Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Poly(A) selection”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 recordsLinked to original sources

Hydrogen ion-selective poly(vinyl chloride) membrane electrode based on a calix[4]arene.

A hydrogen ion-selective poly(vinyl chloride) membrane electrode was constructed using 5,11,17,23-tetra-tert-butyl-25,26,27,28-tetracyanomethoxycalix[4]arene as a neutral carrier. The electrode showed an apparent Nernstian response in the 2-11.5 pH range with a slope of 54.0 +/- 0.2 mV/pH at 20 +/- degrees C. This electrode showed a rapid response of the emf to changes in the pH, high ion selectivity with respect to lithium, sodium and potassium, and characteristics similar to those reported for the conventional pH glass membrane electrode. It can be used as a potentiometric indicator electrode in hydrofluoric acid solutions. The effects of iodide, thiocyanate, perchlorate and bromide on the characteristics of the electrode were also considered.

Calixarenes↗

Discovery of quinazolinone and quinoxaline derivatives as potent and selective poly(ADP-ribose) polymerase-1/2 inhibitors.

Two classes of quinazolinone derivatives and quinoxaline derivatives were identified as potent and selective poly(ADP-ribose) polymerase-1 and 2 (PARP-1) and (PARP-2) inhibitors, respectively. In PARP enzyme assays using recombinant PARP-1 and PARP-2, quinazolinone derivatives displayed relatively high selectivity for PARP-1 and quinoxaline derivatives showed superior selectivity for PARP-2. SBDD analysis via a combination of X-ray structural study and homology modeling suggested distinct interactions of inhibitors with PARP-1 and PARP-2. These findings provide a new structural framework for the design of selective inhibitors for PARP-1 and PARP-2.

Crystallography, X-Ray↗

Different positioning elements select poly(A) sites at the 3'-end of GCN4 mRNA in the yeast Saccharomyces cerevisiae.

Cleavage and polyadenylation of eukaryotic mRNA requires efficiency and positioning elements in the 3'-untranslated region (3'-UTR) of the mRNA. Specific point mutations were introduced into the yeast GCN4 3'-UTR to detect sequence motifs which are involved in the positioning of the poly(A) site. 3'-End proces-sing activities of different GCN4 3'-UTR alleles were measured in an in vivo test system. Point mutations in an AAGAA motif defocussed selection of the poly(A) sites of the GCN4 3'-UTR to various additional poly(A) sites instead of the single site of the wild-type GCN4 3'-UTR. A strain with an intact wild-type GCN4 3'-UTR but impaired in RNA15 encoding an RNA-binding processing factor showed a similar defocussed pattern of poly(A) site selection. Remarkably, two additional sequence motifs upstream of the AAGAA motif which resemble yeast efficiency motifs independently affected poly(A) site positioning but not efficiency of 3'-end processing. Mutations in one motif resulted in an additional upstream poly(A) site. Alterations of the other motif shifted the poly(A) sites exclusively to two downstream poly(A) sites. These data suggest several contact points between the precursor mRNA and the polyadenylation machinery in yeast.

3' Untranslated Regions↗

Characterization of a crude selective PolI transcription system from Tetrahymena pyriformis.

A crude in vitro transcription system which selectively transcribes DNA fragments containing the promoter region of the Tetrahymena pyriformis rRNA gene has been prepared from T. pyriformis. The system requires both an S100 fraction of lysed isolated macronuclei and an S100 extract of whole cells. When a HhaI-HindIII fragment of the promoter containing plasmid pEN 19-1 is employed as a template, transcription yields two major products of about 560 (A) and 510 (B) bases in length. The analysis of the transcription products of truncated templates showed that RNA A is a runoff transcript and RNA B is produced by nucleolytic cleavage of RNA A at a site about 50 nucleotides to the left of the HindIII cleavage site. S1 nuclease mapping was used to demonstrate that the 5' end of RNA A is identical with that predicted for a transcript which was initiated at the same site on the gene as the in vivo 35S rRNA precursor. Transcription is dependent upon the addition of promoter containing DNA, is inhibited by 1 microgram/mL actinomycin D, and is insensitive to 200 micrograms/mL alpha-amanitin. Transcription is dependent upon the salt levels in the assay exhibiting activity peaks at 58 mM KCl, 28 mM (NH4)2SO4, and 3 mM MgCl2. Several minor transcription start sites to the left of the major initiation site become active at high salt, yielding several minor longer transcripts. High salt also inhibits the RNA cleavage activity, reducing the levels of RNA B produced.

Animals↗

A hydrogen ion-selective poly(aniline) solid contact electrode based on dibenzylpyrenemethylamine ionophore for highly acidic solutions.

Hydrogen-ion selective solid contact electrodes based on tribenzylamine, dibenzylnaphthalenemethylamine, and dibenzylpyrenemethylamine ionophores were prepared. With these electrodes, we showed that the response ranges were influenced by the number of phenyl rings in the ionophores. The lower limits for a linear pH response in acidic solutions were pH 2.50, 0.65, and 0.50, respectively. As the number of phenyl rings in the ionophores increased, the slopes of the EMF responses of these electrodes did not change significantly, but their response extended toward an acidic range (shifted to pH 0.50). Thus, their dynamic response range became wider. A solid contact electrode with dibenzylpyrenemethylamine ionophore, in particular, showed the best selectivity, from the interference of cations and anions, and the best reproducibility of the EMF. This electrode was stored in Tris buffer solutions, artificial serum, and hydrofluoric acid solutions for one month without any loss of performance. Their response time was 8 s. Satisfactory results were obtained when it was tested directly with artificial serum (in pH range 6.0 - 8.5) and hydrofluoric acid.

Acids↗

Inhibition of ADP-evoked platelet aggregation by selected poly(ADP-ribose) polymerase inhibitors.

Pathologic platelet activation has been implicated in the pathogenesis of ischemic heart disease. Since cardiomyocytes can be protected from ischemia-reoxygenation injury by poly(ADP-ribose) polymerase (PARP) inhibitors mimicking the adenine/ADP part of NAD, their structural resemblance to ADP may also enable the blockade of platelet aggregation via binding to ADP receptors. Blood samples drawn from healthy volunteers were pre-incubated with different concentrations of PARP inhibitors: 4-hydroxyquinazoline, 2-mercapto-4(3 H)-quinazolinone, or HO-3089. ADP-, collagen- and epinephrine-induced platelet aggregation was evaluated according to the method described by Born. The effect of PARP inhibitors on thrombocyte aggregation was also examined when platelets were sensitized by heparin and in the presence of incremental concentrations of ADP. All examined PARP inhibitors reduced the ADP-induced platelet aggregation in a dose-dependent manner (significant inhibition at 20 microM for HO-3089 and at 500 microM for the other agents; P < 0.05), even if platelets were sensitized with heparin. However, their hindrance on platelet aggregation waned as the concentration of ADP rose (no effect at 40 microM ADP). PARP inhibitors had minimal effect on both collagen- and epinephrine-induced platelet aggregation. Our study first demonstrates the feasibility of a design for PARP inhibitors that does not only protect against ischemia-reperfusion-induced cardiac damage but may also prevent thrombotic events.

Blood Platelets↗

The behavior of a poly(aniline) solid contact pH selective electrode based on N,N,N',N'-tetrabenzylethanediamine ionophore.

A hydrogen ion-selective solid-contact electrode based on N,N,N',N'-tetrabenzylethanediamine has shown the best Nernstian slope and selectivity and the widest response range in a Tris buffered pH sample solution. Its linear dynamic range was pH 3.50-11.94, and the Nernstian slope showed 52.1 mV/pH (at 20 +/- 0.2 degrees C). When it was directly applied to human whole blood (in pH range 6.0-8.5) we could obtain the same satisfying results. This electrode continuously contacted a Tris 7.47 buffered solution, human whole blood and a hydrofluoric acid solution for one month without any loss of performance. Also, hydrofluoric acid did not influence the surface of this electrode, and thus it was maintained without showing any changes in potentials after being used in a hydrofluoric acid solution. The standard deviation in the determined e.m.f. differences was 1.5 mV (N = 5) for Tris buffer solutions of pH 6.5 and 1.1 mV at a Tris buffer solutions of pH 8.5. The 90% response time of the electrodes obtained by injecting of hydrochloric acid into the Tris buffer sample solution was less than 10 s. Especially, in the this paper, with these potential response characteristics of hydrogen ion selective poly(aniline) solid contact electrode, we have also presented the pH response mechanism of this electrode and the role of poly(aniline) and a doped anion in a poly(aniline) layer.

Journal Article↗

[Selectivity of poly (4-methyl-5-vinylthiazole) stationary phase in reversed-phase liquid chromatography].

In this paper, the selectivity of poly(4-methyl-5-vinylthiazole) stationary phase (PMV CA phase) is comprehensively studied in reversed-phase liquid chromatography (RPLC) mode with methanol-water system. The selectivity difference between PMV CA phase and three commonly used RPLC stationary phases (C18, C8 and Phenyl phase) is shown. Four typical species of standards (alkylbenzens, chlorobenzenes, nitrobenzenes and PAHs) are selected for the selectivity study. It is shown that the PMV CA phase has some special selectivities: 1) It has different selectivity from C18 and C8 phase because the PMV CA phase may form diploe interaction, pi-electron interaction and hydrogen bonding interaction (with the nitrogen atom and oxygen atom on the phase) with solutes owing to its polar aromatic thiazole ring and polar ester bond etc. on the phase; 2) It has similar property as phenyl phase because both of them can form pi-electron interaction with solutes. But owing to its polar thiazole ring and other polar group on the phase, which may form dipole interaction and hydrogen bonding interaction with solutes, there are still some differences between these two phases.

Benzo(a)pyrene↗

Size-based separation of polyelectrolytes by capillary zone electrophoresis: migration regimes and selectivity of poly(styrenesulphonates) in solutions of derivatized cellulose.

The migration regimes and the separation selectivity of linear poly(styrenesulfonates) (PSS) were investigated in solutions of linear polymeric hydroxyethylcellulose (HEC). Variable parameters were the number of PSS monomer units (in the range of 25-6520), HEC concentration (below and above the entanglement threshold), molecular mass of HEC (between 35900 and 438000 Da) and electric field strength (from 190 to 1140 V/cm). Besides those regimes which are known for migration of polyelectrolytes in physical networks (Ogston sieving, reptation without and with orientation), the observed separation below the entanglement threshold indicates an effect of solute-chain interactions similar to that observed for the separation of double-stranded DNA. From the dependence of the separation selectivity on HEC concentration and molecular weight it was found that both parameters increase the separation. The selectivity of the solutions of higher concentrated low molecular HEC was compared to lower concentrated high molecular HEC, which has a similar bulk viscosity, and therefore obeys comparable peak dispersion due to thermal broadening. At high field strengths (preferably used in capillary electrophoresis) the former gave better separation only for shorter PSS molecules. For separation of longer PSS molecules, only high molecular HEC is applicable due to the deformation of the low molecular matrix by large analyte molecules.

Cellulose↗

pH dependence and protein selectivity of poly(ethyleneimine)/poly(acrylic acid) multilayers studied by in situ ATR-FTIR spectroscopy.

The selective interaction between polyelectrolyte multilayers (PEM) consecutively adsorbed from poly(ethyleneimine) (PEI) and poly(acrylic acid) (PAC) and a binary mixture containing concanavalin A (COA) and lysozyme (LYZ) based on electrostatic interaction is reported. The composition and structure of the PEM and the uptake of proteins were analyzed by in situ attenuated total reflection (ATR) Fourier transform infrared (FTIR) spectroscopy, and the morphology and thickness were characterized by atomic force microscopy (AFM) and ellipsometry. The PEM dissociation degree and charge state and the protein adsorption were shown to be highly dependent on the outermost layer type and the pH in solution. High protein uptake was obtained under electrostatically attractive conditions. This was used to bind selectively one protein from a binary mixture of LYZ/COA. In detail it could be demonstrated that six-layered PEM-6 at pH = 7.3 showed a preferential sorption of positively charged LYZ, while at PEM-5 and pH = 7.3 negatively charged COA could be selectively bound. No protein sorption from the binary mixture was observed at pH = 4.0 for both PEM, when COA, LYZ, and the outermost PEI layer of PEM-5 were positively charged or the outermost PAC layer of PEM-6 was neutral. Furthermore, from factor analysis of the spectral data the higher selectivity was found for PEM-5 compared to PEM-6. Increasing the ionic strength revealed a drastic decrease in the selectivity of both PEM. Evidence was found that the proteins were predominantly bound at the surface and to a minor extent in the bulk phase of PEM. These results suggest possible working regimes and application fields of PEI/PAC multilayer assemblies related to the preparative separation of binary and multicomponent protein mixtures (biofluids, food) as well as to the design of selective protein-resistant surfaces.

Acrylic Resins↗

Chiral selection in poly(C)-directed synthesis of oligo(G).

Theories of the origin of optical asymmetry in living systems place fundamental importance on the amplification of optical asymmetry by an autocatalytic process. The replication of a polynucleotide is one obvious choice for such an autocatalytic growth mechanism. If an optically homogeneous polynucleotide could replicate by directing the polymerization of monomers of the same handedness, while excluding monomers of the opposite handedness, its chiral descendants would come to dominate what was once an achiral environment. Recently, two highly efficient template-directed reaction systems have been developed for the oligomerization of activated guanosine mononucleotides (Fig. 1) on a poly(C) template. The synthesis of L-guanosine 5'-mononucleotide makes it possible to study chiral selection in these systems. We report here that poly(C)-directed oligomerization of activated guanosine mononucleotides proceeds readily if the monomers are of the same optical handedness as the template, and is indeed far less efficient if the monomers are of the opposite handedness. However, in template-directed reactions with a racemic mixture, monomers of the opposite handedness to the template are incorporated as chain terminators at the 2'(3') end of the products. This inhibition raises an important problem for many theories of the origin of life.

Chromatography, High Pressure Liquid↗

A novel principle for conferring selectivity to poly(A)-binding proteins: interdependence of two ATP synthase beta-subunit mRNA-binding proteins.

Based on electrophoretic mobility-shift assays and UV cross-linking experiments, we present evidence in the present work for the existence of two mammalian cytosolic proteins that selectively interact with the 3'-untranslated region of the mRNA coding for the catalytic beta-subunit of mitochondrial ATP synthase (beta-mtATPase). One of the proteins, beta-mtATPase mRNA-binding protein (BARB)1, is a novel poly(A)-binding protein that specifically binds the poly(A) tail of the beta-mtATPase transcript. BARB1 achieves this mRNA selectivity through its interaction with a second protein, BARB2, that binds the beta-mtATPase mRNA through a 22-bp element with a uridylate core, located 75 bp upstream of the poly(A) tail. Conversely, in the absence of BARB1, BARB2 is still able to bind the beta-mtATPase mRNA, but does so with lower affinity. Thus the interaction between BARB1 and BARB2 and beta-mtATPase mRNA involves the formation of a complex between the two BARB proteins. We conclude that BARB1 and BARB2 selectively bind the 3'-untranslated region of beta-mtATPase mRNA in a novel and interdependent manner. The complex between these two proteins may be involved in post-transcriptional regulation of gene expression.

3' Untranslated Regions↗

Preparation and characterization of monovalent cation selective sulfonated poly(ether ether ketone) and poly(ether sulfone) composite membranes.

Highly charged cation permeable composite membranes were prepared by blending of sulfonated poly(ether sulfone) (SPES) with sulfonated poly(ether ether ketone) (SPEEK) in 0 to 90% weight ratio, to adjust the hydrophobic properties and ion selective nature. Extent of sulfonation was confirmed by 1H NMR and ion exchange capacity and degree of sulfonation depending on blending composition. These membranes were characterized as a function of weight fraction of SPEEK by recording ion-exchange capacity, water uptake, thermogravimetric analysis, membrane conductivity and membrane potential in equilibration with different electrolytic solutions. Membrane permselectivity and solute flux were estimated using these data on the basis of non-equilibrium thermodynamic principles and for observing the selectivity of different membranes for mono- or bivalent counter-ions. It was observed that relative selectivity for monovalent in comparison to bivalent counter-ions were increased with the decrease in SPEEK content in the composite membrane matrix. The range of SPEEK content in the blend from 60 to 80% appears the most suitable for the selective separation of monovalent ions from bivalent ions. Furthermore, highly charged nature and stabilities of these membranes extend their applications for the electro-assisted separations of similarly charged ions as well as other electro-membrane processes.

Journal Article↗

Oxidation-responsive polymeric vesicles.

Vesicles formed in water by synthetic macro-amphiphiles have attracted much attention as nanocontainers having properties that extend the physical and chemical limits of liposomes. We sought to develop ABA block copolymeric amphiphiles that self-assemble into unilamellar vesicles that can be further oxidatively destabilized. We selected poly(ethylene glycol) (PEG) as the hydrophilic A blocks, owing to its resistance to protein adsorption and low toxicity. As hydrophobic B blocks, we selected poly(propylene sulphide) (PPS), owing to its extreme hydrophobicity, its low glass-transition temperature, and most importantly its oxidative conversion from a hydrophobe to a hydrophile, poly(propylene sulphoxide) and ultimately poly(propylene sulphone). This is the first example of the use of oxidative conversions to destabilize such carriers. This new class of oxidation-responsive polymeric vesicles may find applications as nanocontainers in drug delivery, biosensing and biodetection.

Hydrogen Peroxide↗

Highly selective iodide poly(vinyl chloride) membrane electrode based on a nickel(II) tetraazaannulene macrocyclic complex.

A PVC membrane electrode based on a nickel(II) tetraazaannulene macrocyclic complex as the carrier is described. The electrode exhibits an anti-Hofmeister selectivity sequence with a preference for iodide at pH 3.0-4.0. It has a linear response to iodide from 8.0 x 10(-6) to 1 x 10(-1) mol dm-3 with a slope of -54.7 +/- 0.2 mV per decade (20 degrees C), a satisfactory reproducibility and a rapid response time. The pH dependence of the potential response is discussed. The response mechanism of the electrode was investigated by ac impedance, quartz crystal microbalance and spectroscopic techniques. The electrode can be used for the determination of iodide in drug preparations.

Heterocyclic Compounds↗

pH regulates cation selectivity of poly-(R)-3-hydroxybutyrate/polyphosphate channels from E. coli in planar lipid bilayers.

Poly-(R)-3-hydroxybutyrate/polyphosphate (PHB/polyP) complexes, whether isolated from the plasma membranes of bacteria or prepared from the synthetic polymers, form ion channels in planar lipid bilayers that are highly selective for Ca(2+) over Na(+) at physiological pH. This preference for divalent over monovalent cations is attributed to a high density of negative charge along the polyP backbone and the higher binding energies of divalent cations. Here we modify the charge density of polyP by varying the pH, and observe the effect on cation selectivity. PHB/polyP complexes, isolated from E. coli, were incorporated into planar lipid bilayers, and unitary current-voltage relations were determined as a function of pH. When Ca(2+) was the sole permeant cation, conductance diminished steadily from 97 +/- 6 pS at pH 7.4 to 47 +/- 3 pS at pH 5.5. However, in asymmetric solutions of Ca(2+) and Na(+), there was a moderate increase in conductance from 98 +/- 4 at pH 7.4 to 129 +/- 4 pS at pH 6.5, and a substantially larger increase to 178 +/- 6 pS at pH 5.6, signifying an increase in Na(+) permeability or disorganization of channel structure. Reversal potentials point to a sharp decrease in preference for Ca(2+) over Na(+) over a relatively small decrease in pH. Ca(2+) was strongly favored over Na(+) at physiological pH, but the channels became nonselective near the pK(2) of phosphate (approximately 6.8), and displayed weak selectivity for Na(+) over Ca(2+) at acidic pH. Evidently, PHB/polyP complexes are versatile ion carriers whose selectivity may be modulated by small adjustments of the local pH. The results may be relevant to the physiological function of PHB/polyP channels in bacteria and the role of PHB and polyP in the Streptomyces lividans potassium channel.

Calcium↗

Highly selective thiocyanate poly(vinyl chloride) membrane electrode based on a cadmium-Schiff's base complex.

A PVC membrane electrode based on a cadmium-salen (N,N'-bis-salicylidene-1,2-ethylenediamine) complex as an anion carrier is described. The electrode has an anti-Hofmeister selectivity sequence with a preference for thiocyanate at pH 1.5-11.0. It has a linear response to thiocyanate from 1.0 x 10(-6) to 1.0 x 10(-1) mol L(-1) with a slope of 59.1 +/- 0.2 mV per decade, and a detection limit of 7 x 10(-7) mol L(-1). This electrode has high selectivity for thiocyanate relative to many common organic and inorganic anions. The proposed sensor has a fast response time of approximately 15 s. It was applied to the determination of thiocyanate in a milk sample.

Journal Article↗

Matrix effects on selectivities of poly(ethylene glycol)s for alkali metal ion complexation in matrix-assisted laser desorption/ionization.

The effect of the matrix on poly(ethylene glycol) (PEG) cationization was investigated using an equimolar mixture of CsCl and LiCl as cationizing agents. It was observed that for both carboxylic acid and non-carboxylic acid matrices used, PEG cationization by a given alkali metal ion depends on the matrix used. For example, cesiated PEG ion intensities were much stronger than those of the corresponding lithiated PEG ions when equimolar concentrations of Cs(+) and Li(+) were present and IAA (indolacrylic acid) was the matrix. However, an opposite result was obtained when the same experimental conditions were utilized, but with HABA (2-(4-hydroxyphenylazo)benzoic acid) in place of IAA as the matrix.

Acrylates↗