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At least 19 records

A 'Warm Formamide' Scenario for the Origins of Life Might Not Be so Hot Comment on 'Formamide and the Origin of Life' by E. Di Mauro Et Al.

In this review, Saladino et al. present an intriguing hypothesis surrounding the role of formamide in the originsof life on Earth, backed by experimental results supporting each step from formamide to RNA polymers [1]. The overall premise is that, from formamide and inorganic phosphate, RNA molecules over 100 nucleotides in length canbe produced. In addition, many carboxylic acids likely relevant to prebiotic metabolism are formed along the way. Thus, from a rather simple organic molecule that has been observed in outer space (formamide), you can generatemany of the compounds necessary for the origins of life. However, because high temperatures (160 C) are requiredfor the formamide reactions, it remains unclear where the warm formamide scenario could have occurred.Low-temperature, aqueous hydrogen counter to the observation that all protein-catalyzed ligation and polymerization reactions of RNA and DNA requireactivated substrates. Detailed mechanistic studies of the reported reactions are warranted and could provide important insights for understanding the chemistry behind the origins of life.Because the authors have produced many of the experimental results supporting their hypothesis, they coulddemonstrate the validity of their hypothesis by converting formamide into 100 nucleotide RNA oligomers, usingthe products of one reaction as the reactants for the next reaction, under specific conditions plausible on the pre-bioticEarth. Such a demonstration would represent a milestone for our understanding of the origins of life.cyanide-based prebiotic chemistry that we know actually happened has beenshown to produce many of the molecules invoked in the formamide hypothesis: amino acids, carboxylic acids, sugaracids, and nucleobases have all been found in meteorites recovered on Earth [e.g. [24]], providing a plausible routefor their synthesis and delivery. In contrast, a large portion of the formamide hypothesis is based on relatively high-temperature reactions. A plausible milieu for high-temperature reactions with concentrated formamide is yet to bedescribed, and is critical for this hypothesis to be validated. Hydrothermal vents are attractive heat sources, and the higher boiling point of formamide has been invoked as a mechanism to concentrate it from an aqueous solution.Unless the water can actually evaporate, however, there would be no net enrichment. For example, in the context of a deep-sea vent, any water removed by heating would be quickly replaced.Some of the individual reactions underpinning the present hypothesis [1] have been met with skepticism becausethey go against conventional wisdom. To name a few of the surprising results: the observation that nucleosides can beconverted to cyclic phosphates when heated in the presence of minerals and inorganic phosphate [5]; that 35 cGMPand cAMP nucleotides polymerize rapidly into RNA oligomers, even in the absence of monovalent counterions [6];and that end-to-end ligation reactions between RNA oligomers occur in essentially pure water, without requiring any activating groups or counterions [7,8]. Because the polymerization reactions are simply transesterification reactions,that they readily occur in the absence of cations makes one wonder why nearly all ribozyme-catalyzed transesterification reactions are metal-ion dependent; similarly, that the end-to-end ligation reactions do not require activation runs.

life↗

A "Warm Formamide" Scenario for the Origins of Life Might not be so Hot: Comment on "Formamide and the Origin of Life"

In this review, Saladino et al. present an intriguing hypothesis surrounding the role of formamide in the origins of life on Earth, backed by experimental results supporting each step from formamide to RNA polymers. The overall premise is that, from formamide and inorganic phosphate, RNA molecules over 100 nucleotides in length can be produced. In addition, many carboxylic acids likely relevant to prebiotic metabolism, are formed along the way. Thus, from a rather simple organic molecule that has been observed in outer space (formamide), you can generate many of the compounds necessary for the origins of life. However, because high temperatures (160 C) are required for the formamide reactions, it remains unclear where the "warm formamide" scenario could have occurred. Low-temperature, aqueous hydrogen cyanide-based prebiotic chemistry that we know actually happened has been shown to produce many of the molecules invoked in the formamide hypothesis: amino acids, carboxylic acids, sugar acids, and nucleobases have all been found in meteorites recovered on Earth, providing a plausible route for their synthesis and delivery. In contrast, a large portion of the formamide hypothesis is based on relatively hightemperature reactions, A plausible milieu for high-temperature reactions with concentrated formamide is yet to be described, and is critical for this hypothesis to be validated. Hydrothermal vents are attractive heat sources, and the higher boiling point of formamide has been invoked as a mechanism to concentrate it from an aqueous solution, Unless the water can actually evaporate, however, there would be no net enrichment. For example, in the context of a deep-sea vent, any water "removed" by heating would be quickly replaced. Some of the individual reactions underpinning the present hypothesis have been met with skepticism because they go against conventional wisdom, To name a few of the surprising results: the observation that nucleosides can be converted to cyclic phosphates when heated in the presence of minerals and inorganie phosphate; that 3'-5' cGMP and cAMP nucleotides polymerize rapidly into RNA oligomers, even in the absence of monovalent counterions and that end-to-end ligation reactions between RNA oligomers occur in essentially pure water, without requiring any activating groups or counterions. Because the polymerization reactions are simply transesterification reactions, that they readily occur in the absence of cations makes one wonder why nearly all ribozyme-catalyzed transesterification reactions are metal-ion dependent; similarly, that the end-to-end ligation reactions do not require activation runs counter to the observation that all protein-catalyzed ligation and polymerization reactions of RNA and DNA require activated substrates. Detailed mechanistic studies of the reported reactions are warranted and could provide important insights for understanding the chemistry behind the origins of life. Because the authors have produced many of the experimental results supporting their hypothesis, they could demonstrate the validity of their hypothesis by converting formamide into approx 100 nucleotide RNA oligomers, using the products of one reaction as the reactants for the next reaction, under specific conditions plausible on the pre-biotic Earth. Such a demonstration would represent a milestone for our understanding of the origins of life.

Burton, Aaron S.↗

Prebiotic phosphorylation of nucleosides in formamide

Results are presented for an experimental study intended to assess phosphorylation under neither aqueous nor dry thermal conditions. Instead, phosphorylations were attempted in possible nonaqueous prebiotic solvents. Formamide appeared to be the most obvious candidate for phosphorylation studies. Three main classes of phosphorylated products were formed in formamide solution: adenosine monophosphates, cyclic adenosine phosphate, and adenosine diphosphates. Experiments were designed to investigate the extent of phosphorylation of nucleosides in formamide, the relative amounts of nucleoside monophosphate, diphosphates and cyclic phosphate formed and the relative effectiveness of different sources of phosphate as phosphorylating agents in formamide. Reaction variables were temperature, nature of the phosphate or condensed phosphate, nucleoside, concentration of reactants and possible effects of additives. Product identification was based on qualitative and quantitative thin layer chromatography.

Schoffstall, A. M.↗

Single-base-pair discrimination of terminal mismatches by using oligonucleotide microarrays and neural network analyses

The effects of single-base-pair near-terminal and terminal mismatches on the dissociation temperature (T(d)) and signal intensity of short DNA duplexes were determined by using oligonucleotide microarrays and neural network (NN) analyses. Two perfect-match probes and 29 probes having a single-base-pair mismatch at positions 1 to 5 from the 5' terminus of the probe were designed to target one of two short sequences representing 16S rRNA. Nonequilibrium dissociation rates (i.e., melting profiles) of all probe-target duplexes were determined simultaneously. Analysis of variance revealed that position of the mismatch, type of mismatch, and formamide concentration significantly affected the T(d) and signal intensity. Increasing the concentration of formamide in the washing buffer decreased the T(d) and signal intensity, and it decreased the variability of the signal. Although T(d)s of probe-target duplexes with mismatches in the first or second position were not significantly different from one another, duplexes with mismatches in the third to fifth positions had significantly lower T(d)s than those with mismatches in the first or second position. The trained NNs predicted the T(d) with high accuracies (R(2) = 0.93). However, the NNs predicted the signal intensity only moderately accurately (R(2) = 0.67), presumably due to increased noise in the signal intensity at low formamide concentrations. Sensitivity analysis revealed that the concentration of formamide explained most (75%) of the variability in T(d)s, followed by position of the mismatch (19%) and type of mismatch (6%). The results suggest that position of the mismatch at or near the 5' terminus plays a greater role in determining the T(d) and signal intensity of duplexes than the type of mismatch.

Non-NASA Center↗

New methods for preparing N,N-dialkyltrifluoroacetamides

The customary preparative methods for N,N-dialkyltrifluoroacetamides involve the acylation of an amine by trifluoroacetic acid or its derivatives. The synthesis of N,N-dialkyltrifluoroacetamides by reacting trifluoroacetic anhydride or acid with disubstituted formamides and acetamides is discussed. These reactions were interpreted with the aid of gas chromatographic analysis. Different reaction mechanisms are proposed for the reactions of formamides and acetamides with trifluoroacetic anhydride or acid. The use of the proposed reaction mechanisms for the synthesis of other fluorinated compounds is discussed.

Hsu, L.↗

New methods for preparing n, n-dialkyltrifluoroacetamides

The customary preparative methods for N,N-dialkyltrifluoroacetamides involve the acylation of an amine by trifluoroacetic acid or its derivatives. In this report the synthesis of N,N-dialkyltrifluoroacetamides by reacting trifluoroacetic anhydride or acid with disubstituted formamides and acetamides is discussed. These reactions are interpreted with the aid of gas chromatographic analysis. Different reaction mechanisms are proposed for the reactions of formamides and acetamides with trifluoroacetic anhydride or acid. The use of the proposed reaction mechanisms for the synthesis of other fluorinated compounds is discussed.

Hsu, L.↗

Ultraviolet-gas phase and -photocatalytic synthesis from CO and NH3

Ammonium cyanate is identified as the major product of the photolysis of gaseous NH3-CO mixtures at 206.2 or 184.9 nm. Lesser amounts of urea, biurea, biuret semicarbazide, formamide and cyanide are observed. A series of 18 reactions underlying the formation of photolysis products is presented and discussed. Photocatalytic syntheses of C-14-urea, -formamide, and -formaldehyde are carried out through irradiation of (C-14)O and NH3 in the presence of Vycor, silica gel, or volcanic ash shale surfaces. The possible contributions of the relevant reactions to the abiotic synthesis of organic nitrogen compounds on Mars, the primitive earth, and in interstellar space are examined.

Hubbard, J. S.↗

Asymmetric adsorption by quartz - A model for the prebiotic origin of optical activity

One mechanism previously proposed for the abiotic accumulation of molecules of one chirality in nature is asymmetric adsorption on the chiral surfaces of optically active quartz crystals. Earlier literature in this field is reviewed, with the conclusion that previous investigations of this phenomenon, using optical rotation criteria, have afforded ambiguous results. We now have studied the adsorption of radioactive D- and L-alanine on powdered d- and l-quartz, using change in radioactivity level as a criterion for both gross and differential adsorption, d-Quartz preferentially adsorbed D-alanine from anhydrous dimethyl-formamide solution, and l-quartz L-alanine. The differential adsorption varied between 1.0 and 1.8%. The implications of these observations are discussed from the viewpoint of early chemical evolution and the origin of optically active organic compounds in nature.

Bonner, W. M.↗

A comparison of certain extracting agents for extraction of adenosine triphosphate (ATP) from microorganisms for use in the firefly luciferase ATP assay

Firefly luciferase ATP assay is used in clinical and industrial applications, such as determination of urinary infection levels, microbial susceptibility testing, and monitoring of yeast levels in beverages. Three categories of extractants were investigated for their extracting efficiency. They were ionizing organic solvents, nonionizing organic solvents, and inorganic acids. Dimethylsulfoxide and formamide represented the ionizing organic solvents, while n-butanol, chloroform, ethanol, acetone, and methylene chloride were used for the nonionizing organic solvents. Nitric acid and perchloric acid were chosen for the inorganic acids category. Pathogens were tested with each solvent. They included: Saccharomyces carlsbergensis, E. coli, Staphylococcus aureus, Klebsiella pneumoniae, Enterobacter species, Proteus mirabilis, Proteus vulgaris, Staphylococcus epidermidis, Streptococcus faecalis, Pseudomonas aeruginosa, and Candida albicans. These results are shown in graphic representations.

Knust, E. A.↗

Influence of adsorbed fluids on the rolling contact deformation of MgO single crystals

Basic phenomena associated with rolling contact deformation were studied using MgO as a model bearing material. A hardened steel ball was rolled on MgO single crystals in slow-speed reciprocating motion and in high-speed circular motion. The resulting deformation was studied by dislocation etch-pit techniques. The presence of adsorbed fluids, such as silicone oil, white mineral oil, and toluene, with slow-speed sliding caused a dramatic change in slip mode and premature surface spalling compared with similar experiments in air or under water. In contrast, dimethyl formamide inhibited these slip processes. The results are consistent with the dependence of dislocation mobility on adsorbed species. High-speed hydrodynamic rolling with mineral oil lubrication produced a different slip phenomena entirely from the slow-speed rolling. The slip bands resembled those produced in tensile tests, and all slip apparently initiated at subsurface sites.

Dufrane, K. F.↗

Nucleoside phosphorylation in amide solutions

The paper deals with phosphorylation in possible prebiotic nonaqueous solvents. To this end, phosphorylation of nucleosides using inorganic phosphates in amide solutions is studied at room and elevated temperatures. Reaction proceeds most readily in formamide and N-methylformamide. Products obtained at elevated temperature are nucleotides, nucleoside 2',3'-cyclic phosphates, and when the phosphate concentration is high, nucleoside diphosphates. At room temperature, adenosine afforded a mixture of nucleotides, but none of the cyclic nucleotide. Conditions leading to the highest relative percentage of cyclic nucleotide involve the use of low concentrations of phosphate and an excess of nucleoside.

Schoffstall, A. M.↗

Observations of some oxygen-containing and sulfur-containing organic molecules in cold dark clouds

Observations of nine oxygen- and sulfur-containing organic molecules have been made toward the cold dark clouds TMC-1 and L134N. The presence of paraketene (H2C2O) in TMC-1 is confirmed for orthoketene, and has been observed for the first time and a total ketene column density of about 10 to the 13th/sq cm is found. Thioformaldehyde (H2CS) is easily detectable in both TMC-1 and L134N, with a column density about five times larger in the former source. The fractional abundance of ketene is comparable to the predictions of ion-molecule chemistry, while that of thioformaldehyde in TMC-1 is one to two orders of magnitude greater than that expected from such models at steady state. Interstellar sulfur chemistry thus continues to be poorly understood. Upper limits are set for the column densities of formic acid (HCOOH), vinyl alcohol (CH2CHOH), methyl formate (HCO2CH3), formamide (NH2CHO), methyl mercaptan (CH3SH), isothiocyanic acid (HNCS), and thioketene (H2C2S) in both sources.

Irvine, W. M.↗