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At least 595 records · Page 33Linked to original sources
PubMed1983

Structural defects in DNA from primary hepatocyte cultures.

Structural analysis of DNA from primary hepatocytes has been made by chromatography on benzoylated-DEAE-cellulose. DNA was labelled in vivo by incorporation of 3H-TdR after partial hepatectomy 2 weeks prior to animals being used to establish hepatocyte cultures. Structural change in DNA associated with the transition to primary culture was assessed by comparison of data with that obtained when DNA was isolated from the intact organ immediately after death. In terms of this comparison, DNA from primary hepatocytes was bound more extensively to benzoylated-DEAE-cellulose in the presence of 1.0 M NaCl. Thus 32% of primary hepatocyte DNA was recovered in the formamide-eluted fraction after chromatography, a result which regions. This proportion of formamide-eluted DNA in primary hepatocytes could not be further reduced by extensive shearing and could not be affected by manipulation of the isolation procedure. Analysis of DNA isolated from hepatocyte cell lines revealed structural characteristics similar to DNA isolated from intact liver. The data imply that extensive structural damage to DNA is a consequence of the primary status of the hepatocytes examined.

Animals↗
PubMed2006

Degradation of cyanide by Trichoderma mutants constructed by restriction enzyme mediated integration (REMI).

REMI technique was used to construct mutants with improved cyanide-degradation ability from biocontrol fungus Trichoderma koningii strain T30. The plasmid pV2 transformation was confirmed by PCR and Southern blot analysis. Out of 21 transformants, 15 single-copied transformants (71.4%) were found. To compare enzyme activities of rhodanese and cyanide hydratase, T. atroviride T23, T. harzianum T21 and their transformants constructed by REMI previously were also included. Transformants TkB6 (0.173 micromols thiocyanate formed min(-1)mg protein(-1)) from T30 and TaK1 (0.174 micromols thiocyanate formed min(-1)mg protein(-1)) from T23 showed higher rhodanese activity than other transformants and their wild strains. TkA9 (5.53 micromols formamide formed h(-1)mg protein(-1)) from T30 and Th64 (5.35 micromols formamide formed h(-1)mg protein(-1)) from T21 had higher cyanide hydratase activity than other transformants and their wild strains.

Base Sequence↗
PubMed2005

Genosensor on gold films with enzymatic electrochemical detection of a SARS virus sequence.

A hybridisation-based genosensor was designed on a 100 nm sputtered gold film. This material worked as an immobilisation and transduction surface. A 30-mer sequence that encodes a short lysine-rich region, unique to SARS (severe acute respiratory syndrome) virus, was chosen as target. A complementary strand (probe), labelled with a thiol group at the 3'-end, was immobilised on the film. After blocking the surface, hybridisation with the biotin-conjugated SARS strand (at the 3'-end) took place. Interaction with alkaline phosphatase-labelled streptavidin permits amplified indirect electrochemical detection. The analytical signal is constituted by an electrochemical process of indigo carmine, the soluble product of the enzymatic hydrolysis of 3-indoxyl phosphate. The use of a sensitive electrochemical technique such as square wave voltammetry allowed a detection limit of 6 pM to be obtained for this DNA sequence, lower than any other found in the bibliography. The parameters affecting the methodology were studied, with special attention being placed on selectivity. Specificity was clearly enhanced when interaction time and stringency (in the form of formamide percentage) were increased. With 1h of strand interaction and employing 50% of formamide in the hybridisation buffer, a 3-base mismatch strand was perfectly distinguished from the complementary.

Biosensing Techniques↗
PubMed2004

Impact of lipopolysaccharide coating on clay particle wettability.

Impact of lipopolysaccharide coating on kaolinite and Na-montmorillonite wettability was investigated. Kaolinite had greater diiodomethane contact angles, smaller water and formamide contact angles than Na-montmorillonite. After lipopolysaccharide coating, diiodomethane and formamide contact angles decreased, while water contact angles increased for both kaolinite and Na-montmorillonite. The decrease and increase in liquid contact angles after lipopolysaccharide coating were most pronounced for lipopolysaccharide extracted from Pseudomonas aeruginosa, followed by Pseudomonas fluorescens and Echerichia coli. Clay particle wettability was determined by particle surface thermodynamic properties. Both kaolinite and Na-montmorillonite exhibited a monopolar surface and the monopolarity decreased after lipopolysaccharide coating, indicating an increase in hydration or surface wetness. The origins of interactions of clay particles with water molecules were discussed and related to clay particle water wettability.

Aluminum Silicates↗
PubMed2005

Characterization of the PCR inhibitory effect of bile to optimize real-time PCR detection of Helicobacter species.

The inhibitory effect of human and porcine bile samples to detect Helicobacter DNA was studied by adding different concentrations of bile samples to PCR mixtures of six thermostable DNA polymerases containing cagA specific primers and Helicobacter pylori DNA. PCR products were amplified by using the Rotorgene system and SYBR Green I. Among the six DNA polymerases tested, rTth had the lowest sensitivity to bile inhibitors, whereas Taq and Tfl had the highest sensitivity. Bile proteins did not inhibit AmpliTaq DNA polymerase, whereas the fraction containing mainly bile acids and their salts inhibited the amplification capacity of AmpliTaq. Heating human bile at 98 degrees C and adding casein and formamide to the reaction mixture reduced the PCR inhibitory effect of bile. Therefore, a pre-PCR treatment based on dilution and heating of bile, adding casein and formamide to the reaction mixture of rTth DNA polymerase was found efficient to amplify DNA directly in bile.

Animals↗
PubMed2005

Percolation phenomenon in mixed reverse micelles: the effect of additives.

The conductivity of AOT/IPM/water reverse micellar systems as a function of temperature, has been found to be non-percolating at three different concentrations (100, 175 and 250 mM), while the addition of nonionic surfactants [polyoxyethylene(10) cetyl ether (Brij-56) and polyoxyethylene(20) cetyl ether (Brij-58)] to these systems exhibits temperature-induced percolation in conductance in non-percolating AOT/isopropyl myristate (IPM)/water system at constant compositions (i.e., at fixed total surfactant concentration, omega and X(nonionic)). The influence of total surfactant concentration (micellar concentration) on the temperature-induced percolation behaviors of these systems has been investigated. The effect of Brij-58 is more pronounced than that of Brij-56 in inducing percolation. The threshold percolation temperature, Tp has been determined for these systems in presence of additives of different molecular structures, physical parameters and/or interfacial properties. The additives have shown both assisting and resisting effects on the percolation threshold. The additives, bile salt (sodium cholate), urea, formamide, cholesteryl acetate, cholesteryl benzoate, toluene, a triblock copolymer [(EO)13(PO)30(EO)13, Pluronic, PL64], polybutadiene, sucrose esters (sucrose dodecanoates, L-1695 and sucrose monostearate S-1670), formamide distinctively fall in the former category, whereas sodium chloride, cholesteryl palmitate, crown ether, ethylene glycol constitute the latter for both systems. Sucrose dodecanoates (L-595) had almost marginal effect on the process. The observed behavior of these additives on the percolation phenomenon has been explained in terms of critical packing parameter and/or other factors, which influence the texture of the interface and solution properties of the mixed reverse micellar systems. The activation energy, Ep for the percolation process has been evaluated. Ep values for the AOT/Brij-56 systems have been found to be lower than those of AOT/Brij-58 systems. The concentration of additives influence the parameters Tp and Ep for both systems. A preliminary report for the first time on the percolation phenomenon in mixed reverse micelles in presence of additives has been suggested on the basis of these parameters (Tp and Ep).

Journal Article↗
PubMed2004

A study of vehicles for dosing rodent whole embryo culture with non aqueous soluble compounds.

In rodent whole embryo culture (WEC), finding vehicles for non-aqueous-soluble compounds has been problematic due to developmental toxicity associated with many solvents. The purpose of this study was to identify alternative vehicles for insoluble compounds. In WEC, we evaluated carrier solutions containing bovine serum albumin (BSA) and glycerol as well as the solvents, formamide, dimethylformamide (DMF), dimethyl sulfoxide (DMSO) and ethanol, for relative teratogenicity and delivery of the insoluble teratogen, all-trans retinoic acid (RA). At a concentration of <or=0.04%, formamide and DMF exhibited no significant toxicity to cultured rat embryos and were effective at delivering RA to the embryo. The BSA and glycerol carrier solutions were not teratogenic, although both inhibited robust formation of yolk sac vasculature. Both solutions delivered RA to the cultured rat embryos at higher doses. In summary, all four solvents/solutions may have utility as vehicles dependent upon the chemical properties of the compound to be solubilized.

Animals↗
PubMed1975

Liquid ion exchangers in paper chromatography of steroidal glucosiduronic acids, glucosiduronic esters and free steroids. Influence of concentration of exchanger and counterion.

The chromatographic mobility of steroidal glucosiduronic acids on paper in chloroform-formamide increases as the concentration of ion exchanger in the chloroform phase increases; mobility decreases as the concentration of counterion in formamide increases. Mobility of glucosiduronic esters and of hydroxylated free steroids increases with an increase in concentration of exchanger; small changes in concentration of counterion in the stationary phase do not alter the migration of these nonionizable compounds. Data are presented which suggest that partition of the glucosiduronic acids between the two phases occurs predominantly by an ion-exchange process and that hydrogen bonding plays a secondary role. Partition of the glucosiduronic esters and hydroxylated free steroids appears to occur primarily by a hydrogen-bonding process.

Cholesterol↗
PubMed1998

Nonaqueous capillary electrophoresis chiral separations with quaternary ammonium beta-cyclodextrin.

Chiral separation of nonsteroidal anti-inflammatory drugs (profens), 1,1'-binaphthyl-2,2'-diyl-hydrogen phosphate, N-[1-(1-naphthyl)ethyl]phthalamic acid, and derivatized amino acids by a cationic cyclodextrin, quaternary ammonium beta-cyclodextrin (QA-beta-CD), was investigated by capillary electrophoresis (CE) in both aqueous and nonaqueous media. Several profens and amino acids could only be separated by QA-beta-CD in pure formamide system. No chiral separation of the profens was achieved in the following solvents: N-methylformamide, methanol, dimethyl sulfoxide, and water; however, chiral separations of most of the amino acids were obtained in all of these solvents. The effects of other experimental parameters such as the CD concentration and apparent pH (pH*) were also investigated. The first application of nonaqueous CE chiral separation of ketoprofen in a commercially available sample, Actron, was also examined. In addition, the reversal of electroosmotic flow by QA-beta-CD was observed in water, formamide, N-methylformamide, methanol, and dimethyl sulfoxide media.

Anti-Inflammatory Agents, Non-Steroidal↗
PubMed1979

Repair and de novo replication of rat lung DNA following instillation of 3-methylcholanthrene.

Structural analysis of rat lung DNA was made by stepwise elution of the nucleic acid from benzoylated--DEAE-cellulose with 1.0 M NaCl and 30% formamide solutions respectively, the DNA content of collected fractions being determined by absorbance. The proportion of the minor fraction, which was eluted with formamide and thought to contain DNA having single-stranded regions, was increased by intratracheal instillation of 3-methylcholanthrene prior to death of the animal. Maximum initial increase was observed 14 h after treatment. Analysed up to 10 days after treatment, there was a biphasic response, the early maxima being dose dependent and the second apparently independent of the amount of hydrocarbon administered. The data implicate DNA repair processes and cellular proliferation stimulated by 3-methylcholanthrene as being involved in recovery of the lung from this potentially carcinogenic insult.

Animals↗
PubMed1999

Extracellular nuclease from Rhizopus stolonifer: purification and characteristics of - single strand preferential - deoxyribonuclease activity.

An extracellular nuclease from Rhizopus stolonifer (designated as nuclease Rsn) was purified to homogeneity by chromatography on DEAE-cellulose followed by Blue Sepharose. The M(r) of the purified enzyme determined by native PAGE was 67¿ omitted¿000 and it is a tetramer and each protomer consists of two unidentical subunits of M(r) 21¿ omitted¿000 and 13¿ omitted¿000. It is an acidic protein with a pI of 4.2 and is not a glycoprotein. The purified enzyme showed an obligate requirement of divalent cations like Mg(2+), Mn(2+) and Co(2+) for its activity but is not a metalloprotein. The optimum pH of the enzyme was 7.0 and was not influenced by the type of metal ion used. Although, the optimum temperature of the enzyme for single stranded (ss) DNA hydrolysis in presence of all three metal ions and for double stranded (ds) DNA hydrolysis in presence of Mg(2+) was 40 degrees C, it showed higher optimum temperature (45 degrees C) for dsDNA hydrolysis in presence of Mn(2+) and Co(2+). Nuclease Rsn was inhibited by divalent cations like Zn(2+), Cu(2+) and Hg(2+), inorganic phosphate and pyrophosphate, low concentrations of SDS, guanidine hydrochloride and urea, organic solvents like dimethyl sulphoxide, dimethyl formamide and formamide but not by 3'- or 5'-mononucleotides. The studies on mode and mechanism of action showed that nuclease Rsn is an endonuclease and cleaves dsDNA through a single hit mechanism. The end products of both ssDNA and dsDNA hydrolysis were predominantly oligonucleotides ending in 3'-hydroxyl and 5'-phosphoryl termini. Moreover, the type of metal ion used did not influence the mode and mechanism of action of the enzyme.

Cations, Divalent↗
PubMed2001

Synthesis, characterization and reactions of 2-deoxo-5-deazaalloxazines.

5-Deazaflavins and their homologues have been known as potential riboflavin antagonists, bioreductives, and compounds with potent antitumor activity. 2-Amino-4-methylquinoline-3-carbonitrile (2) was prepared as unreported starting material for several interesting 2-deoxo-5-deazalloxazine derivatives. Cyclization of 2 using formamide afforded the 2,4-deoxo-5-deazaalloxazine derivative 7, which was subjected to deamination with nitrous acid to give the 2-deoxo-5-deazaalloxazine (8). The compound 8 was also obtained via 13 by treating the latter with refluxing formic acid or formamide and used as a precursor for synthesis of several 2-deoxo-5-deazaalloxazines 18, 19, 20, 21 and 22. The pharmacological and biological properties of these compounds are still under investigation.

Antineoplastic Agents↗
PubMed2000

Formation of [M - nH] + mNA](m-n)+ and [M - nH + mK](m-n)+ ions in electrospray mass spectrometry of peptides and proteins.

The [M - nH + mNa](m-n)+ and [M - nH + mK](m-n)+ ions are common in the electrospray mass spectra of proteins and peptides. The feasibility of forming these ions in the gas phase via collision activation and/or ion-molecule reaction is investigated. Sodium and potassium affinities of the N-methylacetamide anion, the acetate anion, and the 1-propanamide anion have been calculated using density functional theory at the B3LYP/6-311+ +G(d,p) level of theory. These anions were chosen as models for the functional groups on a protein or peptide. These affinity values are then used to calculate reaction enthalpies of alkali hydroxides, chlorides, and hydrates with N-methylacetamide, acetic acid, the acetate anion, and 1-propanamine, model reactions that may lead to formation of the [M - nH + mNa](m-n) and [M - nH + mK](m-n)+ ions. It is found that a number of these reactions are exothermic or slightly endothermic (deltaH(o) < + 20 kcal/mol) and are accessible after collision activation in the lens region. The potential energy hypersurfaces of model reactions between NaOH and formamide as well as NaCl and formamide show relatively flat surfaces devoid of significant barriers.

Hydroxides↗
PubMed1994

Evidence that alternate foldings of the hepatitis delta RNA confer varying rates of self-cleavage.

The pentapurine sequence GGAGA, located between 80 and 84 nucleotides downstream of the cleavage site in the self-cleaving antigenomic RNA of hepatitis delta virus, is necessary for highly efficient cleavage and for stability in up to 20 M formamide. Yet much of the cleavage activity lost upon its removal from the 3' end of an 84-nucleotide RNA can be restored by elongation of the 5' end of the RNA with the polypyrimidine sequence found in the virus. We propose that this sequence alteration causes a refolding of the RNA, resulting in a "structural compensation" of the active core of the molecule. Restoration of the self-cleavage activity did not restore the ability to cleave in high concentrations of formamide. Deletion mutagenesis was carried out and supported the alternate RNA folding. The ability to assume more than one active conformation and for one RNA structure to compensate for another in supporting ribozyme activity may be unique to RNA enzymes and could be a useful adaptation in viruses or in prebiotic RNAs.

Base Sequence↗
PubMed1981

Solvent effects on thermodynamics of double-helix formation in (dG-dC)3.

The thermodynamics of double-helix formation by (dG-dC)3 have been measured in aqueous solvent mixtures containing 10 mol % methanol, ethanol, 1-propanol, formamide, N,N-dimethylformamide, or urea and 20 mol % ethanol. Optical activity measurements indicate the conformation of the double helix at 3 degree C is the same in all the solvent mixtures except 20 mol % ethanol. All the cosolvents destabilize the helix relative to water. With 10 mol % alcohol cosolvents, this destabilization is associated with a more unfavorable entropy change averaging approximately 8% and a more favorable enthalpy change averaging approximately 5%. This is consistent with a small contribution of hydrophobic bonding to stability. In contrast, the destabilization by formamide, N,N-dimethylformamide, and urea is associated with a more unfavorable enthalpy change averaging approximately 23% and a more favorable entropy change averaging approximately 21%. Since all three of these cosolvents have dipole moments larger than water, this is consistent with increased competition for dipolar interactions between the nucleic acid bases. None of the results correlate with any one bulk solvent parameter such as surface tension, viscosity, or dielectric constant. With 20 mol % ethanol, optical activity measurements are consistent with a partial B to C form transition. This is associated with a 27% less favorable enthalpy and 25% more favorable entropy for helix formation relative to water. Since the B to C transition is associated with helix dehydration, this may imply a significant contribution of bound water to stability.

Ethanol↗
PubMed1975

Sequence homology of the mitochondrial leucyl-tRNA cistron in different organisms.

Sequence divergence of the mitochondrial leucytl-tRNA cistron in several eukaryotes has been examined by RNA-DNA hybridized. Rat mitochondria Leucyl-tRNA was hybridized with rat, mouse, guinea pig, monkey, chicken, and yeast mitochondrial DNAs (mtDNA) immobilized onfilters. Hybridization was carried out in 50% formamide (Tm -12degrees) or in 20% fromamide (Tm -21degrees). melting profiles of the hybrids were obtained for evaluation of the extent of base sequence micmatching. Under the more stringent hybridization conditions (50% formamide, Tm -12degrees), only mouse and quines pig mtDNAs hybridized with rat mitochondrial leucyl-tRNA. The Tm's of the heterohybrids were depressed by 2 and 9 degrees, respectively. Under less stringent hybridization conditions (Tm-21 degrees), monkey mtDNA also hybridized, and the Tm was depressed by about 15 degrees. Chicken and yeast mtDNAs did not form specific hybrids with rat mibochondrial leucyl-tRNA under these hybridization conditions. Mitochondrial leucyl-tRNA sequences in different eukaryotes appear to be conserved to a less extent than cytoplasmic rRNA, 5S RNA, or hemoglobin mRNA sequences.

Animals↗
PubMed1975

Molecular mobility and structure of elastin deduced from the solvent and temperature dependence of 13C magnetic resonance relaxation data.

13C relaxation parameters, T1, line width, and NOE, have been determined for backbone carbons of ligamentum nuchae elastin swollen by 0.15 M NaCl, 0.15 M NaCl-formamide, 0.15 M NaCl-ethanol, dimethyl sulfoxide, and formamide. The data have been analyzed in terms of (a) a single correlation time model and (b) a model employing a log-chi2 distribution of correlation times used by Schaefer (1973) to analyze solid cis-polyisoprene 13C relaxation data. Employing the latter mode, one obtains an approximately self-consistent quantitative analysis of all the elastin data. An average backbone correlation time, tau, of ca. 2 nsec is calculated for elastin swollen in the presence of polar organic solvents at 37 degrees, in approximate agreement with tau of 0.4 nsec obtained for bulk cis-polyisoprene at 35 degrees. The influence of solvent and temperature on elastin spectra indicate that the larger tau value (approximately 80 nsec) obtained for elastin swollen by 0.15 M NaCl at 37 degrees is a consequence of weak interchain polar and hydrophobic interactions, a result which is in accord with the reported viscoelastic behavior exhibited by water-swollen elastin at 37 degrees. The results obtained further suggest that Gly, Pro, and Val residues are significantly more mobile than Ala residues, which are located in the cross-link regions. Hence, the NMR data support the view that water-swollen elastin is composed of a network of mobile chains, except possibly in the cross-link regions.

Animals↗
PubMedDate not supplied

Scleroglucan gelation by in situ neutralization of the alkaline solution.

Scleroglucan gels were prepared by neutralization of aqueous alkaline solution of scleroglucan by in situ release of acid. Transition of scleroglucan chains in a disordered state to the triple-helical state result in cross-linking of the polysaccharide. The pH and the storage and loss moduli, G' and G' ', were determined as a function of time after initiating the pH reduction. Experiments were performed in the temperature range from 20 to 90 degrees C and in the polymer concentration range from C(p) = 10-200 mg/mL. The concentration dependence of the apparent plateau value of the storage modulus showed a lower critical concentration, C(p,0), in the range 12-15 mg/mL needed for gelation and a second power dependence of G' on concentration in the range 50-200 mg/mL. In situ pH reduction was achieved using formamide (methanoic acid) or ethyl acetate (ethyl ethanoate) which hydrolyze in alkaline solution, yielding carboxylic acids. The more rapid hydrolyses of ethyl acetate compared to formamide yielded a faster decrease of pH in solution and a more rapid increase of the storage modulus. The present gelation process of scleroglucan based on the in situ reduction of pH has advantages in applications where external control of the conditions is difficult to achieve.

Alkalies↗