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At least 847 records · Page 47Linked to original sources
PubMed1998

UV light-induced duplex-to-duplex crosslinking of DNA molecules in aqueous ethanol solutions.

Ultraviolet light is known to generate crosslinks between the complementary strands of DNA and between DNA and proteins. Here we demonstrate that the UV light also crosslinks DNA duplexes to other DNA duplexes. However, the duplex-to-duplex crosslinks only appear in the presence of about 75% (vol/vol) ethanol plus a millimolar or submillimolar concentration of monovalent or divalent cations, e.g. 2 mM Na+. Methanol or formamide are ineffective. The present observations provide a direct means to detect physical contacts of DNA molecules or their parts, e.g. during recombination. It is remarkable that the solution conditions leading to the duplex-to-duplex UV light-induced crosslink formation are the same as those inducing the B-to-A conformational transition of DNA.

Bacteriophage phi X 174↗
PubMed1996

A theoretical study of torsional flexibility in the active site of aspartic proteinases: implications for catalysis.

We have performed ab initio Hartree-Fock self-consistent field calculations on the active site of endothiapepsin. The active site was modeled as a formic acid/formate anion moiety (representing the catalytic aspartates, Asp-32 and -215) and a bound water molecule. Residues Gly-34, Ser-35, Gly-217, and Thr-218, which all form hydrogen bonds to the active site, were modeled using formamide and methanol molecules. The water molecule, which is generally believed to function as the attacking nucleophile in catalysis, was allowed to bind to the active site in four distinct configurations. The geometry of each configuration was optimized using two basis sets (4-31G and 4-31G*). The results indicate that in the native enzyme the nucleophilic water is bound in a catalytically inert configuration. However, by rotating the carboxyl group of Asp-32 by about 90 degrees the water molecule can be reorientated to attack the scissile bond of the substrate. A model of the bound enzyme-substrate complex was constructed from the crystal structure of a difluorostatone inhibitor complexed with endothiapepsin. This model suggests that the substrate itself initiates the reorientation of the nucleophilic water immediately prior to catalysis by forcing the carboxyl group of Asp-32 to rotate. The theoretical results predict that the active site of endothiapepsin undergoes a large distortion during substrate binding and this observation has been used to explain some of the kinetics results which have been reported for mutant aspartic proteinases.

Aspartic Acid Endopeptidases↗
PubMed1998

Change of thermal stability of colicin E7 triggered by acidic pH suggests the existence of unfolded intermediate during the membrane-translocation phase.

Purified colicin E7 was analyzed by CD spectrum and gel filtration chromatography in a mimicking membrane-translocation phase. It was found that the CD spectra of colicin E7 at pH 7 and pH 2.5 were similar. Although the melting temperature of the protein shifted from 54.5 degrees C to 34 degrees C at low pH, the thermal denaturation curves of colicin E7 at different pH conditions still fit a two-state model. These experimental results imply that a minor structural change, triggered by acidic pH, for instance, may reduce the energy required for protein melting. In contrast to the minor change in secondary structure at different pH conditions, we observed that, in vitro, all monomeric colicin E7s converted into multimer-like conformations after recovering from the partial unfolding process. This multimeric form of colicin can only be dissociated by formamide and guanidine hydrochloride, indicating that this protein complex is indeed formed by aggregation of the monomeric colicins. Most interestingly, the aggregated colicins still perform in vivo bacteriocidal activity. We suggest that in a partial unfolding state the colicin is prepared for binding to the specific targets for translocation through the membrane. However, in the absence of specific targets in vitro these unfold intermediates may therefore aggregate into the multimeric form of colicins.

Bacterial Proteins↗
PubMed1999

Thermodynamics of the conformational transition of biopolyelectrolytes: the case of specific affinity of counterions.

A formal development of the Counterion Condensation theory (CC) of linear polyelectrolytes has been performed to include specific (chemical) affinity of condensed counterions, for polyelectrolyte charge density values larger than the critical value of condensation. It has been conventionally assumed that each condensed counterion exhibits an affinity free-energy difference for the polymer, (DeltaG(aff)). Moreover, the model assumes that the enthalpic and entropic contributions to DeltaG(aff), i.e., DeltaH(aff) and DeltaS(aff), are both independent of temperature, ionic strength and polymer concentration. Equations have been derived relative to the case of the thermally induced, ionic strength dependent, conformational transition of a biopolyelectrolyte between two conformations for which chemical affinity is supposed to take place. The experimental data of the intramolecular conformational transition of the ionic polysaccharide kappa-carrageenan in dimethylsulfoxide (DMSO) have been successfully compared with the theoretical predictions. This novel approach provides the enthalpic and entropic affinity values for both conformations, together with the corresponding thermodynamic functions of nonpolyelectrolytic origin pertaining to the biopolymer backbone change per se, i.e., DeltaH(n.pol) and DeltaS(n.pol), according to a treatment previously shown to be successful for lower values of the biopolyelectrolyte linear charge density. The ratio of DeltaH(n.pol) to DeltaS(n.pol) was found to be remarkably constant independent of the value of the dielectric constant of the solvent, from formamide to water to DMSO, pointing to the identity of the underlying conformational process.

Biopolymers↗
PubMed2000

Structural stability of DNA in nonaqueous solvents.

One of the defining physicochemical features of DNA in aqueous solution is its ability to maintain a double-helical structure and for this structure to undergo a cooperative, heat-induced denaturation (melting). Herein we show that a 21-mer synthetic DNA can form and maintain such a duplex structure not only in water but even in 99% glycerol; moreover, this double-helical structure reversibly and cooperatively melts in that solvent, with a T(m) value of some 30 degrees lower than in water. Two much larger, natural DNAs, from calf thymus and salmon testes, exhibit similar behavior in glycerol. All three DNAs can also sustain a double-helical structure in 99% ethylene glycol, although its thermostability (as reflected by the melting temperature) is some 20 degrees lower than in glycerol. In contrast, no duplex structure of any of the DNAs was detected in 99% formamide, methanol, or DMSO. This solvent trend resembles that previously observed in studies of protein structure and folding and underscores the importance of hydrophobic interactions in both protein and DNA structure and stability. Our findings suggest that water may not be unique as a suitable medium not only for protein structure but also for that of nucleic acids.

DNA↗
PubMed1998

Fast-FISH technique for rapid, simultaneous labeling of all human centromeres.

Fluorescence in situ hybridization (FISH) has become a powerful tool in chromosome analysis. This report describes the systematic optimization of the Fast-FISH technique for centromere labeling of human metaphase chromosomes for radiobiological dosimetry purposes. For the present study, the hybridization conditions and the efficiency of two commercially available alpha-satellite DNA probes were compared ("human chromosome 1 specific", Oncor, Gaithersburg, MD, vs. "all-human chromosomes specific", Boehringer-Mannheim, Germany). These probes were hybridized to human lymphocyte metaphase plates by using a hybridization buffer without formamide and without any other equivalent denaturing chemical agents. The results indicate the suitability of the method for automated image analysis on the basis of thresholding. The optimal conditions concerning hybridization time and temperature were determined by a systematic quantitative evaluation of the fluorescent labeling sites after the hybridization procedures. Under defined "low stringency" conditions, we found that the "human chromosome 1 specific" DNA probe labeled not only the centromere of the human chromosome 1 but also the other human centromeres in the same way as the "all-human chromosome specific" DNA probe. The optimized conditions to complete all centromere labeling were applied to the detection of dicentric chromosomes on irradiated human lymphocyte samples (gamma-rays of 60Co source, 0.5 Gy/min, for doses of 1, 3, and 4 Gy). The yield of dicentrics was determined after Fast-FISH and compared with results obtained after Giemsa staining. These results are very compatible and indicate that, because of its simplicity, this optimized Fast-FISH procedure would be useful for fast screening purposes in biological dosimetry after accidental overexposure.

Cells, Cultured↗
PubMed2000

RET and GDNF gene scanning in Hirschsprung patients using two dual denaturing gel systems.

Hirschsprung disease (HSCR) is a congenital disorder characterised by intestinal obstruction due to an absence of intramural ganglia along variable lengths of the intestine. RET is the major gene involved in HSCR. Mutations in the GDNF gene, and encoding one of the RET ligands, either alone or in combination with RET mutations, can also cause HSCR, as can mutations in four other genes (EDN3, EDNRB, ECE1, and SOX10). The rare mutations in the latter four genes, however, are more or less restricted to HSCR associated with specific phenotypes. We have developed a novel comprehensive mutation detection system to analyse all but three amplicons of the RET and GDNF genes, based on denaturing gradient gel electrophoresis. We make use of two urea-formamide gradients on top of each other, allowing mutation detection over a broad range of melting temperatures. For the three remaining (GC-rich) PCR fragments we use a combination of DGGE and constant denaturing gel electrophoresis (CDGE). These two dual gel systems substantially facilitate mutation scanning of RET and GDNF, and may also serve as a model to develop mutation detection systems for other disease genes. In a screening of 95 HSCR patients, RET mutations were found in nine out of 17 familial cases (53%), all containing long segment HSCR. In 11 of 78 sporadic cases (14%), none had long segment HSCR. Only one GDNF mutation was found, in a sporadic case.

Amino Acid Substitution↗
PubMed1999

Analysis of the binding surfaces of proteins.

We have developed an experimental approach to map the complete binding surface of any crystalline macromolecule that is fast and flexible. Crystals of the target protein are transferred into organic solvents and the crystal structures are determined at high (about 2A) resolution. The sites where the solvent molecules bind to the protein are thus identified directly. Different solvents serve as probes for different organic functional groups; thus, benzene is a probe for where aromatic groups like to bind, dimethyl formamide is a probe for peptide binding sites, and so forth. A series of about six such experiments suffices to locate the major binding regions on the protein surface unambiguously. These different sites can then be targeted with "Hydra-headed" inhibitors that interact simultaneously with more that one site, thereby providing specificity for the desired target. We have used this method to map the complete binding surface of elastase, and find that three regions, including the active site cleft, are generally "sticky" and can make interactions with almost any functional group. Analyses of these binding sites on elastase and other proteins suggests that what makes a binding site is amphipathicity and the ease with which water can be displaced.

Binding Sites↗
PubMed1998

Follow-up biological and genotoxicological monitoring of acrylonitrile- and dimethylformamide-exposed viscose rayon plant workers.

In order to investigate the genotoxic effects of occupational acrylonitrile (ACN) and dimethylformamide (DMF) exposures, clinical serum and urine parameters and genotoxicological endpoints such as chromosome aberration (CA), sister chromatid exchange (SCE), high frequency SCE (HFC), cell cycle kinetics, and UV-induced unscheduled DNA synthesis (UDS) were followed up three times during a 20-month period in peripheral blood lymphocytes (PBL) of 26 workers (13 maintainers and 13 fiber producers) occupationally exposed to ANC and/or DMF in a viscose rayon plant, 26 matched control subjects, and six industrial controls (all males). Six of the 26 exposed subjects were hospitalized because of liver dysfunction that had developed due to inhalative DMF exposure. The rate of smoking was estimated on the basis of serum thiocyanate (SCN) levels. Average peak air ACN and DMF concentrations were over the maximum concentration limits at the time of both investigations. Urine ACN and monomethyl-formamide (MMF) excretions of the exposed subjects were almost doubled after work shifts. An increase in lymphocyte count (in months 0 and 7), and severe alterations in the liver function were observed in the exposed subjects. In PBLs the proliferative rate index (PRI) was already increased in month 0 compared with the controls. In each study, significant increases in CA and SCE frequencies, as well as increases in UDS were found in PBLs of the exposed subjects. The frequencies of chromatid breaks and acentric fragments further increased in month 7 and remained constantly elevated in month 20. Increased yields of both chromatid and chromosome-type exchange aberrations first appeared in month 20, when HFCs were 2.72 times more frequent in fiber producers than in maintainers. The role of some important biological confounding factors (age, white blood cell count, and hematocrit) and lifestyle confounding factors (smoking and drinking habits) were subjected to an analysis of variance during the second study. Increased CA, SCE, and UDS were found both in control and exposed smokers when current smoking was established on the basis of the serum SCN levels. The cytogenetic data suggest that occupational exposures to ACN and DMF induce considerable genotoxic consequences and may increase the cancer risk in the exposed human populations.

Acrylonitrile↗
PubMed1999

Molecular genetic diagnosis of de novo and recurrent bladder cancer.

Bladder cancer, the second most common urological tumor, is usually diagnosed by endoscopy and biopsy of the lower urinary tract. However, this procedure is expensive, can cause discomfort to the patient and is a source of infection. Commercially available diagnostic systems measure protein byproducts of bladder carcinoma in voided urine; their sensitivity is only between 60-80%. Polymerase chain reaction (PCR)-based microsatellite analysis of the urine sediment (MAUS) is a noninvasive, inexpensive and easily performed analytical method which was introduced in the de novo diagnosis and follow-up of bladder cancer. By utilizing the PCR with 20 polymorphic microsatellite markers on different chromosomes and separating PCR products by electrophoresis on 7% denaturing polyacrylamide-formamide-urea slab gels, a 91% diagnostic sensitivity could be achieved. In order to minimize costs and analysis time, the separation and detection of PCR products was carried out by capillary array electrophoresis and two-color fluorescent primer labeling/laser beam detection in another study. The accuracy of both methods was the same. In either detection system, MAUS is an accurate and promising tool in the noninvasive diagnosis of bladder cancer.

Carcinoma, Transitional Cell↗
PubMed1999

Truncated fragments in polymerase chain reaction-based DNA sequencing.

Reconstitution experiments were performed by using an ordinary dye-primer protocol of a template spiked with known amounts of truncated fragments. We observed that as little as 0.2 mole-percentage of the truncated fragment caused sequence interpretation problems. Two protocols were developed for sequencing with dye-labeled terminators; this eliminates the problems with truncated fragments, which are adapted to a one-dye chemistry. One was designed for single extension sequencing using T7 DNA polymerase and one for cycle sequencing. To avoid precipitation and centrifugation and to facilitate automation, the dye-terminator protocols included the use of a biotinylated sequencing primer. Thus, the Sanger fragments were recovered and, by magnetic separation, washed and released by formamide, EDTA, and heat treatment before loading on the electrophoresis gel. Integrated procedures for sequencing PCR products using one-dye-labeled terminators suitable for automation are described. High quality data in terms of long reads and detection of polymorphisms is obtained. The protocols serve as attractive alternatives to internal labeling and dye-primer approaches.

Base Sequence↗
PubMed2000

Kinetics of small ion evaporation from the charge and mass distribution of multiply charged clusters in electrosprays

The distribution of charge z and radii R in clusters electrosprayed from formamide solutions of tetraheptylammonium bromide was investigated by selecting those within a narrow range of electrical mobilities Z(1) in a first differential mobility analyzer (DMA), reducing their charge to unity by passage through a neutralizing chamber containing a radioactive (alpha) source, and measuring the mobilities Z(z) of the resulting discrete set of singly charged clusters in a second DMA. After correcting for the polarization contribution to cluster drag, the tandem DMA data yield the range of radii present at detectable levels for each charge state up to z = 9. Because small ion evaporation from electrospray drops leads to charge loss when a drop reaches a certain critical radius R(crit)(z), the measured maximum and minimum cluster radii associated with a given z can be used to infer the activation energy Delta for ion evaporation as a function of drop charge and curvature. These results confirm the Iribarne-Thomson ion-evaporation mechanism, and support earlier theoretical expressions for the functional form of Delta(z,R). The different phenomenon of ion evaporation from metastable multiply charged dry clusters is also observed at characteristic times of 1 s. Its activation energy is estimated as approximately 0.3 eV larger than for ion evaporation from the drops. This new process complicates the interpretation of the present measurements in terms of ion evaporation from liquid surfaces, but introduces no radical change in the picture. It helps understand why salt clusters with more than two or three charges are harder to see in mass spectrometers than in mobility studies under ambient conditions. Copyright 2000 John Wiley & Sons, Ltd.

Journal Article↗
PubMed1983

The use of a tumor colony assay in predicting chemotherapeutic drug response in murine bladder cancer.

A tumor colony assay (TCA) was evaluated for its ability to predict anticancer drug responses in an N-[4-(5-nitro-2-furyl)-2-thiazolyl]-formamide (FANFT)-induced murine bladder tumor (MBT) model. Ten anticancer drugs were evaluated in vivo and in vitro using four MBT cell lines (40 drug responses). Using the optimum criteria for drug response, the TCA accurately predicted drug responses in the murine model 65% of the time with a true-positive predictive rate of 54% and a true-negative predictive rate of 70%. Drug testing tumor cells immediately on removal from the mouse resulted in a true-positive predictive rate of 77% and a true-negative predictive rate of 100%. The authors conclude that the TCA can predict response to chemotherapy in the MBT model and may be useful in screening investigation compounds for the subsequent evaluation in this murine bladder tumor model.

Animals↗
PubMed2000

Identification of a possible association between carbon tetrachloride-induced hepatotoxicity and interleukin-8 expression.

Hepatotoxicants can elicit liver damage by various mechanisms that can result in cell necrosis and death. The changes induced by these compounds can vary from gross alterations in DNA repair mechanisms, protein synthesis, and apoptosis, to more discrete changes in oxidative damage and lipid peroxidation. However, little is known of the changes in gene expression that are fundamental to the mechanisms of hepatotoxicity. We have used DNA microarray technology to identify gene transcription associated with the toxicity caused by the hepatotoxicant carbon tetrachloride. Labeled poly A+ RNA from cultured human hepatoma cells (HepG2) exposed to carbon tetrachloride for 8 hours was hybridized to a human microarray filter. We found that 47 different genes were either upregulated or downregulated more than 2-fold by the hepatotoxicant compared with dimethyl formamide, a chemical that does not cause liver cell damage. The proinflammatory cytokine interleukin-8 (IL-8) was upregulated over 7-fold compared with control on the array, and this was subsequently confirmed at 1 hour and 8 hours by Northern blot analyses. We also found that carbon tetrachloride caused a time-dependent increase in interleukin-8 protein release in HepG2 cells, which was paralleled by a decrease in cell viability. These data demonstrate that carbon tetrachloride causes a rapid increase in IL-8 mRNA expression in HepG2 cells and that this increase correlates with a later and significant increase in the levels of interleukin-8 protein. These results illustrate the potential of microarray technology in the identification of novel gene changes associated with toxic processes.

Carbon Tetrachloride↗
PubMed2000

Synthesis and solution properties of deferoxamine amides.

The poor membrane permeability and oral bioavailability of the iron chelating agent deferoxamine (DFO) mesylate result from the low octanol/water partition coefficient and high aqueous solubility. With the ultimate aim to improve biomembrane permeability while retaining the iron-binding ability of DFO, a series of more lipophilic amides were prepared by reacting the terminal primary amino group with fatty and aromatic acid chlorides or anhydrides. Octanol/water partition coefficients and equilibrium solubilities of these analogs in solvents, chosen to delineate physicochemical interactions, were determined as a function of temperature. Solid-state properties were evaluated by calorimetry. All DFO amide derivatives had higher melting points, indicating that derivatives formed strong intermolecular interactions in the solid phase. Formamidation of the primary amine of deferoxamine resulted in a 200-fold increase in the octanol/water partition coefficient and reduced aqueous solubility at least 2000-fold compared with the parent molecule. The partition coefficient increased and aqueous solubility decreased 2-fold with the addition of each methylene group in the homologous series of aliphatic amides. Solubilities of the derivatives in water-saturated octanol and hexane showed irregular profiles as a function of increasing aliphatic chain length that were attributed to intermolecular packing in the solid state. The temperature dependence of the partition coefficients was interpreted to indicate that interfacial transfer of the deferoxamine amides was, in part, affected by an apparent diminished ability to form energetically favorable interactions in the water-saturated organic phase.

Amides↗
PubMed2001

Novel galactosylated liposomes for hepatocyte-selective targeting of lipophilic drugs.

Novel galactosylated neutral liposomes containing cholesten-5-yloxy-N-(4-((1-imino-2-beta-D-thiogalactosylethyl)amino)butyl)formamide (Gal-C4-Chol) as a "homing" device were developed for hepatocyte-selective drug targeting. Distearoylphosphatidylcholine (DSPC)/cholesterol (Chol) (60:40) and DSPC/Chol/Gal-C4-Chol (60:35:5) liposomes were prepared and labeled with [3H]cholesteryl hexadecyl ether (CHE). [3H]Prostaglandin E1 (PGE1) and [14C]probucol were incorporated in liposomes as model lipophilic drugs. After intravenous injection of the liposomes, mice were sacrificed at suitable time periods, and the lung, liver, kidney, spleen, and heart were excised. DSPC/Chol/Gal-C4-Chol liposomes rapidly disappeared from the blood, and 85% of the dose had accumulated in the liver within 10 min compared with hepatic accumulation of DSPC/Chol liposomes of 12%. The liver was perfused with collagenase, and liver parenchymal cells (PC) and liver nonparenchymal cells (NPC) were separated by centrifugal differentiation to determine the cellular distribution. The PC/NPC ratios for DSPC/Chol/Gal-C4-Chol and DSPC/Chol liposomes were 15.1 and 1.1, respectively. The hepatic uptake of DSPC/Chol/Gal-C4-Chol liposomes, but not that of DSPC/Chol liposomes, was significantly inhibited by the predosing of galactosylated bovine serum albumin. [14C]Probucol and [3H]PGE1 incorporated in DSPC/Chol/Gal-C4-Chol liposomes was also efficiently delivered to the liver. In conclusion, newly developed galactosylated liposomes have been proven to be a useful carrier for hepatocyte-selective targeting that will have many practical applications.

Animals↗
PubMed2002

Synthesis, stability, and conformation of the formamidopyrimidine G DNA lesion.

The formamidopyrimidine (FapydGua) lesion, derived from the nucleobase guanine, is a major DNA lesion involved in mutagenesis and carcinogenesis. To date, the chemical information available about this main lesion is very limited. Herein, we describe a synthesis and a detailed characterization of the acetyl-protected monomer of the FapydGua lesion. Stability studies in DMSO and in water/acetonitrile show that the N-glycosidic bond, previously thought to be highly labile, is much more stable than anticipated. Decomposition of the FapydGua lesion proceeds with half-life times of 37.8 h for the beta-anomer and 65.2 h for the alpha-anomer in water/acetonitrile. The relaxation time for the anomerization reaction was determined to tau = 6.5 h at room temperature. Most important, it was found that the formamido group, which is critical for the lesion recognition process by repair enzymes, is fixed in the cis-conformation in apolar solvents such as chloroform. This conformation enables the formation of a hydrogen bond between the carbonyl oxygen of the formamide and the NH of the N-glycosidic bond within the framework of a seven-membered ring system. This has consequences for the recognition of the lesion by repair enzymes (hOGG1 and Fpg protein). These enzymes were so far believed to recognize the carbonyl group of the FapydGua lesion. Our investigations show that this carbonyl group is not readily accessible because it is almost buried in the dominating cis-conformation. In agreement with the recent X-ray structure of hOGG1 in complex with 8-oxo-7,8-dihydroguanine-containing DNA, we can conclude that repair enzymes can contact both lesions only via the N(7)-H group, which is a hydrogen-bond acceptor in guanine.

8-Hydroxy-2'-Deoxyguanosine↗
PubMed2000

Polymer solutions as a pseudostationary phase for capillary electrochromatographic separation of DNA diastereomers.

The solutions of linear polymers traditionally used for DNA separation have been employed for the capillary electrophoresis (CE) of diastereomers of chemically modified DNA. The selectivity of diastereomeric separation of the phosphorothioate (PS) and 2'-O-methylated (2-OMe) PS oligonucleotides depends on the nature of the polymer additive in the CE background electrolyte. The selectivity of separation for different polymers increases in the line: linear polyacrylamide < polyethylene glycol < polyvinyl pyrrolidone. The separation of oligomer diastereomers was shown to be primarily based on the hydrophobic interaction with the polymer network that acts as a pseudostationary phase. While lowering the temperature resulted in improved separation, the addition of organic modifiers such as formamide, methanol or acetonitrile counteracts the solute adsorption on the polymer network, and decreases the selectivity of DNA diastereoseparation. The effect of molecular mass and concentration of the polymer on the separation selectivity was investigated.

Animals↗