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PubMed1989

The use of monoclonal antibodies in the characterization and purification of cell surface antigens of Listeria monocytogenes serogroup 4.

Soluble antigen was prepared from Listeria monocytogenes serovar 4b using a formamide extraction method. Antigenic material was detected in this extract by gel diffusion and ELISA using anti-Listeria monoclonal antibodies. Using this ELISA, antigen was detected in cerebrospinal fluid (CSF) during infection due to L. monocytogenes serovar 4b with wells coated with three of the monoclonal antibodies (CL1, CL2 and CL3). The antigen binding of CL3 was found to be greatly influenced by changes in ionic strength, and these properties were utilized in an affinity purification method. An analysis of the antigens was carried out using crossed immunoelectrophoresis and this indicated that the crude formamide extract contains a number of distinct antigens. A group of three antigens of differing electrophoretic mobilities were demonstrated in the affinity purified material.

Animals↗
PubMed1987

An investigation of the relationship between the hepatotoxicity and the metabolism of N-alkylformamides.

The hepatotoxicity and metabolism of the following close analogs of the hepatotoxic antitumor agent N-methylformamide (NMF) were investigated in CBA/CA mice: N-ethylformamide (NEF), dimethylformamide (DMF), formamide and N-methylacetamide (NMA). Apart from NMF only NEF was potently hepatotoxic as measured by the elevation of plasma activities of the enzymes sorbitol dehydrogenase and alanine and aspartate aminotransferases 24 hr after drug administration. In freeze-dried urine samples of mice which had received NEF or NMF, but not in the case of DMF, formamide or NMA, thioesters were detected by thin-layer chromatography. Evidence based on high-pressure liquid chromatography analysis and 400 MHz 1H-NMR and mass spectrometry suggests that the thioester metabolite of NEF is S-(N-ethylcarbamoyl)-N-acetylcysteine. It has been shown previously that NMF is metabolized to S-(N-methylcarbamoyl)-N-acetylcysteine. NEF also underwent extensive metabolism to ethylamine; similarly NMF was biotransformed to methylamine. In contrast, the urine of mice which had received DMF contained only very small amounts of dimethylamine and methylamine could not be detected as a metabolite of NMA. Instead, the major metabolite of NMA was identified by 400 MHz 1H-NMR spectrometry as N-(hydroxymethyl)acetamide. DMF is known to undergo extensive metabolism to its N-hydroxymethyl derivative. The results suggest that two metabolic pathways of N-alkylformamides can be distinguished: Hydroxylation at the alpha-carbon of the N-alkyl group and oxidation of the formyl moiety. The former pathway presumably constitutes a detoxification route, and the latter may well be associated with hepatotoxicity, and affords a glutathione conjugate, excreted in the urine as a mercapturate.

Acetamides↗
PubMed1975

Variable effects of a lipotrope-deficient, high-fat diet on chemical carcinogenesis in rats.

Earlier studies demonstrated enhanced chemical carcinogenesis in the liver, colon, and probably esophagus of male rats that were fed a lipotrope-deficient, high-fat diet. In further experiments, designed to examine the range of the dietary effect on chemical carcinogenesis, rats were fed either the marginally lipotrope-deficient, high-fat diet or an adequate control diet, and treated wit- N-2-fluorenylacet-amide, 3,3 diphenyl-3-diemthylcarbamoyl-1-propyne, N-methyl-N-nitroso-N'-nitroguanidine, N-[4-(5-nitro-2-furyl)-2-thiazolyl]formamide, aflatoxin G1, or ethionine. N-2-Fluorenylacetamide indiced hepatocarcinomas more rapidly and in higher incidence in deficient rats than in control rats. 3,3-Diphenyl-3-dimethylcarbamoyl-1-propyne induced a higher incidence of hepatocarcinomas but not gastric tumors in deficient rats. Aflatoxin B1, included as a positive control, was significantly more hepatocarcinogenic in deficient rats. Gastric tumor induction by N-methyl-N-nitroso-N'-nitroguanidine and induction of tumors of the urinary bladder by N-[4-(5-nitro-2-furyl)-2thiazylyl]formamide were not influenced by diet. Aflatoxin G1 and ethionine were toxic to deficient rats, and carcinogenic doses could not be administered.

2-Acetylaminofluorene↗
PubMed1982

Studies on the structure of avian myeloblastosis virus (AMV) RNA. III. Electron microscopic definition of secondary structure.

The secondary structure of avian myeloblastosis virus (AMV) RNA was characterized by electron microscopy under moderately denaturing spreading conditions. Under denaturation by aqueous 44% formamide or 77% formamide in the presence of salts, partly stretched RNA molecules with measurable double-stranded regions were observed. This approach allowed the localization from 5 to 11 regions of preserved secondary structure on AMV RNA molecules. Topographic analysis revealed a nonrandom occurrence of stable secondary structures in several prevalent regions. These regions with higher secondary structure stability revealed certain similarity to hairpin structures localized by electron microscopy on Rous sarcoma virus RNA or to highly structured regions found on this RNA by T1 ribonuclease oligonucleotide analysis.

Avian Leukosis Virus↗
PubMed1993

FoLT PCR: a simple PCR protocol for amplifying DNA directly from whole blood.

FoLT (formamide low temperature) PCR is a protocol for amplifying DNA directly from whole blood without any preparative steps. Up to 10% (vol/vol) whole blood can be added directly into the tube containing the PCR mixture. There is no need for transfers, centrifugations, pre-boiling or any preparative step. It involves the use of formamide (18% vol/vol) as well as reduced incubation temperatures (cycles of 85 degrees, 40 degrees, 60 degrees C). The type of anticoagulant used was critical: sodium heparin or EDTA being superior to lithium or fluoride heparin. Our studies indicate that FoLT PCR probably works by reducing the amount of protein coagulation and allowing more DNA template to be accessible for amplification. The sensitivity of FoLT PCR is such that a single copy gene from 5.5 nucleated cells in 1 microliter of whole blood can be detected.

Anticoagulants↗
PubMed1998

Cryochemistry: freezing effect on peptide coupling in different organic solutions.

The freezing effect on peptide coupling in organic solutions of different polarity has been investigated and compared with the results obtained in liquid phase. The model reaction of DCC-activated coupling of Boc-Ala-Phe-OH with H-Ala-OBu(t) has been carried out in dioxane, dimethylsulfoxide and formamide, as well as in mixtures (90%/10%, v/v) of dioxane with acetonitrile, dimethylformamide, dimethylsulfoxide and formamide. The reactions have been traced and evaluated by RP-HPLC analysis. Freezing the reaction mixture resulted in all cases in a significant suppression of the N-dipeptidylurea side-product formation together with a slight decrease of tripeptide epimerization. The coupling yields and the side effects depended on the solvent, with the dioxane and dioxane/acetonitrile mixture produced the best results. The role of freezing and solvent in the improved results is discussed.

Chromatography, High Pressure Liquid↗
PubMed1999

Polymer solution-filled column for the analysis of antisense phosphorothioates by capillary electrophoresis.

A capillary electrophoresis (CE) column filled with 13% poly(ethylene glycol) (PEG) solution is demonstrated to resolve different lengths of antisense phosphorothioates in 100 mM Tris-borate (pH 9.0) buffer containing 30% formamide at 50 degrees C. Two sets of mixtures composed of 15-20 mers of either antisense phosphorothioate or phosphodiester oligonucleotides were synthesized based on a sequence of the antisense orientation directed against DNA-methyltransferase (denoted as MT-AS) and were used as model compounds. It was found that column coating reduced electroosmotic flow, as well as wall adsorption, and led to the separation of both phosphorothioate and phosphodiester molecules. Substantial peak broadening, however, specifically occurred to the phosphorothioates and was reduced statisfactorily by the addition of formamide into the buffer solution, raising the temperature, and raising the pH value. Under experimental conditions, a linear relationship between the migration time and the base number was observed, indicating that no peak compression artifacts existed. Without tedious pretreatment, antisense phosphorothioates were spiked into human serum, followed by water dilution, and then directly injected into the column. Separation of different lengths of phosphorothioates was observed using pressure injection, which did not suffer from injection bias.

Electrophoresis, Capillary↗
PubMed2001

Solvent-induced dimensional changes in EDTA-demineralized dentin matrix.

The purpose of this study was to test the null hypothesis that the re-expansion of dried matrix and the shrinkage of moist, demineralized dentin is not influenced by polar solvents. Dentin disks were prepared from midcoronal dentin of extracted human third molars. After complete demineralization in 0.5M of EDTA (pH 7), the specimens were placed in the well of a device that measures changes in matrix height in real time. Dry, collapsed matrices were created by blowing dry N(2) on the specimens until they shrank to a stable plateau. Polar solvents [water, methanol, ethanol, n-propanol, n-butanol, formamide, ethylene glycol, hydroxyethyl methacrylate (HEMA), or mixtures of water-HEMA] as model primers then were added and the degree of re-expansion measured. These same solvents also were applied to moist, expanded matrices and the solvent-induced shrinkages measured. Regression analysis was used to test the correlations between matrix height and Hansen's dispersive, polar, hydrogen bonding, and total solubility parameters (delta(d), delta(p), delta(h), delta(t)). The results indicate that water-free polar solvents of low hydrogen bonding (H-bond) ability (e.g., neat HEMA) do not re-expand dried matrices and that they shrink moist matrices. When HEMA was mixed with progressively higher water concentrations, the model water-HEMA primers expanded the dried matrix in proportion to their water concentrations and they produced less shrinkage of moist matrices. Solvents with higher H-bonding capacities (methanol, ethanol, ethylene glycol, formamide, and water) re-expanded the dried matrix in proportion to their solubility parameters for H-bonding (delta(h)). They also induced small transient shrinkages of moist matrices, which slowly re-expanded. The results require rejection of the null hypothesis.

Biocompatible Materials↗
PubMed2000

Quantum chemical modeling of through-hydrogen bond spin-spin coupling in amides and ubiquitin.

Through-hydrogen bond spin-spin coupling has been investigated computationally in the formamide dimer and in fragments of the protein ubiquitin. The Fermi-contact term was calculated by finite perturbation theory with the B3LYP DFT method with several basis sets. The distance and angular dependence of the 3J(N,C') coupling constant (N-H--O=C) in the hydrogen-bonded formamide dimer was firstly examined for a wide range of mutual arrangements, also in relation to the stability of the dimer. The magnitude of 3J(N,C') is relatively insensitive to the dihedral angle between the two amide planes, whereas values between 1-2 Hz are calculated for a variety of arrangements, including non-linear hydrogen bonds, in agreement with the shape of some occupied, low-lying molecular orbitals which connect donor and acceptor. Then, fragments of the ubiquitin protein (for which such coupling constants are experimentally available) were generated by removing from the experimental structure all amino acids except those involved in hydrogen bonding, and coupling constants were calculated for such fragments. Although calculated 3J(N,C') values are sometimes overestimated, they generally correlate with the corresponding experimental values.

Amides↗
PubMed2001

Solvent-dependent C-OH homolysis and heterolysis in electronically excited 9-fluorenol: the life and solvation time of the 9-fluorenyl cation in water.

The primary pathways of the photodecomposition of 9-fluorenol (FOH) were studied in polar and nonpolar solvents by use of laser flash-photolysis with a resolution time of 10 ps. In solvents of high polarity, that is, in 1,1.1,3,3,3-hexafluoroisopropanol (HFIP), 2,2,2-trifluoroethanol (TFE), formamide or water, the fluorenyl cation, F+, forms by heterolytic C-O bond cleavage. In H2O, the initial (10 ps) spectrum of F+ has lambdamax at <460 nm. This absorption red-shifts with T = 25 ps to the "classical" spectrum with lambdamax = 510-515 nm. This process is assigned to the solvation of the initial "naked" cation, or rather, the contact ion pair. The lifetime of the solvated fluorenyl cation in H2O (or D2O) and TFE was measured to be tau 20 ps and 1 ns, respectively. In solvents of lower polarity such as alkanes, ethers and alcohols, the long-lived (tau 1/2 1 micros) fluorenyl radical, F., (lambdamax = 500 nm) forms through homolytic C-O cleavage. In addition to the radical and the cation, the vibrationally relaxed excited singlet state of FOH is seen with its absorption at approximately 640 nm; its lifetime is strongly dependent on the solvent, from 10 ps for formamide to 1.7 ns for cyclohexane. The rate constant for singlet decay increases exponentially with the polarity of the solvent (as expressed by the Dimroth-Reichardt ET value) or with the Gutmann solvent acceptor number. The relaxation of S1 to S0 is accompanied by homolytic C9-O bond cleavage (except in HFIP, TFE, and water, where S1 is not seen).

Journal Article↗
PubMed2003

Effect of water potential on sol-gel transition and intermolecular interaction of gelatin near the transition temperature.

The sol-gel transition of gelatin, measured by thermal analysis and viscosity measurement, was analyzed in terms of the change in hydration state of polymer molecules. A new thermodynamic model was proposed in which the effect of water potential is explicitly taken into account for the evaluation of the free energy change in the sol-gel transition process. Because of the large number of water molecules involved and the small free energy change in the transition process, the contribution of water activity, a(W), was proved to be not negligible in the sol-gel transition process in solutions containing such low-molecular cosolutes as sugars, glycerol, urea, and formamide. The gel-stabilization effect of sugars and glycerol was linear with a(W), which seemed consistent with the contribution of water potential in the proposed model. The different stabilization effect among sugars and glycerol was explained by the difference in solvent ordering, which affects hydrophobic interaction among protein molecules. The gel-destabilization effect of urea and formamide could be explained only by the direct binding of them to protein molecules through hydrogen bonding. On the contrary, the polymer-polymer interaction, measured by the viscosity analysis, in polyethyleneglycol and dextran solutions was not sensitive to the change in a(W), suggesting that no substantial change in hydration state with a(W) occurred in these polymer solutions.

Animals↗
PubMed1986

Quantitation of branched-chain alpha-keto acids as their N-methylquinoxalone derivatives: comparison of O- and N-alkylation versus -silylation.

Quantitative estimation of isotopic enrichment and concentrations of keto analogs of branched-chain amino acids in biological fluid has been used for the study of protein metabolism in animal and human studies. At present, O-trimethylsilyl-quinoxalinol derivative is used widely in the quantification of branched-chain alpha-keto acids. In the present study, N-methyl-quinoxalone derivative was developed and its use in quantification in human studies verified. O-phenylenediamine and alpha-keto acid react in acidic media to yield phenolic and amide tautomers. O-trimethylsilyl-quinoxalinol derivative of the phenolic tautomer is used at present for quantification by chemical ionization/selected ion monitoring. We have prepared N-methyl-quinoxalone derivative using N,N-dimethyl formamide dimethyl acetal. This derivative is characterized by a major amide form and a minor phenolic form. The mass spectrum has a characteristic fragment, which facilitates easy identification and quantitation by electron impact/selected ion monitoring. Because m/z 174 was observed as the base peak for alpha-ketoisocaproate, alpha-keto-beta-methylvalerate and alpha-ketoisovalerate, "single ion monitoring' could be performed for the quantification of isotopic enrichment as well as plasma concentration of these three branched-chain alpha-keto acids. Isotopic enrichment from 0.25 to 7.5 at% excess could be measured easily, with an average coefficient of variation of less than 8%. Plasma concentrations as low as 10 microM l-1 in a 200-microliters aliquot could be measured. Methyl migration was an interesting feature of the mass spectrometric fragmentation pattern of the alpha-keto acids. The mechanism of methyl migration is proposed and discussed. This paper also describes some of the studies involved in the formation of isomeric O- and N-alkyl, -quinoxaline and -quinoxalone using a number of N,N-dimethyl formamide dialkyl acetals.

Alkylation↗
PubMed1985

Cytochemistry for bromodeoxyuridine/DNA analysis: stoichiometry and sensitivity.

This report describes an improved immunochemical procedure for staining cells in suspension for amount of incorporated bromodeoxyuridine (BrdUrd) and total DNA. In this procedure, cellular DNA is partially denatured by extracting the cells with 0.1 M HCl and then heating them to 80 degrees C in a 50% formamide solution. The cells are then immunofluorescently stained using a monoclonal antibody against BrdUrd in single-strand DNA (ssDNA) and counterstained for DNA content with propidium iodide (PI), a dye that fluoresces preferentially when bound to double-strand DNA (dsDNA). We show that the relative amounts of immunofluorescently stained BrdUrd in ssDNA and PI in dsDNA can be altered reciprocally by changing the formamide concentration, denaturation time, and denaturation temperature. We show that this new immunochemical staining procedure allows more complete DNA denaturation so that fivefold lower levels of BrdUrd incorporation can be quantified. In addition, we show that the BrdUrd-linked immunofluorescence achieved using the new denaturation procedure is more linearly related to cellular BrdUrd content than that achieved after acid DNA denaturation. However, cell loss is sufficiently severe with the thermal denaturation procedure that it may not be applicable to all cell types.

Animals↗
PubMed2002

Intruder state avoidance multireference Møller-Plesset perturbation theory.

A new perturbation approach is proposed that enhances the low-order, perturbative convergence by modifying the zeroth-order Hamiltonian in a manner that enlarges any small-energy denominators that may otherwise appear in the perturbative expansion. This intruder state avoidance (ISA) method can be used in conjunction with any perturbative approach, but is most applicable to cases where small energy denominators arise from orthogonal-space states-so-called intruder states-that should, under normal circumstances, make a negligible contribution to the target state of interests. This ISA method is used with multireference Møller-Plesset (MRMP) perturbation theory on potential energy curves that are otherwise plagued by singularities when treated with (conventional) MRMP; calculation are performed on the 1(3)Sigma(-)(u) state of O(2); and the 2(1)Delta, 3(1)Delta, 2(3)Delta, and 3(3)Delta states of AgH. This approach is also applied to other calculations where MRMP is influenced by intruder states; calculations are performed on the (3)Pi(u) state of N(2), the (3)Pi state of CO, and the 2(1)A' state of formamide. A number of calculations are also performed to illustrate that this approach has little or no effect on MRMP when intruder states are not present in perturbative calculations; vertical excitation energies are computed for the low-lying states of N(2), C(2), CO, formamide, and benzene; the adiabatic (1)A(1)-(3)B(1) energy separation in CH(2), and the spectroscopic parameters of O(2) are also calculated. Vertical excitation energies are also performed on the Q and B bands states of free-base, chlorin, and zinc-chlorin porphyrin, where somewhat larger couplings exists, and-as anticipated-a larger deviation is found between MRMP and ISA-MRMP.

Journal Article↗
PubMed1993

Rapid colorimetric detection of epidermal growth factor receptor mRNA by in situ hybridization.

We describe a rapid, formamide-free, random oligomer-enhanced in situ hybridization method in formalin-fixed, paraffin-embedded tissue sections using a biotinylated oligonucleotide probe for colorimetric detection of the mRNA transcript of the epidermal growth factor receptor (EGFR) gene, a putative protooncogene. Transitional cell carcinomas (TCC) of the urinary bladder and oral squamous cell carcinomas (SCC) were examined. A431, a human squamous carcinoma cell line that overexpresses EGFR mRNA, and mature skeletal muscle, known to express EGFR, served as control tissues. A biotinylated poly-T oligonucleotide probe was used to evaluate the preservation of mRNA in the formalin-fixed, paraffin-embedded tissues. The EGFR mRNA and poly-T oligonucleotide probes were constructed with a target-specific, 5' region and a 3' non-hybridizing, biotinylated tail. Random sequence oligomers nine bases long added to the probe cocktail eliminated the need for formamide and sheared carrier DNA in the method. The assay produced strong, specific staining for EGFR mRNA in all cases of TCC and SCC, and in the A431 tumors, but not in skeletal muscle. The assay was completed in approximately 90 minutes. This method may have widespread utility for rapid and specific detection of other mRNA sequences.

Base Sequence↗
PubMed2000

DNA binding properties of novel distamycin analogs that lack the leading amide unit at the N-terminus.

First examples of distamycin (Dst) analogs which lack hydrogen bond donor or acceptor groups at the N-terminus have been synthesized. The first molecule of this series, which is a bispyrrole peptide, did not exhibit any detectable binding with double-stranded (ds) DNA. However, all other analogs did bind strongly to AT-rich sequences of ds-DNA, with the binding affinities increasing as a function of the number of repeating pyrrole carboxamide units. These results imply that a hydrogen bond donor or acceptor atom per se at the N-terminus is not a prerequisite for DNA binding in the case of pyrrole carboxamide-based Dst analogs. However, in the absence of H-bond donor or acceptor at the N-terminus, a minimum of three pyrrole carboxamide units is necessary for the onset of DNA binding. Beyond this minimum number, the binding affinity increases as a function of the number of pyrrole units, as a result of the greater availability of hydrogen bonding and van der Waals surface. Experiments with poly[d(G-C)] have shown that the presence of the N-terminus formamide group is not inevitable for GC binding of this class of molecules. The observation that the N-terminus formamide unit can be dispensed with suggests that these molecules, which are much easier to synthesize and functionalize, can be used in place of the conventional analogs of distamycin for the development of novel minor groove binders with extended sequence recognition properties.

Binding Sites↗
PubMed1997

Stability of Nonaqueous Emulsions

We examined the stability of emulsions of oil in several nonaqueous polar liquids using commercially available nonionic surfactants. Stable nonaqueous emulsions were only obtained with formamide and dimethylsulfoxide. Hydrogen bonding, and not polarity, appears to be the important factor determining the emulsifying power of a solvent. Ostwald ripening plays a much more important role in the stability of these nonaqueous emulsions than in the corresponding aqueous systems. This destabilizing process can be prevented, however, by addition to the oil phase of a small amount (1%) of an oil that has a very low solubility in the continuous phase. Furthermore, a larger size of the surfactant molecule protects emulsions against droplet coalescence. Thus, emulsions in formamide and dimethylsulfoxide did not show any breakdown when stabilized with a triblock copolymer of polyoxyethylene-polyoxypropylene-polyoxyethylene. Copyright 1997Academic Press

Journal Article↗
PubMed1981

Chain length heterogeneity of nucleosomal DNA in mouse liver after dimethylnitrosamine administration.

The effect of dimethylnitrosamine on the nucleosomal structure of mouse liver chromatin was studied. After a single oral dose of dimethylnitrosamine (2-75 mg/kg body weight 45 min before sacrifice) liver nuclei were isolated and incubated with micrococcus nuclease. Nucleosomes were separated on sucrose density gradients. There were no differences in nucleosomal sedimentation velocities between preparations from control and dimethylnitrosamine treated animals. The supernatant obtained after centrifugation of the lysed nuclei (2 min at 4,000 gav) and nucleosomal peak fractions were used for isolation of DNA. DNA was heat denatured in 7 M urea or formamide. After electrophoresis on polyacrylamide gels areas under mononucleosomal DNA and smaller fragments were measured and compared with the total DNA area. The increase in DNA fragmentation was dimethylnitrosamine dose response dependent. When expressed as per cent of controls it amounted to 106% for 2 mg; 115% for 10 mg; 127% for 25 mg; 164% for 75 mg dimethylnitrosamine/kg body weight. A good correlation between mobility and log of chain length of phi chi 174 RF DNA-Hae III digest was obtained in nondenaturing 5% polyacrylamide gels and denaturing non-aqueous formamide polyacrylamide gels but not in 12% polyacrylamide gels containing 7 M urea. DNA of mononucleosomal peak fractions contained 200 and that of dinucleosomal peak fractions 400 nucleotides. Fragmentation of DNA was closely related to in vivo dimethylnitrosamine treatment but was not detected in measurements of protein-DNA complexes in the chromatin. It was disclosed on denaturation of DNA followed by polyacrylamide gel electrophoresis.

Animals↗