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PubMed2005

Hydrogen bonding patterns in the cocrystals of 5-nitrouracil with several donor and acceptor molecules.

: Cocrystals of 5-nitrouracil with solvent molecules, dioxane, pyridine, DMSO, formamide and ethanol as well as with piperazine, N, N'-dimethylpiperazine, 3-aminopyridine and diazabicyclo [2.2.2]octane obtained by deliberate inclusion, have been examined by X-ray crystallography. The tape structure found in the parent centric form of nitrouracil is retained with some modifications in the cocrystals with dioxane, piperazine, diazabicyclo [2.2.2]octane, N,N'-dimethylpiperazine, pyridine and DMSO, with the guest molecules forming alternate tapes. In cocrystals involving formamide, ethanol and 3-aminopyridine, the molecular tapes exhibit mixed compositions. The observed bonding patterns have been classified into six schemes. Interestingly, quadruple type hydrogen bonding patterns are seen in cocrystals containing 3-aminopyridine or ethanol and water, while a network of acyclic tetrahedral pentamers of water is found in the cocrystal containing diazabicyclo [2.2.2]octane and water.

Journal Article↗

PubMed1982

Effects of organic solvents on flagellar asymmetry and quiescence in sea urchin sperm.

Low concentrations of methanol, 2-propanol and ethylene glycol increase the asymmetry of the flagellar waveforms ad the turning rate of both live sperm and potentially symmetrical sperm reactivated with 1 mM-MgATP2-, while at the same time causing a decrease in the heat frequency. Similar effects are observed if the solvents are added to preparations of potentially symmetrical sperm reactivated in the presence of 1 mM free Ca2+, or to potentially asymmetrical sperm reactivated without added Ca2+, A second group of solvents, N,N-dimethylformamide, formamide and p-dioxane, also decrease the flagellar beat frequency, but have the opposite effect on symmetry, reducing the asymmetry of the waveforms and the turning rate of potentially symmetrical sperm reactivated in the presence of 1 mM free Ca2+. These effects of solvents are all reversible within about 5 min after initial exposure to solvent. Higher concentrations of methanol and 2-propanol (above approximately 5 and 0.8 mole %, respectively) induce quiescence in potentially asymmetrical sperm reactivated with concentrations of MgATP2- ranging from 10 microM to 1 mM. The quiescent flagella initially assume a bent form very similar to that seen in Ca2+-induced quiescence, and show a subsequent time-dependent distortion of the initial bent from with eventual disintegration and splitting off of bundles of microtubules. Dimethylformamide, formamide and dioxane have almost no effect on the intrinsic asymmetry of potentially asymmetrical sperm reactivated in the absence of added Ca2+, but addition of these solvents to potentially asymmetrical sperm that have been induced to become quiescent by addition of 0.1 mM free Ca2+ causes the sperm to resume swimming with flagellar waveforms that are substantially more symmetrical that those of the starting preparation before the addition of Ca2+. Mild digestion with trypsin of reactivated sperm that have been induced either to beat asymmetrically or to become quiescent by addition of methanol causes a gradual appearance of symmetrical flagellar beating, as in the case of Ca2+-induced quiescence. The flagellar beat frequency, however, remains low, at about 20 Hz. The results suggest that the solvents either mimic or block the action of CA2+ by interaction with a Ca2+-dependent regulatory protein, and may also induce alteration in the rate constants of dynein ATPase.

1-Propanol↗

PubMed1975

Characteristics of DNA fractionated on benzoylated DEAE-cellulose.

Chromatography on BD-cellulose columns with a salt gradient and formamide separates cellular DNA into two fractions (fraction I eluted within the salt gradient, fraction II with formamide), the proportions of these two fractions (ca. 2:1) being similar for DNA from a number of eucaryotic organisms. Yeast DNA was chosen for a detailed study of the mode of fractionation. Several physicochemical parameters, binding to nitrocellulose filters, sensitivity towards nuclease S1, labelling properties in vivo, and hybridization properties of the two DNA fractions were compared. It was shown that both fractions are native DNA and that the fractionation does not depend on the size or the (G + C) content of the DNA. Fraction I DNA contains only a small portion of molecules having single-stranded ends. Fraction II DNA is a heterogeneous population, containing molecules with peculiar structural characteristics: (a) It contains DNA molecules with single-stranded ends and/or gaps sensitive to nuclease S1; labeling experiments suggested that these are molecules undergoing repair and replication. (b) Another portion of fraction II is molecules sensitive to nuclease S1 in regions which are not single-stranded. (c) A third portion is DNA which, after treatment with nuclease S1, is still strongly bound to the resin. Indications that the segregation may be due to the presence of specific DNA sequences comes from the above experiments and from the finding that fraction I DNA is enriched in ribosomal genes and fraction II DNA in tRNA genes.

Centrifugation, Density Gradient↗

PubMed2000

Modified AFLP technique for rapid genetic characterization in plants.

The standard amplified fragment-length polymorphism (AFLP) technique was modified to develop a convenient and reliable technique for rapid genetic characterization of plants. Modifications included (i) using one restriction enzyme, one adapter molecule and primer, (ii) incorporating formamide to generate more intense and uniform bands and (iii) using agarose gel electrophoresis. Sea oats (Uniola paniculata L.), pickerel-weed (Pontederia cordata L.), Bermudagrass (Cynodon dactylon L.) and Penstemon heterophyllus Lindl. were used to determine the ability to generate adequate resolution power with both self- and cross-pollinated plant species including cultivars, ecotypes and individuals within populations. Reproducibility of bands was higher in all the AFLP experiments compared to random amplified polymorphic DNA (RAPD). Formamide with or without bovine serum albumin improved band intensities compared to dimethyl sulfoxide and the standard reaction mixture with no organic solvents. Comparison between RAPD and modified AFLP using sea-oats population samples proved that modified AFLP exhibits (i) a low number of faint bands with increased specificity of amplified bands, (ii) a significantly higher number of polymorphic loci per primer, (iii) less primer screening time, (iv) easy scoring associated with fewer faint bands and (v) greatly enhanced reproducibility. The technique described here can be applied with a high degree of accuracy for plant genetic characterization.

Plants↗

PubMed1998

Fast-painting of human metaphase spreads using a chromosome-specific, repeat-depleted DNA library probe.

For chromosome painting, in situ suppression of repetitive DNA sequences has been well established. Such standard protocols usually require large amounts of Cot-I DNA. Recently, it has become possible to deplete repetitive DNA sequences from library probes by magnetic purification and PCR-assisted affinity chromatography. These "repeat-depleted library probes" appear to be extremely useful for Fast-FISH, a technique that omits denaturing chemical agents such as formamide in the hybridization buffer, resulting in a substantial acceleration and simplification of the complete protocol. Shown here is the application of Fast-FISH to a repeat-depleted, directly fluorochrome-labeled library probe of the q-arm of chromosome 15 (Fast-Painting) for human lymphocyte metaphase spreads. Following painting without Cot-I DNA and without formamide, visual inspection revealed sufficient chromosome painting after a few hours of hybridization. The fluorescence signals of the labeling sites were analyzed after hybridization times of 1 and 2 h (in one case, 4 h) using digital fluorescence microscopy. The painting efficiency expressed in values of relative fluorescence signal ratios was quantitatively evaluated by image analysis using line-scan procedures and area-morphometry of mean luminance. Two preparation protocols (ethanol dehydration without and with RNase A treatment followed by pepsin digestion for four different exposure times) were compared. These results indicated that RNase A treatment and pepsin digestion are steps that can be omitted.

Adult↗

PubMed1990

Identification of the biliary metabolites of (+/-)-3-dimethylamino-1,1-diphenylbutane HCl (recipavrin) in rats.

1. The in vivo biliary metabolites of (+/-)-3-dimethylamino-1,1-diphenylbutane hydrochloride (recipavrin) isolated from Wistar rats have been characterized by g.l.c.-mass spectrometry. 2. Non-conjugated metabolites include recipavrin (1), norrecipavrin (2), diphenylbutanone (3), diphenylbutanone oxime (4), diphenylbutanone phenol (12), diphenylbutanone oxime phenol (14), recipavrin phenol (19), diphenylbutanone O-methylcatechol (16) and diphenylbutanone oxime O-methylcatechol (18). 3. Following beta-glucuronidase hydrolysis and extraction from pH 10 solution, diphenylbutanone (3), diphenylbutanone oxime (4), an unidentified compound (6), primary amine (8), norrecipavrin (2), recipavrin (1), phenols (12, 14, 15), norrecipavrin phenol (13), O-methylcatechols (16, 18), diphenylbutanol O-methylcatechol (17), recipavrin O-methylcatechol (19) and a secondary formamide (5) were identified by g.l.c.-mass spectrometry. 4. Various extraction solvents were employed in sample workup. The formamide (5) was present regardless of solvent used, while the trace presence of secondary acetamide (7) may be associated with the use of ethyl acetate. 5. Metabolites isolated after beta-glucuronidase hydrolysis were characterized by g.l.c.-mass spectrometry of the underivatized form, and as the trimethylsilyl (TMS) derivatives, or following methylation with diazomethane or trimethylanilinium hydroxide (TMAH).

Animals↗

PubMed1991

A non-invasive monitoring of exposure to an industrial organic solvent, dimethylformamide.

A urinary metabolite, N-hydroxymethyl-N-methyl formamide (DMF-OH) was measured by a colorimetric method in Wistar and Sprague-Dawley rat urine after a single exposure to N,N-dimethyl formamide (DMF). A linear relationship was found between the total excretion of DMF-OH in 2 days versus the exposure ranging from 1 to 20% of the LD50 of DMF i.e. 47.2 to 944 mg DMF per kg b. wt. This is proposed to be a non-invasive biological method for monitoring exposure to DMF.

Animals↗

PubMed2002

Activity of HDV ribozymes to trans-cleave HCV RNA.

AIM: To explore whether HDV ribozymes have the ability to trans-cleave HCV RNA. METHODS: Three HDV genomic ribozymes were designed and named RzC1, RzC2 and RzC3. The substrate RNA contained HCV RNA 5'-noncoding region and 5'-fragment of C region (5'-NCR-C). All the ribozymes and HCV RNA 5'-NCR-C were obtained by transcription in vitro from their DNA templates, and HCV RNA 5'-NCR-C was radiolabelled at its 5'-end. Under certain pH, temperature, appropriate concentration of Mg(2+) and deionized formamide, these ribozymes were respectively or simultaneously mixed with HCV RNA 5'-NCR-C and reacted for a certain time. The trans-cleavage reaction was stopped at different time points, and the products were separated with polyacrylamide gel electrophoresis (PAGE), displayed by autoradiography. Percentage of trans-cleaved products was measured to indicate the activity of HDV ribozymes. RESULTS: RzC1 and RzC2 could trans-cleave 26 % and 21.8 % of HCV RNA 5'-NCR-C under our reaction conditions with 2.5 mol.L(-1) deionized formamide respectively. The percentage of HCV RNA 5'-NCR-C trans-cleaved by RzC1, RzC2 or combined usage of the three ribozymes increased with time, up to 24.9 %, 20.3 % and 37.3 % respectively at 90 min point. Almost no product from RzC3 was observed. CONCLUSION: HDV ribozymes are able to trans-cleave specifically HCV RNA at certain sites under appropriate conditions, and combination of several ribozymes aiming at different target sites can trans-cleave the substrate more efficiently than using only one of them.

Base Sequence↗

PubMed1999

Postulated effects on water structure of some salts and protein denaturants as inferred from measurements of viscosity B coefficients: example of HbS polymerization.

Viscosity measurements have been performed on aqueous solutions of some solutes commonly used in biochemical practice, with a view to determine the B coefficients and their temperature dependence. The temperature dependence measured for some anions leads to a ranking of the latter in an order similar to that reported earlier from entropy data for their postulated efficiency in disrupting "water structure". The well known dependence of denaturing power of guanidinium salts on the anions is shown to be related to the temperature dependence of B coefficients. Urea and formamide do not appear from this criterion to be significantly "structure-breaking"; alkyl-substituted derivatives of urea and formamide, on the other hand, possess significant "structure-forming" properties. The results are of interest in relation to the known effects of salts and other solutes on the stability of protein structures in respect of denaturation, subunit dissociation or self assembly. A typical application is illustrated by studying the effect of two anions, namely nitrate and sulphate, on the polymerization of sickle cell hemoglobin (HbS). Nitrate, which is believed to disrupt water structure, acts as an inhibitor of HbS polymerization which, on the contrary, is favoured by sulphate, a postulated structure- former.

Biopolymers↗

PubMed1975

Characterization of globin messenger ribonucleic acids in membrane polysomes of mouse reticulocytes.

Between 20 and 30% of the polysomes in mouse reticulocytes are associated with the cell membrane fraction. These polysomes are not liberated by washing with 0.5 m KCl and are therefore thought to be attached to membranes. They have the same percentage of polyadenylic acid-containing RNA, as determined by oligo(dT)-cellulose affinity chromatography, as cytoplasmic polysomes. Analysis of the RNA by polyacrylamide gel electrophoresis in aqueous solutions shows that at least 95% of the RNA migrates identically with the cytoplasmic polysomal globin mRNAs. Electrophoresis in 99% formamide resolves the membrane mRNAs into two bands which migrate identically with the cytoplasmic alpha- and beta-globin mRNAs. The molar ratio of the alpha- and beta-globin mRNAs, as determined by quantitating the bands on the formamide gels, is similar to that of the cytoplasmic mRNAs. There is also no difference in biological activity between the two messenger preparations. The polyadenylic acid in the membrane mRNAs, isolated after labeling mice in vivo for 20 hours with (32P)orthophosphate, migrates with the three broad size classes previously shown to be present in the cytoplasmic globin mRNAs. The 32P specific activity of the membrane mRNAs and ribosomal RNA fractions after different times of labeling with 32Pi are similar to those from cytoplasmic polysomes. These observations show that the reticulocyte membranes contain approximately 20% of the cellular globin nRNAs, and that these mRNAs are similar to those from cytoplasmic polysomes.

Animals↗

PubMed2001

[Reconstruction of hepatitis D virus ribozymes and their ability to trans-cleave hepatitis C virus RNA].

OBJECTIVE: To study whether reconstructed hepatitis D virus (HDV) ribozymes have the ability to trans-cleave hepatitis C virus (HCV) RNA. METHODS: We reconstructed the stem IV and substrate-binding region of HDV genomic ribozymes, thus obtained three HDV ribozymes named RzC1, RzC2 and RzC3 expected to be able to trans-cleave HCV RNA at predicted sites. The substrate containing HCV RNA 5'-noncoding region (5'-NCR) and 5'-fragment of C region (HCV RNA 5'-NCR-C) was synthesized by transcription in vitro, then radiolabelled at its 5'-end. Under certain pH and appropriate concentration of Mg(2+) with or without deionized formamide, the ribozymes and their substrate were mixed at mol ratio of 100 : 1 and reacted for two hours. Trans-cleaved products were shown by denatured polyacrylamide gel electrophoresis and autoradiography, and the percentage of trans-cleaved substrate was calculated as the activity indicator of these ribozymes. RESULTS: RzC1 and RzC2 were able to trans-cleave HCV RNA 5'-NCR-C site specifically, and their activity could be enhanced by certain concentration of deionized formamide. RzC3 could not trans-cleave the substrate. CONCLUSIONS: Optimized HDV genomic ribozymes can trans-cleave HCV RNA.

5' Untranslated Regions↗

PubMed2001

Rapid method for comparing the cytotoxicity of organic solvents and their ability to destabilize proteins of the erythrocyte membrane.

Cytotoxicities of a group of frequently used organic solvents were assessed by their effect on thermal stability of erythrocyte membrane proteins. The denaturation temperatures Tm of membrane proteins, peripheral and intrinsic, were detected by the increase in the derivative of suspension impedance during heating. These Tm linearly changed by delta Tm in the presence of organic solvents indicating labilization (negative delta Tm) or stabilization (positive delta Tm) of the structure of respective membrane protein. The potency P of the solvent with molar concentration Cex to affect the conformation stability of membrane protein was defined as delta Tm/Cex. This potency decreased as both polarity of solvent and its capability to form hydrogen bonds increased. In some solvents (dimethyl sulfoxide and dimethyl formamide) the potencies to destabilized peripheric and intrinsic proteins were equal. Formamide destabilized selectively peripheral proteins. Some solvents (glycerol, especially erythritol) stabilised thermally proteins. As the hydrophobicity of the solvents increased (ethylene glycol, methanol, ethanol, acetone, pyridine, ethyl acetate, diethyl maleate) the potency for destabilization of intrinsic proteins strongly increased. Thus, the use of more polar solvents capable of forming more hydrogen bonds appears preferable when low cytotoxicity should be attained.

Blood Proteins↗

PubMedDate not supplied

[Ethanol formation by methane-utilizing bacteria at ethane co-metabolism].

It was established, that EDTA (1.0 mM) and formamide (100 mM) are inhibitors of methanol dehydrogenase in Methylobacter luteus 12b, Methylomonas rubra 15sh and Methylococcus thermophilus 111p. The investigated strains co-metabolised ethane with the use of formate as the co-substrate. The application of formamide (or EDTA) as inhibitors of methanol dehydrogenase prevented from further transformation of ethanol and resulted in accumulation of extracellular ethanol. It was shown, that M. rubra 15sh accumulated extracellular ethanol under cultivation in a chemostate. The carried out researches have shown a regulation path of co-metabolism process of hydrocarbons by methane utilizing bacteria. Using the specific inhibitors of methanol dehydrogenase and a source of reducing agent (energy) for methane monooxygenase with the help of the cells of methane-oxidizing bacteria it is possible to obtain from ethane or other hydrocarbons the products of their monooxygenation--alcohols.

Ethane↗

PubMed2002

Effect of sample preparation and pH-mediated sample stacking on the analysis of multiplexed short tandem repeats by capillary electrophoresis.

An amplification system was used in this study to evaluate the effect of sample preparation and its injection on the electrophoretic separation by capillary electrophoresis using a commercially available capillary electrophoresis instrument. The effect of dilution of amplified samples in water and in different sources of formamide (with conductivity values ranging from 47 to 1000 microS) was evaluated, as was contamination of the sample with high DNA concentrations or buffer salts. Although resolution remained constant in the different solvents tested, the sensitivity increased in samples diluted in water and high-purity formamide. An on-column sample preconcentration method for capillary-based DNA analysis was evaluated to increase the sensitivity of low-quality samples. This technique, pH-mediated sample stacking, is based on the injection of NaOH immediately before sample injection: A neutralization reaction occurs between OH- and tris+ ions so that a low-conductivity zone is created at the head of the capillary. DNA fragments are concentrated at the front of this zone. Using coated capillaries with hydroxycellulose 2% (MW 250,000) as a separation matrix, an improvement in sensitivity was detected in all the solvents studied. The gain in sensitivity was higher for more conductive solvents, and was not correlated with the size of the DNA fragments.

Electrophoresis, Capillary↗

PubMed2004

Effect of cationic charge on receptor-mediated transfection using mannosylated cationic liposome/plasmid DNA complexes following the intravenous administration in mice.

The purpose of this study was to evaluate the effect of cationic charge of complexes after intravenous administration of cholesten-5-yloxy-N-[4-[(1-imino-2-D-thiomannosyl-ethyl)amino]butyl]formamide (Man-C4-Chol) containing cationic liposomes/pDNA complexes in mice. Transfection efficiency after intravenous administration of complex at a charge ratio (- : +) of 1.0:2.3 and/or 1.0:3.1 in liver and spleen expressing a mannose receptor on the cell surface were higher than those in lung. When complexes were formed at a charge ratio (- : +) of 1.0:4.7, on the other hand, transfection efficiency in the lung was highest, suggesting a non-specific interaction. Although asialoglycoprotein receptors are expressed on hepatocytes, a liver-selective gene transfection was not achieved by the intravenous administration of pDNA complexed with cholesten-5-yloxy-N-[4-[(1-imino-2-D-thiogalactosyl-ethyl)-amino]butyl]formamide (Gal-C4-Chol)/DOPE liposomes at a charge ratio (- : +) of 1.0 : 2.3. This information supports the design of pDNA/ligands-grafted cationic liposome complexes for cell-specific gene delivery after intravenous administration.

Animals↗

PubMed1990

[Synthesis of 3-[4-[(3-alkylamino-2-hydroxy)propoxy]phenyl (benzyl)]-substituted 4(3H)-quinazolines as antimyocardial ischemic agents].

In order to search for effective antimyocardial ischemic agents, fourteen new 3-[4-[(3-alkylamino-2-hydroxy)propoxy]phenyl(benzyl)]-substituted 4(3H)-quinazolinones (II) were synthesized. Substituted o-aminobenzoic acids used as the starting materials were allowed to react with acetic anhydride and then p-amino-phenol (method A), or with N-(4-hydroxyphenyl)formamide (method B), or with thionyl chloride and then N-(4-hydroxybenzyl)formamide (method C) to form 3-[(4-hydroxyphenyl(benzyl)]-substituted 4(3H)-quinazolinones (III). The intermediate III reacted with epichlorohydrin to form the epoxides (IV). The reaction of IV with an excess of isopropylamine or tert-butylamine in boiling chloroform gave the desired products. Of all the compounds synthesized, compounds II3-5 and II13 were found to increase the tolerance of mice to hypoxia. Further evaluation is in progress.

Adrenergic beta-Antagonists↗

PubMed1989

Synthesis and anticonvulsant evaluation of 1,2-diphenylethane derivatives, potential metabolites of denzimol.

A number of new 1,2-diphenylethane derivatives were synthesized and tested for anticonvulsant activity. Their structure was designed on the basis of the potential metabolic degradation of the imidazole ring present in denzimol ( ( +/- )-N-[2-[4-(beta-phenylethyl)phenyl]-2-hydroxethyl]imidazole), a potent anticonvulsant. The compounds which inhibited the electroshock-induced seizures (MES) in mice, namely N-[4-(beta-phenylethyl)phenacyl]formamide (VII) and N-[2-[4-(beta-phenylethyl)phenyl]-2-hydroxyethyl]formamide (IX), proved active also as inhibitors of the pentylenetetrazole-induced tonic seizures. The results of the pharmacological screening were evaluated in relation to the lipophilicity of the compounds.

Animals↗

PubMed1987

A method of in situ molecular hybridization applied to the study of viral papillomas in man.

Thirty nine papillomas and 14 precancerous lesions, from skin and mucosa were studied for the presence of human papillomavirus (HPV) infection on frozen sections or on paraffin embedded sections by comparison of 2 methods: (1) Detection of group specific viral antigen by immunohistochemical techniques with a rabbit antiserum raised to highly purified virus dissociated by SDS (sodium dodecylsulfate) and heating: (2) detection of viral DNA by an in situ molecular hybridization technique with biotinylated probes. In non-stringent conditions of hybridization (20 p. 100 formamide, Tm = -33 degrees C) viral DNA sequences were more frequently detected (85%) than viral antigen (32%). They were detected in a high proportion of cutaneous and mucosal papillomas as well as in precancerous lesions. They were found in 7 out of 8 biopsies from Bowen's disease and bowenoid papulosis, which were viral antigen negative. Under stringent conditions (50 p. 100 formamide, Tm = -12 degrees C) in situ hybridization allowed typing of HPV. Identical results were obtained in most lesions using in situ hybridization and the Southern technique. Some discrepancies were observed in mucosal lesions, which could be due to the presence or absence of infected foci in the different fragments. Thus, with in situ hybridization it is possible to evaluate the risk of evolution towards malignancy when potentially oncogenic types are present in the biopsies. In the absence of viral DNA in lesions, complementary methods should be used (detection of viral DNA with Southern technique or detection of RNA transcripts).

Adolescent↗