The prebiotic synthesis of deoxythymidine oligonucleotides

Summary A reaction shown to oligomerize nucleotides under possible prebiotic conditions has been made more plausible by the finding that the reaction can proceed at initial neutral pH in the presence of acid salts or NH₄Cl.     

Non-enzymatic transfer of sequence information under plausible prebiotic conditions

We simulated in our laboratory a prebiotic environment where dry and wet periods were cycled. Under anhydrous conditions, lipid molecules present in the medium could form fluid lamellar matrices and work as organizing agents for the condensation of nucleic acid monomers into polymers. We exposed a mixture of 2′-deoxyribonucleoside 5′-monophosphates and a ssDNA oligomer template to this dry environment at 90 °C under a continuous gentle stream of CO₂ and we followed it with rehydration periods. After five dry/wet cycles we were able to detect the presence of a product that was complementary to the template. The reaction had a 0.5% yield with respect to the template, as measured by staining with the Pico Green^® fluorescent probe. Absent initial template, the product of the reaction remained below the detection limit. In order to characterize the fidelity of replication, the synthesized strand was ligated to adapters, amplified by PCR, and sequenced. The alignment of the sequenced DNA to the expected complementary sequence revealed that the misincorporation rate was 9.9%. We present these results as a proof of concept for the possibility of having non-enzymatic transfer of sequence information in a prebiotically plausible environment.     

In vitro study on gas generation and prebiotic effects of some carbohydrates and their mixtures

This study was carried out to examine the effect of inulin (IN), fructooligosaccharide (FOS), polydextrose (POL) and isomaltooligosaccharides (ISO), alone and in combination, on gas production, gas composition and prebiotic effects. Static batch culture fermentation was performed with faecal samples from three healthy volunteers to study the volume and composition of gas generated and changes in bacterial populations. Four carbohydrates alone or mixed with one another (50:50) were examined. Prebiotic index (PI) was calculated and used to compare the prebiotic effect. The high amount of gas produced by IN was reduced by mixing it with FOS. No reduction in gas generation was observed when POL and ISO mixed with other substrates. It was found that the mixture of IN and FOS was effective in reducing the amount of gas produced while augmenting or maintaining their potential to support the growth of bifidobacteria in faecal batch culture as the highest PI was achieved with FOS alone and a mixture of FOS and IN. It was also found that high volume of gas was generated in presence of POL and ISO and they had lower prebiotic effect. The results of this study imply that a mixture of prebiotics could prove effective in reducing the amount of gas generated by the gut microflora.     

Steps Towards the Formation of A Protocell: The Possible Role of Short Peptides

The paper deals with molecular self-organization leading to formation of a protocell. Plausible steps towards a protocell include: polymerization of peptides and oligonucleotides on mineral surfaces; coevolution of peptides and oligonucleotides with formation of collectively autocatalytic sets; self-organization of short peptides into vesicles; entrapment of the peptide/oligonucleotide systems in mixed peptide and simple amphiphile membranes; and formation of functioning protocells with metabolism and cell division. The established propensity of short peptides to self-ordering and to formation of vesicles makes this sequence plausible. We further suggest that evolution of a protocell produced cellular ancestors of viruses as well as ancestors of cellular organisms.     

Alternative bases in the RNA world: The prebiotic synthesis of urazole and its ribosides

Urazole is five-membered heterocyclic compound which is isosteric with uracil's hydrogen-bonding segment. Urazole reacts spontaneously with ribose (and other aldoses) to give mixture of four ribosides: and pyranosides and furanosides. This reaction occurs in aqueous solution at mild temperatures. Thermodynamic and kinetic parameters for the reaction of urazole with ribose were determined. In contrast, uracil is completely unreactive with ribose under these conditions. Urazole's unusual reactivity is ascribed to the hydrazine portion of the molecule. Urazole can be synthesized from biuret and hydrazine under prebiotic conditions. The prebiotic synthesis of guanazole, which is isosteric in part to diaminopyrimidine and cytosine, is accomplished from dicyandiamide and hydrazine. Kinetic parameters for both prebiotic reactions were measured. Urazole and guanazole are transparent in the UV, which would be favorable property in the absence of an ozone layer on the early Earth. Urazole makes hydrogen bonds with adenine in DMSO similar to those of uracil, as established by IH NMR. All of these properties make urazole an attractive potential precursor to uracil and guanazole a potential precursor to cytosine in the RNA or pre-RNA world.Correspondence to: S.L. Miller 0805Presented at the ISSOL Meeting in Barcelona, 5 July 1993 V.M. Kolb is on sabbatical leave from the University of Wisconsin-Parkside, Kenosha, WI 53141     

From prebiotic chemistry to cellular metabolism--the chemical evolution of metabolism before Darwinian natural selection

It is generally assumed that the complex map of metabolism is a result of natural selection working at the molecular level. However, natural selection can only work on entities that have three basic features: information, metabolism and membrane. Metabolism must include the capability of producing all cellular structures, as well as energy (ATP), from external sources; information must be established on a material that allows its perpetuity, in order to safeguard the goals achieved; and membranes must be able to preserve the internal material, determining a selective exchange with external material in order to ensure that both metabolism and information can be individualized. It is not difficult to understand that protocellular entities that boast these three qualities can evolve through natural selection. The problem is rather to explain the origin of such features under conditions where natural selection could not work. In the present work we propose that these protocells could be built by chemical evolution, starting from the prebiotic primordial soup, by means of chemical selection. This consists of selective increases of the rates of certain specific reactions because of the kinetic or thermodynamic features of the process, such as stoichiometric catalysis or autocatalysis, cooperativity and others, thereby promoting their prevalence among the whole set of chemical possibilities. Our results show that all chemical processes necessary for yielding the basic materials that natural selection needs to work may be achieved through chemical selection, thus suggesting a way for life to begin.     

The first peptides: The evolutionary transition between prebiotic amino acids and early proteins

The issues we attempt to tackle here are what the first peptides did look like when they emerged on the primitive earth, and what simple catalytic activities they fulfilled. We conjecture that the early functional peptides were short (3-8 amino acids long), were made of those amino acids, Gly, Ala, Val and Asp, that are abundantly produced in many prebiotic synthesis experiments and observed in meteorites, and that the neutralization of Asp's negative charge is achieved by metal ions. We further assume that some traces of these prebiotic peptides still exist, in the form of active sites in present-day proteins. Searching these proteins for prebiotic peptide candidates led us to identify three main classes of motifs, bound mainly to Mg²⁺ ions: D(F/Y)DGD corresponding to the active site in RNA polymerases, DGD(G/A)D present in some kinds of mutases, and DAKVGDGD in dihydroxyacetone kinase. All three motifs contain a DGD submotif, which is suggested to be the common ancestor of all active peptides. Moreover, all three manipulate phosphate groups, which was probably a very important biological function in the very first stages of life. The statistical significance of our results is supported by the frequency of these motifs in today's proteins, which is three times higher than expected by chance, with a P-value of 3×10⁻². The implications of our findings in the context of the appearance of life and the possibility of an experimental validation are discussed.     

The catalytic effect of L- and D-histidine on alanine and lysine peptide formation

A starting phase of chemical evolution on our ancient Earth around 4 billion years ago was the formation of amino acids and their combination to peptides and proteins. The salt-induced peptide formation (SIPF) reaction has been shown to be appropriate for this condensation reaction under moderate and plausible primitive Earth conditions, forming short peptides from amino acids in aqueous solution containing sodium chloride and Cu(II) ions. In this paper we report results about the formation of dialanine and dilysine from their monomers in this reaction. The catalytic influence of l- and d-histidine dramatically increases dialanine yields when starting from lower alanine concentrations, but also dilysine formation is markedly boosted by these catalysts. Attention is paid to measurable preferences for one enantiomeric form of alanine and lysine in the SIPF reaction. Alanine, especially, shows stereospecific behaviour, mostly in favour of the l-form.     

Oxovanadium(IV) complexes of carbohydrates: A brief overview

In this brief review the most recent studies and the most relevant aspects of the complexes generated by interaction of carbohydrates and related molecules with the oxovanadium(IV) cation, VO²⁺, are presented and discussed. The survey includes complexes of mono-, di- and polysaccharides, and of other molecules related to simple sugars. First studies with conduritols and related molecules are also described. Moreover, complexes of ascorbic and quinic acids and of some peculiar flavonoids are also included. Some comments on the general physicochemical properties of these complexes are made and their biological activities and effects are also briefly discussed.     

A possible role of fluctuating clay-water systems in the production of ordered prebiotic oligomers

Summary A model is proposed for the intermediate stages of prebiotic evolution, based on the characteristics of the adsorption and condensation of amino acids and nucleotides on the surface area of clay minerals in a fluctuating environment. Template replication and translation of adsorbed oligonucleotides and catalytic effects by peptide products on further condensation are proposed, due to specific properties of hypohydrous clay surfaces as well as the biomolecules themselves. Experimental evidence supports some of the proposed interactions, and all of them can be tested experimentally.on leave from the Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel, 1975–76     

A conformational rationale for the replication of nucleic acids under prebiotic conditions

The Watson-Crick model at once gave an explanation for the mechanism of replication of DNA. But the hydrogen-bonding forces between the bases alone are not enough for the specificity of base-pairing mechanisms, since any pair of bases can be positioned to have at least two hydrogen bonds. In the present-day biological organisms, sophisticated enzymatic machinery is supposed to constrain the ribose-phosphate backbone to have regular structure, aiding the self-templating duplication. For the prebiotic stage, whence sophisticated enzymes would not have been evolved, we propose a novel double helical conformation of DNA wherein the two sugar-phosphate backbones are pulled towards each other by (CH  O) hydrogen bonds conferring stereospecificity for the formation of (A : T)- and (G : C)-pairs, in the self-templating chains of DNA. Our model-building efforts and computer calculations endorse the stereochemical feasibility of the conformation. The pairing of homologous sequences of two double helices of DNA is explained by direct hydrogen-bonding interactions in our model and it is thus relevant to the present-day biological functions also, at least in some stages of the cell-cycle.     

Clusterin in cerebrospinal fluid: analysis of carbohydrates and quantification of native and glycosylated forms

Clusterin is suggested to be involved in the pathogenesis of Alzheimer's disease. Clusterin expression is increased in brain tissue in affected regions of Alzheimer patients, and intense clusterin staining is found in both senile plaques and in neuronal and glia cells. In contrast, the cerebrospinal fluid level of clusterin in Alzheimer patients has, thus far, been found unchanged. Clusterin is a glycosylated protein, and an alteration of its glycosylation in Alzheimer's disease might influence accurate quantification in cerebrospinal fluid through interference of antibody binding to the protein. Using enzymatic deglycosylation of clusterin isolated from cerebrospinal fluid, we found that the carbohydrates attached to clusterin were of the N-linked type and sialic acids. Based on this finding, cerebrospinal fluid samples from Alzheimer patients (n = 99) and controls (n = 39) were analysed. The samples were treated with peptide: N-glycanase F, cleaving off N-linked carbohydrates, and clusterin was quantified before and after deglycosylation using a new sandwich enzyme-linked immunosorbent assay. Clusterin was significantly increased in Alzheimer patients, in both native (7.17 ± 2.43 AU versus 5.73 ± 2.09 AU; p = 0.002), and deglycosylated samples (12.19 ± 5.00 AU versus 9.68 ± 4.38 AU; p = 0.004). Deglycosylation led to increased measured levels of clusterin by 70% (p < 0.001) in Alzheimer patients and 67% (p < 0.001) in controls. These findings indicate that glycosylation of proteins may interfere with their quantification. The results show that clusterin is significantly increased in cerebrospinal fluid from Alzheimer patients as a group, supporting that clusterin might be involved in the pathogenesis of Alzheimer's disease. However, the individual clusterin levels overlap between the two groups, and thus cerebrospinal fluid clusterin measurement is not suitable as a biochemical marker in the diagnosis of Alzheimer's disease.     

The Effects of Ferrous and other Ions on the Abiotic Formation of Biomolecules using Aqueous Aerosols and Spark Discharges

It has been postulated that the oceans on early Earth had a salinity of 1.5 to 2 times the modern value and a pH between 4 and 10. Moreover, the presence of the banded iron formations shows that Fe⁺² was present in significant concentrations in the primitive oceans. Assuming the hypotheses above, in this work we explore the effects of Fe⁺² and other ions in the generation of biomolecules in prebiotic simulation experiments using spark discharges and aqueous aerosols. These aerosols have been prepared using different sources of Fe⁺², such as FeS, FeCl₂ and FeCO₃, and other salts (alkaline and alkaline earth chlorides and sodium bicarbonate at pH = 5.8). In all these experiments, we observed the formation of some amino acids, carboxylic acids and heterocycles, involved in biological processes. An interesting consequence of the presence of soluble Fe⁺² was the formation of Prussian Blue, Fe₄[Fe(CN)₆]₃, which has been suggested as a possible reservoir of HCN in the initial prebiotic conditions on the Earth.     

Tritrichomonas foetus: ultrastructural localization of basic proteins and carbohydrates

The postformalin ammoniacal silver (AS) and the ethanolic phosphotungstic acid (E-PTA) techniques were used to localize basic proteins at the ultrastructural level in the protozoa, Tritrichomonas foetus. The periodic acid-thiosemicarbazide-silver proteinate technique was used to localize carbohydrates. With the AS technique reaction product was seen only in the hydrogenosomes. With the E-PTA technique, reaction product was seen in the microtubules that form the basal bodies, flagella, pelta, and axostyle, in the costa, in the hydrogenosomes, and at the region of the recurrent flagellum's adhesion to the cell body. Previous acetylation of the cells under conditions that block most free amino groups abolished (AS technique) or greatly reduced (E-PTA technique) staining. Carbohydrates were localized on the cell surface; in the membranes of the hydrogenosomes, Golgi complex, and cytoplasmic vesicles; and in the glycogen particles. The specificity of the AS and E-PTA techniques to detect basic proteins is based on observations made with T. foetus as well as with other cell types.     

Direct one-pot conversion of acylated carbohydrates into their alkylated derivatives under heterogeneous reaction conditions using solid NaOH and a phase transfer catalyst

A convenient one-pot protocol for the direct conversion of acyl-protected carbohydrates into their alkylated counterparts has been developed by using alkyl halides in the presence of solid sodium hydroxide and a phase transfer catalyst. These economically convenient, mild, two-phase reaction conditions allow the preparation of a variety of monosaccharide intermediates for use in the synthesis of complex oligosaccharides.     

Functional petit-suisse cheese: measure of the prebiotic effect

Prebiotics and probiotics are increasingly being used to produce potentially synbiotic foods, particularly through dairy products as vehicles. It is well known that both ingredients may offer benefits to improve the host health. This research aimed to evaluate the prebiotic potential of novel petit-suisse cheeses using an in vitro fermentation model. Five petit-suisse cheese formulations combining candidate prebiotics (inulin, oligofructose, honey) and probiotics (Lactobacillus acidophilus, Bifidobacterium lactis) were tested in vitro using sterile, stirred, batch culture fermentations with human faecal slurry. Measurement of prebiotic effect (MPE) values were generated comparing bacterial changes through determination of maximum growth rates of groups, rate of substrate assimilation and production of lactate and short chain fatty acids. Fastest fermentation and high lactic acid production, promoting increased growth rates of bifidobacteria and lactobacilli, were achieved with addition of prebiotics to a probiotic cheese (made using starter+probiotics). Addition of probiotic strains to control cheese (made using just a starter culture) also resulted in high lactic acid production. Highest MPE values were obtained with addition of prebiotics to a probiotic cheese, followed by addition of prebiotics and/or probiotics to a control cheese. Under the in vitro conditions used, cheese made with the combination of different prebiotics and probiotics resulted in the most promising functional petit-suisse cheese. The study allowed comparison of potentially functional petit-suisse cheeses and screening of preferred synbiotic potential for future market use.     

A radical solution for the biosynthesis of the H-cluster of hydrogenase

Fe-only or FeFe hydrogenases, as they have more recently been termed, possess a uniquely organometallic enzyme active site, termed the H-cluster, where the electronic properties of an iron-sulfur cluster are tuned with distinctly non-biological ligands, carbon monoxide and cyanide. Recently, it was discovered that radical S-adenosylmethionine enzymes were involved in active hydrogenase expression. In the current work, we present a mechanistic scheme for hydrogenase H-cluster biosynthesis in which both carbon monoxide and cyanide ligands can be derived from the decomposition of a glycine radical. The ideas presented have broader implications in the context of the prebiotic origin of amino acids.     

Carbohydrate-directed synthesis of silver and gold nanoparticles: effect of the structure of carbohydrates and reducing agents on the size and morphology of the composites

A monosaccharide (β-d-glucose) and polysaccharide (soluble starch) were used as structure directing and subsequently stabilizing agents for the synthesis of spherical nanoparticles (NPs) and nanowires of silver and gold. Homogeneous monodispersed Ag(0) nanoparticles (Ag NPs) of 15 nm diameter were obtained when 10⁻⁴ M AgNO₃ precursor salt was reduced in starch (1 wt %)–water gel by 1 wt % β-d-glucose. For a second preparation the effect of reducing agents on the synthesis of Au(0) metallic nanoparticles (Au NPs) of 2 × 10⁻⁴ M concentration prepared in a β-d-glucose (0.03 M)–water dispersion was studied first in detail. Different equivalent amounts of NaBH₄ and a number of pH values were evaluated for the reduction of the Au salt HAuCl₄·3H₂O to obtain Au NPs. The type and the amount of reducing agent, as well as the pH of the solution was shown to affect the size and morphology of the NPs. NaBH₄ (4 equiv) produced the smallest (5.3 nm (σ 0.7)) metallic particles compared to larger particles (10.0 nm (σ 1.4)) when the salt was reduced by 1 equiv of NaBH₄. Addition of excess NaBH₄ caused the NPs to settle out as a precipitate forming a mesh or wire structure rather than monodispersed particles. Low pH (pH 6) resulted in incomplete reduction, while at pH 8 the salt was completely reduced. When the salt was reduced by NaOH at pH 8, the particles were larger (14.2 nm) and less homogeneous (σ 2.8) compared to those from NaBH₄ reduction.     

An Extended Model for the Evolution of Prebiotic Homochirality: A Bottom-Up Approach to the Origin of Life

A generalized autocatalytic model for chiral polymerization is investigated in detail. Apart from enantiomeric cross-inhibition, the model allows for the autogenic (non-catalytic) formation of left and right-handed monomers from a substrate with reaction rates epsilon L and epsilon R, respectively. The spatiotemporal evolution of the net chiral asymmetry is studied for models with several values of the maximum polymer length, N. For N = 2, we study the validity of the adiabatic approximation often cited in the literature. We show that the approximation obtains the correct equilibrium values of the net chirality, but fails to reproduce the short time behavior. We show also that the autogenic term in the full N = 2 model behaves as a control parameter in a chiral symmetry-breaking phase transition leading to full homochirality from racemic initial conditions. We study the dynamics of the N--> infinity model with symmetric (epsilon L = epsilon R) autogenic formation, showing that it only achieves homochirality for epsilon > epsilon c, where epsilon c is an N-dependent critical value. For epsilon 相似文献   

On the basics of carbohydrate-metal chemistry: complexes of palladium(II) with hydroxyaldehyde and -ketone hydrates

In this work, we present novel complexes of hydroxyaldehydes and ketones with palladium(II). The compounds are studied by two-dimensional NMR spectroscopy in solution (COSY, HMQC, HMBC). Glycolaldehyde, d-glyceraldehyde, glyoxal and 2,4-O-ethylidene-d-erythrose were used as aldehydes, d-erythrulose was used as an alpha-hydroxyketone. Although different species are present in solution, only the hydrated forms of the aldehydes can coordinate to the metal centre. These complexes are stable at 4 degrees C in aqueous solution. The crystal structure of a complex formed by mesoxalic acid and palladium(II) is reported and shows coordination by both hydroxy groups of the hydrated ketone.