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At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
NASA NTRS1991

On the origin and early evolution of biological catalysis and other studies on chemical evolution

One of the lines of research in molecular evolution which we have developed for the past three years is related to the experimental and theoretical study of the origin and early evolution of biological catalysis. In an attempt to understand the nature of the first peptidic catalysts and coenzymes, we have achieved the non-enzymatic synthesis of the coenzymes ADPG, GDPG, and CDP-ethanolamine, under conditions considered to have been prevalent on the primitive Earth. We have also accomplished the prebiotic synthesis of histidine, as well as histidyl-histidine, and we have measured the enhancing effects of this catalytic dipeptide on the dephosphorylation of deoxyribonucleotide monophosphates, the hydrolysis of oligo A, and the oligomerization 2', 3' cAMP. We reviewed and further developed the hypothesis that RNA preceded double stranded DNA molecules as a reservoir of cellular genetic information. This led us to undertake the study of extant RNA polymerases in an attempt to discover vestigial sequences preserved from early Archean times. In addition, we continued our studies of on the chemical evolution of organic compounds in the solar system and beyond.

Oro, J.↗
NASA NTRS1991

Disulfide-linked oligonucleotide phosphorothioates - Novel analogues of nucleic acids

The synthesis of phosphorothioate analogs of oligonucleotides by the oxidation of deoxyadenosine 3',5'-bisphosphorothioate (3) was attempted. Cyclization of 3 is much more efficient than oligomerization under all the conditions investigated. However, a preformed oligonucleotide carrying a 5'-terminal phosphorotioate group undergoes efficient chain-extension when oxidized in the presence of 3.

Wu, Taifeng↗
NASA NTRS1993

Crosslinked polyimides prepared from N-(3-ethynylphenyl)maleimide

The compound N-(3-ethynylphenyl)maleimide (NEPMI) was used to prepare thermally stable, glassy polyimides which did not exhibit glass transition temperatures below 500 C. NEPMI was blended with the maleimide of methylene dianiline (BMI) and heated to form the polyimide. NEPMI was also mixed with Thermid 600 R, a commercially available bisethynyl oligomeric material, and heated to form a thermally stable, glassy polyimide. Lastly, NEPMI was blended with both BMI and Thermid 600 R to form thermally stable, glassy polyimides.

Gerber, Margaret K.↗
NASA NTRS1990

Separation of rat pituitary secretory granules by continuous flow electrophoresis

The separation of growth hormone-containing cytoplasmic secretory granules from the rat pituitary gland by continuous flow electrophoresis is described. The results are consistent with the hypothesis that granule subpopulations can be separated due to differences in surface charge; these, in turn, may be related to the oligomeric state of the hormone.

Hayes, Daniel↗
NASA NTRS1994

Oligomers Terminated By Maleimide And Acetylene

Oligomeric molecules terminated with maleimide and acetylene groups synthesized and thermally treated to form cross-linked polymers exhibiting high or undetectable glass-transition temperatures and high thermo-oxidative stabilities. Compounds used to make thermally stable, glassy polymers.

St. Clair, Terry L.↗
NASA NTRS1994

Double layer hydroxide minerals as host structures for bioorganic molecules

A central problem in molecular evolution concerns the selective concentration from dilute, multicomponent solution of source molecules into a reactive environment, where formation of larger molecular assemblages can take place. Minerals consisting of positively charged, separable metal hydroxide sheets have proven capable of these functions. This common structural type is represented by minerals such as pyroaurite (Mg-Fe(3+) hydroxide), hydrotalcite (Mg-Al), green rust Fe(2+)-Fe(3+) and others. Effective interlayer sorption is demonstrated for orthophosphate and condensed phosphates, anionic alkyl compounds, polypeptides, nucleic acids, cyanide complexes and glycolaldehyde phosphate, the latter shown to readily oligomerize to form and selectively retain racemic hexose -2, 4, 6-phosphates, preferentially of altrose (Pitsch, et al, 1993). The selective aldomerization and retention effects correlate with the charge distribution in the host mineral structure and the stereochemistry of the substrate molecules. Interaction between nucleic acid bases, and between the cyanide groups of glycolaldehyde phosphate nitrile at the low water activity in the mineral interlayer is indicated by doubling of the monomeric separation of the hydroxide mineral sheets.

Lee, Ton↗
NASA NTRS1993

Is ligation the only solution to the pyrophosphate problem?

Pyrophosphate linkages are easily formed during the nonenzymatic oligomerization of activated nucleotides. They often form `caps' which terminate an oligonucleotide with a 5'-5' pyrophosphate. Owing to their structural resemblance to the intermediates in enzymatic ligation reactions, it has been suggested that pyrophosphate caps might have been capable of acting as activating groups in chain elongation processes. We argue that an alternative possibility would have been the specific hydrolysis of pyrophosphates.

Visscher, J.↗
NASA NTRS1981

Flammability and Photo-Stability of Selected Polymer Systems

A systematic approach to the improvement of the flammability of epoxy resins, bisphenol-A polycarbonate poly(butylene terephthalate), and Nylon 6.6 by introducing halogens and loop functionality into the flame retardants is described. The phthalides (the loop functionality containing molecules) include 3,3-bis(4-bromophenyl)-phthalide, 3,3-bis(4-chlorophenyl)phthalide, and phenolphthalein. The phthalide containing epoxy resins are synthesized and characterized in comparison with the bisphenol-A epoxy resins in terms of flammability in the copolymer systems. The resins include diglycidyl ethers of phenolphthalein, bisphenol-A. tetrabromobisphenol-A, and tetraoromophenolphthalein. The vaporization of the phthalide additive in the polymers is observed in Thermal Gravimetric Analysis. The flame retardancy is primarily due to the presence of halogens. In the poly(butylene terephthalate) system, the cleavage of the C(sub aromatic) -B bond of the flame retardant additive enhances the crosslinking react ions between the aromatic rings resulting in an increase of char formation. In the epoxy resin systems, loop functionality contributes to char formation to a larger extent. The interaction between the epoxy resin and poly-(butylene terephthalate) follows the mechanism of insertion of the oxirane ring into the ester bond. This mechanism is studied by FT-IR. The investigation of the thermal properties of the char-forming phenol-formaldehyde resins is conducted to provide information for the systematic design of high temperature flame-resistant phenolics. NMR and FT-IR are used to characterize the oligomeric resins and the cured resins. The curing agents used in the study include formaldehyde, s-trioxane and terephthaloyl chloride. The brominated phenolic resins are found to have higher oxygen indices with lower char yields.

Lo, Jeelin↗
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 NTRS1997

New Approaches to Waterproofing of Space Shuttle Insulating Materials

Future reusable space vehicles will be in service much more frequently than current space shuttles. Therefore, rapid reconditioning of spacecraft will be required. Currently, the waterproofing of space shuttles after each re-entry takes 72 hours and requires substantial labor. In addition, the currently used waterproofing reagent, DiMethylEthoxySilane (DMES), is considered toxic, and ethanol fumes are released during its hydrolytic activation. Consequently, a long time period, which is not acceptable for future operations, is needed to ensure that 0 the excess volatile compounds are removed before further maintenance of the space vehicle can be performed. The objective of this project was to assist NASA Ames in finding improved waterproofing systems by identifying suitable waterproofing agents that can be applied by vapor phase deposition and will be less toxic, bond more rapidly to the insulation material surface, and potentially have higher thermal stability than the DMES system. Several approaches to achieve faster waterproofing with less toxicity were assessed using the following alternatives: Reactive volatile compounds that are rapidly deposited by chemical bonding at the surface and leave no toxic volatiles. Reactive reagents that are the least toxic. Nonvolatile reagents that are very reactive and bond strongly to the insulating material surface. Three specific types of potential reagents were chosen for evaluation in this project: 1. Volatile reagents with Si-Cl functional groups for vapor deposition 2. Volatile reagents with Si-H functional groups for vapor deposition 3. Nonvolatile oligomeric or polymeric reactive siloxanes that are assumed to have higher thermal stability and/or strong bonding to the insulating material. The chemistry involved in the project was targeted at the generation of intermediates having reactive Si-OH bonds for the formation of either volatile species or polymeric species that bond rapidly to the surface and also cure rapidly. We focused on two chemical reactions@-hydrolysis of Si-Cl bonds and catalytic dehydrocoupling of Si-H bonds.

Blum, Yigal D.↗
NASA NTRS1997

Dimerization in Highly Concentrated Solutions of Phosphoimidazolide Activated Mononucleotides

Phosphoimidazolide activated ribomononucleotides (*pN) are useful substrates for the non-enzymatic synthesis of polynucleotides. However, dilute neutral aqueous solutions of *pN typically yield small amounts of dimers and traces of polymers; most of *pN hydrolyzes to yield nucleoside 5'-monophosphate. Here we report the self-condensation of nucleoside 5'-phosphate 2- methylimidazolide (2-MeImpN with N = cytidine, uridine or guanosine) in the presence of Mg2(+) in concentrated solutions, such as might have been found in an evaporating lagoon on prebiotic Earth. The product distribution indicates that oligomerization is favored at the expense of hydrolysis. At 1.0 M, 2-MelmpU and 2-MelmpC produce about 65% of oligomers including 4% of the 3',5'-Iinked dimer. Examination of the product distribution of the three isomeric dimers in a self-condensation allows identification of reaction pathways that lead to dimer formation. Condensations in a concentrated mixture of all three nucleotides (U,C,G mixtures) is made possible by the enhanced solubility of 2-MeImpG in such mixtures. Although percent yield of intemucleotide linked dimers is enhanced as a function of initial monomer concentration, pyrophosphate dimer yields remain practically unchanged at about 20% for 2-MelmpU, 16% for 2-MeImpC and 25% of the total pyrophosphate in the U,C,G mixtures. The efficiency by which oligomers are produced in these concentrated solutions makes the evaporating lagoon scenario a potentially interesting medium for the prebiotic synthesis of dimers and short RNAs.

Kanavarioti, Anastassia↗
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.↗