Water regulation of actinomycin-D binding to DNA: the interplay among drug affinity, DNA long-range conformation, and hydration

Actiaomycin-D (actD) binds to natural DNA at two different classes of binding sites, weak and strong. The affinity for these sites is highly dependent on DNA se(sequence and solution conditions, and the interaction appears to be purely entropic driven Although the entropic character of this reaction has been attributed to the release of water molecules upon drug to DNA complex formation, the mechanism by which hydration regulates actD binding and discrimination between different classes of binding sites on natural DNA is still unknown. In this work, we investigate the role of hydration on this reaction using the osmotic stress method. We skew that the decrease of solution water activity, due to the addition of sucrose, glycerol ethylene glycol, and betaine, favors drug binding to the strong binding sites on DNA by increasing both the apparent binding affinity Delta G, and the number of DNA base pairs apparently occupied by the bound drug n(bp/actD). These binding parameters vary linearly with the logarithm of the molar fraction of water in solution log(X-w), which indicates the contribution of water binding to the energetic of the reaction. It is demonstrated that the hydration change measured upon binding increases proportionally to the apparent size of the binding site n(bp/uctD). This indicates that n(bp/actD) measured from the Scatchard plod is a measure of the size of the DNA molecule changing conformation due to ligand binding. We also find that the contribution of DNA deformation, gauged by n(bp/act) to the total free energy of binding Delta G, is given by Delta G = Delta G(local) + n(bp/actD) x delta G(DNA), where Delta G(local), = -8020 +/- 51 cal/mol of actD bound and delta G(DNa) = -24.1 +/- 1.7cal/mol of base pair at 25 degrees C. We interpret Delta G(local), as the energetic contribution due to the direct interactions of actD with the actual tetranucleotide binding site, and it n(bp/actB) X delta G(DNA) as that due to change inconformation, induced by binding, of it n(bp/actD) DNA base pairs flanking the local site. This interpretation is supported by the agreement found between the value of delta G(DNA) and the torsional free energy change measured independently. We conclude suggesting an allosteric model for ligand binding to DNA, such that the increase in binding affinity is achieved by increasing the relaxation of the unfavorable free energy of binding storage at the local site through a larger number of DNA base pairs. The new aspect on this model is that the size of the complex is not fixed but determined by solutions conditions, such as water activity, which modulate the energetic barrier to change helix conformation. These results may suggest that long-range allosteric transitions of duplex DNA are involved in the inhibition of RNA synthesis by actD, and more generally, in the regulation of transcription. (C) 2000 John Wiley & Sons, Inc.

Determination of rice herbicides, their transformation products and clofibric acid using on-line solid-phase extraction followed by liquid chromatography with diode array and atmospheric pressure chemical ionization mass spectrometric detection

A simultaneous method for the trace determination of acidic, neutral herbicides and their transformation products in estuarine waters has been developed through an on-line solid-phase extraction method followed by liquid chromatography with diode array and mass spectrometric detection. An atmospheric pressure chemical ionization (APCI) interface was used in the negative ionization mode after optimization of the main APCI parameters. Limits of detection ranged from 0.1 to 0.02 ng/ml for 50 mi of acidified estuarine waters preconcentrated into polymeric precolumns and using time-scheduled selected ion monitoring mode. Two degradation products of the acidic herbicides (4-chloro-2-methylphenol and 2,4-dichlorophenol) did not show good signal response using APCI-MS at the concentration studied due to the higher fragmentor voltage needed for their determination For molinate and the major degradation product of propanil, 3,4-dichloroaniline, positive ion mode was needed for APCI-MS detection. The proposed method was applied to the determination of herbicides in drainage waters from rice fields of the Delta del Ebro (Spain). During the S-month monitoring of the herbicides, 8-hydroxybentazone and 4-chloro-2-methylphenoxyacetic acid were successively found in those samples. (C) 2000 Elsevier B.V. B.V. All rights reserved.

Application of low-pressure gas chromatography-ion-trap mass spectrometry to the analysis of the essential oil of Turnera diffusa (Ward.) Urb.

Turnera diffusa Willd. var. afrodisiaca (Ward) Urb. (syn. T. aphrodisiaca) belongs to the family of Turneraceae and is an aromatic plant growing wild in the subtropical regions of America and Africa. It is widely used in the traditional medicine as e.g. anti-cough, diuretic, and aphrodisiac agent. This work presents a 3 min chromatographic analysis using low-pressure (LP) gas chromatography (GC)-ion-trap (IT) mass spectrometry (MS). The combination of a deactivated 0.6 m x 0.10 mm i.d., restrictor with a wide-bore CP-Wax 52 capillary column (10 m x 0.53 mm i.d., 1 mum) reduces the analysis time by a factor of 3-7 in comparison to the use of a conventional narrow bore column. Chromatographic conditions have been optimized to achieve the fastest separation with the highest signal/noise ratio in MS detection. These results allow fast and reliable quality control of the essential oil to be achieved. (C) 2003 Elsevier B.V. All rights reserved.

Determination of aldehydes and ketones in fuel ethanol by high-performance liquid chromatography with electrochemical detection

A new methodology was developed for analysis of aldehydes and ketones in fuel ethanol by high-performance liquid chromatography (HPLC) coupled to electrochemical detection. The electrochemical oxidation of 5-hydroxymetkylfurfural, 2-furfuraldehyde, butyraldehyde, acetone and methyl ethyl ketone derivatized with 2,4-dinitrophenylhydrazine (DNPH) at glassy carbon electrode present a well defined wave at +0.94 V; +0.99 V; +1.29 V; +1.15 V and +1.18 V, respectively which are the basis for its determination on electrochemical defector. The carbonyl compounds derivatized were separated by a reverse-phase column under isocratic conditions with a mobile phase containing a binary mixture of methanol /LiClO4(aq) at a concentration of 1.0 x 10(-3) mol L-1 (80:20 v/v) and a flow-rate of 1.1 mL min(-1). The optimum potential for the electrochemical detection of aldehydes-DNPH and ketones-DNPH was +1.0 V vs. Ag/AgCl. The analytical curve of aldehydes-DNPH and ketones-DNPH presented linearity over the range 5.0 to 400.0 ng mL(-1), with detection limits of 1.7 to 2.0 ng mL(-1) and quantification limits from 5.0 to 6.2 ng mL(-1), using injection volume of 20 mu L. The proposed methodology was simple, low time-consuming (15 min/analysis) and presented analytical recovery higher than 95%.

Pharmacokinetic Study of Nobiletin and Tangeretin in Rat Serum by High-Performance Liquid Chromatography-Electrospray Ionization-Mass Spectrometry

Nobiletin (NOB) and tangeretin (TAN), two of the main polymethoxylated flavones (PMFs) in citrus, influence a number of key biological pathways in mammalian cells. Although the impacts of NOB and TAN on glucose homeostasis and cholesterol regulation have been investigated in human clinical trials, much information is still lacking about the metabolism and oral bioavailability of these compounds in animals. In this study, NOB and TAN were administered to rats by gavage and intraperitoneal (ip) injection, and the blood serum concentrations of these compounds and their main metabolites were monitored by high-performance liquid chromatography-electrospray ionization-mass spectrometry (HPLC-ESI-MS). In addition to the administered compounds, two metabolites of TAN and eight metabolites of NOB were detected and measured over 24 h. With identical oral doses, nearly 10-fold higher absorption of NOB occurred compared to TAN. For both compounds, maximum levels of glucuronidated metabolites occurred in the blood serum at later time points (similar to 5-8 h) compared to the earlier T(max) a values for NOB and TAN. In most cases the glucuronides occurred at substantially higher concentrations than the aglycone metabolites. Low levels of NOB and TAN and their metabolites were detectable in rat blood serum even at 24 h after treatment.

Determination of the sodium monofluoroacetate in serum by gas chromatography

Sodium monofluoroacetate (NAFAc) has been widely used for vertebrate pest control, such as rabbits in Australia. However NAFAc is extremely toxic to all vertebrates and its use is restricted. Although this compound is stringently restricted, the occurrence of accidental and homicidal poisoning is no ever-present possibility.The method developed in this work shows the applicability of SPE with alumina cartridges for the extraction of NAFAc from serum samples. The method is efficient with recoveries of at least 96.8% from spiked serum. The samples were subsequently derivatized with dicyclohexylcabodiimide (DCC), using 2,4-dichloroaniline (DCA), to make the product volatile for GC analysis.

Determination of organochlorine pesticides and polychlorinated biphenyls residues in municipal solid waste compost by gas chromatography with electron-capture detection

A simple and efficient method for the simultaneous gas chromatographic determination of ten organochlorine pesticides (alpha-HCH, beta-HCH, gamma-HCH, p,p'-DDT, o,p'-DDT, p,p'-DDD, p,p'-DDE, aldrin, endrin, and dieldrin) and six congeners of PCBs (PCB 28, 52, 118, 138, 153, and 180) in municipal solid waste compost is described. The procedure involves a solid-phase dispersion matrix using celite as dispersant sorbent, alumina as clean up sorbent and hexane-dichloromethane (7:3, v/v) mixture as eluting solvent. An additional purification step with copper was necessary to eliminate sulphur. Analysis of the sample was performed by GC-ECD. The method was validated with fortified samples at two concentration levels (0.025 and 0.05 mg kg(-1)). Average recovery ranged from 77 to 121% with relative standard deviation between 1 and 18%. The detection limits, which ranged from 0.003 to 0.01 mg kg-1, were lower than those established by the Baden-Wurttemberg directive (0.033 mg kg(-1)).

Jacalin interaction with human immunoglobulin A1 and bovine immunoglobulin G1: Affinity constant determined by piezoelectric biosensoring

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Real-time monitoring and kinetic parameter estimation of the affinity interaction of jArtinM and rArtinM with peroxidase glycoprotein by the electrogravimetric technique

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

High resolution ultra high pressure liquid chromatography-time-of-flight mass spectrometry dereplication strategy for the metabolite profiling of Brazilian Lippia species

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Purification of a PHA-Like chitin-binding protein from Acacia farnesiana seeds: A time-dependent oligomerization protein

A lectin-like protein from the seeds of Acacia farnesiana was isolated from the albumin fraction, characterized, and sequenced by tandem mass spectrometry. The albumin fraction was extracted with 0.5 M NaCl, and the lectin-like protein of A. farnesiana (AFAL) was purified by ion-exchange chromatography (Mono-Q) followed by chromatofocusing. AFAL agglutinated rabbit erythrocytes and did not agglutinate human ABO erythrocytes either native or treated with proteolytic enzymes. In sodium dodecyl sulfate gel electrophoresis under reducing and nonreducing conditions, AFAL separated into two bands with a subunit molecular mass of 35 and 50 kDa. The homogeneity of purified protein was confirmed by chromatofocusing with a pI=4.0+/-0.5. Molecular exclusion chromatography confirmed time-dependent oligomerization in AFAL, in accordance with mass spectrometry analysis, which confers an alteration in AFAL affinity for chitin. The protein sequence was obtained by a liquid chromatography quadrupole time-of-flight experiment and showed that AFAL has 68% and 63% sequence similarity with lectins of Phaseolus vulgaris and Dolichos biflorus, respectively.

Detection of the 43,000-molecular-weight glycoprotein in sera of patients with paracoccidioidomycosis

The 43,000-molecular-weight (43K) soluble glycoprotein was detected in sera of patients with paracoccidioidomycosis by the immunoblot technique by using as the probe rabbit monospecific antisera to this fraction. The 43K antigen was present before treatment in sera of patients with the acute (juvenile) form; it started to disappear from circulation after 10 months of chemotherapy, and it was undetectable afer 2 years of treatment. In the chronic cases, the 43K antigen was detected in patients without treatment, and it was absent in the healed cases. The detection of the 43K protein specific to Paracoccidioides brasiliensis may be important for its diagnostic value as well as for modulation of the host immune response.