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PubMed1995

A method for the purification of oligonucleotides containing strong intra- or intermolecular interactions by reversed-phase high-performance liquid chromatography.

Synthetic oligodeoxyribonucleotides containing a high guanine content have a tendency to form intra- or intermolecular complexes in solution make HPLC purification difficult or sometimes impossible. We have developed a simple method that has enabled us to purify a series of highly guanine-rich and self-complementary oligonucleotides by HPLC on a reverse-phase PRP-1 column. Although others have shown that this type of oligonucleotide can be purified on an ion-exchange column by adding formamide to the mobile phase, the resulting resolution is poor and the formamide must subsequently be removed from the purified product. We find that simply having 20% formamide in the loading buffer is sufficient to remove the interfering interactions. This small amount of formamide passes quickly through the reverse-phase column, far removed the peak position of the oligonucleotides. Quantities of up to 35 ODs have been satisfactorily purified with recoveries of 95% or better. This procedure was particularly suitable for purification of oligonucleotides containing base-labile modifications, such as acetylaminofluorene-modified oligonucleotides,since other denaturing HPLC purification methods usually employ strong alkaline conditions or high temperatures that might result in damage to the adduct.

Base Sequence↗
PubMed1989

DNA denaturation for ultrastructural banding and the mechanism underlying the fluorochrome-photolysis-Giemsa technique studied with anti-5-bromodeoxyuridine antibodies.

G- and R-bands produced by an immunochemical approach were studied by electron microscopy (EM) to evaluate the role of DNA denaturation on banding quality. Excellent banding was observed only after adequate denaturation by HCl, NaOH and formamide, used in appropriate concentrations to provide uniform 5-bromodeoxyuridine (BrdUrd) exposure by generating single-stranded DNA. Formamide treatment resulted in less intercellular variability. High temperature and high concentrations of NaOH and HCl altered chromosomal morphology. Besides formamide, Hoechst 33258 prestaining which does not interfere with the binding of the anti-BrdUrd antibody and UV irradiation associated with formamide also produced high quality banding. On the other hand, consecutive Hoechst and UV treatment completely inhibited the immunochemical banding. The data indicate that Hoechst and UV act synergistically to disintegrate BrdUrd-substituted chromatin from which DNA is then extracted, leaving only the unsubstituted DNA stainable with Giemsa.

Animals↗
PubMed1995

Application of in situ hybridization with a novel phenytoin-labeled probe to conventional formalin-fixed, paraffin-embedded tissue sections.

Non-isotopic in situ hybridization with a novel phenytoin (PHE)-labeled probe was developed. The mixture of cloned cytomegalovirus (CMV) DNA fragments was labeled by random primer technique using PHE-11(spacer)-dUTP, instead of dTTP. The tissue sections were treated with 0.2 N HCl and with proteinase K (1 microgram/ml), and then heated at 70 degrees C in the presence of 50 or 75% formamide. The sections were hybridized with PHE-labeled probe at 37 degrees C overnight. The hybridization signal was visualized by alkaline phosphatase-5-bromo-4-chloro-3-indolyl phosphate (BCIP)/4-nitroblue tetazolium (NBT) system. Strong hybridization signals were detected in sections of the small intestine and the placenta, even when denatured in the presence of 50% formamide. In the case of small intestine, CMV DNA was also detected in the endothelial cells of the mucosa where apparent infected cell was not observed histologically. In the sections of the submaxillary gland, the lung, the adrenal gland and the ovary, hybridization signal was not detected when denatured in the presence of 50% formamide, but detected after denaturation with 75% formamide. Thus, in situ hybridization with the novel PHE-labeled probe is applicable to conventional formalin-fixed, paraffin-embedded tissue sections.

Adrenal Glands↗
PubMed1992

Adaptation of a radioactive L. donovani complex DNA probe to a chemiluminescent detection system gives enhanced sensitivity for diagnostic and epidemiological applications.

The cDNA probe, Lmet2, was labelled with digoxigenin and used in a chemiluminescent system to detect fewer than 100 membrane-immobilized Leishmania parasites. The probe was found to hybridize primarily with members of the L. donovani complex but a slight cross-reaction was also observed with greater than 5 x 10(4) L. major. This cross-reaction was reduced by hybridizations in 50% formamide at 37 degrees C. Formamide also significantly reduced non-specific binding of the digoxigenin-labelled probe to the membrane support which, in hybridizations without formamide, masked the specific hybridization signal. This background was not observed with the corresponding radio-isotope labelled probe. With hybridizations in formamide the sensitivity achieved by the chemiluminescent system after exposure to film for 3 h was greater than that achieved by the isotopic system even after autoradiography for 24 h.

Animals↗
PubMed1998

Solvent effects on horse apomyoglobin dynamics.

The effects of the solvent conditions (buffer pH 9, 8, or 7 or buffer pH 6.5 alone or mixed with 3.2% ethanol or 6.2% formamide) on the protein dynamics of horse apomyoglobin were investigated through tryptophan fluorescence quenching, spectra, and decay properties. Raising the pH (which induces discontinuous protein conformation changes) increases the structural fluctuations inside the hydrophobic A, G, and H helix core. Mixed solutions containing either 3.2% ethanol or 6.2% formamide (which redistribute water molecules on the protein surface) produce protein dynamics changes in the vicinity of the two Trp residues, without inducing particular constraints on these very residues. Formamide increases, in the same way, the polarity and the protein flexibility while ethanol reduces both. The present fluorescence work also shows that, whatever the outside solvent, the two Trp residues W7 and W14, embedded in the A, G, and H helix core, are equally and statistically reached by small molecules diffusing inside the protein matrix. Hydrogen-tritium exchange measurements on the protein in mixed solvents reveal that the dynamics of the A, G, and H helix cluster and of the B and E helixes are greatly influenced by the nature of the outside medium. A small amount of formamide in the buffer increases the protein fluctuations while an ethanol-water mixture reduces them. We suggest that the hydratation state of the protein surface could be the relevant parameter of the protein dynamics.

Animals↗
PubMed1989

Fusion of phospholipid vesicles with a planar membrane depends on the membrane permeability of the solute used to create the osmotic pressure.

Phospholipid vesicles fuse with a planar membrane when they are osmotically swollen. Channels in the vesicle membrane are required for swelling to occur when the vesicle-containing compartment is made hyperosmotic by adding a solute (termed an osmoticant). We have studied fusion using two different channels, porin, a highly permeable channel, and nystatin, a much less permeable channel. We report that an osmoticant's ability to support fusion (defined as the magnitude of osmotic gradient necessary to obtain sustained fusion) depends on both its permeability through lipid bilayer as well as its permeability through the channel by which it enters the vesicle interior. With porin as the channel, formamide requires an osmotic gradient about ten times that required with urea, which is approximately 1/40th as permeant as formamide through bare lipid membrane. When nystatin is the channel, however, fusion rates sustained by osmotic gradients of formamide are within a factor of two of those obtained with urea. Vesicles containing a porin-impermeant solute can be induced to swell and fuse with a planar membrane when the impermeant bathing the vesicles is replaced by an isosmotic quantity of a porin-permeant solute. With this method of swelling, formamide is as effective as urea in obtaining fusion. In addition, we report that binding of vesicles to the planar membrane does not make the contact region more permeable to the osmoticant than is bare lipid bilayer. In the companion paper, we quantitatively account for the observation that the ability of a solute to promote fusion depends on its permeability properties and the method of swelling. We show that the intravesicular pressure developed drives fusion.

Bacterial Outer Membrane Proteins↗
PubMed1992

Deriving a 67-nucleotide trans-cleaving ribozyme from the hepatitis delta virus antigenomic RNA.

RNAs derived from the genomic and antigenomic hepatitis delta virus are capable of self-cleavage, and thus have the potential for serving as ribozymes in a trans-cleaving reaction. Because the catalytic core of such an enzymatic RNA was not evident from phylogenetic data, we took a step-wise approach to identifying the core, reducing the RNA in size, and characterizing various properties for each size class. Thus, a 186-nucleotide antigenomic RNA (termed Ag180) was found to be capable of cleaving well in 20 M formamide (Smith and Dinter-Gottlieb, 1991), and this unusual stability in formamide was lost by reducing the 3' end of the molecule, leaving a 140-nucleotide RNA (Ag 140). Both RNAs showed only intramolecular cleavage at a wide range of concentrations, and a number of conformers could be seen in the Ag140 RNA, some of which were resistant to cleavage at 37 degrees C. Since Ag140 could not cleave in 20 M formamide, the 5' and 3' termini of Ag180 were truncated and produced Ag5-84, which cleaved to 100% at 37 degrees C in less than 0.25 min. Internal deletions of the Stem IV region resulted in Ag5-73, still capable of efficient cleavage, although with a lessened stability in formamide. A trans-cleaving enzyme-substrate pair was finally derived from this RNA, and it consisted of a 67-nucleotide enzyme that cleaved a 13-nucleotide RNA substrate.

Base Sequence↗
PubMed1978

Antigens of Streptococcus mutans: isolation of a serotype-specific and a cross-reactive antigen from walls of strain V-100 (serotype e).

Two cell wall-associated polysaccharide antigens were extracted from purified cell walls of Streptococcus mutans serotype e strain V-100. One of these purified antigens (I) is specific for serotype e, whereas the other (II) has antigenic determinants reactive with both heterologous anti-serotype c serum (GS-5) and the homologous (e) serum. When crude formamide extracts of V-100 cell walls were loaded onto a Cellex-D column and eluted with a linear gradient of ammonium carbonate (0.02 to 0.40 M), the two products mentioned above could be recovered. The purified, antigenically reactive products (I and II) were each composed only of rhamnose and glucose in approximately a 2:1 molar ratio. Immunoelectrophoresis of the crude formamide extract, peak I, and peak II showed the purified fractions to have opposite mobilities and the crude extract to have a mobility that encompassed both purified peaks when reacted with homologous antiserum (V-100). When these three fractions were immunoelectrophoresed and reacted with heterologous anti-serotype c serum (GS-5), only the anodic portion of the crude V-100 formamide extract and purified peak II formed precipitates. Ouchterlony analysis with homologous antiserum produced precipitin patterns between the crude formamide extract and both purified peaks, indicating complete identity. However, only crude extracts of V-100 and the purified peak II material reacted with heterologous (c) antiserum; peak I did not cross-react in these Ouchterlony assays. Hapten inhibition studies revealed that a beta-glucosyl moiety is the immunodeterminant for serotype e and is present on each purified fraction. The basis of the cross-reaction between anti-c sera and the purified antigen II of e is discussed.

Cell Wall↗
PubMed2000

From fertilization to cancer: the role of centrosomes in the union and separation of genomic material.

Centrosomes play crucial roles in the union of sperm and egg nuclei during fertilization and in the equal separation of genomic material during cell division. While many studies in recent years have focused on the molecular composition of centrosomes, this article focuses on the structural behavior of centrosomes and on factors that play a role in centrosome functions under normal, artificially altered, and abnormal conditions. We review here how studies in the classic sea urchin egg model have contributed to our knowledge on the centrosome cycle within the cell cycle, on compaction and decompaction of centrosomal material, and on the contributions of maternal and paternal centrosomes during fertilization. Centrosome material is activated in unfertilized eggs by increasing pH with ammonium and by increasing calcium with the ionophore A23187, which are conditions that are normally induced by sperm. D(2)O and taxol also induce centrosome aggregation in the unfertilized egg. Maternal and paternal centrosome material both contribute to the formation of a functional centrosome but the formation of a bipolar centrosome requires material from the paternal centrosome. Fertilization of taxol-treated eggs reveals that the male centrosome possesses the capability to attract maternal centrosome material. When pronuclear fusion of the male and female pronuclei is inhibited with agents such as the disulfide reducing agent dithiothreitol (DTT) a bipolar mitotic apparatus is formed from the paternal centrosome. Furthermore, one centrosome of the bipolar mitotic apparatus is capable of organizing an additional half spindle that attaches to the female pronucleus indicating a functional and perhaps structural connection between centrosomes and chromatin. Sea urchin eggs are also useful to study centrosome abnormalities and consequences for the cell cycle. While classic studies by Theodor Boveri have shown that dispermic fertilization will result in abnormal cell division because of multiple centrosomes contributed by sperm, abnormal cell division can also be induced by chemical alterations of centrosomes. Compaction and decompaction of centrosome structure is studied using chloral hydrate or the chaotropic agent formamide, which reveals that centrosomes can be chemically altered to produce mono- or multipolar abnormal mitosis and unequal distribution of genomic material upon release from formamide. The patterns of abnormal centrosome reformations after recovery from formamide treatment resemble those seen in cancer cells which argues that structural defects of centrosomes can account for the formation of abnormal mitosis and multipolar cells frequently observed in cancer. In summary, the sea urchin model has been most useful to gain information on the role of centrosomes during fertilization and cell division as well as on adverse conditions that play a role in centrosome dysfunctions and in disease.

Animals↗
PubMed2002

Elimination of polymer interference in chromatographic analysis of estradiol degradation products in a transdermal drug delivery formulation by proper selection of extraction solvents.

This article describes the proper selection of extraction solvents to eliminate interference from a polymer matrix to the quantitation of estradiol degradation products in a transdermal formulation by reversed-phase liquid chromatography. The separation is performed by gradient elution with acetonitrile and water as the mobile phase on Inertsil ODS columns. Severe band distortion and insufficient recovery are observed for two geometric degradation products (or impurities) when the sample is prepared by acetonitrile. It is anticipated that the poor resolution and recovery are caused by multiple retention processes due to the reversible binding of degradation products to the polymer matrix (or the impurity-polymer interaction). This interaction is eliminated by adding formamide, a solvent that possesses similar properties to the matrix, in the extraction solvent. It is believed that the favorable interaction between formamide and the polymer matrix releases the impurity molecules, and they can then be separated by a single retention mode. It has been confirmed experimentally that the use of formamide in the extraction solvent not only sharpens the peaks tremendously, but also recovers the degradation products completely.

Administration, Cutaneous↗
PubMed1995

Biological monitoring of workers exposed to N, N-dimethylfomamide. I. Methods of analysis.

Some methods for analysing N,N-dimethylformamide and its metabolites [hydroxymethyl-N-methylformamide, hydroxymethylformamide and N-acetyl-S-(N-methylcarbamoyl)cysteine] in the urine of exposed workers are described. Unchanged dimethylformamide was measured after pretreatment of urine (2 ml) with silica gel cartridges and elution with methanol. The gas chromatographic analysis using a nitrogen phosphor detector made it possible to detect N,N-dimethylformamide in urine even when workers were exposed to low concentrations of the solvent (about 1 mg/m3). N-Hydroxymethyl-N-methylformamide and N-hydroxymethylformamide were analysed as N-methylformamide and formamide respectively after direct injection of urine into the gas chromatograph. The injection port temperature played an important role in the gas chromatographic determination of these products. Reliable results were obtained when direct or split injections were performed at 250 degrees C. The splitless injection gave the same reliable results at 150 degrees C. In urine samples from occupationally non-exposed persons, N-methylformamide could not be detected. In contrast, formamide (or its precursor, hydroxymethylformamide) was present in every urine sample. Our results in respect of 19 urine samples analysed with the injection port of the gas chromatograph at 250 degrees C gave a mean of 8.6 mg/l of formamide. N-Acetyl-S-(N-methylcarbamoyl)cysteine was determined using a modified method for analysing organic acid in urine samples. The metabolite was extracted with ethyl ether in an acid environment, treated with a silylating reagent and measured by gas chromatography/mass spectrometry.

Acetylcysteine↗
PubMed1988

Formate ester formation in amide solutions.

Simple aliphatic alcohols, deoxynucleosides and nucleosides undergo reaction with formamide yielding formate esters. Formate ester formation was observed to occur slowly at 100 degrees C and more rapidly at 130 degrees C. As expected, formate esters were hydrolyzed to the alcohol and formic acid upon heating in aqueous solution. It was proposed to study the possibility that formate esters are formed initially in amide solvents, followed by displacement of formate by dihydrogen phosphate ion to form monophosphate esters. Experiments are described which demonstrate the formation and hydrolysis of formate esters, as well as their lack of reaction with hydrogen phosphate ion. Formate esters are not intermediates in the phosphorylation of nucleosides in formamide. Their formation has been observed and such an esterification is a side reaction during the phosphorylation of nucleosides in formamide.

Adenosine↗
PubMed2006

Cryogenic synthesis of molecules of astrobiological interest: catalytic role of cosmic dust analogues.

We have studied the effects of the substrate, namely amorphous olivine (MgFeSiO(4)) cosmic dust analogues (CDAs), in synthesis of molecules obtained after 200 keV proton irradiation of formamide (NH(2)COH). Formamide has been deposited on the olivine substrate at 20 K. The abundances of new molecular species formed after an irradiation dose of 12 eV/16 amu in formamide pure (i.e. deposited on an inert silicon substrate) and deposited on CDAs have been compared. Specifically, MgFeSiO(4) amorphous olivine is a selective catalyst preventing formation of NH(3) and CN(-) molecules and changing the relative abundances of NH4(+)OCN(-), CO(2), HNCO, CO. We have shown that the role of CDAs has to be taken into account in experiments simulating processes occurring in astronomical environments.

Ammonia↗
PubMed1987

Selective modification of sodium channel gating by solvents and drugs.

In Myxicola heavy water (D2O) does not alter Na+ gating currents, but slows activation and inactivation. In this study, the solvent formamide (5-20% v/v) is shown to proportionately and reversibly block Na+ currents and charge movement, suggesting it may be useful for fractionating gating currents. Formamide- and prepulse-sensitive (inactivating) gating currents were identical, comprising 60-80% of total charge. Both had rising phases and decayed as single exponential functions. Formamide-insensitive and non-inactivating charge movements had no rising phases and decayed slowly with more complex kinetics. Another solvent, dimethylsulfoxide (1% v/v), had no effect on Na+ activation or charge movement, though it did affect inactivation. Amantadine (0.1 mM) did not change Na+ activation or charge movement, but slowed inactivation and shifted the foot of the steady state Na+ inactivation curve. Sotalol (0.1 mM) slowed inactivation, but also inhibited Na+ activation and gating current.

Amantadine↗
PubMed1996

Pseudo-coulometric loading in capillary electrophoresis DNA sequencing.

While injection volumes in capillary electrophoresis are typically in the nanoliter range, it is difficult to physically prepare and manipulate samples much smaller than a microliter. As a result, only a small fraction of the analyte contained with the sample volume is transferred to the capillary. This problem is particularly acute in DNA sequencing applications, where on-column stacking is difficult and where the sequencing sample is relatively expensive to prepare. We report a method that transfers 75% of the DNA contained within a 3 microliters sample onto a capillary for DNA sequencing. This method relies on the use of very low ionic strength formamide to resuspend the DNA after an ethanol precipitation. The use of low ionic strength formamide achieves two tasks. First, it produces a very high resistance sample, which increases the voltage drop across the sample and decreases the field across the capillary. This electric field manipulation ensures that DNA fragments do not migrate down the capillary during the loading process, allowing long injection periods without excessive band-broadening. Second, the low ionic strength of the formamide increases the transference number of the DNA; more of the current passing through the injection tip of the capillary is carried by DNA fragments. In the limit of complete elimination of impurity ions from the loading solvent, current passing through the sample is carried only by DNA fragments and loading becomes a coulometric process.

DNA, Single-Stranded↗
PubMed1995

Measurement of vascular permeability in spinal cord using Evans Blue spectrophotometry and correction for turbidity.

Vascular permeability can be visualized by Evans Blue (EB) extravasation and quantified by spectrophotometry after formamide extraction of the tissue. However, formamide extracts show significant turbidity, which may contribute to the total optical density at the wavelength of measurement (e.g., 620 lambda). We developed a simple method for estimating the component of the total optical density of a dyed specimen contributed by turbidity. Our method, which uses a determination of turbidity made at another point of the light spectrum (740 lambda), was more precise than two other EB quantification techniques. We therefore recommend it for individual correction of formamide extracts of spinal cord specimens. The application of this technique to the brain remains to be determined.

Animals↗
PubMed2003

Biosynthesis of pteridines. Reaction mechanism of GTP cyclohydrolase I.

GTP cyclohydrolase I catalyses the hydrolytic release of formate from GTP followed by cyclization to dihydroneopterin triphosphate. The enzymes from bacteria and animals are homodecamers containing one zinc ion per subunit. Replacement of Cys110, Cys181, His112 or His113 of the enzyme from Escherichia coli by serine affords catalytically inactive mutant proteins with reduced capacity to bind zinc. These mutant proteins are unable to convert GTP or the committed reaction intermediate, 2-amino-5-formylamino-6-(beta-ribosylamino)-4(3H)-pyrimidinone 5'-triphosphate, to dihydroneopterin triphosphate. The crystal structures of GTP complexes of the His113Ser, His112Ser and Cys181Ser mutant proteins determined at resolutions of 2.5A, 2.8A and 3.2A, respectively, revealed the conformation of substrate GTP in the active site cavity. The carboxylic group of the highly conserved residue Glu152 anchors the substrate GTP, by hydrogen bonding to N-3 and to the position 2 amino group. Several basic amino acid residues interact with the triphosphate moiety of the substrate. The structure of the His112Ser mutant in complex with an undefined mixture of nucleotides determined at a resolution of 2.1A afforded additional details of the peptide folding. Comparison between the wild-type and mutant enzyme structures indicates that the catalytically active zinc ion is directly coordinated to Cys110, Cys181 and His113. Moreover, the zinc ion is complexed to a water molecule, which is in close hydrogen bond contact to His112. In close analogy to zinc proteases, the zinc-coordinated water molecule is suggested to attack C-8 of the substrate affording a zinc-bound 8R hydrate of GTP. Opening of the hydrated imidazole ring affords a formamide derivative, which remains coordinated to zinc. The subsequent hydrolysis of the formamide motif has an absolute requirement for zinc ion catalysis. The hydrolysis of the formamide bond shows close mechanistic similarity with peptide hydrolysis by zinc proteases.

Amino Acid Sequence↗
PubMed2003

Redefining the structure-activity relationships of 2,6-methano-3-benzazocines. Part 2: 8-formamidocyclazocine analogues.

High affinity binding for mu and kappa opioid receptors has been observed in analogues of cyclazocine, ethylketocyclazocine and naltrexone where the prototypic (of opiates) phenolic OH group was replaced with a formamide (-NHCHO) group. For the 8-formamide analogue of cyclazocine, binding is highly enantiospecific (eudismic ratios approximately 2000 for mu and kappa) with K(i) values </=1 nM observed for the (2R,6R,11R)-isomer, (-)-4. A preliminary SAR revealed that affinity is very sensitive to substitution on the formamide appendage.

Analgesics, Non-Narcotic↗