A nonenzymatic method for determination of hydrogen peroxide and organic peroxides

Reduction of hydrogen peroxide and organic peroxides (t-butyl hydroperoxide and linoleic acid hydroperoxide) was achieved with homovanillic acid as hydrogen donor in the presence of the triethylenetetramine-Fe3+ complex. By the catalytic action of this complex, homovanillic acid is oxidized to its fluorescent dimer. Based on this reaction a fluorometric method for the measurement of the hydroperoxides mentioned above is described. The method can be extended to the determination of substrate-enzyme systems that produce hydrogen peroxide, e.g., glucose-glucose oxidase. The method allows the determination of substances such as hydrogen peroxide and t-butyl hydroperoxide with an accuracy and precision of less than 3%. Glucose can be determined with similar precision and an accuracy of 4.7%.     

Artifact-inducing enrichment of ethylenediaminetetraacetic acid and ethyleneglycoltetraacetic acid on anion exchange resins

Multivalent metal chelators, ethylenediaminetetraacetic acid (EDTA) and ethyleneglycoltetraacetic acid (EGTA), are used extensively during protein purification. Both strong (Q) and weak (DEAE) anion exchange resins were found to adsorb surprisingly large quantities of EDTA and EGTA that elute from the resin at NaCl concentrations of approximately 240 mM (EDTA) and 140 mM (EGTA). The EDTA/EGTA elution and saturation parameters were determined for five commonly used anion exchange resins. The resulting concentration of eluted EDTA was 10- to 200-fold higher than that originally present in the sample or in the mobile phase. Samples from fractions containing such a high concentration of EDTA were found to inhibit Mg²⁺-dependent polymerase chain reaction (PCR). EDTA binding to the anion exchange resins could saturate the resin, decrease its binding capacity, and displace weakly bound proteins such as green fluorescent protein (GFP). Several steps are suggested to minimize on-column EDTA concentration, including column equilibration in the absence of any EDTA, lower concentrations (0.1–0.5 mM) of EDTA, monitoring eluate absorbance at 280 nm as well as at 215 nm, adding EDTA back into fractions eluting before the EDTA peak, and performing blank column runs to control for the effect of changes in EDTA concentration in downstream assays.     

Routine acid decalcification of bone marrow samples can preserve DNA for FISH and CGH studies in metastatic prostate cancer.

Production of paraffin-section material from tissue samples that contain bone requires decalcification. Techniques such as acidic decalcification or EDTA chelation are suitable methods. Acid decalcification is generally quicker than EDTA chelation but studies have suggested that it may result in hydrolysis of DNA. Here we show that limited acid decalcification (less than 24 hr) in 5% formic acid can preserve DNA sufficient for fluorescent in situ hybridization (FISH) or comparative genomic hybridization (CGH) and that prolonged 10% formic acid decalcification results in failure of FISH and only limited retrieval of DNA for CGH studies.     

Synthesis of affinity-label chelates: a novel synthetic method of coupling ethylenediaminetetraacetic acid to amine functional groups

An affinity-label chelate for the enzyme trypsin was synthesized by a novel synthetic technique which takes advantage of the presence of a dangling carboxylate arm in the [Co(EDTA)Cl]2- complex anion. The dangling carboxylate group was coupled to the amino group of p-aminobenzamidine, an effective inhibitor of trypsin activity, via the carbodiimmide reaction to produce a trypsin affinity label at one end and a strong EDTA-like chelating agent at the other, coupled through an amide bond. The cobalt ion can be removed if desired by reduction with Fe2+ + ascorbate, and alternate metal ions inserted in its place. The reaction is general, and affinity labels which contain amino groups can be easily coupled via this procedure, allowing the introduction of a paramagnetic or fluorescent probe into a protein or nucleotide system. The same method has been used to prepare a highly effective chelating gel which is capable of removing calcium and lanthanide ions from the binding protein parvalbumin.     

A quantitative study of the complexation of cadmium in hemolyzed human erythrocytes by 1H NMR spectroscopy

The stability of complexes formed by Cd2+ in hemolyzed human erythrocytes was studied by spin-echo 1H NMR spectroscopy. Changes in resonances for the carbon-bonded protons of glutathione (GSH) upon addition of the ethylenediaminetetraacetic acid complex of Cd2+ (Cd(EDTA)2-) and the appearance of resonances for Mg(EDTA)2- indicate that the Cd(EDTA)2- complex dissociates in hemolyzed erythrocytes with the formation of Cd(GSH)x and Mg(EDTA)2- complexes. A semiquantitative estimate of the overall stability constant for the complexation of Cd2+ in hemolyzed erythrocytes was obtained from spin-echo 1H NMR data. The stability constant is consistent with the majority of the Cd2+ in erythrocytes present as Cd(SG)2(2-). A conditional equilibrium constant was also determined for the complexation of Mg2+ by ligands in hemolyzed human erythrocytes.     

The Nucleic Acids and Cellular Differentiation in the Root Apex of Pisum sativum: I. A FLUORIMETRIC METHOD FOR THE ESTIMATION OF NUCLEIC ACIDS IN ROOT CELLS

A method is described for the estimation of RNA and DNA in microscopicpreparations of pea roots by measuring the fluorescent intensityof a dye-nucleate complex. By this method the nucleic acid contentmay be determined of small groups of cells in different tissuesof the root. The limitations of the method are outlined.     

Homogeneous TR-FRET high-throughput screening assay for calcium-dependent multimerization of sorcin

A homogeneous high-throughput screening method based on time-resolved fluorescence resonance energy transfer (TR-FRET) for the measurement of calcium-dependent multimerization of an EF-hand protein, sorcin, is described. The assay is based on a specific sorcin binding peptide conjugated either with an intrinsically highly fluorescent europium chelate (donor) or an Alexa Fluor 700 fluorophore (acceptor). Addition of calcium results in multimerization of sorcin, allowing several peptides to bind simultaneously to the epitopes of the multimeric protein complex, and the proximity of peptides labeled either with donor or acceptor label results in fluorescence resonance energy transfer between the 2 labels. When no calcium is present, the protein remains in a monomer form, and thus no FRET can take place. In the optimized assay construct, the assay was performed in 45 min, and a more than 20-fold signal-to-background ratio was achieved. The reversibility of sorcin multimerization was shown by chelating free calcium with ethylenediamine tetraacetic acid (EDTA). The developed homogeneous assay can be used in screening molecules that either inhibit or enhance multimerization of sorcin, and the assay format is applicable to various noncompetitive high-throughput screening assays detecting protein multimerization reactions.     

Lactoferrin-catalysed hydroxyl radical production. Additional requirement for a chelating agent.

The ability of lactoferrin to catalyse hydroxyl radical production was determined by measuring ethylene production from methional (2-amino-4-methylthiobutyraldehyde) or 4-methylthio-2-oxobutyrate. Lactoferrin, isolated from human milk and saturated by adding the exact equivalents of Fe3+-nitrilotriacetic acid and dialysing, give little if any catalysis of the reaction between H2O2 and either O2-. or ascorbic acid at either pH 7.4 or pH 5.0. However, in the presence of chelating agents such as EDTA or nitrilotriacetic acid that can complex with lactoferrin, hydroxyl radical production by both mechanisms was observed.     

Complementary addressed modification of single-stranded DNA using a [Fe-EDTA] derivative of oligonucleotide

A one-tube synthesis scheme for coupling EDTA residue to the 5'-terminus of unprotected oligonucleotides via propylenediamine linker is described. The EDTA derivative of oligonucleotide d(pTGACCCTCTTCCC)A forms a kinetically stable complex with Fe2+ ion. In the presence of ascorbic acid with O2 limiting, this complex modifies single-stranded DNA (a 302-mer) in a site-specific way near the target complementary nucleotide sequence. The DNA fragment can be then cleaved predominantly at modified pyrimidine nucleotides (hidden breaks) by hot piperidine treatment, whereas few direct breaks (i.e. without piperidine) occurs at this site. No autocleavage of the [Fe.EDTA]-oligonucleotide derivative is observed under the experiment's conditions.     

Label-Free and Sensitive Fluorescent Detection of Sequence-Specific Single-Strand DNA Based on S1 Nuclease Cleavage Effects

The ability to detect sequence-specific single-strand DNA (ssDNA) in complex, contaminant-ridden samples, using a fluorescent method directly without a DNA extraction and PCR step could simplify the detection of pathogens in the field and in the clinic. Here, we have demonstrated a simple label-free sensing strategy to detect ssDNA by employing its complementary ssDNA, S1 nuclease and nucleic acid fluorescent dyes. Upon clearing away redundant complementary ssDNA and possibly mismatched double strand DNA by using S1 nuclease, the fluorescent signal-to-noise ratio could be increased dramatically. It enabled the method to be adaptable to three different types of DNA fluorescent dyes and the ability to detect target ssDNA in complex, multicomponent samples, like tissue homogenate. The method can distinguish a two-base mismatch from avian influenza A (H1N1) virus. Also, it can detect the appearance of 50 pM target ssDNA in 0.5 µg·mL⁻¹ Lambda DNA, and 50 nM target ssDNA in 5 µg·mL⁻¹ Lambda DNA or in tissue homogenate. It is facile and cost-effective, and could be easily extended to detect other ssDNA with many common nucleic acid fluorescent dyes.     

Development and characterization of simulant pancreatic islets

Insulin is stored in pancreatic islets as a zinc-insulin complex, and stimulating the islets results in the release of insulin and zinc. Simulant pancreatic islet beads have been developed using agarose beads (50-250 micro m diameter) derivatized with iminodiacetic acid that have been loaded with zinc. A qualitative comparison of the simulant beads with pancreatic islets has been made by staining with dithizone and a zinc-binding fluorescent dye, TSQ. The binding capacity of simulant beads was determined to be 34 micro mol Zn(2+)/g of dried beads using anodic stripping voltammetry. Hydrochloric acid was used to release zinc from beads to mimic the secretion of insulin from pancreatic islets and a release profile was established. The simulant beads can be used to optimize the islet isolation process and reduce the use of real islets in method development.     

7-Amino-actinomycin D as a cytochemical probe. I. Spectral properties.

The optical absorption and fluorescence characteristics of 7-animo-actinomycin D were determined to evaluate its potential as a fluorescent cytochemical probe. At pH 7.0, the absorption maximum and fluorescence excitation maximum are both at 503 nm; the fluorescence emission is at 675 nm. When this compound forms complexes with DNA in solution, the absorption and fluorescence excitation maxima shift to 543 nm and the fluorescence emission shifts to 655 nm. The fluorescence quantum yield is 0.016 for 7-amino-actinomycin D free in solution and 0.01-0.02 for complexes with native DNA. The 7-amino-actinomycin D also exhibits fluorescence shifts characteristic of binding when put into solution with poly(dG-dC) poly(dG-dC), but not with poly(dI-dC) poly(dI-dC). The spectral characteristics are the same at pH 7.0 whether the solvent is 0.01 M PO4 with 0.0001 M EDTA or Earle's salts with 0.025 M N-2-hydroxyethylpiperazine-N1-2-ethanesulfonic acid.     

The use of Magallanic peat as non-conventional sorbent for EDTA removal from wastewater

Kraft mills are responsible for large volumes discharges of highly polluted effluents. Application of new bleaching processes (i.e. total chlorine-free (TCF) process) is already a feasible option to reduce environmental impacts. The current trend in the increase in the production of TCF pulp will proportionally increase the consumption of chelating agents. The most commonly used chelants, ethylenediaminetetraacetic acid (EDTA) and diethylenetriaminepentaacetic acid (DPTA) are supposed to be relatively persistent substances, poorly degradable in biological treatment facilities and are subsequently considered as environmentally critical compounds. Adsorption could be used as a treatment technique to remove recalcitrant compounds from wastewaters. However, in most cases, sorbent and regeneration costs can make the whole process not economically feasible. The goal of this study was to evaluate the use of Magallanic peat as non-conventional sorbent for EDTA removal from wastewater. Adsorption studies were carried out considering a 2(3) factorial design. pH, temperature and sorbent/sorbate (S/S) relationship effects were evaluated in EDTA adsorption onto Magallanic peat. In addition, adsorption isotherm constants were determined according to the Langmuir and Freundlich models. The results showed that the optimal conditions for EDTA adsorption onto Magallanic peat were 20 degrees C, acid pH (4.0) and a low sorbent/sorbate ratio (0.1/100). At these conditions Magallanic peat showed an adsorption capacity for EDTA (Cs(sat)) of 128.2mg/g, comparable and even better than activated carbon (Cs(sat) 56.5mg/g). EDTA adsorption data at 60 degrees C obtained are not shown due to Magallanic peat degradation phenomena.     

Structural and thermodynamic analysis of the GFP:GFP-nanobody complex

The green fluorescent protein (GFP)-nanobody is a single-chain VHH antibody domain developed with specific binding activity against GFP and is emerging as a powerful tool for isolation and cellular engineering of fluorescent protein fusions in many different fields of biological research. Using X-ray crystallography and isothermal titration calorimetry, we determine the molecular details of GFP:GFP-nanobody complex formation and explain the basis of high affinity and at the same time high specificity of protein binding. Although the GFP-nanobody can also bind YFP, it cannot bind the closely related CFP or other fluorescent proteins from the mFruit series. CFP differs from GFP only within the central chromophore and at one surface amino acid position, which lies in the binding interface. Using this information, we have engineered a CFP variant (I146N) that is also able to bind the GFP-nanobody with high affinity, thus extending the toolbox of genetically encoded fluorescent probes that can be isolated using the GFP-nanobody.     

A simple and effective method to overcome the inhibition of Fe to PCR

Fe inhibition to PCR can be overcome by adding greatly excessive EDTA first, and then the same amount Mg(2+) as EDTA to PCR mix. By this method impure DNA was amplified successfully. DNA samples containing metals whose complexation constant with EDTA was much higher than Mg(2+) can also be amplified.     

Interpretation of the thiobarbituric acid reactivity of rat liver and brain homogenates in the presence of ferric ion and ethylenediaminetetraacetic acid.

The thiobarbituric acid (TBA) reactivity of rat liver and brain homogenates was characterized to elucidate what kinds of aldehyde species contributed to the reactivity. Characteristic pH dependence of the reactivity with a maximum at around pH 3 and marked enhancement of the reactivity by t-butyl hydroperoxide (t-BuOOH) and ferric ion were similar to those of alkadienals. The amounts of aldehyde species, including alkadienals determined as 2,4-dinitrophenylhydrazones, were high enough to account for the enhanced reactivity. The reactivity was inhibited by ethylenediaminetetraacetic acid (EDTA) but not completely, suggesting the presence of malonaldehyde whose reactivity was not affected by EDTA. The amounts of malonaldehyde determined as 1-(2,4-dinitrophenyl)pyrazole could account for a part of the reactivity in the presence of EDTA. Hence, the TBA reactivity of liver and brain homogenates at around pH 3 in the presence of t-BuOOH and ferric ion may be accounted for by alkadienals and malonaldehyde and that in the presence of EDTA by malonaldehyde.     

Interaction of a protein, BSA, and a fluorescent probe, Mag-Indo-1, influence of EDTA and calcium on the equilibrium.

Recent findings indicate that ion-chelator probes with tetracarboxylate structure bind proteins. It was suggested that these fluorescent probes are valuable tools to gain information on protein structure through the energy transfer from tryptophans to the bound probe. Here, the binding of the fluorescent probe Mag-Indo-1 to bovine serum albumin (BSA) was investigated. Mag-Indo-1 was reported previously to serve as a probe for magnesium cations (Kd = 2.8 x 10(-4) M for zero ionic strength) which can also interact with calcium cations (Kd = 7.5 x 10(-7) M). Probe complexation with protein results in a shift of the emission fluorescence spectrum of the probe from 480 to 457 nm. We used emission fluorescence techniques to monitor this interaction. Computational resolution of the complex fluorescence spectra and a new software to test the theoretical model were developed in our laboratory. This enabled us to calculate the number of interacting sites and the dissociation constants. The fluorescent probe Mag-Indo-1 binds at a singular site with high affinity (Kd = 1.8 x 10(-7) M) to bovine serum albumin (BSA). Since proteins are known to bind several compounds unspecifically, we have studied the influence of EDTA as a competitor of the probe. Our findings suggest that the BSA binding site is identical for both Mag-Indo-1 and EDTA. We found that EDTA binds the protein with Kd = 0.4 x 10(-3) M. We studied the influence of calcium and found that Mag-Indo-1 does not bind the calcium free Apo-protein anymore.     

Saint Louis Encephalitis Viral Ribonucleic Acid Replication Complex

Pulse-labeled Saint Louis encephalitis viral ribonucleic acid (RNA) is found in the cytoplasm of infected cells associated with a membranous structure which sediments with an average value of 250S. The integrity of the complex is destroyed by detergents and ribonuclease; however, it is stable in ethylenediaminetetraacetic acid (EDTA) which differentiates this structure from cellular polyribosomes. With cultures in which cellular RNA was highly labeled prior to infection, ribosomal RNA could not be demonstrated in the complex isolated from EDTA-sucrose gradients. Single-stranded 43S and the 26S and 20S forms of viral RNA were found in the complex. Viral RNA polymerase activity in sucrose-gradient fractions sedimented in the same region as the fractions which contained the pulse-labeled viral RNA. The polymerase incorporated (3)H-guanosine triphosphate into acid-precipitable material in the absence of added template. It was also found that the replication complex contains viral-specific proteins.     

壳聚糖-g-N.羧甲基-二(2-苯并眯唑)-1,2-乙二醇的制备及其性能

以2-溴乙酸、壳聚糖、二（2-苯并咪唑）-1,2-乙二醇为原料,利用接枝作用将化学修饰后的小分子药物二（2-苯并咪唑）-1,2-乙二醇连接在天然高分子壳聚糖（CTS）上。并以。HNMR,IR,热分析及XRD等方法对其结构进行表征并研究接枝聚合物的理化性质。本文采用络合滴定法测定了接枝聚合物对一系列重金属离子的吸附作用;采用震荡法进行悬菌定量杀菌实验;还以经典的静态失重法研究了合成的聚合物在腐蚀介质中对N80钢片腐蚀的抑制作用。结果表明：小分子药物-（2-苯并咪唑）-1,2-乙二醇在接枝到天然高分子壳聚糖后热稳定性提高,在酸中具有良好的溶解度,对金属离子吸附能力在一个较宽温度范围内得以保持;同时增强了抑菌力,降低了最小抑菌浓度;利用BBIE与CTS韵协同作用提高了聚合物对金属腐蚀的抑制能力。     

Artificial restriction DNA cutter for site-selective scission of double-stranded DNA with tunable scission site and specificity

The artificial restriction DNA cutter (ARCUT) method to cut double-stranded DNA at designated sites has been developed. The strategy at the base of this approach, which does not rely on restriction enzymes, is comprised of two stages: (i) two strands of pseudo-complementary peptide nucleic acid (pcPNA) anneal with DNA to form 'hot spots' for scission, and (ii) the Ce(IV)/EDTA complex acts as catalytic molecular scissors. The scission fragments, obtained by hydrolyzing target phosphodiester linkages, can be connected with foreign DNA using DNA ligase. The location of the scission site and the site-specificity are almost freely tunable, and there is no limitation to the size of DNA substrate. This protocol, which does not include the synthesis of pcPNA strands, takes approximately 10 d to complete. The synthesis and purification of the pcPNA, which are covered by a related protocol by the same authors, takes an additional 7 d, but pcPNA can also be ordered from custom synthesis companies if necessary.