Anticipating an RNA world. Some past speculations on the origin of life: where are they today?
No abstract available
Biography↗
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A computer modeling study of acetylcholine receptor-ligand interactions
No abstract available
NASA Discipline Number 52-20↗
Marine hydrothermal systems and the origin of life: future research
No abstract available
Review, Tutorial↗
Conformational influence of the ribose 2'-hydroxyl group: crystal structures of DNA-RNA chimeric duplexes
We have crystallized three double-helical DNA-RNA chimeric duplexes and determined their structures by X-ray crystallography at resolutions between 2 and 2.25 A. The two self-complementary duplexes [r(G)d(CGTATACGC)]2 and [d(GCGT)r(A)d(TACGC)]2, as well as the Okazaki fragment d(GGGTATACGC).r(GCG)d(TATACCC), were found to adopt A-type conformations. The crystal structures are non-isomorphous, and the crystallographic environments for the three chimeras are different. A number of intramolecular interactions of the ribose 2'-hydroxyl groups contribute to the stabilization of the A-conformation. Hydrogen bonds between 2'-hydroxyls and 5'-oxygens or phosphate oxygens, in addition to the previously observed hydrogen bonds to 1'-oxygens of adjacent riboses and deoxyriboses, are observed in the DNA-RNA chimeric duplexes. The crystalline chimeric duplexes do not show a transition between the DNA A- and B-conformations. CD spectra suggest that the Okazaki fragment assumes an A-conformation in solution as well. In this molecule the three RNA residues may therefore lock the complete decamer in the A-conformation. Crystals of an all-DNA strand with the same sequence as the self-complementary chimeras show a morphology which is different from those of the chimera crystals. Moreover, the oligonucleotide does not match any of the sequence characteristics of DNAs usually adopting the A-conformation in the crystalline state (e.g., octamers with short alternating stretches of purines and pyrimidines). In DNA-RNA chimeric duplexes, it is therefore possible that a single RNA residue can drive the conformational equilibrium toward the A-conformation.
NASA Discipline Number 52-20↗
Meteorite organics in planetary environments: hydrothermal release, surface activity, and microbial utilization
Up to 50% of the organics in the Murchison meteorite, possibly including some of the polymer, is released in high temperature and pressure aqueous environments, to 350 degrees C and 250 bar, that simulate submarine volcanic, hydrothermal or impact-induced conditions. Meteorite organics of prebiotic significance, such as nonanoic acid, glycine, and pyrene survive the hydrothermal conditions. The released material is surface active with surface pressures up to 19.8 x 10(-3) N m-1, and exhibits an extended surface tension isotherm which suggests a mixture of amphiphilic components. One component, nonanoic acid, is shown to form vesicles. The materials extracted under mild conditions, at 120 degrees C, are nutrients for the humic acid bacterium Pseudomonas maltophilia and efficient nutrients for the oligotroph Flavobacterium oryzihabitans, demonstrating the capability of microorganisms to metabolize extraterrestrial organics.
NASA Program Exobiology↗
Structural investigation of protein kinase C inhibitors
The phospholipid and Ca2+ dependent protein kinase (PKC) plays an essential role in a variety of cellular events. Inhibition of PKC was shown to arrest growth in tumor cell cultures making it a target for possible antitumor therapy. Calphostins are potent inhibitors of PKC with high affinity for the enzyme regulatory site. Structural characteristics of calphostins, which confer the inhibitory activity, are investigated by comparing their optimized structures with the existing models for PKC activation. The resulting model of inhibitory activity assumes interaction with two out of the three electrostatic interaction sites postulated for activators. The model shows two sites of hydrophobic interaction and enables the inhibitory activity of gossypol to be accounted for.
NASA Discipline Exobiology↗
A method to identify and characterize Z-DNA binding proteins using a linear oligodeoxynucleotide
An oligodeoxynucleotide that readily flips to the Z-DNA conformation in 10mM MgCl2 was produced by using Klenow enzyme to incorporate 5-bromodeoxycytosine and deoxyguanosine into a (dC-dG)22 template. During synthesis the oligomer can be labeled with 32P to high specific activity. The labeled oligodeoxynucleotide can be used in bandshift experiment to detect proteins that bind Z-DNA. This allows the binding specificity of such proteins to be determined with high reliability using unlabeled linear and supercoiled DNA competitors. In addition, because the radioactive oligodeoxynucleotide contains bromine atoms, DNA-protein complexes can be readily crosslinked using UV light. This allows an estimate to be made of the molecular weight of the proteins that bind to the radioactive probe. Both techniques are demonstrated using a goat polyclonal anti-Z-DNA antiserum.
NASA Program Exobiology↗
Rate of production, dissolution and accumulation of biogenic solids in the ocean
The equatorial current system, by its response to global circulation changes, provides a unique recording mechanism for long range climatic oscillations. A permanent record of the changes in rate of upwelling and organic production is generated in the equatorial deep sea sediments, particularly by such biogenic components which are unaffected by secondary dissolution. In order to determine the rates of accumulation of various sedimentary components, a reliable differential measurement of age of the strata must be obtained. Various approaches to this problem are reviewed, and sources of error discussed. Secondary dissolution of calcium carbonate introduces a substantial and variable difference between the dissolution-modified, and hence a priori unknown, rate of deposition on one hand and the rate of accumulation, derivable from the observed concentration, on the other. The cause and magnitude of these variations are of importance, particularly since some current dating schemes are based on assumed constancy in the rate of accumulation of this and, in some cases, also all other sedimentary components. The concepts used in rate evaluation are discussed with emphasis on the difference between the state of dissolution, an observable property of the sediment, and the rate of dissolution, a parameter that requires deduction of the carbonate fraction dissolved, and of the time differential. As a most likely cause of the enhanced state of dissolution of the interglacial carbonate sediments is proposed the lowered rates of biogenic production and deposition, which cause longer exposure of the carbonate microfossils to corrosion in the bioturbated surface layer of the sediment. Historical perspective is included in the discussion in view of the dedication of the Symposium to Hans Pettersson, the leader of the Swedish Deep Sea Expedition 1947-1948, an undertaking that opened a new era in deep sea research and planetary dynamics.
NASA Discipline Exobiology↗
Determination of O2(a1 delta g) and O2(b1 sigma+ g) yields in the reaction O + ClO --> Cl + O2: implications for photochemistry in the atmosphere of Venus
A discharge flow apparatus with chemiluminescence detector has been used to study the reaction O + ClO --> Cl + O2, where O2 = O2(a1 delta g) or O2(b1 sigma+ g). The measured quantum yields for producing O2(a1 delta g) and O2(b1 sigma+ g) in the above reaction are less than 2.5 x 10(-2) and equal to (4.4 +/- 1.1) x 10(-4), respectively. The observed O2(a1 delta g) airglow of Venus cannot be explained in the context of standard photochemistry using our experimental results and those reported in recent literature. The possibility of an alternative source of O atoms derived from SO2 photolysis in the mesosphere of Venus is suggested.
Non-NASA Center↗
REE chemistry and Sm-Nd systematics of late Archean weathering profiles in the Fortescue Group, Western Australia
Two weathering profiles, each consisting of an upper, sericite-rich zone and a lower, chlorite-rich zone, are preserved between flows of the Mt. Roe Basalt in the Fortescue Group, Hamersley Basin, Western Australia. REE concentrations in samples from these two profiles, which originally developed ca 2,760 Ma, show large variations depending on stratigraphic position. LREE abundances and (La/Yb)N are greatest at depths of 3-6 m below the paleosurface of the Mt. Roe #1 profile and are somewhat lower in samples above this level. The LREEs reach concentrations 6-9 times greater than in the underlying basalt, and thus appear to have been mobilized downward in the paleosol and concentrated in its middle part. LREE concentrations in the #2 profile show a similar distribution but with a sharp increase in all REE concentrations within 50 cm of the paleosurface. The distinction between the REE profiles in the two paleosols may be related to the difference in the overlying material. The #1 paleosol is overlain by a few meters of sediments and then by basalt, whereas the #2 paleosol is directly overlain by basalt. The LREEs appear to have been mobilized both during chemical weathering of the parental basalt and during later lower-greenschist-facies metamorphism and metasomatism of the paleosols. Remobilization of the REEs during the regional metamorphism of the Fortescue Group is confirmed by a whole-rock Sm-Nd reference isochron of Mt. Roe #1 samples with an age of 2,151 +/- 360 Ma. Variable initial 143Nd/144Nd values of unweathered basalt samples which may represent the paleosol protolith prevents a confident determination of the magnitude of LREE mobility. Both the initial mobilization of the REEs during weathering and the metasomatic remobilization appear to have taken place under redox conditions where Ce was present dominantly as Ce3+, because Ce anomalies are not developed within the sericite zone samples regardless of concentration. Europium anomalies in the paleoweathering profile are somewhat variable and were probably modified by mobilization of Eu2+ at metamorphic conditions. In all samples, the HREEs appear to have been relatively immobile and correlate with Al, Ti, Cr, V, Zr, and Nb. Sm-Nd systematics and REE patterns of four unweathered basalt samples indicate derivation of the Mt. Roe Basalts from a heterogeneous and enriched source having epsilon Nd between -4.0 and -7.4. Initial 143Nd/144Nd values of these basalts are even lower than those reported by NELSON et al. (1992) for Fortescue Group basalts and indicate a substantial crustal component in the generation of Mt. Roe Basalts.
NASA Discipline Exobiology↗
The Sturgeon Falls paleosol and the composition of the atmosphere 1.1 Ga BP
A paleosol is exposed along the north bank of the Sturgeon River, some 25 km SW of Baraga, Michigan. The paleosol was developed on hydrothermally altered Keweenawan basalt and is overlain by the Jacobsville sandstone. Textures, mineralogy, and chemical composition change gradually upwards from unweathered metabasalt, through the paleosol, to the contact of the paleosol with the Jacobsville sandstone. Many of these changes are similar to those in modern soils developed on basaltic rocks. However, K has clearly been added to the paleosol, probably by solutions which had equilibrated with K-feldspar in the Jacobsville sandstone. The Keweenawan basalt was oxidized quite extensively during its conversion to greenstone. During weathering, the remaining Fe2+ was oxidized to Fe3+ and was retained in the paleosol. The composition of the parent greenstone and its change during weathering can be used to define an approximate lower limit to the ratio of the O2 pressure to the CO2 pressure in the atmosphere during the formation of the paleosol [formula: see text]. Free O2 must have been present in the atmosphere 1.1 Ga ago, but its partial pressure could have been 10(3) times lower than in the atmosphere today.
NASA Program Exobiology↗
The oxygen content of ocean bottom waters, the burial efficiency of organic carbon, and the regulation of atmospheric oxygen
Data for the burial efficiency of organic carbon with marine sediments have been compiled for 69 locations. The burial efficiency as here defined is the ratio of the quantity of organic carbon which is ultimately buried to that which reaches the sediment-water interface. As noted previously, the sedimentation rate exerts a dominant influence on the burial efficiency. The logarithm of the burial efficiency is linearly related to the logarithm of the sedimentation rate at low sedimentation rates. At high sedimentation rates the burial efficiency can exceed 50% and becomes nearly independent of the sedimentation rate. The residual of the burial efficiency after the effect of the sedimentation rate has been subtracted is a weak function of the O2 concentration in bottom waters. The scatter is sufficiently large, so that the effect of the O2 concentration in bottom waters on the burial efficiency of organic matter could be either negligible or a minor but significant part of the mechanism that controls the level of O2 in the atmosphere.
Non-NASA Center↗
Evolution of catalytic function
An RNA-based evolution system was constructed in the laboratory and used to develop RNA enzymes with novel catalytic function. By controlling the nature of the catalytic task that the molecules must perform in order to survive, it is possible to direct the evolving population toward the expression of some desired catalytic behavior. More recently, this system has been coupled to an in vitro translation procedure, raising the possibility of evolving protein enzymes in the laboratory to produce novel proteins with desired catalytic properties. The aim of this line of research is to reduce darwinian evolution, the fundamental process of biology, to a laboratory procedure that can be made to operate in the service of organic synthesis.
NASA Program Exobiology↗
Experimental dehydration of natural obsidian and estimation of DH2O at low water contents
Water diffusion experiments were carried out by dehydrating rhyolitic obsidian from Valles Caldera (New Mexico, USA) at 510-980 degrees C. The starting glass wafers contained approximately 0.114 wt% total water, lower than any glasses previously investigated for water diffusion. Weight loss due to dehydration was measured as a function of experiment duration, which permits determination of mean bulk water diffusivity, mean Dw. These diffusivities are in the range of 2.6 to 18 X 10(-14) m2/s and can be fit with the following Arrhenius equation: ln mean Dw (m2/s) = -(25.10 +/- 1.29) - (46,480 +/- 11,400) (J/mol) / RT, except for two replicate runs at 510 degrees C which give mean Dw values much lower than that defined by the above equation. When interpreted according to a model of water speciation in which molecular H2O is the diffusing species with concentration-independent diffusivity while OH units do not contribute to the transport but react to provide H2O, the data (except for the 510 degrees C data) are in agreement with extrapolation from previous results and hence extend the previous data base and provide a test of the applicability of the model to very low water contents. Mean bulk water diffusivities are about two orders of magnitude less than molecular H2O diffusivities because the fraction of molecular H2O out of total water is very small at 0.114 wt% total water and less. The 510 degrees C experimental results can be interpreted as due to slow kinetics of OH to H2O interconversion at low temperatures.
NASA Program Exobiology↗
Titan: a laboratory for prebiological organic chemistry
When we examine the atmospheres of the Jovian planets (Jupiter, Saturn, Uranus, and Neptune), the satellites in the outer solar system, comets, and even--through microwave and infrared spectroscopy--the cold dilute gas and grains between the stars, we find a rich organic chemistry, presumably abiological, not only in most of the solar system but throughout the Milky Way galaxy. In part because the composition and surface pressure of the Earth's atmosphere 4 x 10(9) years ago are unknown, laboratory experiments on prebiological organic chemistry are at best suggestive; but we can test our understanding by looking more closely at the observed extraterrestrial organic chemistry. The present Account is restricted to atmospheric organic chemistry, primarily on the large moon of Saturn. Titan is a test of our understanding of the organic chemistry of planetary atmospheres. Its atmospheric bulk composition (N2/CH4) is intermediate between the highly reducing (H2/He/CH4/NH3/H2O) atmospheres of the Jovian planets and the more oxidized (N2/CO2/H2O) atmospheres of the terrestrial planets Mars and Venus. It has long been recognized that Titan's organic chemistry may have some relevance to the events that led to the origin of life on Earth. But with Titan surface temperatures approximately equal to 94 K and pressures approximately equal to 1.6 bar, the oceans of the early Earth have no ready analogue on Titan. Nevertheless, tectonic events in the water ice-rich interior or impact melting and slow re-freezing may lead to an episodic availability of liquid water. Indeed, the latter process is the equivalent of a approximately 10(3)-year-duration shallow aqueous sea over the entire surface of Titan.
Non-NASA Center↗
Synthesis of the coenzymes adenosine diphosphate glucose, guanosine diphosphate glucose, and cytidine diphosphoethanolamine under primitive Earth conditions
The nonenzymatic synthesis of the coenzymes adenosine diphosphate glucose (ADPG), guanosine diphosphate glucose (GDPG), and cytidine diphosphoethanolamine (CDP-ethanolamine) has been carried out under conditions considered to have been prevalent on the early Earth. The production of these compounds was performed by allowing simple precursor molecules to react under aqueous solutions, at moderate temperatures and short periods of time, with mediation by cyanamide or urea. These two condensing agents are considered to have been present in significant amounts on the primitive Earth and have been previously used in the nonenzymatic synthesis of several other important biochemical compounds. In our experiments, ADPG was obtained by heating glucose-1-phosphate (G1P) and ATP in the presence of cyanamide for 24 h at 70 degrees C. The reaction of G1P and GTP under the same conditions yielded GDPG. The cyanamide-mediated production of CDP-ethanolamine was carried out by reacting a mixture of ethanolamine phosphate and CTP for 24 h at 70 degrees C. The separation and identification of the reaction products was carried out by paper chromatography, thin-layer chromatography, high performance thin-layer chromatography, high performance liquid chromatography, both normal and reverse-phase, UV spectroscopy, enzymatic assays, and acid hydrolysis. Due to the mild conditions employed, and to the relative ease of these reactions, these studies offer a simple attractive system for the nonenzymatic synthesis of phosphorylated high-energy metabolic intermediates under conditions considered to have been prevalent on the ancient Earth.
NASA Discipline Exobiology↗
An RNA motif that binds ATP
RNAs that contain specific high-affinity binding sites for small molecule ligands immobilized on a solid support are present at a frequency of roughly one in 10(10)-10(11) in pools of random sequence RNA molecules. Here we describe a new in vitro selection procedure designed to ensure the isolation of RNAs that bind the ligand of interest in solution as well as on a solid support. We have used this method to isolate a remarkably small RNA motif that binds ATP, a substrate in numerous biological reactions and the universal biological high-energy intermediate. The selected ATP-binding RNAs contain a consensus sequence, embedded in a common secondary structure. The binding properties of ATP analogues and modified RNAs show that the binding interaction is characterized by a large number of close contacts between the ATP and RNA, and by a change in the conformation of the RNA.
NASA Discipline Exobiology↗
Modeling study on the cleavage step of the self-splicing reaction in group I introns
A three-dimensional model of the Tetrahymena thermophila group I intron is used to further explore the catalytic mechanism of the transphosphorylation reaction of the cleavage step. Based on the coordinates of the catalytic core model proposed by Michel and Westhof (Michel, F., Westhof, E. J. Mol. Biol. 216, 585-610 (1990)), we first converted their ligation step model into a model of the cleavage step by the substitution of several bases and the removal of helix P9. Next, an attempt to place a trigonal bipyramidal transition state model in the active site revealed that this modified model for the cleavage step could not accommodate the transition state due to insufficient space. A lowering of P1 helix relative to surrounding helices provided the additional space required. Simultaneously, it provided a better starting geometry to model the molecular contacts proposed by Pyle et al. (Pyle, A. M., Murphy, F. L., Cech, T. R. Nature 358, 123-128. (1992)), based on mutational studies involving the J8/7 segment. Two hydrated Mg2+ complexes were placed in the active site of the ribozyme model, using the crystal structure of the functionally similar Klenow fragment (Beese, L.S., Steitz, T.A. EMBO J. 10, 25-33 (1991)) as a guide. The presence of two metal ions in the active site of the intron differs from previous models, which incorporate one metal ion in the catalytic site to fulfill the postulated roles of Mg2+ in catalysis. The reaction profile is simulated based on a trigonal bipyramidal transition state, and the role of the hydrated Mg2+ complexes in catalysis is further explored using molecular orbital calculations.
NASA Discipline Exobiology↗