A Prebiotic Ribosylation of Pyrimidine Nucleobases Enabled by Metal Cations and Clay Minerals.
Ontology highlight
ABSTRACT:
SUBMITTER: Chen QQ
PROVIDER: S-EPMC8707481 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:According to a current "RNA first" model for the origin of life, RNA emerged in some form on early Earth to become the first biopolymer to support Darwinism here. Threose nucleic acid (TNA) and other polyelectrolytes are also considered as the possible first Darwinian biopolymer(s). This model is being developed by research pursuing a "Discontinuous Synthesis Model" (DSM) for the formation of RNA and/or TNA from precursor molecules that might have been available on early Earth from prebiotic reactions, with the goal of making the model less discontinuous. In general, this is done by examining the reactivity of isolated products from proposed steps that generate those products, with increasing complexity of the reaction mixtures in the proposed mineralogical environments. Here, we report that adenine, diaminopurine, and hypoxanthine nucleoside phosphates and a noncanonical pyrimidine nucleoside (zebularine) phosphate can be formed from the direct coupling reaction of cyclic carbohydrate phosphates with the free nucleobases. The reaction is stereoselective, giving only the β-anomer of the nucleotides within detectable limits. For purines, the coupling is also regioselective, giving the N-9 nucleotide for adenine as a major product. In the DSM, phosphorylated carbohydrates are presumed to have been available via reactions explored previously [Krishnamurthy R, Guntha S, Eschenmoser A (2000) Angew Chem Int Ed 39:2281-2285], while nucleobases are presumed to have been available from hydrogen cyanide and other nitrogenous species formed in Earth's primitive atmosphere.
| S-EPMC5664531 | biostudies-literature
Project description:A nucleoside analogue comprising the ligand 1H-imidazo[4,5-f][1,10]phenanthroline (P) was applied to develop a molecular beacon capable of discriminating the canonical nucleobases cytosine and thymine. The beacon is based on the formation of a stable Ag+-mediated base pair between P and cytosine, whereas the presence of Ag+ strongly destabilizes nucleic acids comprising an artificial base pair between P and thymine. Metal-mediated base pair formation was investigated by temperature-dependent UV spectroscopy and CD spectroscopy and complemented by extensive DFT calculations. The molecular beacon significantly extends the application spectrum of nucleic acids with metal-mediated base pairs. It is of potential use in the detection of single-nucleotide polymorphisms.
| S-EPMC5360170 | biostudies-literature
Project description:Clay minerals, charcoal and metal oxides are essential parts of the soil matrix and strongly influence the formation of biogeochemical interfaces in soil. We investigated the role of these parental materials for the development of functional microbial guilds using the example of alkane-degrading bacteria harbouring the alkane monooxygenase gene (alkB) in artificial mixtures composed of different minerals and charcoal, sterile manure and a microbial inoculum extracted from an agricultural soil. We followed changes in abundance and community structure of alkane-degrading microbial communities after 3 and 12 months of soil maturation and in response to a subsequent 2-week plant litter addition. During maturation we observed an overall increasing divergence in community composition. The impact of metal oxides on alkane-degrading community structure increased during soil maturation, whereas the charcoal impact decreased from 3 to 12 months. Among the clay minerals illite influenced the community structure of alkB-harbouring bacteria significantly, but not montmorillonite. The litter application induced strong community shifts in soils, maturated for 12 months, towards functional guilds typical for younger maturation stages pointing to a resilience of the alkane-degradation function potentially fostered by an extant 'seed bank'.
| S-EPMC4478698 | biostudies-literature
Project description:The objective of this research was to examine the potential for intercalation of trichloroethene (TCE) by clay minerals associated with aquifer sediments. Sediment samples were collected from a field site in Tucson, AZ. Two widely used Montmorillonite specimen clays were employed as controls. X-ray diffraction, conducted with a controlled-environment chamber, was used to characterize smectite interlayer d-spacing for three treatments (bulk air-dry sample, sample mixed with synthetic groundwater, sample mixed with TCE-saturated synthetic groundwater). The results show that the d-spacing measured for the samples treated with TCE-saturated synthetic groundwater are larger (~26%) than those of the untreated samples for all field samples as well as the specimen clays. These results indicate that TCE was intercalated by the clay minerals, which may have contributed to the extensive elution tailing observed in prior miscible-displacement experiments conducted with this sediment.
| S-EPMC3548623 | biostudies-literature
Project description:Formamide is one of the important compounds from which prebiotic molecules can be synthesized, provided that its concentration is sufficiently high. For nucleotides and short DNA strands, it has been shown that a high degree of accumulation in hydrothermal pores occurs, so that temperature gradients might play a role in the origin of life [Baaske P, et al. (2007)Proc Natl Acad Sci USA104(22):9346-9351]. We show that the same combination of thermophoresis and convection in hydrothermal pores leads to accumulation of formamide up to concentrations where nucleobases are formed. The thermophoretic properties of aqueous formamide solutions are studied by means of Infrared Thermal Diffusion Forced Rayleigh Scattering. These data are used in numerical finite element calculations in hydrothermal pores for various initial concentrations, ambient temperatures, and pore sizes. The high degree of formamide accumulation is due to an unusual temperature and concentration dependence of the thermophoretic behavior of formamide. The accumulation fold in part of the pores increases strongly with increasing aspect ratio of the pores, and saturates to highly concentrated aqueous formamide solutions of ?85 wt% at large aspect ratios. Time-dependent studies show that these high concentrations are reached after 45-90 d, starting with an initial formamide weight fraction of[Formula: see text]wt % that is typical for concentrations in shallow lakes on early Earth.
| S-EPMC4843465 | biostudies-literature
Project description:Given the high surface reactivity of clay minerals, it is assumed that flocculation will lead to metal accumulation in marginal marine settings. However, the degree of metal sorption to clays is impacted by solution pH and ionic strength, and it remains unknown whether riverine clays indeed serve as a metal sink once they encounter seawater where pH and ionic strength markedly increase. Here, we conducted cadmium (Cd) adsorption experiments to three types of common clay minerals - kaolinite, illite and montmorillonite. We found that 20-30% of Cd from illite and montmorillonite surfaces were desorbed when transitioning from freshwater to seawater pH and ionic strength conditions, while kaolinite showed no discernible differences. Synchrotron X-ray adsorption spectroscopy confirmed that Cd release corresponded to a change in bonding from outer- to inner-sphere complexes when clays encountered seawater pH and ionic strength conditions. If other trace nutrients (such as Cu, Zn, Co) adsorbed onto riverine clay minerals behave in a similar manner to Cd, we speculate that their desorption in marginal marine settings should exert a significant impact on the productivity of the biosphere.
| S-EPMC7320025 | biostudies-literature
Project description:Flavylium cations are synthetic analogues of anthocyanins, the natural plant pigments that are responsible for the majority of the red, blue, and purple colors of flowers, fruits, and leaves. Unlike anthocyanins, the properties and reactivity of flavylium cations can be manipulated by the nature and position of substituents on the flavylium cation chromophore. Currently, the most promising strategies for stabilizing the color of anthocyanins and flavylium cations appear to be to intercalate and/or adsorb them on solid surfaces and/or in confined spaces. We report here that hybrid pigments with improved thermal stability, fluorescence, and attractive colors are produced by the cation-exchange-mediated adsorption of flavylium cations (FL) on two synthetic clays, the mica-montmorillonite SYn-1, and the laponite SYnL-1. Compared to the FL/SYn-1 hybrid pigments, the FL/SYnL-1 pigments exhibited improved thermal stability as judged by color retention, better preferential adsorption of the cationic form of FL1 at neutral to mildly basic pH (pH 7-8), and lower susceptibility to color changes at pH 10. Although both clays adsorb the cationic form on their external surfaces, SYnL-1 gave more evidence of adsorption in the interlayer regions of the clay. This interlayer adsorption appears to be the contributing factor to the better properties of the FL/SYnL-1 hybrid pigments, pointing to this clay to be a promising inorganic matrix for the development of brightly colored, thermally more stable hybrid pigments based on cationic analogues of natural plant pigments.
| S-EPMC7581255 | biostudies-literature
Project description:The data presented in this article are generated as part of the research article entitled "from a naturally occurring material (clay mineral) to the production of porous ceramic membranes" (Elgamouz and Tijani, 2018) [1]. This article describe how clays as very abundant versatile materials that have many properties not available in pure materials namely, silica, alumina and zirconia can be used for the preparation of ceramic membranes (Karaborni et al., 1996; Oun et al., 2017; Hollanders et al., 2016; de Oliveira Henriques et al., 2017) [2], [3], [4], [5]. This paper presents data obtained at different stages of the fabrication of a clay-zeolite composite ceramic membrane made from a largely available clay from the central region of Morocco (Meknes). The data include the characterization of the clay powder using XRD, FTIR, thermogravimetric (TGA and TDA) analysis of the clay powder. The data of porosity, mesoporosity, specific surface area, volumes of the pores, volumes of mesopores, diameters of the pores using mercury intrusion porosimetry and adsorption desorption of nitrogen data that was computed from BET and BJH theories of the clay supports at different firing temperatures (700, 750, 800, 850 and 900 °C). Data obtained from measurement of nitrogen permeation of support alone and that of the silicalite membranes are also represented.
| S-EPMC6141442 | biostudies-literature
Project description:This article presents clay minerals and major elements data of Miocene red clay from Zhuanglang core (ZL) from the eastern Longzhong Basin, China. The dataset including the contents of main clay minerals such as smectite, kaolinite, illite and chlorite and other important clay minerals parameters as illite crystallinity, Illite 5 Å/10 Å, kaolinite/(illite +chlorite) ratio and major elements and its ratio as SiO2, Al2O3, MgO, Na2O, K2O, K2O/Al2O3 and SiO2/Al2O3 in the Mid-Miocene climatic optimum (MMCO). The X-ray diffraction (XRD) and X-ray Fluorescence (XRF) experiments were made at the State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences. The data provide the evidence for understanding the MMCO and its driving factors.
| S-EPMC5988317 | biostudies-literature
Project description:DNA purification is essential for the detection of human clinical specimens. A non-destructive, controllable, and low reagent consuming DNA extraction method is described. Negatively charged DNA is absorbed onto a negatively charged montmorillonite to achieve non-destructive DNA extraction based on cation bridge construction and electric double layer formation. Different valence cation modified montmorillonite forms were used to validate the charge-dependent nature of DNA adsorption on montmorillonite. Electric double layer thickness thinning/thickening with the high/lower valence cations exists, and the minerals tended to be sedimentation-stable due to the Van der Waals attraction/electrostatic repulsion. Li-modified montmorillonite with the lowest charge states showed the best DNA adsorption efficiency of 8-10 ng/μg. Charge-dependent regulating research provides a new perspective for controllable DNA extraction and a deep analysis of interface engineering mechanisms.
| S-EPMC6497631 | biostudies-literature