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PubMed1991

Small iminium ions block gramicidin channels in lipid bilayers.

Guanidinium and acetamidinium, when added to the bathing solution in concentrations of approximately 0.1M, cause brief blocks in the single channel potassium currents from channels formed in planar lipid bilayers by gramicidin A. Single channel lifetimes are not affected indicating that the channel structure is not modified by the blockers. Guanidinium block durations and interblock times are approximately exponential in distribution. Block frequencies increase with guanidinium concentration whereas block durations are unaffected. Increases in membrane potential cause an increase in block frequency as expected for a positively charged blocker but a decrease in block duration suggesting that the block is relieved when the blocker passes through the channel. At low pH, urea, formamide, and acetamide cause similar blocks suggesting that the protonated species of these molecules also block. Arginine and several amines do not block. This indicates that only iminium ions which are small enough to enter the channel can cause blocks in gramicidin channels.

Amidines↗

PubMed1995

Aggregation of chlorophyll a probed by resonance light scattering spectroscopy.

We report the resonance light scattering (RLS) spectra of chlorophyll a aggregated in a 9:1 solution of formamide and pH 6.8 phosphate buffer. The aggregate formed after 2 h of mixing, referred to as Chl469, shows a strong scattering feature at 469 nm (Soret band) and a much weaker feature at 699 nm (Qy band). A kinetic investigation confirmed that the aggregation process is cooperative, and also detected one intermediate (Chl458) with a strong RLS spectrum but only a weak CD spectrum. We propose that aggregation proceeds via at least three steps: 1) formation of a nucleating species, probably a dimer of chlorophylls; 2) formation of large aggregates with little or no secondary structure (e.g., Chl458); and 3) conformational change to form helical aggregate (Chl469).

Biophysical Phenomena↗

PubMed2002

Validity of PCR with emphasis on variable number of tandem repeat analysis.

OBJECTIVES: Variable number of tandem repeat polymorphisms (VNTR) are frequently analyzed by PCR in genetic, epidemiologic and forensic studies. We wanted to explore the validity of these PCR analyses. DESIGN AND METHODS: The amplification of the different alleles of the 17- and the 44-bp VNTR of the serotonin transporter gene and the 39-bp VNTR of the glycoprotein Ibalpha gene was analyzed. We studied the effects of the parameters magnesium, dimethylsulfoxide, 7-deaza-dGTP, formamide, betaine, PCR temperatures and different types of polymerases. RESULTS: In all three VNTR polymorphisms selective amplification of one of the alleles of heterozygous individuals could be obtained by change of the magnesium concentration. This problem could be minimized by a combination of Taq- and Pwo-polymerases and by use of 7-deaza-dGTP. CONCLUSION: PCR analysis of all of these VNTRs may give reproducibly wrong results in truly heterozygous subjects due to selective amplification of only one of the alleles.

Betaine↗

PubMed2003

Thermal expansion measurements of cryoprotective agents. Part II: measurements of DP6 and VS55, and comparison with DMSO.

As part of an ongoing effort to characterize the mechanical behavior of biological tissues in the cryogenic temperature range, the current study focuses on thermal expansion measurements of cryoprotective agents. Utilizing the experimental apparatus described in the previous report (Part I), the current report (Part II) includes thermal expansion measurements of the cryoprotectant mixtures DP6 and VS55, and comparison with available data from the literature on DMSO. In the temperature range in which the cryoprotectant mixture behaves like low viscosity liquid, results of this study show that the thermal expansion coefficient of VS55 and DP6 is 22% and 40% lower than that of 3M DMSO, respectively, where 3M DMSO is only one component of each cryoprotectant mixture. This significant difference is attributed to the presence of 3M formamide in VS55.

Cryoprotective Agents↗

PubMed1992

Non-planar structure of nitrous bases and non-coplanarity of Watson-Crick pairs.

We discuss the non-planar structural stability of the NH2-group in formamide, cytosine, adenine, guanine and aniline molecules. Based on the microwave data available on small amino derivatives and on the results of PCILO conformation study it is shown that the slope of the amino group HNH plane to the molecular plane in nitrous bases should be close to 40 degrees. One of the main consequences of the non-planar structure of bases is a comparatively large (approximately equal to 15 degrees) propeller twisting of purine and pyrimidine planes in the complementary adenine-thymine and guanine-cytosine pairs. It is concluded that the non-coplanarity of single Watson-Crick base pairs is their intrinsic property. The specificity of hydrogen bonding in pairs along with stacking is believed to be the original cause of their peculiar packing in crystals and in DNA and RNA structures.

Adenine↗

PubMed1984

The N-lines of skeletal muscle.

The N-lines of skeletal muscle, although known for a century, have remained elusive and neglected structures. Their fortuitous appearance in diverse experiments on beef sternomandibularis muscle, involving stretch, heat denaturation, and myosin extraction, have been collected and related to the literature. Treatments with pyroantimonate and formamide solutions have proved a more reliable way of visualizing N-lines. It is concluded that there are at least seven N-lines: an N1-line always near the Z-line, four N2-lines in the mid-I-band, and two N3-lines at the extremity of the I-filaments or in the "gap." There is evidence for suspension of both N2- and N3-lines on G-filaments.

Actins↗

PubMed2003

The effect of the cyclopropyl group on the conformation of chemotactic formyl tripeptides.

Certain formyl peptides are powerful chemoattractants towards neutrophils. In this study, several formyl tripeptides were synthesized and used to investigate the effects of different amino acid residues in position 1 on their ability to stimulate neutrophil chemotaxis. Pig neutrophil chemotaxis towards the formyl tripeptide, HCO-Ac(3)C-Leu-Phe-OMe 1, where Ac(3)C represents 1-amino-1-cyclopropane carboxylic acid, was observed. Pig neutrophil chemotaxis towards a very similar formyl tripeptide, HCO-Aib-Leu-Phe-OMe 2, where Aib represents alpha-amino isobutyric acid, was not observed. Compared to the isopropyl group, it was shown that the cyclopropyl group induces a greater percentage of the E conformation about the formamide functionality in these peptides. For 1 and 2, the E isomer distributions in CDCl3 are 36 and 9%, respectively. Since a major difference between these two peptides is the Z/E isomeric distribution, one implication is that the peptide-receptor site interactions involving the E conformer are more effective than those of the Z conformer. No pig neutrophil chemotaxis towards the formyl tripeptides, HCO-Ala-Leu-Phe-OMe 3 and HCO-Gly-Leu-Phe-OMe 4 was observed. These formyl tripeptides exhibit a low percentage of the E isomer, similar to that of peptide 2.

Animals↗

PubMed2004

A protocol for determining the surface free energy of dental materials.

OBJECTIVE: The purpose of this study was to develop a standard methodology for measuring the surface free energy (SFE), and its component parts, of dental biomaterials. METHODS: The contact angle of each of four samples of two materials--low density polyethylene and poly(methyl methacrylate)--was measured three times in each of six liquids (1-bromonaphthalene, diiodomethane, ethylene glycol, formamide, glycerol and distilled water). Critical surface tension estimates were obtained from Zisman plots. Data were then analyzed by the least-squares method to estimate the components of SFE. Estimates were also made for each of 12 liquid triplets, and by maximum likelihood and Bayesian analyses. RESULTS: The use of liquid triplets could yield misleading estimates of the components of SFE. A testing protocol is suggested in which multiple test liquids are used, and multiple methods of statistical analyses employed. SIGNIFICANCE: SFE is important, in that high SFE is desirable when adhesion is required, but undesirable if plaque resistance is needed. Methodology that avoids some of the limitations of existing studies has been proposed.

Bayes Theorem↗

PubMed1999

Non-aqueous capillary electrophoresis of drugs: properties and application of selected solvents.

The electrophoretic mobility of selected acidic and basic test solutes have been determined in non-aqueous media prepared by adding various combinations of ammonium acetate, sodium acetate, methane sulphonic acid and acetic acid to acetonitrile, propylene carbonate, methanol, formamide, N-methylformamide, N,N-dimethylformamide and dimethylsulphoxide, respectively. The apparent pH (pH*) of these non-aqueous media have been measured and it was found that pH* is an important factor for the separations in non-aqueous capillary electrophoresis. However, in some solvents the concentration of sodium acetate has a strong influence on the mobility despite very small changes in pH*. Due to the fact that a change in one parameter influences a number of other parameters it is very difficult to conduct systematic studies in non-aqueous media and to compare the migration of the species at fixed pH* values from one solvent to another. Thus pH* is only of value for comparison when used with a specific solvent or solvent mixture. The viscosity of the above-mentioned solvents were measured at various temperatures and means to adjust the viscosity of the non-aqueous media used for capillary electrophoresis are discussed and the separation of ibuprofen and its major metabolites in urine is used as an example.

4-Aminobenzoic Acid↗

PubMed2001

The effect of acquired salivary pellicle on the surface free energy and wettability of different denture base materials.

OBJECTIVE: The objective of the present study was to evaluate the effect of salivary coating on the wettability and surface free energy of different denture base materials. METHODS: Five acrylic resin and two metallic denture base materials were investigated. Ten specimens of each material (20 x 15x1.5mm) were fabricated and a standardized method was used for polishing the test specimens. Whole unstimulated saliva was collected from a single healthy donor. The wettability properties of the materials were tested before and after organic layer formation. The wetting forces were determined according to the Wilhelmy Plate Technique. Diiodomethane, ethylene glycol and formamide were used as probe liquids. The contact angles, Lifshitz-van der Waals surface energy components, Lewis acid-base surface energy components and total surface energies were calculated using the equations described in the paper. The significance of the differences in the experimentally determined surface energies of different denture materials are calculated by statistical methods. CONCLUSIONS: Light-cured acrylic resin was the most wettable material with a significant basic character. Organic layers decreased the total surface free energies of all materials and at the same time imparted a more basic character. The coatings had a homogenizing effect in terms of the surface free energy components of the denture materials, nevertheless, their adhesive properties were still influenced by the substrate employed.

Acrylic Resins↗

PubMed1988

Gas chromatographic method for the determination of N-acetyl-S-(N-methylcarbamoyl)cysteine, a metabolite of N,N-dimethylformamide and N-methylformamide, in human urine.

A simple method has been developed for the determination of N-acetyl-S-(N-methylcarbamoyl)cysteine in human urine. Treatment of a urine sample (1 ml) with ethanol (2 ml) and potassium carbonate (1.5 g) produces ethyl N-methylcarbamate, which is extracted into ethanol and measured by packed column gas chromatography with nitrogen-sensitive detection. The limit of quantitation in human urine is 1 microgram/ml and the between-sample coefficient of variation is 5-11%. Simultaneously, N,N-dimethylformamide, N-methylformamide and formamide can also be determined.

Acetylcysteine↗

PubMed1999

Non-aqueous capillary electrophoresis chiral separations with sulfated beta-cyclodextrin.

This paper reports the application of an anionic cyclodextrin (CD), sulfated beta-cyclodextrin with a degree of substitution of four (beta-CD-(SO4-)4, in chiral separations of pharmaceutical enantiomers by non-aqueous capillary electrophoresis (NACE). Upon complexation with the anionic CD, electrophoretic mobilities of the basic enantiomers decreased, however, both separation selectivity and resolution were enhanced. The advantage of NACE chiral separations over the aqueous CE with the charged CD is that higher electric field strength and higher ionic strength could be applied due to the characteristics of the solvent formamide. The higher ionic strength leads to stacking of peaks and reduces the electrodispersion caused by the mobility mismatch between beta-CD-(SO4-)4-analyte complexes and the co-ions in the running buffer. As a result, better peak shapes and higher separation efficiency were obtained. Comparing with NACE chiral separations with neutral CDs, lower concentration of beta-CD-(SO4-)4 was needed due to the fact that the electrostatic attraction caused stronger binding between beta-CD-(SO4-)4 and the enantiomers. The effects of the experimental parameters, such as concentration of the CD, apparent pH (pH*), degree of substitutions of the CDs, percentage of water in mixed solvent systems, and type of solvents were also studied.

Cyclodextrins↗

PubMed2003

Synthesis, characterization and in vitro release of 5-aminosalicylic acid and 5-acetyl aminosalicylic acid of polyanhydride--P(CBFAS).

A novel polyanhydride, poly[(5-carboxybutyl formamide)-2-acetyl salicylic anhydride] (P(CBFAS)), with 5-aminosalicylic acid (5-ASA) incorporated into the polymer backbone was synthesized and characterized by infrared, (1)H-nuclear magnetic resonance, differential scanning calorimetry, vapor pressure osmometry, etc. The polyanhydride was subjected to degradation and simultaneously released 5-ASA and its derivative 5-acetyl aminosalicylic acid (5-acetyl ASA) in vitro under various conditions. The factors influencing the release profiles of 5-ASA and 5-acetyl ASA, including polymer molecular weights, pH value, enzyme and rat gastrointestinal contents, were examined. The results showed that the release rate of 5-ASA and 5-acetyl ASA increases with increasing pH value and with decreasing molecular weights. In PBS (pH 8.0, 37 degrees C) total ASA released was 8.0% for P(CBFAS)(1) (Mn 10770) in 13 h, but only 1.1 and 2.6% at pH 2.0 and 6.5, respectively. Enzymes including pepsin and trypsin, as well as rat gastric and jejunum contents had little effect on the release rate of 5-ASA and 5-acetyl ASA at pH 2.0 and 6.5 (less than 4% in 13 h). However, the release rate of 5-ASA and 5-acetyl ASA was much fast in PBS(pH 8.0) containing 5% of cecal contents, the total ASA released was 13.6% for the polymer in 13 h. Considering the high drug loading of the polymer (50.2% of 5-ASA moieties in the backbones) and the degradation characters, it is possible to reach high local concentration of 5-ASA in the colon site via oral administration. Therefore, P(CBFAS) may be potentially useful in the colon specific delivery of 5-ASA.

Aminosalicylic Acids↗

PubMed1997

beta-Lactam antibiotics. Spectroscopy and molecular orbital (MO) calculations. Part I: IR studies of complexation in penicillin-transition metal ion systems and semi-empirical PM3 calculations on simple model compounds.

IR studies were preformed to determine possible transition metal ion binding sites of penicillin, the observed changes in spectral position and shape of characteristic IR bands of cloxacillin in the presence of transition metal ions (both in solutions and in the solid state) indicate formation of M-L complexes with engagement of -COO- and/or -CONH- functional groups. The small shift of vC=O towards higher frequencies rules out direct M-L interaction via beta-lactam carbonyl. PM3 calculations on simple model compounds (substituted formamide, cyclic ketones, lactams and substituted monocyclic beta-lactams) have been performed. All structures were fully optimized and the calculated bond lengths, angles, heats of formation and C=O stretching frequencies were discussed to determine the beta-lactam binding sites and to explain its susceptibility towards nucleophilic attack (hydrolysis in vitro) and biological activity. The relative changes of calculated values were critically compared with available experimental data and same correlation between structural parameters and in vivo activity was shown.

Amides↗

PubMed2005

Ionic liquids as advantageous solvents for headspace gas chromatography of compounds with low vapor pressure.

The potential of ionic liquids as solvents for headspace gas chromatography was investigated. Three compounds with boiling points above 200 degrees C were selected to demonstrate the feasibility of the concept described. 2-Ethylhexanoic acid, formamide, and tri-n-butylamine as examples of acidic, neutral, and basic analytes were dissolved in acidic 1-n-butyl-3-methylimidazolium hydrogen sulfate (1), neutral 1-n-butyl-2,3-dimethylimidazolium dicyanamide (2), and 2 containing 1,8-diazabicyclo[5.4.0]undec-7-ene to adjust basic conditions. All analytes could be determined with limits of detection and limits of quantification in the low-ppm concentration range.

Ampicillin↗

PubMed1997

Behavior and use of nonaqueous media without supporting electrolyte in capillary electrophoresis and capillary electrochromatography.

Five nonaqueous solvents (acetonitrile, methanol, N,N-dimethylformamide, dimethyl sulfoxide, formamide) and deionized water were investigated for their ability to support electroosmotic flow (EOF) without electrolytic additives. In general, flow was found to be equal to or greater than flow with typical CE buffer systems. The magnitude of EOF was determined for each solvent by open tubular capillary electrophoresis (CE) and related to viscosity (eta), dielectric constant (epsilon), and the ratio of dielectric constant to viscosity (eta/epsilon). Zeta potentials (zeta) were derived indirectly from flow data and tabulated. Comparisons of flow behavior and zeta were made between pure solvents and conventional CE buffers, and questions of equilibrium and reproducibility were addressed. Similar experiments were performed using hydroorganic mobile phases (ACN/water, MeOH/water) across the complete compositional range (100% water-100% organic), with flow characteristics and zeta reported for each mobile phase system. Packed capillary columns (5-microns ODS) were evaluated for flow and retention stability under capillary electrochromatographic (CEC) conditions. A separation of 11 polycyclic aromatic hydrocarbons was performed in under 13 min by CEC with an ACN/water mobile phase. Reduced plate heights (h) were calculated between 2.5 and 3.0 for solutes with capacity factors (k') up to 4.5 for the most retained solute.

Acetonitriles↗

PubMed1993

Reaction conditions and kinetics of self-cleavage of a ribozyme derived from Neurospora VS RNA.

We have investigated the self-cleavage reaction performed by a ribozyme that contains 164 nucleotides of Neurospora VS RNA. Self-cleavage requires a divalent cation, magnesium being more effective than manganese or calcium. Spermidine or monovalent cations stimulate the reaction but cannot replace magnesium. The temperature optimum is rather broad, around 40-50 degrees C. Unlike some other ribozymes, VS self-cleavage is inhibited by even low concentrations of urea or formamide. The rate of cleavage is the same from pH 5.5 to 8.9, suggesting either that hydroxide is not directly involved in the cleavage chemistry or that a step that precedes the actual cleavage event is rate-limiting.

Formamides↗

PubMed1991

Reaction of formate with the fast form of cytochrome oxidase: a model for the fast to slow conversion.

The ability to isolate preparations of cytochrome oxidase which are highly homogeneous has facilitated a study of the effects of various reagents on the purified enzyme. The addition of either sodium formate, formamide, formaldehyde, or sodium nitrite to enzyme which reacts in a single rapid kinetic phase with cyanide causes a blue-shift of 4-6 nm of the net (cytochrome a + cytochrome a3) Soret maximum. Only the derivative prepared by adding sodium formate demonstrates measurable intensity in the g' = 12 region of the low-temperature electron paramagnetic resonance (EPR) spectrum. This g' = 12 resonance is characteristic of cytochrome oxidase which has undergone a modification at the binuclear center and thereby reacts sluggishly with cyanide. As the site of cyanide binding in resting enzyme as been demonstrated to be CuB [Yoshikawa, S., & Caughey, W.S. (1990) J. Biol. Chem. 265, 7945-7958], it is proposed that formate can bind to CuB and the fast to slow transition is rationalized by using this proposal. The g' = 12 signal is also produced upon the addition of sodium formate to mitochondrial preparations, suggesting that the species responsible for this behavior may have possible physiological relevance. Physical properties of the formate derivative and data for other reagents reacted with the fast-reacting enzyme preparation are presented.

Animals↗