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At least 415 records · Page 23
All sourcesNASA NTRSDOE OSTI
NASA NTRS1996

Synthesis of long Prebiotic Oligomers on Mineral Surfaces

Most theories of the origin of biological organization assume that polymers with lengths in the range of 30-60 monomers are needed to make a genetic system viable. But it has not proved possible to synthesize plausibly prebiotic polymers this long by condensation in aqueous solution, because hydrolysis competes with polymerization. The potential of mineral surfaces to facilitate prebiotic polymerization was pointed out long ago. Here we describe a system that models prebiotic polymerization by the oligomerization of activated monomers -both nucleotides and amino acids. We find that whereas the reactions in solution produce only short oligomers (the longest typically being a 10-mer), the presence of mineral surfaces (montmorillonite for nucleotides, illite and hydroxylapatite for amino adds) induces the formation of oligomers up to 55 monomers long. These are formed by successive "feedings" with the monomers; polymerization takes place on the mineral surfaces in a manner akin to solid-phase synthesis of biopolymers.

Ferris, James P.↗
NASA NTRS1995

Enzymatic Synthesis of Polymers Containing Nicotinamide Mononucleotide

Nicotinamide mononucleoside 5'-diphosphate in its reduced form is an excellent substrate for polynucleotide phosphorylase from Micrococcus luteus both in de novo polymerization reactions and in primer extension reactions. The oxidized form of the diphosphate is a much less efficient substrate; it can be used to extend primers but does not oligomerize in the absence of a primer. The cyanide adduct of the oxidized substrate, like the reduced substrate, polymerizes efficiently. Loss of cyanide yields high molecular weight polymers of the oxidized form. Terminal transferase from calf thymus accepts nicotinamide mononucleoside 5'-triphosphate as a substrate and efficiently adds one residue to the 3'-end of an oligodeoxynucleotide. T4 polynucleotide kinase accepts oligomers of nicotinamide mononucleotide as substrates. However, RNA polymerases do not incorporate nicotinamide mononucleoside 5'-triphosphate into products on any of the templates that we used.

Liu, Rihe↗
NASA NTRS1998

Structure of Pseudoknot PK26 Shows 3D Domain Swapping in an RNA

3D domain swapping provides a facile pathway for the evolution of oligomeric proteins and allosteric mechanisms and a means for using monomer-oligomer equilibria to regulate biological activity. The term "3D domain swapping" describes the exchange of identical domains between two protein monomers to create an oligomer. 3D domain swapping has, so far, only been recognized in proteins. In this study, the structure of the pseudoknot PK26 is reported and it is a clear example of 3D domain swapping in RNA. PK26 was chosen for study because RNA pseudoknots are required structures in several biological processes and they arise frequently in in vitro selection experiments directed against protein targets. PK26 specifically inhibits HIV-1 reverse transcriptase with nanomolar affinity. We have now determined the 3.1 A resolution crystal structure of PK26 and find that it forms a 3D domain swapped dimer. PK26 shows extensive base pairing between and within strands. Formation of the dimer requires the linker region between the pseudoknot folds to adopt a unique conformation that allows a base within a helical stem to skip one base in the stacking register. Rearrangement of the linker would permit a monomeric pseudoknot to form. This structure shows how RNA can use 3D domain swapping to build large scale oligomers like the putative hexamer in the packaging RNA of bacteriophage Phi29.

Lietzke, Susan E↗
NASA NTRS2000

Size Exclusion Chromatography Studies of the Initial Self-Association Steps of Chicken Egg White Lysozyme Nucleation

Nucleation is one of the least understood aspects of crystallogenesis. In the case of macromolecule nucleation, this understanding is further hampered by uncertainty over what precisely is being discussed. We define the process of solute self-association (aggregation, oligomerization, interaction, clustering, etc.) whereby n-mers (n > or = 2) having a crystallographic or nascent crystallographic arrangement leading to the critical nucleus reversibly form in the solution, to be part of the nucleation process. This reversible self-association process is a fundamental part of the nucleation process, and occurs as a function of the solute concentration. In the case of chicken egg white lysozyme, a considerable body of experimental evidence leads us to the conclusion that it also forms the crystal growth units. Size exclusion chromatography is a simple and direct method for determining the equilibrium constants for the self-association process. A Pharmacia FPLC system was used to provide accurate solution flow rates. The column, injection valve, and sample loop were all mounted within a temperature-controlled chamber. Chromatographically re-purified lysozyme was first dialyzed against the column equilibration buffer, with injection onto the column after several hours pre-incubation at the running temperature. Preliminary experiments, were carried out using a Toyopearl HW-50F column (1 x 50cm), equilibrated with 0.1 M sodium acetate, 5% sodium chloride, pH 4.6, at 15C. Protein concentrations from 0.1 to 4 mg/ml were employed (C(sub sat) = 1.2 mg/ml). The data from several different protein preparations consistently shows a progressively decreasing elution volume with increasing protein concentration, indicating that reversible self-association is occurring. The dotted line indicates the monomeric lysozyme elution volume. However, lysozyme interacts with the column matrix in these experiments, which complicates data analysis.Accordingly, we are testing silica-based HPLC columns in an effort to eliminate this problem and substantially reduce the column volume and experimental run time. The results and data analysis from these and subsequent experiments will be presented.

Ewing, Felecia↗
NASA NTRS2000

Phenylethynyl Containing Imide Oligomers

As part of a program to develop high performance/high temperature adhesives and composite matrices for a Mach 2.4 high speed civil transport, imide oligomers containing phenylethynyl groups were investigated. Phenylethynyl groups were placed on the ends of oligomers of different molecular weights (1250, 2500 and 5000 g/mol), pendent along the backbone of oligomers and both pendent and terminal on oligomers. Many different compositions of phenylethynyl containing imide oligomers had been previously prepared and evaluated before selecting the composition based upon 3,3'.4,4'-biphenyltetracarboxcylic dianhydride (BPDA), 3.4'-oxydianiline (3,4'-ODA) and 1,3-bis(3-aminophenoxy)benzene (APB) for extensive work. 4-Phenylethynylphthalic anhydride (PEPA) was used to place phenylethynyl groups on the ends of the oligomers and 3,5-diamino-4'-phenylethynylbenzophenone (DPEB) was used to introduce pendent phenylethynyl groups along the oligomeric backbone. Upon heating above 300 C, the phenylethynyl groups react to provide chain extension, branching and cross linking. Several of these materials exhibited excellent properties as adhesives and composite matrices. The chemistry, processability and properties of the oligomers, the cured polymers, bonded specimens and composites from phenylethynyl containing oligomers are presented.

Hergenrother, P. M.↗
NASA NTRS1999

Approaches to New Endcaps for Improved Oxidation Resistance

Norbornenyl-end capped PMR polyimide resins are widely used as polymer matrix composite materials for aircraft engine applications, since they combine ease of processing with good oxidative stability up to 300 C. PMR resins are prepared by a two-step approach involving the initial formation of oligomeric pre-polymers capped at both ends by a latent reactive end cap. The end cap undergoes cross-linking during higher temperature processing, producing the desired low density, high specific strength materials, for PMR- 15. The end cap facilitates processing by controlling the molecular weight of the oligomer and allowing flow before it cross-links. However, after cross-linking, this very end cap accounts for much of the weight loss in the polymer on aging in air at elevated temperatures. Understanding this degradation provides clues for designing new end caps to slow down degradation, and prolong the lifetime of the material.

Meador, Mary Ann B.↗
NASA NTRS1998

Fluoropolymer Films Deposited by Argon Ion-Beam Sputtering of Polytetrafluoroethylene

The FT-IR, XPS and UV spectra of fluoropolymer films (SPTFE-I) deposited by argon ion-beam sputtering of polytetrafluoroethylene (PTFE) were obtained and compared with prior corresponding spectra of fluoropolymer films (SPTFE-P) deposited by argon rf plasma sputtering of PTFE. Although the F/C ratios for SPTFE-I and -P (1.63 and 1.51) were similar, their structures were quite different in that there was a much higher concentration of CF2 groups in SPTFE-I than in SPTFE-P, ca. 61 and 33% of the total carbon contents, respectively. The FT-IR spectra reflect that difference, that for SPTFE-I showing a distinct doublet at 1210 and 1150 per centimeter while that for SPTFE-P presents a broad, featureless band at ca. 1250 per centimeter. The absorbance of the 1210-per centimeter band in SPTFE-I was proportional to the thickness of the film, in the range of 50-400 nanometers. The SPTFE-I was more transparent in the UV than SPTFE-P at comparable thickness. The mechanism for SPTFE-I formation likely involves "chopping off" of oligomeric segments of PTFE as an accompaniment to "plasma" polymerization of TFE monomer or other fluorocarbon fragments generated in situ from PTFE on impact with energetic Ar ions. Data are presented for SPTFE-I deposits and the associated Ar(+) bombarded PTFE targets where a fresh target was used for each run or a single target was used for a sequence of runs.

Golub, Morton A.↗
NASA NTRS2002

Solid State Electrolytes Prepared from PEO (360) Silanated Silica

All solid state composite electrolytes were prepared using fumed silica (SiO2) silanated with an oligomeric polyethylene oxide (PEO) silane containing 6-9 ethylene oxide repeat units, a PEO matrix and LiClO4 (8/1 O/Li). The PEO-silane covalently attached to the silica was amorphous, with a T(sub g) that increased from -90 C to -53 C after attachment. The conductivity of films prepared using the PEO-silanated silica increased to approx. 6 x 10(exp -5) S/cm at RT compared with approx. 1 x 10(-5) S/cm for films prepared with unsilanated SiO2.

Maitra, P.↗
NASA NTRS2002

NMR Guided Design of Endcaps With Improved Oxidation Resistance

A polyimide is a polymer composed of alternating units of diamine and dianhydride, linked to each other via an imide bond. PMR polyimides, commonly used in the aerospace industry, are generally capped at each end by a norbornene endcap which serves a double function: (1) It limits the number of repeating units and, hence, the average molecular weight of the various polymer chains (oligomers), thereby improving processibility; (2) Upon further treatment (curing), the endcap crosslinks the various oligomer strands into a tough heat-resistant piece. Norbornenyl-end capped PMR polyimide resins' are widely used as polymer matrix composite materials for aircraft engine applications,2 since they combine ease of processing with good oxidative stability up to 300 C. PMR resins are prepared by a twestep approach involving the initial formation of oligomeric pre-polymers capped at both ends by a latent reactive end cap. The end cap undergoes cross-linking during higher temperature processing, producing the desired low density, high specific strength materials, as shown for PMR-15.

Meador, Mary Ann B.↗
NASA NTRS2001

Organic-Inorganic Hybrids Using Novel Phenylethynyl Imide Silanes

In this presentation, polyimide-silica hybrids using novel phenylethynyl imide silanes are reported. The phenylethynyl group is present in the organic precursor as either a pendent or an end group to bond chemically with the polyimide adhesive containing phenylethynyl groups during processing, while the silane group of the organic precursor would chemically react with the inorganic precursor through oxane bond formation. The chemical compositions of these novel hybrids were examined using X-ray mapping modes of scanning electron microscopy (SEM), which revealed a silicon gradient interphase between the high surface energy substrate and the polyimide adhesive. Novel aromatic phenylethynyl imide silanes (APEISs) and pendent phenylethynyl imide oligomeric disilanes (PPEIDSs) have been synthesized, and sol-gel solutions containing the new silanes, a phenylethynyl terminated imide oligomer (PETI-5), and an inorganic precursor were formulated to develop a gradient hybrid interphase between a titanium alloy and the adhesive. Two different sol-gel systems were investigated to develop organic-inorganic hybrids. Hybrid I was composed of an organic precursor containing both phenylethynyl and silane groups (PPEIDS) and an inorganic precursor. Functional group concentrations were controlled by the variation of the molecular weight of the imide backbone of PPEIDS. Hybrid II was composed of organic and inorganic precursors and a coupling agent containing both phenylethynyl and silane groups. Morphology and chemical composition of the hybrid interphase between the inorganic substrate and the adhesive were investigated, and the bond strength and durability were evaluated using lap shear tests at various conditions. The assessment of how the bonding at an interface is affected by various sol-gel solution compositions and environments is reported.

Park, C.↗
NASA NTRS1994

Effect of phosphate activating group on oligonucleotide formation on montmorillonite: the regioselective formation of 3',5'-linked oligoadenylates

The effects of amine structure on the montmorillonite-catalyzed oligomerization of the 5'-phosphoramidates of adenosine are investigated. 4-Aminopyridine derivatives yielded oligoadenylates as long as dodecamers with a regioselectivity for 3',5'-phosphodiester bond formation averaging 88%. Linear and cyclic oligomers are obtained and no A5'ppA-containing products are detected. Oligomers as long as the hexanucleotide are obtained using 2-aminobenzimidazole as the activating group. A predominance of pA2'pA is detected in the dimer fraction along with cyclic 3',5'-trimer; no A5'ppA-containing oligomers were detected. Little or no oligomer formation was observed when morpholine, piperidine, pyrazole, 1,2,4-triazole, and 2-pyridone are used as phosphate-activating groups. The effects of the structure of the phosphate activating group on the oligomer structure and chain lengths are discussed.

Non-NASA Center↗
NASA NTRS1993

Kinetic dissection of individual steps in the poly(C)-directed oligoguanylate synthesis from guanosine 5'-monophosphate 2-methylimidazolide

A kinetic study of oligoguanylate synthesis on a polycytidylate template, poly(C), as a function of the concentration of the activated monomer, guanosine 5'-monophosphate 2-methylimidazolide, 2-MeImpG, is reported. Reactions were run with 0.005-0.045 M 2-MeImpG in the presence of 0.05 M poly(C) at 23 degrees C. The kinetic results are consistent with a reaction scheme (eq 1) that consists of a series of consecutive steps, each step representing the addition of one molecule of 2-MeImpG to the growing oligomer. This scheme allows the calculation of second-order rate constants for every step by analyzing the time-dependent growth of each oligomer. Computer simulations of the course of reaction based on the determined rate constants and eq 1 are in excellent agreement with the product distributions seen in the HPLC profiles. In accord with an earlier study (Fakhrai, H.; Inoue, T.; Orgel, L. E. Tetrahedron 1984, 40, 39), rate constants, ki, for the formation of the tetramer and longer oligomers up to the 16-mer were found to be independent of length and somewhat higher than k3 (formation of trimer), which in turn is much higher than k2 (formation of dimer). The ki (i > or = 4), k3, and k2 values are not true second-order rate constants but vary with monomer concentration. Mechanistic models for the dimerization (Scheme I) and elongation reactions (Scheme II) are proposed that are consistent with our results. These models take into account that the monomer associates with the template in a cooperative manner. Our kinetic analysis allowed the determination of rate constants for the elementary processes of covalent bond formation between two monomers (dimerization) and between an oligomer and a monomer (elongation) on the template. A major conclusion from our study is that bond formation between two monomer units or between a primer and a monomer is assisted by the presence of additional next-neighbor monomer units. This is consistent with recent findings with hairpin oligonucleotides (Wu, T.; Orgel, L. E. J. Am. Chem. Soc. 1992, 114, 317). Our study is the first of its kind that shows the feasibility of a thorough kinetic analysis of a template-directed oligomerization and provides a detailed mechanistic model of these reactions.

Non-NASA Center↗
NASA NTRS1993

Redox regulation of energy transfer efficiency in antennas of green photosynthetic bacteria

The efficiency of energy transfer from the peripheral chlorosome antenna structure to the membrane-bound antenna in green sulfur bacteria depends strongly on the redox potential of the medium. The fluorescence spectra and lifetimes indicate that efficient quenching pathways are induced in the chlorosome at high redox potential. The midpoint redox potential for the induction of this effect in isolated chlorosomes from Chlorobium vibrioforme is -146 mV at pH 7 (vs the normal hydrogen electrode), and the observed midpoint potential (n = 1) decreases by 60 mV per pH unit over the pH range 7-10. Extraction of isolated chlorosomes with hexane has little effect on the redox-induced quenching, indicating that the component(s) responsible for this effect are bound and not readily extractable. We have purified and partially characterized the trimeric water-soluble bacteriochlorophyll a-containing protein from the thermophilic green sulfur bacterium Chlorobium tepidum. This protein is located between the chlorosome and the membrane. Fluorescence spectra of the purified protein indicate that it also contains groups that quench excitations at high redox potential. The results indicate that the energy transfer pathway in green sulfur bacteria is regulated by redox potential. This regulation appears to operate in at least two distinct places in the energy transfer pathway, the oligomeric pigments in the interior of the chlorosome and in the bacteriochlorophyll a protein. The regulatory effect may serve to protect the cell against superoxide-induced damage when oxygen is present. By quenching excitations before they reach the reaction center, reduction and subsequent autooxidation of the low potential electron acceptors found in these organisms is avoided.

NASA Discipline Exobiology↗
NASA NTRS2000

Caveolin-1 regulates shear stress-dependent activation of extracellular signal-regulated kinase

Fluid shear stress activates a member of the mitogen-activated protein (MAP) kinase family, extracellular signal-regulated kinase (ERK), by mechanisms dependent on cholesterol in the plasma membrane in bovine aortic endothelial cells (BAEC). Caveolae are microdomains of the plasma membrane that are enriched with cholesterol, caveolin, and signaling molecules. We hypothesized that caveolin-1 regulates shear activation of ERK. Because caveolin-1 is not exposed to the outside, cells were minimally permeabilized by Triton X-100 (0.01%) to deliver a neutralizing, polyclonal caveolin-1 antibody (pCav-1) inside the cells. pCav-1 then bound to caveolin-1 and inhibited shear activation of ERK but not c-Jun NH(2)-terminal kinase. Epitope mapping studies showed that pCav-1 binds to caveolin-1 at two regions (residues 1-21 and 61-101). When the recombinant proteins containing the epitopes fused to glutathione-S-transferase (GST-Cav(1-21) or GST-Cav(61-101)) were preincubated with pCav-1, only GST-Cav(61-101) reversed the inhibitory effect of the antibody on shear activation of ERK. Other antibodies, including m2234, which binds to caveolin-1 residues 1-21, had no effect on shear activation of ERK. Caveolin-1 residues 61-101 contain the scaffolding and oligomerization domains, suggesting that binding of pCav-1 to these regions likely disrupts the clustering of caveolin-1 or its interaction with signaling molecules involved in the shear-sensitive ERK pathway. We suggest that caveolae-like domains play a critical role in the mechanosensing and/or mechanosignal transduction of the ERK pathway.

Non-NASA Center↗
NASA NTRS2000

Nonenzymatic template-directed reactions on altritol oligomers, preorganized analogues of oligonucleotides

Altritol nucleic acids (ANAs) are RNA analogues with a phosphorylated D-altritol backbone. The nucleobase is attached at the 2-(S)-position of the carbohydrate moiety. We report that ANA oligomers are superior to the corresponding DNA, RNA, and HNA (hexitol nucleic acid) in supporting efficient nonenzymatic template-directed synthesis of complementary RNAs from nucleoside-5'-phosphoro-2-methyl imidazolides. Activated ANA and HNA monomers do not oligomerize efficiently on DNA, RNA, HNA, or ANA templates.

Non-NASA Center↗
NASA NTRS1998

Formation of RNA oligomers on montmorillonite: site of catalysis

Certain montmorillonites catalyze the self condensation of the 5'-phosphorimidazolide of nucleosides in pH 8 aqueous electrolyte solutions at ambient temperatures leading to formation of RNA oligomers. In order to establish the nature of the sites on montmorillonite responsible for this catalytic activity, oligomerization reactions were run with montmorillonites which had been selectively modified (I) at the edges by (a) fluoride treatment, (b) silylation, (c) metaphosphate treatment of the anion exchange sites (II) in the interlayer by (a) saturation with quaternary alkylammonium ions of increasing size, (b) aluminum polyoxo cations. High pressure liquid chromatography, HPLC, analysis of condensation products for their chain lengths and yields indicated that modification at the edges did not affect the catalytic activity to a significant extent, while blocking the interlayer strongly inhibited product formation.

NASA Discipline Exobiology↗
NASA NTRS1997

Entropy and charge in molecular evolution--the case of phosphate

Biopoesis, the creation of life, implies molecular evolution from simple components, randomly distributed and in a dilute state, to form highly organized, concentrated systems capable of metabolism, replication and mutation. This chain of events must involve environmental processes that can locally lower entropy in several steps; by specific selection from an indiscriminate mixture, by concentration from dilute solution, and in the case of the mineral-induced processes, by particular effectiveness in ordering and selective reaction, directed toward formation of functional biomolecules. Numerous circumstances provide support for the notion that negatively charged molecules were functionally required and geochemically available for biopoesis. Sulfite ion may have been important in bisulfite complex formation with simple aldehydes, facilitating the initial concentration by sorption of aldehydes in positively charged surface active minerals. Borate ion may have played a similar, albeit less investigated role in forming charged sugar complexes. Among anionic species, oligophosphate ions and charged phosphate esters are likely to have been of even more wide ranging importance, reflected in the continued need for phosphate in a proposed RNA world, and extending its central role to evolved biochemistry. Phosphorylation is shown to result in selective concentration by surface sorption of compounds, otherwise too dilute to support condensation reactions. It provides protection against rapid hydrolysis of sugars and, by selective concentration, induces the oligomerization of aldehydes. As a manifestation of life arisen, phosphate already appears in an organic context in the oldest preserved sedimentary record.

NASA Discipline Exobiology↗