Size-exclusion reaction chromatography (SERC): a new technique for protein PEGylation

A new, widely applicable process that combines reaction and separation in a single unit operation is described. The process, size-exclusion reaction chromatography (SERC), simultaneously allows control of the extent of reactions in which molecular size is altered and the separation of products and reactants. In SERC, a moving reaction zone is formed by injection of reactants onto a size-exclusion chromatography column. Reactants and products are partitioned differently within the mobile phase, resulting in different linear flow rates through the column. The products are therefore removed selectively from the reaction zone, minimizing their residence time in the reaction zone and allowing their separation in the downstream section of the column. For reactions such as protein PEGylation, in which successive addition of PEG groups to the protein results in significant molecular size increases, SERC potentially offers a method by which a dominant final PEGylated protein size can be produced at high yield. The SERC PEGylation of two model proteins, alpha-lactalbumin and beta-lactoglobulin, is demonstrated and results show that simultaneous reaction and separation was obtained.     

A rapid, quantitative, non-radioactive bisulfite-SNuPE- IP RP HPLC assay for methylation analysis at specific CpG sites

The precise mapping and quantification of DNA methylation as an epigenetic parameter during development and in diseased tissues is of great importance for functional genomics. Here we describe a rapid, quantitative method to assess methylation levels at specific CpG sites using PCR products of bisulfite-treated genomic DNA. Using single nucleotide primer extension (SNuPE) assays in combination with ion pair reverse phase high performance liquid chromatography (IP RP HPLC) separation techniques, methylated and unmethylated CpGs can be discriminated and quantified based on the different masses and hydrophobicities of the extended primer products. The assay is linear, highly reproducible and several sites can be measured simultaneously in one reaction. It can be semi-automated and eliminates the need for cloning and sequencing of individual bisulfite PCR products.     

Iodo-Gen-mediated radioiodination of nucleic acids

Iodo-Gen (1,3,4,6-tetrachloro-3a,6a-diphenylglycoluril), widely used as an oxidizing agent for iodination of proteins, can also be used for iodination of nucleic acids. Optimal conditions were determined for efficient labeling of RNA and DNA with 125I. The proposed procedure for radioiodination of nucleic acids is more beneficial than the methods utilizing TlCl3 because of the milder reaction conditions, the simplicity and completeness of separation of reaction products from the oxidizing agents, and the absence of a toxic catalyst. Using the standard procedure for Iodo-Gen-mediated iodination a specific radioactivity of up to 1.3 X 10(9) dpm/micrograms RNA can be achieved. The proposed procedure is also suitable for radioiodination of DNA.     

The relationship between compositional phase separation and vesicle morphology: Implications for the regulation of phospholipase A2 by membrane structure

The action of phospholipase A₂ (PLA₂) on bilayer substrates causes the accumulation of reaction products, lyso-phospholipid and fatty acid. These reaction products and the phospholipid substrate generate compositional heterogeneities and then apparently phase separate when a critical mole fraction of reaction product accumulates in the membrane. This putative phase separation drives an abrupt morphologic rearrangement of the vesicle, which may be in turn responsible for modulating the activity of PLA₂. Here we examine the thermotropic properties of the phase-separated lipid system formed upon hydrating colyophilized reaction products (1:1 palmitic acid:1-palmitoyl-2-lyso-phosphatidylcholine) and substrate, dipalmitoylphosphatidylcholine. The mixture forms structures which are not canonical spherical vesicles and appear to be disks in the gel-state. The main gel-liquid transition of these structures is hysteretic. This hysteresis is apparent using several techniques, each selected for its sensitivity to different aspects of a lipid aggregate's structure. The thermotropic hysteresis reflects the coupling between phase separation and changes in vesicle morphology.     

Simultaneous determination of fifteen illegal dyes in animal feeds and poultry products by ultra-high performance liquid chromatography tandem mass spectrometry

With the increasing presence of illegal dyes, such as sudan reds and malachite green, in animal feeds and food products during the last few years, there is an urgent need of accurate quantitative determination methods for these illicit compounds. Here we established an accurate method for the simultaneous determination of 15 illegal dyes in animal feeds, meat, eggs and other food products using ultra-high performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS). The samples were extracted with a simple procedure using acetonitrile and solid phase extraction cleaning up. The application of C(18) rapid column can achieve satisfactory separation of the 15 dyes within 16 min; and multiple reaction monitoring of positive ions ensure confirmative detection of these illegal dyes. With the developed method, a sample can be analyzed in less than 2h. Dyes spiked in feeds, poultry meat and eggs in the range of 0.1-5.0 mg kg(-1) were tested in terms of linearity, sensitivity, repeatability and recovery. Recoveries for the compounds ranged from 60 to 140%. Intra- and inter-day precisions (RSDs) were less than 15%. Limit of quantification ranged from 0.01 to 5.61 μg kg(-1) for different dyes. The developed UHPLC-MS/MS method could be used as a qualitative and quantitative technique for the simultaneous determination of illegal dyes in animal feeds and poultry products.     

Biphasic one-pot synthesis of two useful and separable compounds using nicotinamide cofactor-requiring enzymes: Syntheses of (S)-4-hydroxyhexanoate and its lactone

Several one-pot syntheses of two valuable and separable compounds in a biphasic system using nicotinamide cofactor-requiring enzymes are described. In this system, two synthetic reactions occur in the aqueous phase where the N AD or N ADP cofactor is recycled ≈ 1000 times, and the reduction product is extracted into the organic phase while the oxidation product is retained in the aqueous phase. The effective separation of products and elimination of product inhibition during the reaction makes the biphasic system practical for large-scale synthesis. Several chiral hydroxy compounds of synthetic value have been prepared. Manipulation of N AD-dependent enzymes in synthesis in water-immiscible organic solvent by entrapment of both enzyme and the cofactor in X AD-8 is described.     

Phosphorylation assay in liquid scintillation counter using C̆erenkov radiation of P: Application to photophosphorylation

A simple procedure is described for the assay of phosphorylation using C?erenkov radiation to detect ³²P in a liquid scintillation counter. Unreacted ³²P_i is first removed from the reaction mixture as the phosphomolybdate complex by butanol/benzene extraction. Addition of ammonium hydroxide to the remaining aqueous fraction avoids color quenching, phase separation, and instability in the counting rate during measurement of ³²P. Application of this procedure to several photophosphorylation systems is included.     

Simplified fluorometric assay for sphingosine bases

A simplified procedure for fluorometric determination of sphingosine bases is presented. Nitrogenous bases are reacted with fluorescamine and then extracted into a lower phase solvent, obviating the need to transfer the reaction products prior to quantitation. Consequently, the entire procedure may be carried out in a single set of screw-capped reaction tubes. Chloroform was found to be the best solvent of those tested for the maximal extraction of derivatized sphingosine bases with negligible extraction of nitrogenous contaminants derived from phospholipids and amino sugars. The simplified method retains excellent sensitivity and selectivity and allows for simultaneous processing of large numbers of samples. Furthermore, quantitation of glycolipid-derived hexosamine can be obtained by measuring the fluorescence of the aqueous phase after partitioning.     

An o-phthalaldehyde spectrophotometric assay for proteinases

A rapid and convenient spectrophotometric assay has been devised to measure proteolysis. The assay is based on the reaction of o-phthalaldehyde (OPA) and 2-mercaptoethanol with amino groups released during proteolysis of a protein substrate. The reaction is specific for primary amines in amino acids, peptides, and proteins, approaches completion within 1 to 2 min at 25 degrees C (half-times of approx 10-15 s), and requires no preliminary heating or separation of the hydrolyzed products from the undegraded protein substrate prior to performing the assay. The OPA assay was relatively as successful as a 2,4,6-trinitrobenzenesulfonic acid (TNBS) procedure in predicting the extent of hydrolysis of a protein substrate. The utility of the OPA method was demonstrated by measuring the degree of proteolytic degradation caused by trypsin, subtilisin, Pronase, and chymotrypsin of various soluble protein substrates. Ethanethiol (instead of 2-mercaptoethanol) or 50% of dimethyl sulfoxide can be included in the assay solution to stabilize certain OPA-amine products. The present method approaches the sensitivity of ninhydrin and TNBS procedures, is more convenient and rapid, and could substitute for these reagents in most assay systems.     

A study on enzymatic reaction using a liquid emulsion membrane technique

An enzymatic reaction using a liquid emulsion membrane technique was studied to investigate the effects of some experimental variables on the stability of liquid membrane, enzyme deactivation, and transport of substrates and products. The hydrolysis of L-phenylalanine methyl ester by alpha-chymotrypsin was selected as a model reaction system. First, a transport mechanism for the substrates and products across the membrane was qualitatively identified. Second, it was found that the pH of the internal phase was one of the most important variables to determine the enzyme activity in a liquid membrane. Third, the effect of membrane phase which consists of surfactant, carrier, and organic solvent on the emulsion stability was investigated. It was found that the properties of the organic solvents greatly affect the emulsion stability. For an optimum condition, it was possible to reuse the emulsion which consists of membrane phase and internal phase without further separation. It was finally concluded that the enzyme in a liquid membrane retained 60% of its native activity in spite of vigorous mixing during the emulsification step.     

Ultrafiltration membrane with ribonuclease activity

Summary RNase was immobilized by entrapment in polymer matrix during the formation of the ultrafiltration membrane. The resulting membrane can hydrolyze RNA with simultaneous separation of reaction products (nucleotides) and RNA. The RNase activity has not decreased after one month of operation.     

Ultrafiltration-based assay for heparanase activity

Heparanase, a mammalian endoglycosidase that specifically cleaves heparan sulfate (HS), has been found in many tissues. Platelet, liver, and placenta have been abundant sources for the study of the enzyme. Notably, certain malignant cells also have been found to produce large amounts of the enzyme, the levels of which often correlate with their invasive and metastatic properties. To study roles of heparanase in various biological situations, a reliable method measuring the enzyme activity is indispensable. In the past, measurement of heparanase enzyme activity was done either by the detection of the degradation of fluorescent or radiolabeled HS chains by gel filtration procedures or by the use of radiolabeled substrate conjugated to solid matrices for the easy separation of degraded HS chains. A newly developed procedure, presented in this article, measures degradation of radiolabeled HS chains in the aqueous buffer by detecting their degradation products using an ultrafiltration device, the Centricon 30. This procedure has several advantages over previous assay procedures that involved tedious processing such as gel filtration chromatography of each sample or the preparation of substrate HS proteoglycans conjugated to a solid matrix. The simplicity of the new procedure allows a short setup time and a rapid processing of a large number of samples. Furthermore, the enzymatic reaction during the aqueous phase allows kinetic analyses in standard conditions.     

Hydrolysis of dipalmitoylphosphatidylcholine large unilamellar vesicles by porcine pancreatic phospholipase A2

The interaction between dipalmitoylphosphatidylcholine large unilamellar vesicles and porcine pancreatic phospholipase A2 has been studied under a variety of conditions. It was found that the presence of large unilamellar vesicles inhibits the hydrolysis of small unilamellar vesicles at room temperature, and reaction calorimetric experiments showed that protein-lipid interactions in the absence of Ca2+ occur in the gel state with a stoichiometry of about 40 phospho-lipid molecules/protein-binding site. However, hydrolysis can be induced in the gel state under conditions of osmotic shock. On the other hand, hydrolysis is usually observed within the lipid transition temperature range, but then it occurs only after a latency phase during which the hydrolysis is very slow. The duration of this latency phase reaches a minimum near the phase transition temperature. However, if the enzyme-substrate mixture is heated from low temperatures (continuously or by a temperature jump) to a temperature within the phase transition region, hydrolysis occurs instantaneously. These results are in accordance with the conclusions of the preceding paper (Menashe, M., Romero, G., Biltonen, R. L., and Lichtenberg, D. (1986) J. Biol. Chem. 261, 5328-5333) that effective binding of the enzyme to lipid vesicles occurs relatively rapidly in the gel state and that activation of the enzyme-substrate complex requires the existence of structural irregularities in the lipid bilayer. Although hydrolysis products may have a pronounced effect on the time course of the reaction in the transition range, instantaneous hydrolysis can be induced in the phase transition region in the absence of reaction products by appropriate manipulation of the experimental conditions during which no reaction products are produced. Thus reaction products are not essential for activation of porcine pancreatic phospholipase A2. Furthermore, it is shown that the fraction of lipid hydrolyzed during the latency period is a function of the initial substrate concentration in a manner inconsistent with the proposition that the accumulation of a constant critical fraction of reaction products is the basis for activation. Comparison of the results of this study with those of the preceding paper strongly support the previously proposed reaction scheme.     

A rapid radiometric assay for dihydrofolate reductase

A rapid radiochemical procedure for the measurement of dihydrofolate reductase activity is described. The method employs separation of the radiolabeled substrate from the products of the reaction by precipitation with acetic acid and zinc sulfate. This method permits rapid processing of samples and climinates time-consumlng column chromatography techniques. Good agreement of results is obtained when the radioactive method is compared to the spectrophotometric assay method.     

On-line integration of PCR and cycle sequencing in capillaries: from human genomic DNA directly to called bases

A fully integrated system has been developed for genetic analysis based on direct sequencing of polymerase chain reaction (PCR) products. The instrument is based on a serially connected fused-silica capillary assembly. The technique involves the use of microreactors for small-volume PCR and for dye-terminator cycle-sequencing reaction, purification of the sequencing fragments, and separation of the purified DNA ladder. Four modifications to the normal PCR protocol allow the elimination of post-reaction purification. The use of capillaries as reaction vessels significantly reduced the required reaction time. True reduction in reagent cost is achieved by a novel sample preparation procedure where nanoliter volumes of templates and sequencing reaction reagent are mixed using a micro- syringe pump. The remaining stock solution of sequencing reaction reagent can be reused without contamination. The performance of the whole system is demonstrated by one-step sequencing of a specific 257-bp region in human chromosome DNA. Base calling for the smaller fragments is limited only by the resolving power of the gel. The system is simple, reliable and fast. The entire process from PCR to DNA separation is completed in ~4 h. Feasibilities for development of a fully automated sequencing system in the high-throughput format and future adaptation of this concept to a microchip are discussed.     

1-Acyl-2-[N-(2,4-dinitrophenyl)aminopropionyl]-sn-glycero-3-phosphocholine as a chromogenic substrate for phospholipase A₂ assay

We have developed a spectrophotometric assay for phospholipase A(2) activity using 2,4-dinitrophenyl-labeled phosphatidylcholine as substrate. The assay allows quite simple quantification of phospholipase A(2) activity by measuring the absorbance of the aqueous phase after extraction of the reaction mixture and requires neither chromatographic separation of the reaction products nor the addition of auxiliary coloring reagents.     

Chiral HPLC separation and CD spectra of the C-2 diastereomers of naringin in grapefruit during maturation

Naringin is the chief flavanone glycoside of grapefruit (Citrus paradisi). It is responsible for part of the bitter taste of the fruit and can cause the inhibition of some cytochrome P450s. The direct separation of (2R)- and (2S)-naringin in the albedo of grapefruits was obtained in normal phase HPLC mode using Chiralcel OD as chiral stationary phase and n-hexane/ethanol with 0.1% of TFA as mobile phase. Chiralpak AD was almost ineffective in the separation. This procedure was used to evaluate the stereochemistry at C-2 during maturation of the grapefruit. The CD curves of (2R)- and (2S)-naringin isolated by semipreparative chiral HPLC were determined and the elution order of the chromatographic peaks was related to the absolute C-2 configuration. Partial resolution of the C-2 diastereomers of narirutin was obtained on Chiralpak AD.     

Enzymatic assay for flavonoid sulfotransferase

A novel enzyme assay for flavonoid sulfotransferase is described. It makes use of tetrabutylammonium dihydrogen phosphate which forms a pair of ions with the flavonoid sulfate esters formed. This renders the sulfate ester soluble in organic solvents such as ethyl acetate, whereas the sulfate donor, 3'-phosphoadenosine-5'-phosphosulfate, remains in the aqueous reaction mixture. The procedure is simple, rapid, and reproducible. It eliminates the need for chromatographic separation of the reaction products, except when their identification is required, and is suitable for use in the purification and kinetic studies of sulfotransferases.     

1-Acyl-2-[N-(2,4-dinitrophenyl)aminopropionyl]-sn-glycero-3-phosphocholine as a chromogenic substrate for phospholipase A2 assay

We have developed a spectrophotometric assay for phospholipase A₂ activity using 2,4-dinitrophenyl-labeled phosphatidylcholine as substrate. The assay allows quite simple quantification of phospholipase A₂ activity by measuring the absorbance of the aqueous phase after extraction of the reaction mixture and requires neither chromatographic separation of the reaction products nor the addition of auxiliary coloring reagents.     

Postcolumn nucleic acid intercalation for the fluorescent detection of nucleic acids using ion pair reverse phase high-performance liquid chromatography

Here we report a simple and effective procedure enabling the fluorescent detection of nucleic acids following the rapid, high-resolution separation using ion pair reverse phase chromatography. This approach uses postcolumn nucleic acid intercalation of fluorescent dyes with subsequent fluorescent detection, demonstrating more than a 1000-fold increase in sensitivity in the detection of nucleic acids when compared with traditional UV detection. Moreover, a wide range of intercalating dyes can be incorporated, including those known to disrupt the structure of the nucleic acids, thereby enabling the sensitive detection of DNA and RNA with no adverse effect on resolution of the nucleic acids during ion pair reverse phase chromatography. In addition, such approaches allow one to readily distinguish single-stranded DNA from double-stranded DNA following their separation using ion pair reverse phase high-performance liquid chromatography.