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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
NASA NTRS1991

Product and rate determinations with chemically activated nucleotides in the presence of various prebiotic materials, including other mono- and polynucleotides

We are investigating the reactions of ImpN's in the presence of a number of prebiotically plausible materials, such as metal ions, phosphate, amines and other nucleotides and hope to learn more about the stability/reactivity of ImpN's in a prebiotic aqueous environment. We find that, in the presence of phosphate, ImpN's form substantial amounts of diphosphate nucleotides. These diphosphate nucleotides are not very good substrates for template directed reactions, but are chemically activated and are known to revert to the phosphoimidazolides in the presence of imidazole under solid state conditions. With respect to our studies of the oligomerization reaction, the determination of the dimerization rate constant of a specific ImpN (guanosine 5'-phospho 2 methylimidazolide) both in the absence and the presence of the template leads to the conclusion that at 37 C the dimerization is not template directed, although the subsequent polymerization steps are. In other words, this specific polynucleotide synthesizing system favors the elongation of oligonucleotides as compared with the formation of dimers and trimers. This favoring of the synthesis of long as opposed to short oligonucleotides may be regarded as a rudimentary example of natural selection at the molecular level.

Kanavarioti, A.↗
NASA NTRS1994

Concentration and temperature effects on ovostatin activity

Light scattering experiments performed at Mississippi State University using MSFC ovostatin preparations indicated that at low ovostatin concentrations, below 0.2 mg/ml, the protein was dissociating from a tetramer into dimers. Since the proposed mechanism of action involved the tetrameric form of the protein, we hypothesized that perhaps under the conditions of our assays at various O/T ratios the ovostatin was becoming dissociated into an inactive dimer. To examine this possibility we assayed the ovostatin activity as a function of ovostatin concentration and of temperature of the assay. Data are presented that show the results of these assays at 23 C, 30 C, 37 C and 42 C respectively. The data are highly suggestive that there is a decrease in ovostatin activity as the concentration of the protein falls below 0.06 mg/ml. This may not be of any physiological importance, however, since the concentration of ovostatin in the egg is about 0.5 mg/ml. Curiously, the dissociation of the tetramer into dimers does not show a significant temperature dependence as would be expected for an equilibrium reaction. Whether this is in fact the case, or whether the differences are so small as to not be discerned from the current data remains to be seen. Another aspect to consider is that in the egg the primary role of the ovostatin may or may not be as a protease inhibitor. Although the inhibition of collagenase by ovostatin may be an important aspect of embryogenesis, it is also possible that it functions as a binding protein for some substance. In this regard, all ovostatin preparations from MSFC have shown an approximately 88,000 MW protein associated with the ovostatin. The identity of this protein is not currently known and may be the subject of future studies.

Moriarity, Debra M.↗
NASA NTRS1994

(H2)2 mole-fraction altitude profile in the atmosphere of Jupiter: A computational study

The mole fraction x(sub 2) of (H2)2 in equilibrium mixture with H2 under the atmospheric conditions of Jupiter is evaluated from the dimerization equilibrium constant calculated by quantum-chemical treatments and also from the Lennard-Jones potential. The treatments are of an ab initio type with the second and fourth order Moller-Plesset perturbation techniques and a basis set superposition error evaluation. The computed dimerization equilibrium constant is combined with observed height profiles of temperature and pressure. In six treatments considered it is found that the mole fraction decreases with increasing height. Various approximations suggest the dimeric mole fraction at the Jupiter 1 atm pressure level between 0.04 and 1.06%.

Slanina, Zdenek↗
NASA NTRS2000

Macromolecule Crystal Quality Improvement in Microgravity: The Role of Impurities

While macromolecule impurities may affect crystal size and morphology the over-riding question is; "How do macromolecule impurities effect crystal X-ray quality and diffraction resolution?" In the case of chicken egg white lysozyme, crystals can be grown in the presence of a number of impurities without affecting diffraction resolution. One impurity however, the lysozyme dimer, does negatively impact the X-ray crystal properties. Crystal quality improvement as a result of better partitioning of this impurity during crystallization in microgravity has been reported'. In our recent experimental work dimer partitioning was found to be not significantly different between the two environments. Mosaicity analysis of pure crystals showed a reduced mosaicity and increased signal to noise for the microgravity grown crystals. Dimer incorporation however, did greatly reduce the resolution limit in both ground and microgravity grown crystals. These results indicate that impurity effects in microgravity are complex and may rely on the conditions or techniques employed.

Judge, Russell A.↗
NASA NTRS2001

Investigating the Effect of Impurities on Macromolecule Crystal Growth in Microgravity

Chicken egg-white lysozyme (CEWL) crystals were grown in microgravity and on the ground in the presence of various amounts of a naturally occurring lysozyme dimer impurity. No significant favorable differences in impurity incorporation between microgravity and ground crystal samples were observed. At low impurity concentration the microgravity crystals preferentially incorporated the dimer. The presence of the dimer in the crystallization solutions in microgravity reduced crystal size, increased mosaicity and reduced the signal to noise ratio of the X-ray data. Microgravity samples proved more sensitive to impurity. Accurate indexing of the reflections proved critical to the X-ray analysis. The largest crystals with the best X-ray diffraction properties were grown from pure solution in microgravity.

Snell, Edward H.↗
NASA NTRS2001

Simulation of Peptides at Aqueous Interfaces

Behavior of peptides at water-membrane interfaces is of great interest in studies on cellular transport and signaling, membrane fusion, and the action of toxins and antibiotics. Many peptides, which exist in water only as random coils, can form sequence-dependent, ordered structures at aqueous interfaces, incorporate into membranes and self-assembly into functional units, such as simple ion channels. Multi -nanosecond molecular dynamics simulations have been carried out to study the mechanism and energetics of interfacial folding of both non-polar and amphiphilic peptides, their insertion into membranes and association into higher-order structures. The simulations indicate that peptides fold non-sequentially, often through a series of amphiphilic intermediates. They further incorporate into the membrane in a preferred direction as folded monomers, and only then aggregate into dimers and, possibly, further into "dimers of dimers".

Pohorille, Andrew↗
NASA NTRS1998

Computational Studies of the Interaction of H/H2 with Diamond and Silicon Surfaces

The interaction of hydrogen atoms and molecules with diamond and silicon surfaces is important in several important applications. Two areas that we are interested are: 1) tribology (molecular level friction) and 2) the role of H atoms in silicon chemical vapor deposition (CVD). In the tribology area, H atoms can be used to tie off dangling bonds, which otherwise form bonds between adjacent surfaces, and lead to resistance to sliding the surfaces by each other. Processes which are important in understanding molecular level friction include barriers to addition of H/H2 to the surface and barriers to migration of H atoms on the surface. In the silicon CVD area, we have studied the process of H2 elimination from the 100 surface of silicon. Cluster models for the dime surfaces of diamond are presented. The unrelaxed 100 surface has carbene like surface carbon atoms; however, for the relaxed surface these dimerize to give rows of surface dimers and there is a significant amount of p bonding between the radical orbitals of the dimer. The 110 surface has zig-zag rows of carbon atoms with a dangling bond on each carbon atom. These dangling bonds are hybridized away from each other and thus interact less strongly than for the 100 surface. Finally, the 111 surface has surface C atoms arranged in a triangular pattern and the surface dangling bonds are well separated from each other (second nearest neighbor distance) leading to almost no interaction between adjacent dangling bonds. These qualitative features may be quantified by computing the overlap of adjacent dangling bonds in a GVB(pp) calculation. The overlaps are 0.462, 0.292, and 0.016 for the diamond 100, 110, and 111 surfaces, respectively.

Walch, Stephen P.↗
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 NTRS1999

Relative reactivity of ribosyl 2'-OH vs. 3'-OH in concentrated aqueous solutions of phosphoimidazolide activated nucleotides

Phosphoimidazolide activated ribomononucleotides (*pN, see structure) are useful substrates for the non-enzymatic synthesis of oligonucleotides. In the presence of metal ions, aqueous solutions of *pN yield primarily the two internucleotide-linked (pN2' pN and pN3' pN) and the pyrophosphate-linked (N5' ppN) dimers. Small amounts of cyclic dimers and higher oligomers are also produced. In this study the relative reactivity of 2'-OH vs. 3'-OH was determined from the ratio of the yields of pN2' pN vs. pN3' pN. Experiments were performed at 23 degrees C in the range 7.2 < or = pH < or = 8.4 with substrates that differ in nucleobase (guanosine (G), cytidine (C), uridine (U), and adenosine (A)) and leaving group (imidazole (Im), 2-methylimidazole (2-MeIm) and 2,4-dimethylimidazole (2,4-diMeIm)). Two metal ions (Mg2+ or Mn2+) were employed as catalysts. The conditions used here, i.e. a substrate concentration in the range 0.1 M to 1.0 M and metal ion concentration in the range 0.05 M to 0.2 M, favor base-stacking interactions. The ratio pN2' pN: pN3' pN = 2'-5': 3'-5' was found independent of nucleobase and typically varied between 2 to 3 indicating that the 2'-OH is about 2 to 3 times more reactive than the 3'-OH. *pN with Im, compared to 2-MeIm and 2,4-diMeIm leaving group, produce lower yields of internucleotide linked dimers, and a higher pN2' pN: pN3' pN ratio. Trends in the data, observed with all three leaving groups, suggest an increase in pN2' pN: pN3' pN ratio with decreasing substrate concentration (up to 5.47 with 0.051 M ImpG). The observations are in accord with earlier studies reporting a relative reactivity 2'-5': 3'-5' = 6 to 9 obtained with Im as the leaving group, in dilute nucleotide solutions and under conditions that disfavor stacking. It is speculated that the concentration induced change in the relative reactivity is the result of self-association via base-stacking that enhances selectively the proximity of the 3'-OH of one molecule to the reactive P-N bond of an other molecule. The implication of these conclusions for oligomerization/ligation reactions is discussed.

NASA Discipline Exobiology↗
NASA NTRS1999

Kinetics of template-directed pyrophosphate-linked dideoxyguanylate synthesis as a function of 2-MeImpdG and poly(C) concentration: insights into the mechanism

Aqueous solutions of deoxyguanosine 5'-monophosphate 2-methylimidazolide, 2-MeImpdG, yield primarily deoxyguanosine 5'-monophosphate, 5'dGMP, and pyrophosphate-linked dideoxyguanylate, dG5'ppdG, abbreviated G2p (see Chart 1). The initial rate of G2p formation, d[G2p]/dt in M h-1, determined at 23 degrees C, pH 7.8, 1.0 M NaCl and 0.2 M Mg2+ by timed high-performance liquid chromatography (HPLC) analysis, exhibits a second-order dependence on 2-MeImpdG concentration, [G]o, indicating a bimolecular mechanism of dimerization in the range 0.02 M < or = [G]o < or = 0.09 M. In the presence of polycytidylate, poly(C), G2p synthesis is accelerated and oligodeoxyguanylate products are formed by incorporation of 2-MeImpdG molecules. The kinetics of G2p formation as a function of both monomer and polymer concentration, expressed in C equivalents, were also determined under the above conditions and exhibited a complex behavior. Specifically, at a constant [poly(C)], values of d[G2p]/dt typically increased with [G]o with a parabolic upward curvature. At a constant [G]o, values of d[G2p]/dt increase with [poly(C)], but level off at the higher poly(C) concentrations. As [G]o increases this saturation occurs at a higher poly(C) concentration, a result opposite to expectation for a simple complexation of two reacting monomers with the catalyst prior to reaction. Nevertheless, these results are shown to be quantitatively consistent with a template-directed (TD) mechanism of dimerization where poly(C) acts as the template to bind 2-MeImpdG in a cooperative manner and lead, for the first time, to the formulation of principles that govern template-directed chemistry. Analysis of the kinetic data via a proposed TD cooperative model provides association constants for the affinity between polymer and monomer and the intrinsic reactivity of 2-MeImpdG toward pyrophosphate synthesis. To the best of our knowledge, poly(C)/2-MeImpdG is the first system that could serve as a textbook example of a TD reaction under conditions such that the template is fully saturated by monomers and under conditions that it is not.

NASA Discipline Exobiology↗
NASA NTRS1999

CCAAT/enhancer-binding protein delta is a critical regulator of insulin-like growth factor-I gene transcription in osteoblasts

Insulin-like growth factor-I (IGF-I) plays a major role in promoting skeletal growth by stimulating bone cell replication and differentiation. Prostaglandin E2 and other agents that induce cAMP production enhance IGF-I gene transcription in cultured rat osteoblasts through a DNA element termed HS3D, located in the proximal part of the major rat IGF-I promoter. We previously determined that CCAAT/enhancer-binding protein delta (C/EBPdelta) is the key cAMP-stimulated regulator of IGF-I transcription in these cells and showed that it transactivates the rat IGF-I promoter through the HS3D site. We now have defined the physical-chemical properties and functional consequences of the interactions between C/EBPdelta and HS3D. C/EBPdelta, expressed in COS-7 cells or purified as a recombinant protein from Escherichia coli, bound to HS3D with an affinity at least equivalent to that of the albumin D-site, a known high affinity C/EBP binding sequence, and both DNA elements competed equally for C/EBPdelta. C/EBPdelta bound to HS3D as a dimer, with protein-DNA contact points located on guanine residues on both DNA strands within and just adjacent to the core C/EBP half-site, GCAAT, as determined by methylation interference footprinting. C/EBPdelta also formed protein-protein dimers in the absence of interactions with its DNA binding site, as indicated by results of glutaraldehyde cross-linking studies. As established by competition gel-mobility shift experiments, the conserved HS3D sequence from rat, human, and chicken also bound C/EBPdelta with similar affinity. We also found that prostaglandin E2-induced expression of reporter genes containing human IGF-I promoter 1 or four tandem copies of the human HS3D element fused to a minimal promoter and show that these effects were enhanced by a co-transfected C/EBPdelta expression plasmid. Taken together, our results provide evidence that C/EBPdelta is a critical activator of IGF-I gene transcription in osteoblasts and potentially in other cell types and species.

NASA Discipline Musculoskeletal↗
NASA NTRS1998

Mineral catalysis of a potentially prebiotic aldol condensation

Minerals may have played a significant role in chemical evolution. In the course of investigating the chemistry of phosphonoacetaldehyde (PAL), an analogue of glycolaldehyde phosphate, we have observed a striking case of catalysis by the layered hydroxide mineral hydrotalcite ([Mg2Al(OH)6][Cl.nH2O]). In neutral or moderately basic aqueous solutions, PAL is unreactive even at a concentration of 0.1 M. In the presence of a large excess of NaOH (2 M), the compound undergoes aldol condensation to produce a dimer containing a C3-C4 double-bond. In dilute neutral solutions and in the presence of the mineral, however, condensation takes place rapidly, to produce a dimer which is almost exclusively the C2-C3 unsaturated product.

Non-NASA Center↗
NASA NTRS1997

Information transfer from DNA to peptide nucleic acids by template-directed syntheses

Peptide nucleic acids (PNAs) are analogs of nucleic acids in which the ribose-phosphate backbone is replaced by a backbone held together by amide bonds. PNAs are interesting as models of alternative genetic systems because they form potentially informational base paired helical structures. Oligocytidylates have been shown to act as templates for formation of longer oligomers of G from PNA G2 dimers. In this paper we show that information can be transferred from DNA to PNA. DNA C4T2C4 is an efficient template for synthesis of PNA G4A2G4 using G2 and A2 units as substrates. The corresponding synthesis of PNA G4C2G4 on DNA C4G2C4 is less efficient. Incorporation of PNA T2 into PNA products on DNA C4A2C4 is the least efficient of the three reactions. These results, obtained using PNA dimers as substrates, parallel those obtained using monomeric activated nucleotides.

NASA Discipline Exobiology↗
NASA NTRS1977

A production parylene coating process for hybrid microcircuits

The real impetus for developing a production parylene coating process for internal hybrid passivation came as a result of the possibility of loose conductive particles in hybrid microelectronic circuits, causing intermittent and sometimes permanent failures. Because of the excellent mechanical properties of parylene, it is capable of securing the loose particles in place and prevent such failures. The process of coating described consists of (1) vaporizing the initial charge, which is in the form of a dimer; (2) conversion of the dimer into a reactive monomer; and (3) deposition and subsequent polymerization of the monomer in the deposition chamber which forms a uniform parylene film over all the cold surfaces in contact. Experimental results are discussed in terms of wire bond reliability, resistor drift, high-temperature storage characteristics of parylene, and coating acceptance standards. It is concluded that internal cavities of microelectronic circuits can be successfully coated with parylene provided appropriate tooling is used to protect external leads from the parylene monomer.

Kale, V. S.↗
NASA NTRS1977

Nitrogen-induced absorption of oxygen in the Herzberg continuum

Total absorption of O2 induced by collisions with N2 has been measured at room temperature in the Hersberg continuum using a one meter normal incidence grating monochromator. The enhanced absorption is ascribed to the formation of O2-O2 and O2-N2 dimers. The interaction constants for these dimers are determined and utilized to investigate their effect on the absorption of solar radiation in the stratosphere.

Shardanand, MR.↗
NASA NTRS1981

Synthesis of oligoguanylates on oligocytidylate templates

The influence of template length in the self-condensation of guanosine 5'-phosphorimidazole in the presence of oligocytidylate templates is investigated. Reactions were carried out with cyclic cytidine 2',3'-phosphate, oligo- or polyC, and radioactively labeled guanosine 5'-phosphorimidazolide in the presence of Zn(+2) or Pb(+2) catalyst; product yields were determined by paper chromatography, thin-layer chromatography, and high-performance liquid chromatography. In the absence of a catalytic metal or in the presence of Pb(+2), a significant template effect is observed starting with the cytidine dimer and increasing in yield up to the hexamer template. Oligomers longer than the template are observed, and are predominantly 2'-5' linked in the presence of Pb(+2) and of mixed linkages in the uncatalyzed reaction. With the zinc ion as the catalyst, the template effect is first observed with the pentamer and is maximal with the heptamer. Products are predominantly 3'-5', and only a small proportion of them are longer than the template. The importance of the demonstrated formation of molecules with up to 10 guanosine units from oligocytidines as short as the dimer on the primitive earth is noted.

Fakhrai, H.↗
NASA NTRS1989

The rotational spectrum and structure of chlorine peroxide

The dimerization products of the ClO + ClO reaction were investigated in a flowing chemical reactor using submillimeter wave spectroscopy. The major products were identified as the chlorine peroxide (Cl2O2) and chlorine dioxide (OClO). The rotational constants as well as a complete set of quartic centrifugal distortion constants were determined. The identification of the chlorine peroxide supports the earlier proposed ClO-dimer mechanisms, which partly explain the ozone hole formation during the Antarctic springtime.

Birk, Manfred↗
NASA NTRS1990

Reactivity of pi-complexes of Ti, V, and Nb towards dithioacetic acid: Synthesis and structure of novel metal sulfur-containing complexes

In order to use sulfur-containing resources economically and with minimal environmental damage, it is important to understand the desulfurization processes. Hydrodesulfurization, for example, is carried out on the surface of a heterogeneous metal sulfide catalyst. Studies of simple, soluble inorganic systems provide information regarding the structure and reactivity of sulfur-containing compounds with metal complexes. Further, consistent with recent trends in materials chemistry, many model compounds warrant further study as catalyst precursors. The reactivity of low-valent organometallic sandwich pi-complexes toward dithiocarboxylic acids is described. For example, treatment of bisbenzene vanadium with CH3CSSH affords a divanadium tetrakis(dithioacetate) complex. The crystallographically determined V-V bond distance, 2.800(2), is nearly the same as the V-V bond distance in a V(mu-nu squared-S2)2V' unit in the mineral patonite (VS4)n. The stability of the V2S4 core in the dimer is demonstrated by evidence of V2S4(+) in the mass spectrum (70 eV, solid probe) of the vanadium dimer. Several other systems relevant to HDS catalysis are also discussed.

Duraj, Stan A.↗