydrogen bonds with the nucleotides. From the MD simulations, we quantify the interactions between different nucleotides, and between nucleotides and substrates. For comparison, we included graphite as an inert substrate, which is not charged and cannot form hydrogen bonds. We also simulated the dehydration of a nucleotide-only system, which mimics the drying of small droplets. The number of hydrogen bonds between nucleotides and nucleotides and substrates was found to increase significantly when water molecules were removed from the systems. The largest number of C3'-C5' hydrogen bonds between nucleotides occurred in the graphite and nucleotide-only systems. While the surface of the substrates led to an organization and periodic arrangement of the nucleotides, none of the substrates was found to be a catalyst for pre-polymer formation, neither at full hydration, nor when dehydrated. While confinement and dehydration seem to be the main drivers for hydrogen bond formation, substrate interactions reduced the interactions between nucleotides in all cases. Our findings suggest that small supersaturated water droplets that could have been produced by geysers or springs on the primitive Earth may play an important role in non-enzymatic RNA polymerization.

Greenalite Nanoparticles in Alkaline Vent Plumes as Templates for the Origin of Life

Mineral templates are thought to have played keys roles in the emergence of life. Drawing on recent findings from 3.45-2.45 billion-year-old iron-rich hydrothermal sedimentary rocks, we hypothesize that greenalite (Fe3Si2O5(OH)4) was a readily available mineral in hydrothermal environments, where it may have acted as a template and catalyst in polymerization, vesicle formation and encapsulation, and protocell replication. We argue that venting of dissolved Fe2+ and SiO2(aq) into the anoxic Hadean ocean favored the precipitation of nanometer-sized particles of greenalite in hydrothermal plumes, producing a continuous flow of free-floating clay templates that traversed the ocean. The mixing of acidic, metal-bearing hydrothermal plumes from volcanic ridge systems with more alkaline, organic-bearing plumes generated by serpentinization of ultramafic rocks brought together essential building blocks for life in solutions conducive to greenalite precipitation. We suggest that the extreme disorder in the greenalite crystal lattice, producing structural modulations resembling parallel corrugations (∼22 Å wide) on particle edges, promoted the assembly and alignment of linear RNA-type molecules (∼20 Å diameter). In alkaline solutions, greenalite nanoparticles could have accelerated the growth of membrane vesicles, while their encapsulation allowed RNA-type molecules to continue to form on the mineral templates, potentially enhancing the growth and division of primitive cell membranes. Once self-replicating RNA evolved, the mineral template became redundant, and protocells were free to replicate and roam the ocean realm.

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

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

Adenine Adsorbed onto Montmorillonite Exposed to Ionizing Radiation: Essays on Prebiotic Chemistry

Most adsorption and radiolysis experiments related to prebiotic chemistry studies are performed in distilled water or sodium chloride solutions. However, distilled water and sodium chloride solutions do not represent the composition of the primitive seas of Earth. In this work, an artificial seawater with ion abundances Mg²⁺ > Ca²⁺ >> Na⁺ ≈ K⁺ and SO₄^2- >> Cl^- was used, one that is different from the average composition of seawater today. This artificial seawater is named seawater 4.0 Ga, since it better represents the composition of the major constituents of seawater of primitive Earth. The radiolysis of adenine adsorbed onto montmorillonite was studied. The most important result is that adenine is adsorbed onto montmorillonite, when it is dissolved in artificial seawater 4.0 Ga, and the clay protects adenine against gamma radiation decomposition. However, desorption of adenine from montmorillonite was possible only with 0.10 mol L^-1 of KOH. This result indicates that adenine was strongly bonded to montmorillonite. Fourier transform infrared spectroscopy showed that NH₂ group and electrostatic interactions, between negatively charged montmorillonite and positively charged adenine, are responsible for adsorption of adenine onto montmorillonite. In addition, X-ray diffractograms showed that adenine enters in the interlayer space of montmorillonite.

How do Nucleotides Adsorb Onto Clays?

Adsorption of prebiotic building blocks is proposed to have played a role in the emergence of life on Earth. The experimental and theoretical study of this phenomenon should be guided by our knowledge of the geochemistry of the habitable early Earth environments, which could have spanned a large range of settings. Adsorption being an interfacial phenomenon, experiments can be built around the minerals that probably exhibited the largest specific surface areas and were the most abundant, i.e., phyllosilicates. Our current work aims at understanding how nucleotides, the building blocks of RNA and DNA, might have interacted with phyllosilicates under various physico-chemical conditions. We carried out and refined batch adsorption studies to explore parameters such as temperature, pH, salinity, etc. We built a comprehensive, generalized model of the adsorption mechanisms of nucleotides onto phyllosilicate particles, mainly governed by phosphate reactivity. More recently, we used surface chemistry and geochemistry techniques, such as vibrational spectroscopy, low pressure gas adsorption, X-ray microscopy, and theoretical simulations, in order to acquire direct data on the adsorption configurations and localization of nucleotides on mineral surfaces. Although some of these techniques proved to be challenging, questioning our ability to easily detect biosignatures, they confirmed and complemented our pre-established model.

Salinity Effects on the Adsorption of Nucleic Acid Compounds on Na-Montmorillonite: a Prebiotic Chemistry Experiment

Any proposed model of Earth's primitive environments requires a combination of geochemical variables. Many experiments are prepared in aqueous solutions and in the presence of minerals. However, most sorption experiments are performed in distilled water, and just a few in seawater analogues, mostly inconsistent with a representative primitive ocean model. Therefore, it is necessary to perform experiments that consider the composition and concentration of dissolved salts in the early ocean to understand how these variables could have affected the absorption of organic molecules into minerals. In this work, the adsorption of adenine, adenosine, and 5'AMP onto Na+montmorillonite was studied using a primitive ocean analog (4.0 Ga) from experimental and computational approaches. The order of sorption of the molecules was: 5'AMP > adenine > adenosine. Infrared spectra showed that the interaction between these molecules and montmorillonite occurs through the NH2 group. In addition, electrostatic interaction between negatively charged montmorillonite and positively charge N1 of these molecules could occur. Results indicate that dissolved salts affect the sorption in all cases; the size and structure of each organic molecule influence the amount sorbed. Specifically, the X-ray diffraction patterns show that dissolved salts occupy the interlayer space in Na-montmorillonite and compete with organic molecules for available sites. The adsorption capacity is clearly affected by dissolved salts in thermodynamic terms as deduced by isotherm models. Indeed, molecular dynamic models suggest that salts are absorbed in the interlamellar space and can interact with oxygen atoms exposed in the edges of clay or in its surface, reducing the sorption of the organic molecules. This research shows that the sorption process could be affected by high concentration of salts, since ions and organic molecules may compete for available sites on inorganic surfaces. Salt concentration in primitive oceans may have strongly affected the sorption, and hence the concentration processes of organic molecules on minerals.

Effects of salinity on the adsorption of nucleotides onto phyllosilicates

In the context of the origin of life, phyllosilicate surfaces might favor the adsorption, concentration and reactivity of otherwise diluted prebiotic molecules. The primitive oceanic seafloor was certainly rich in Fe-Mg-rich phyllosilicates. The salinity of the primitive seawater remains largely unknown. Values ranging from 1 to 15 times modern salinity have been proposed and the salt composition of the primitive ocean also remains elusive although it may have played a role in the interactions between nucleotides and mineral surfaces. Therefore we studied the adsorption of 5'-monophosphate deoxyguanosine (dGMP) as a model nucleotide onto a Fe-rich swelling clay, i.e. nontronite, and an Al-rich phyllosilicate, i.e. pyrophyllite, for comparison. Experiments were carried out at atmospheric pressure, 25 °C and natural pH, with a series of salts NaCl, MgCl₂, CaCl₂, MgSO₄, NaH₂PO₄ and LaCl₃ in order to evaluate the effect of cations and anions on dGMP adsorption. The present study shows that nucleotides are adsorbed on both phyllosilicates via a ligand exchange mechanism. The phosphate group of the nucleotide is adsorbed on the lateral metal hydroxyls of the broken edges of phyllosilicates. The presence of divalent cations or molecular anions, such as phosphate or sulfate, tends to inhibit this interaction on mineral surfaces. However, in the presence of divalent cations, cationic bridging on the basal surfaces of the swelling clay also occurs and could induce a higher retention capacity of the swelling clays compared to non-swelling phyllosilicates in primitive and modern natural environments.

Surface interaction of ribonucleic acid constituents with spinel ferrite nanoparticles: a prebiotic chemistry experiment

A prebiotic chemistry experiment involving interaction between ribonucleotides and spinel ferrite nanoparticles has been carried out.

Abiotic regioselective phosphorylation of adenosine with borate in formamide

Nearly 40 years ago, Schoffstall and his coworkers used formamide as a solvent to permit the phosphorylation of nucleosides by inorganic phosphate to give nucleoside phosphates, which (due to their thermodynamic instability with respect to hydrolysis) cannot be easily created in water by an analogous phosphorylation (the "water problem" in prebiotic chemistry). More recently, we showed that borate could stabilize certain carbohydrates against degradation (the "asphalt problem"). Here, we combine the two concepts to show that borate can work in formamide to guide the reactivity of nucleosides under conditions where they are phosphorylated. Specifically, reaction of adenosine in formamide with inorganic phosphate and pyrophosphate in the presence of borate gives adenosine-5'-phosphate as the only detectable phosphorylated product, with formylation (as opposed to hydrolysis) being the competing reaction.

Attachment of ribonucleotides on α-alumina as a function of pH, ionic strength, and surface loading

The interactions between nucleic acids and mineral surfaces have been the focus of many studies in environmental sciences, in biomedicine, as well as in origin of life studies for the prebiotic formation of biopolymers. However, few studies have focused on a wide range of environmental conditions and the likely modes of attachment. Here we investigated the adsorption of ribonucleotides onto α-alumina surfaces over a wide range of pH, ionic strength, and ligand-to-solid ratio, by both an experimental and a theoretical approach. The adsorption of ribonucleotides is strongly affected by pH, with a maximum adsorption at pH values around 5. Alumina adsorbs high amounts of nucleotides >2 μmol/m(2). We used the extended triple-layer model (ETLM) to predict the speciation of the surface complexes formed as well as the stoichiometry and equilibrium constants. We propose the formation of two surface species: a monodentate inner-sphere complex, dominant at pH <7, and a bidentate outer-sphere complex, dominant at higher pH. Both complexes would involve interactions between the negatively charged phosphate group and the positively charged surface of alumina. Our results provide a better understanding of how nucleic acids attach to mineral surfaces under varying environmental conditions. Moreover, the predicted configuration of nucleotide surface species, bound via the phosphate group, could have implications for the abiotic formation of nucleic acids in the context of the origin of life.

Structural and energetic factors controlling the enantioselectivity of dinucleotide formation under prebiotic conditions

Recently, it has been reported that the montmorillonite-catalyzed oligomerization of activated nucleotides exhibits remarkable enantioselectivity. In the current paper we investigate the structures and intrinsic energies of homochiral and heterochiral cyclic dinucleotides by means of accurate quantum chemical calculations in gas-phase and in bulk water. The steric effect of the clay is represented with geometrical constraints. Our computations reveal that the heterochiral dimer geometries are systematically less stable than their homochiral counterparts due to steric clashes inside the sugar-phosphate ring geometry. Thus we suggest that the homochiral selectivity observed in the cyclic dinucleotide formation in confined spaces may arise from the energetic destabilization of the heterochiral ring geometries as compared to their homochiral analogues. In the present paper we provide the first model of the 3D structure of d,l cyclic dinucleotides, which until now has eluded experimental observation.

Possible role of metal(II) octacyanomolybdate(IV) in chemical evolution: interaction with ribose nucleotides

We have proposed that double metal cyanide compounds (DMCs) might have played vital roles as catalysts in chemical evolution and the origin of life. We have synthesized a series of metal octacyanomolybdates (MOCMos) and studied their interactions with ribose nucleotides. MOCMos have been shown to be effective adsorbents for 5'-ribonucleotides. The maximum adsorption level was found to be about 50 % at neutral pH under the conditions studied. The zinc(II) octacyanomolybdate(IV) showed larger adsorption compared to other MOCMos. The surface area seems to important parameter for the adsorption of nucleotides. The adsorption followed a Langmuir adsorption isotherms with an overall adsorption trends of the order of 5'-GMP > 5'-AMP > 5'-CMP > 5'-UMP. Purine nucleotides were adsorbed more strongly than pyrimidine nucleotides on all MOCMos possibly because of the additional binding afforded by the imidazole ring in purines. Infrared spectral studies of adsorption adducts indicate that adsorption takes place through interaction between adsorbate molecules and outer divalent ions of MOCMos.

Mineral-organic interfacial processes: potential roles in the origins of life

Life is believed to have originated on Earth ∼4.4-3.5 Ga ago, via processes in which organic compounds supplied by the environment self-organized, in some geochemical environmental niches, into systems capable of replication with hereditary mutation. This process is generally supposed to have occurred in an aqueous environment and, likely, in the presence of minerals. Mineral surfaces present rich opportunities for heterogeneous catalysis and concentration which may have significantly altered and directed the process of prebiotic organic complexification leading to life. We review here general concepts in prebiotic mineral-organic interfacial processes, as well as recent advances in the study of mineral surface-organic interactions of potential relevance to understanding the origin of life.

Genetics first or metabolism first? The formamide clue

Life is made of the intimate interaction of metabolism and genetics, both built around the chemistry of the most common elements of the Universe (hydrogen, oxygen, nitrogen, and carbon). The transmissible interaction of metabolic and genetic cycles results in the hypercycles of organization and de-organization of chemical information, of living and non-living. The origin-of-life quest has long been split into several attitudes exemplified by the aphorisms "genetics-first" or "metabolism-first". Recently, the opposition between these approaches has been solved by more unitary theoretical and experimental frames taking into account energetic, evolutionary, proto-metabolic and environmental aspects. Nevertheless, a unitary and simple chemical frame is still needed that could afford both the precursors of the synthetic pathways eventually leading to RNA and to the key components of the central metabolic cycles, possibly connected with the synthesis of fatty acids. In order to approach the problem of the origin of life it is therefore reasonable to start from the assumption that both metabolism and genetics had a common origin, shared a common chemical frame, and were embedded under physical-chemical conditions favourable for the onset of both. The singleness of such a prebiotically productive chemical process would partake of Darwinian advantages over more complex fragmentary chemical systems. The prebiotic chemistry of formamide affords in a single and simple physical-chemical frame nucleic bases, acyclonucleosides, nucleotides, biogenic carboxylic acids, sugars, amino sugars, amino acids and condensing agents. Thus, we suggest the possibility that formamide could have jointly provided the main components for the onset of both (pre)genetic and (pre)metabolic processes. As a note of caution, we discuss the fact that these observations only indicate possible solutions at the level of organic substrates, not at the systemic chemical level.

Adsorption of ribose nucleotides on manganese oxides with varied mn/o ratio: implications for chemical evolution

Manganese exists in different oxidation states under different environmental conditions with respect to redox potential. Various forms of manganese oxides, namely, Manganosite (MnO), Bixbyite (Mn(2)O(3)), Hausmannite (Mn(3)O(4)) and Pyrolusite (MnO(2)) were synthesized and their possible role in chemical evolution studied. Adsorption studies of ribose nucleotides (5'-AMP, 5'-GMP, 5'-CMP and 5'-UMP) on these manganese oxides at neutral pH, revealed a higher binding affinity to manganosite (MnO) compared to the other manganese oxides. That manganese oxides having a lower Mn-O ratio show higher binding affinity for the ribonucleotides indirectly implies that such oxides may have provided a surface onto which biomonomers could have been concentrated through selective adsorption. Purine nucleotides were adsorbed to a greater extent compared to the pyrimidine nucleotides. Adsorption data followed Langmuir adsorption isotherms, and X( m ) and K( L ) values were calculated. The nature of the interaction and mechanism was elucidated by infrared spectral studies conducted on the metal-oxide and ribonucleotide-metal-oxide adducts.

The adsorption of short single-stranded DNA oligomers to mineral surfaces

We studied the adsorption of short single-stranded deoxyribonucleic acid (ssDNA) oligomers, of approximately 30 nucleotides (nt) in length, of varying sequence, adenine+guanine+cytosine (AGC) content, and propensity to form secondary structure, to equal surface area samples of olivine, pyrite, calcite, hematite, and rutile in 0.1M NaCl, 0.05M pH 8.1 KHCO(3) buffer. Although the mineral surfaces have widely varying points of zero charge, under these conditions they show remarkably similar adsorption of ssDNA regardless of oligomer characteristics. Mineral surfaces appear to accommodate ssDNA comparably, or ssDNA oligomers of this length are able to find binding sites of comparable strength and density due to their flexibility, despite the disparate surface properties of the different minerals. This may partially be due charge shielding by the ionic strength of the solutions tested, which are typical of many natural environments. These results may have some bearing on the adsorption and accumulation of biologically derived nucleic acids in sediments as well as the abiotic synthesis of nucleic acids before the origin of life.

Adsorption of thymine and uracil on 1:1 clay mineral surfaces: comprehensive ab initio study on influence of sodium cation and water

This computational study performed using the density functional theory shows that hydrated and non-hydrated tetrahedral and octahedral kaolinite mineral surfaces in the presence of a cation adsorb the nucleic acid bases thymine and uracil well. Differences in the structure and chemistry of specific clay mineral surfaces led to a variety of DNA bases adsorption mechanisms. The energetically most predisposed positions for an adsorbate molecule on the mineral surface were revealed. The target molecule binding with the surface can be characterized as physisorption, which occurs mainly due to a cation-molecular oxygen interaction, with hydrogen bonds providing an additional stabilization. The adsorption strength is proportional to the number of intermolecular interactions formed between the target molecule and the surface. From the Atoms in Molecules analysis and comparison of binding energy values of studied systems it is concluded that the sorption activity of kaolinite minerals for thymine and uracil depends on various factors, among which are the structure and accessibility of the organic compounds. The adsorption is governed mostly by the surface type, its properties and presence of cation, which cause a selective binding of the nucleobase. Adsorbate stabilization on the mineral surface increases only slightly with explicit addition of water. Comparison of activity of different studied kaolinite mineral models reveals the following order for stabilization: octahedral-Na-water > octahedral-Na > tetrahedral-Na > tetrahedral-Na-water. Further investigation of the electrostatic potentials helps understanding of the adsorption process and confirmation of the active sites on the kaolinite mineral surfaces. Based on the conclusions that clay mineral affinity for DNA and RNA bases can vary due to different structural and chemical properties of the surface, a hypothesis on possible role of clays in the origin of life was made.

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.

Adsorption of nucleic acid components on rutile (TiO(2)) surfaces

Nucleic acids, the storage molecules of genetic information, are composed of repeating polymers of ribonucleotides (in RNA) or deoxyribonucleotides (in DNA), which are themselves composed of a phosphate moiety, a sugar moiety, and a nitrogenous base. The interactions between these components and mineral surfaces are important because there is a tremendous flux of nucleic acids in the environment due to cell death and horizontal gene transfer. The adsorption of mono-, oligo-, and polynucleotides and their components on mineral surfaces may have been important for the origin of life. We have studied here interactions of nucleic acid components with rutile (TiO(2)), a mineral common in many terrestrial crustal rocks. Our results suggest roles for several nucleic acid functional groups (including sugar hydroxyl groups, the phosphate group, and extracyclic functional groups on the bases) in binding, in agreement with results obtained from studies of other minerals. In contrast with recent studies of nucleotide adsorption on ZnO, aluminum oxides, and hematite, our results suggest a different preferred orientation for the monomers on rutile surfaces. The conformations of the molecules bound to rutile surfaces appear to favor specific interactions, which in turn may allow identification of the most favorable mineral surfaces for nucleic acid adsorption.

Analysis of oligonucleotide DNA binding and sedimentation properties of montmorillonite clay using ultraviolet light spectroscopy

Smectite clays such as montmorillonite form complexes with a variety of biomolecules, including the nucleic acids DNA and RNA. Most previous studies of DNA adsorption onto clay have relied on spectrophotometric analysis after the separation of free nucleic acids from bound complexes by centrifugation. In the current work, we demonstrate that such studies produce a consistent error because of (a) incomplete sedimentation of montmorillonite and (b) strong absorbance of the remaining clay at 260 nm. Clay sedimentation efficiency was strongly dependent on cation concentration (Na+ or Mg2+) and on the level of dispersion of the original suspension. An improved clay-DNA adsorption assay was developed and utilized to assess the impact of metal counterions on the binding of single-stranded DNA to montmorillonite. X-ray diffraction demonstrated, for the first time, the formation of intercalated structures consistent with orientation of the DNA strands parallel to the clay surface. Observed gallery spacings were found to match values calculated using atomistic modeling techniques closely.

Role of metal oxides in chemical evolution: interaction of ribose nucleotides with alumina

Interaction of ribonucleotides--namely, 5'-AMP, 5'-GMP, 5'-CMP, and 5'-UMP--with acidic, neutral, and basic alumina has been studied. Purine nucleotides showed higher adsorption on alumina in comparison with pyrimidine nucleotides under acidic conditions. Adsorption data obtained followed Langmuir adsorption isotherm, and X(m) and K(L) values were calculated. On the basis of infrared spectral studies of ribonucleotides, alumina, and ribonucleotide-alumina adducts, we propose that the nitrogen base and phosphate moiety of the ribonucleotides interact with the positive charge surface of alumina. Results of the present study may indicate the importance of alumina in concentrating organic molecules from dilute aqueous solutions in primeval seas in the course of chemical evolution on Earth.

Kinetics and activation parameter analysis for the prebiotic oligocytidylate formation on Na(+)-montmorillonite at 0-100 degrees C

The kinetic analysis of the temperature dependence of the formation of oligocytidylate (oligo(C)) from the 5'-monophosphorimidazolide moiety of cytidine (ImpC) in the presence of Na (+)-montmorillonite (Na (+)-Mont) catalyst has been carried out at 0-100 degrees C. The rate constants for the formation of oligo(C), hydrolysis of ImpC with and without Na (+)-Mont and degradation of oligo(C) were determined. The apparent activation parameters were 30.8 +/- 3.9 kJ mol (-1) ( Ea), 28.3 +/- 4.0 kJ mol (-1) (Delta H++), and -231 +/- 13 J mol (-1) K (-1) (Delta S++) for the formation of the 2-mer; 45.6 +/- 2.9 kJ mol (-1) ( Ea), 43.0 +/- 3.0 kJ mol (-1) (Delta H++), -164 +/- 10 J mol (-1) K (-1) (Delta S++) for the 3-mer; and 45.2 +/- 0.6 kJ mol (-1) ( Ea), 42.7 +/- 0.7 kJ mol (-1) (Delta H++), -159 +/- 2 J mol (-1) K (-1) (Delta S++) for the 4-mer in the presence of Na (+)-Mont. An increasing trend for the rate constants for the formation of oligo(C) in the order 2-mer << 3-mer <4-mer was observed at high temperatures, which is consistent with that observed at low temperatures. These analyses implied for the first time that the associate formation between an activated nucleotide monomer and an elongating oligonucleotide prior to the phosphodiester bond formation during the elongation of an oligonucleotide on a clay surface would be based on the interaction between the two reactants at the phosphoester and/or ribose moieties rather than at the nucleotide bases. The hydrolysis rate of ImpC at 25-100 degrees C was 5.3-10.6 times greater in the presence of Na (+)-Mont than in its absence. Although the degradation of oligo(C) in the presence of Na (+)-Mont was slower than the formation of the 3-mer and longer oligo(C) on Na (+)-Mont, its yield decreased with temperature. This is mainly because the ratios of the rate constant of the 2-mer formation to those of ImpC hydrolysis and the 3-mer and 4-mer formation decrease with an increase in temperature, which is attributed to the enthalpy and entropy changes for the formation of the 2-mer. This trend resembles the case of the template-directed formation of oligo(G) on a poly(C) template but is different from the Pb (2+)-ion-catalyzed oligo(C) formation. According to the kinetics and activation parameter analyses regarding the clay reaction and other prebiotic polymerase models, the possible pathways for the oligonucleotide formation are discussed and compared.

Nucleic acids bind to nanoparticulate iron (II) monosulphide in aqueous solutions

In the hydrothermal FeS-world origin of life scenarios nucleic acids are suggested to bind to iron (II) monosulphide precipitated from the reaction between hydrothermal sulphidic vent solutions and iron-bearing oceanic water. In lower temperature systems, the first precipitate from this process is nanoparticulate, metastable FeSm with a mackinawite structure. Although the interactions between bulk crystalline iron sulphide minerals and nucleic acids have been reported, their reaction with nanoparticulate FeSm has not previously been investigated. We investigated the binding of different nucleic acids, and their constituents, to freshly precipitated, nanoparticulate FeSm. The degree to which the organic molecules interacted with FeSm is chromosomal DNA > RNA > oligomeric DNA > deoxadenosine monophosphate approximately deoxyadenosine approximately adenine. Although we found that FeSm does not fluoresce within the visible spectrum and there is no quantum confinement effect seen in the absorption, the mechanism of linkage of the FeSm to these biomolecules appears to be primarily electrostatic and similar to that found for the attachment of ZnS quantum dots. The results of a preliminary study of similar reactions with nanoparticulate CuS further supported the suggestion that the interaction mechanism was generic for nanoparticulate transition metal sulphides. In terms of the FeS-world hypothesis, the results of this study further support the idea that sulphide minerals precipitated at hydrothermal vents interact with biomolecules and could have assisted in the formation and polymerisation of nucleic acids.

Selectivity of montmorillonite catalyzed prebiotic reactions of D, L-nucleotides

The montmorillonite-catalyzed reactions of the 5'-phosphorimidazolides of D, L-adenosine (D, L-ImpA) (Figure 1a. N = A, R = H) and D, L-uridine (Figure 1a., N = U, R = H) yields oligomers that were as long as 7 mers and 6 mers, respectively. The reactions of dilute solutions of D-ImpA and D-ImpU under the same conditions gave oligomers as long as 9 and 8 mers respectively. This demonstrated that oligomer formation is only partially inhibited by incorporation of both the D- and L-enantiomers. The structures of the dimers, trimers and tetramer fractions formed from D, L-ImpA was investigated by selective enzymatic hydrolysis, comparison with authentic samples and mass spectrometry. Homochiral products were present in greater amounts than would be expected if theoretical amounts of each were formed. The ratio of the proportion of homochiral products to that of the amount of each expected for the dimers (cyclic and linear), trimers and tetramers, was 1.3, 1.6, and 2.1, respectively. In the D, L-ImpU reaction homochiral products did not predominate with ratios of dimers (cyclic and linear), trimers and tetramers 0.8, 0.44, and 1.4, respectively. The proportions of cyclic dimers in the dimer fraction were 52-66% with D, L-ImpA and 44-69% with D, L-ImpU. No cyclic dimers were formed in the absence of montmorillonite. The differences in the reaction products of D, L-ImpA and D, L-ImpU are likely to be due to the difference in the orientations of the activated monomers when bound to the catalytic sites on montmorillonite. The consequences of the selectivity of montmorillonite as a prebiotic catalyst are discussed.

Catalytic activity of hammerhead ribozymes in a clay mineral environment: implications for the RNA world

The hypothesized RNA-based world would have required the presence of a protected environment in which RNA, or an RNA-like molecule, could originate and express its biological activity. Recent studies have indicated that RNA molecules adsorbed/bound on clay minerals are able to persist in the presence of degrading agents, to interact with surrounding molecules, and to transmit the information contained in their nucleotide sequences. In this study, we assessed the ability of RNA molecules with catalytic activity to perform a specific reaction in a mineral environment. For this purpose, we investigated the self-cleavage reaction of the hammerhead ribozyme of the Avocado Sun Blotch Viroid (ASBVd), both in the monomeric and in dimeric forms. The monomeric transcript was tightly bound on the clay mineral montmorillonite to form a stable complex, while the behaviour of the dimeric transcript was studied in the presence of the clay particles in the reaction mixture. The results indicated that the hammerhead ribozyme was still active when the monomeric transcript was adsorbed on the clay surface, even though its efficiency was reduced to about 20% of that in solution. Moreover, the self-cleavage of clay-adsorbed molecule was significantly enhanced ( approximately four times) by the presence of the 5' reaction product. The self-cleavage reaction of the dimeric transcript in the presence of montmorillonite indicated that the mineral particles protected the RNA molecules against aspecific degradation and increased the rate of cleavage kinetics by about one order of magnitude. These findings corroborate the hypothesis that clay-rich environments would have been a good habitat in which RNA or RNA-like molecules could originate, accumulate and undergo Darwinian evolutionary processes, leading to the first living cells on Earth.

Catalysis and selectivity in prebiotic synthesis: initiation of the formation of oligo(U)s on montmorillonite clay by adenosine-5'-methylphosphate

Adenosine-5'-methylphosphate (MepA) initiates the oligomerization of the 5'-phosphorimidazolide of uridine (ImpU) in the presence of montmorillonite clay. Longer oligomers form because the 5'-phosphate is blocked with a methyl group that prevents the formation of cyclic- and pyrophosphate-containing compounds. The MepA initiates 69-84% of the 5-9 charge oligomers, respectively. The montmorillonite catalyst also provides selectivity in the oligomerization reactions so that the main reaction pathway is MepA --> MepA3'pU --> MepA3'pU2'pU --> MepA3'pU2'pU3'pU. MepA did not enhance the oligomerization of ImpA. The relative rates of the reactions were determined from an investigation of the products in competitive reactions. Selectivity was observed in the reaction of ImpU with equimolar amounts of MepA3'pU and MepA2'pU where the relative reaction rates are 10.3:1, respectively. In the reaction of ImpA with MepA3'pA and MepA2'pA the ImpA reacts 5.2 times faster with MepA3'pA. In the competitive reaction of ImpU and ImpA with MepA3'pA and MepA3'pU the elongation proceeds on MepA3'pA 5.6 times more rapidly than with MepA3'pU. There is no correlation between the extent of binding to the montmorillonite and reaction rates in the formation of longer oligomers. The formation of more than two sequential 2',5'-linkages in the oligomer chain proceeds more slowly than the addition to a single 2',5'-link or a 3',5'-link and either chain termination or elongation by a 3',5'-linage occurs. The central role that catalysis may have had in the prebiotic formation of biopolymers is discussed.

Synthesis and degradation of nucleobases and nucleic acids by formamide in the presence of montmorillonites

We describe the role of formamide, a product of the hydrolysis of hydrogen cyanide, as precursor of several components of nucleic acids under prebiotic conditions. When formamide is heated in the presence of montmorillonites, the efficient one-pot synthesis of purine, adenine, cytosine, and uracil is obtained. Along with these nucleobases, several components of the inosine pathway are obtained: 5-aminoimidazole-4-carboxamide, 5-formamidoimidazole-4-carboxamide and hypoxanthine. This almost complete catalogue of nucleic acid precursors is accompanied by N(9)-formylpurine, which, containing a masked glycosidic bond in its formyl moiety, is a plausible precursor of purine acyclonucleosides. In addition, montmorillonites differentially affect the rate of degradation of nucleobases when embedded in 2'-deoxyoligonucleotides; namely, montmorillonites protect adenine and guanine from the degradative action of formamide, while thymine degradation is enhanced. The oligonucleotide backbone reactivity to formamide is also affected; this shows that the interaction with montmorillonites modifies the rate of abstraction of the Halpha and Hbeta protons on the sugar moieties.

Montmorillonite, oligonucleotides, RNA and origin of life

Na-montmorillonite prepared from Volclay by the titration method facilitates the self-condensation of ImpA, the 5'-phosphorimidazolide derivative of adenosine. As was shown by AE-HPLC analysis and selective enzymatic hydrolysis of products, oligo(A)s formed in this reaction are 10 monomer units long and contain 67% 3',5'-phosphodiester bonds (Ferris and Ertem, 1992a). Under the same reaction conditions, 5'-phosphorimidazolide derivatives of cytidine, uridine and guanosine also undergo self-condensation producing oligomers containing up to 12-14 monomer units for oligo(C)s to 6 monomer units for oligo(G)s. In oligo(C)s and oligo(U)s, 75-80% of the monomers are linked by 2',5'-phosphodiester bonds. Hexamer and higher oligomers isolated from synthetic oligo(C)s formed by montmorillonite catalysis, which contain both 3',5'- and 2',5'-linkages, serve as catalysts for the non-enzymatic template directed synthesis of oligo(G)s from activated monomer 2-MeImpG, guanosine 5'-phospho-2-methylimidazolide (Ertem and Ferris, 1996). Pentamer and higher oligomers containing exclusively 2',5'-linkages, which were isolated from the synthetic oligo(C)s, also serve as templates and produce oligo(G)s with both 2',5'- and 3',5'-phosphodiester bonds. Kinetic studies on montmorillonite catalyzed elongation rates of oligomers using the computer program SIMFIT demonstrated that the rate constants for the formation of oligo(A)s increased in the order of 2-mer < 3-mer < 4-mer ... < 7-mer (Kawamura and Ferris, 1994). A decameric primer, dA(pdA)8pA bound to montmorillonite was elongated to contain up to 50 monomer units by daily addition of activated monomer ImpA to the reaction mixture (Ferris, Hill and Orgel, 1996). Analysis of dimer fractions formed in the montmorillonite catalyzed reaction of binary and quaternary mixtures of ImpA, ImpC, 2-MeImpG and ImpU suggested that only a limited number of oligomers could have formed on the primitive Earth rather than equal amounts of all possible isomers (Ertem and Ferris, 2000). Formation of phosphodiester bonds between mononucleotides by montmorillonite catalysis is a fascinating discovery, and a significant step forward in efforts to find out how the first RNA-like oligomers might have formed in the course of chemical evolution. However, as has been pointed out in several publications, these systems should be regarded as models rather than a literal representation of prebiotic chemistry (Orgel, 1998; Joyce and Orgel, 1999; Schwartz, 1999).

Eutectic phase polymerization of activated ribonucleotide mixtures yields quasi-equimolar incorporation of purine and pyrimidine nucleobases

The RNA world hypothesis requires a plausible mechanism by which RNA itself (or precursor RNA-like polymers) can be synthesized nonenzymatically from the corresponding building blocks. Simulation experiments have exploited chemically reactive mononucleotides as monomers. Solutions of such monomers in the prebiotic environment were likely to be very dilute, but in experimental simulations of polymerization reactions dilute solutions of activated mononucleotides in the millimolar range hydrolyze extensively, and only trace amounts of dimers and trimers are formed. We report here that random medium-size RNA analogues with mixed sequences (5- to 17-mers with traces of longer products) can be synthesized in ice eutectic phases that are produced when dilute solutions of activated monomers and catalysts (Mg(II) and Pb(II)) are frozen and maintained at -18 degrees C for periods up to 38 days. Under these conditions, the monomers are concentrated as eutectics in an ice matrix. Hydrolysis of the activated mononucleotides was suppressed at low-temperature ranges, and polymerization was enhanced with yields up to 90%. Analysis of the mixed oligomers established that incorporation of both purine and pyrimidine bases proceeded at comparable rates and yields. These results suggest that ice deposits on the early Earth could have facilitated the synthesis of short- and medium-size random sequence RNA analogues and thereby provided a microenvironment suitable for the formation of biopolymers or their precursors.

Adenine and RNA in mineral samples. Surface-enhanced Raman spectroscopy (SERS) for picomole detections

Studies on the interactions of biological macromolecules with mineral surfaces are crucial for the detecting biomarkers. But before this can be done for real samples like rocks or sediments, rational methods based on mineral models plus known amounts of nucleic acids must be developed. The methods must be very sensitive, as the amount of bound macromolecule may be very small. Surface-enhanced Raman spectroscopy (SERS) is perfect for detecting picomolar amounts of nucleic acid materials. In this study, the models used were adenine and GAAA hairpin for nucleic acids materials and a clay (montmorillonite) plus colloidal silver (used for SERS detection) for mineral supports. We have shown that OH(-) anions compete with adenine and the adenyl residues in the GAAA loop for adsorption onto nano-sized silver particles in basic medium. The GAAA adenyl moieties are less well adsorbed onto either clay or silver than is adenine. Also, the transfer of either adenine or the RNA hairpin from the clay to the silver aggregates is pH-dependent. Contact between adenine and the montmorillonite also seems to disperse adenine aggregates. The clay could also increase the flexibility of the RNA hairpin so that it is released from the clay at pH 10, and the affinity of its adenyl moieties for the metallic substrate is enhanced.

Cations as mediators of the adsorption of nucleic acids on clay surfaces in prebiotic environments

Monovalent ([Na+] > 10 mM) and divalent ([Ca2+], [Mg2+] > 1.0 mM) cations induced the precipitation of nucleic acid molecules. In the presence of clay minerals (montmorillonite and kaolinite), there was adsorption instead of precipitation. The cation concentration needed for adsorption depended on both the valence of the cations and the chemical nature of the nucleic acid molecules. Double-stranded nucleic acids needed higher cation concentrations than single-stranded ones to be adsorbed to the same extent on clay. Divalent cations were more efficient than monovalent ones in mediating adsorption. Adsorption to the clay occurred only when both nucleic acids and cations were present. However, once the complexes were formed, the cations could not be removed from the system by washing, indicating that they are directly involved in the association between nucleic acids and mineral surfaces. These observations indicate that cations take part directly in the formation of nucleic acid-clay complexes, acting as a 'bridge' between the negative charges on the mineral surface and those of the phosphate groups of the genetic polymer. The relatively low cation concentrations needed for adsorption and the ubiquitous presence of clay minerals in the environment suggest that the adsorption of nucleic acids on mineral surfaces could have taken place in prebiotic habitats. This may have played an important role in the formation and preservation of nucleic acids and/or their precursor polymers.

Oligomerization reactions of ribonucleotides: the reaction of the 5'-phosphorimidazolide of nucleosides on montmorillonite and other minerals

The reaction of ImpA in the presence of Na+ -montmorillonite 22A or Na+ -Volclay in aqueous, pH 8 solution gives a 50-60% yield of dimers and trimers (pA)2 and (pA)3. The ratio of 3',5'-phosphodiester bond formation is twice as great as 2',5'-bond formation. The reaction requires the presence of Mg2+ and is inhibited by 0.4 M imidazole. N-methylimidazole enhances the rate of the reaction but does not cause major changes in yield or product composition. Higher yields were obtained when Li+ -or Ca2+ -montmorillonites were used in place of Na+ -montmorillonite. Little or no phosphodiester bond formation was observed with Mg2+ - or Al3+ -montmorillonite. Montmorillonites other than 22A and Volclay exhibited little or no catalysis. In addition, little or no catalysis was exhibited in ferrugenous smectite, nontronite, allophane, imogolite or sepiolite. Oligomers were also formed by the reaction of ImpG, 2-methylImpG, ImpC and ImpU in the presence of Na+ -montmorillonite. The pyrimidine nucleotides gave significantly lower yields of oligomers.

Oligomerization reactions of deoxyribonucleotides on montmorillonite clay: the effect of mononucleotide structure on phosphodiester bond formation

Adenine deoxynucleotides bind more strongly to Na(+)-montmorillonite than do the corresponding ribonucleotides. Thymidine nucleotides binds less strongly to Na(+)-montmorillonite than do the corresponding adenine deoxynucleotides. Oligomers of 2'-dpA up to the tetramer were detected in the reaction 2'-d-5'-AMP with EDAC (a water-soluble carbodiimide) in the presence of Na(+)-montmorillonite. Reaction of 3'-d-5'-AMP with EDAC on Na(+)-montmorillonite yields 3'-d-2',5'-pApA while the reaction of 2'-d-3'-AMP yields almost exclusively 3',5'-cdAMP. The reaction of 5'-TMP under the same reaction conditions give 3',5'-cpTpT and 3',5'-pTpT while 3'-TMP gives mainly 3',5'-cpT. The yield of dinucleotide products (dpNpN) containing the phosphodiester bond is 1% or less when Na(+)-montmorillonite is omitted from the reaction mixture.

Oligomerization reactions of deoxyribonucleotides on montmorillonite clay: the effect of mononucleotide structure, phosphate activation and montmorillonite composition on phosphodiester bond formation

2'-d-5'-GMP and 2'-d-5'-AMP bind 2 times more strongly to montmorillonite 22A than do 2'-d-5'-CMP and 5'-TMP. The dinucleotide d(pG)2 forms in 9.2% yield and the cyclic dinucleotide c(dpG)2 in 5.4% yield in the reaction of 2'-d-5'-GMP with EDAC in the presence of montmorillonite 22A. The yield of d(pC)2 (2.0%) is significantly lower but comparable to that obtained from 5'-TMP. The yield of dimers which contain the phosphodiester bond decreases as the reaction medium is changed from 0.2 M NaCl to a mixture of 0.2 M NaCl and 0.075 M MgCl2. A low yield of d(pA)2 was observed in the condensation reaction of 5'-ImdpA on montmorillonite 22A. The cyclic nucleotide (3',5'-cdAMP) was obtained in 14% yield from 3'-ImdpA. The yield of d(pA)2 obtained when EDAC is used as the condensing agent increases with increasing iron content of the Na(+)-montmorillonite used as a catalyst. Evidence is presented which shows that the acidity of the Na(+)-montmorillonite is a necessary but not sufficient factor for the montmorillonite catalysis of phosphodiester bond formation.

Effect of inhibitors on the montmorillonite clay-catalyzed formation of RNA: studies on the reaction pathway

The Langmuir adsorption isotherms of the phosphoroimidazolides of adenosine (ImpA) and uridine (ImpU), dA5' ppdA and N6,N6-dimethyladenine binding on montmorillonite are consistent with their forming a monolayer on the clay surface. This suggests the condensation of ImpA and ImpU to oligomers proceeds on the surface of the clay and not in groups of monomers stacked on the clay surfaces. The binding and reactions of ImpU and ImpA on montmorillonite are blocked by N6,N6-dimethyladenine and dA5' ppdA. dA5' ppdA is a better inhibitor of oligomer formation than N6,N6-dimethyladenine because both adenine rings of dA5' ppdA bind to the clay surface and block adjacent catalytic sites. An upper limit of 5-10 x 10(15) catalytic sites on 50 mg of clay was estimated from the binding of ImpU and the inhibition of oligomer formation by dA5' ppdA.

Eutectic phases in ice facilitate nonenzymatic nucleic acid synthesis

Polymeric compounds similar to oligonucleotides are relevant to the origin of life and particularly to the concept of an RNA world. Although short oligomers of RNA can be synthesized nonenzymatically under laboratory conditions by second-order reactions in concentrated solutions, there is no consensus on how these polymers could have been synthesized de novo on the early Earth from dilute solutions of monomers. To address this question in the context of an RNA world, we have explored ice eutectic phases as a reaction medium. When an aqueous solution freezes, the solutes become concentrated in the spaces between the ice crystals. The increased concentration offsets the effect of the lower temperature and accelerates the reaction. Here we show that in the presence of metal ions in dilute solutions, frozen samples of phosphoimidazolide-activated uridine react within days at -18 degrees C to form oligouridylates up to 11 bases long. Product yields typically exceed 90%, and approximately 30% of the oligomers include one or more 3'-5' linkages. These conditions facilitate not only the notoriously difficult oligouridylate synthesis, but also the oligomerization of activated cytidylate, adenylate, and guanylate. To our knowledge, this represents the first report to indicate that ice matrices on the early Earth may have accelerated certain prebiotic polymerization reactions.

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.

Clay catalysis of oligonucleotide formation: kinetics of the reaction of the 5'-phosphorimidazolides of nucleotides with the non-basic heterocycles uracil and hypoxanthine

The montmorillonite clay catalyzed condensation of activated monocleotides to oligomers of RNA is a possible first step in the formation of the proposed RNA world. The rate constants for the condensation of the phosphorimidazolide of adenosine were measured previously and these studies have been extended to the phosphorimidazolides of inosine and uridine in the present work to determine of substitution of neutral heterocycles for the basic adenine ring changes the reaction rate or regioselectivity. The oligomerization reactions of the 5'-phosphoromidazolides of uridine (ImpU) and inosine (ImpI) on montmorillonite yield oligo(U)s and oligo(I)s as long as heptamers. The rate constants for oligonucleotide formation were determined by measuring the rates of formation of the oligomers by HPLC. Both the apparent rate constants in the reaction mixture and the rate constants on the clay surface were calculated using the partition coefficients of the oligomers between the aqueous and clay phases. The rate constants for trimer formation are much greater than those dimer synthesis but there was little difference in the rate constants for the formation of trimers and higher oligomers. The overall rates of oligomerization of the phosphorimidazolides of purine and pyrimidine nucleosides in the presence of montmorillonite clay are the same suggesting that RNA formed on the primitive Earth could have contained a variety of heterocyclic bases. The rate constants for oligomerization of pyrimidine nucleotides on the clay surface are significantly higher than those of purine nucleotides since the pyrimidine nucleotides bind less strongly to the clay than do the purine nucleotides. The differences in the binding is probably due to Van der Waals interactions between the purine bases and the clay surface. Differences in the basicity of the heterocyclic ring in the nucleotide have little effect on the oligomerization process.