Using Fluorescence Resonance Energy Transfer (FRET) for Measuring 2-5A Analogues Ability to Activate RNase L

Abstract

The development of a method for measuring the ability of 2-5A analogues to activate the cleavage of an oligoribonucleotide substrate by RNase L is described. This method is based on fluorescence resonance energy transfer. The method is easily performed with 96-well plates, allowing for quantitative high-throughput analyses of 2-5A analogues under different reaction conditions.     

An ab initio algorithm for low-resolution 3-D reconstructions from cryoelectron microscopy images

A statistical method for determining low-resolution 3-D reconstructions of virus particles from cryoelectron microscope images by an ab initio algorithm is described. The method begins with a novel linear reconstruction method that generates a spherically symmetric reconstruction, which is followed by a nonlinear reconstruction method implementing an expectation-maximization procedure using the spherically symmetric reconstruction as an initial condition and resulting in a reconstruction with icosahedral symmetry. An important characteristic of the complete method is that very little need be known about the particle before the reconstruction is computed, in particular, only the type of symmetry and inner and outer radii. The method is demonstrated on synthetic cowpea mosaic virus data, and its robustness to 5% errors in the contrast transfer function, 5% errors in the location of the center of the particles in the images, and 5% distortion in the 3-D structure from which the images are derived is demonstrated numerically.     

结合缺陷型菌株显色法采用离子束诱变筛选高产L-精氨酸突变株

为快速高效筛选L-精氨酸高产突变株,建立一种缺陷菌株平板显色法并采用低能N+离子束对L-精氨酸生产用菌株钝齿棒杆菌SYPA5-5进行诱变处理,通过上述平板显色法筛选获得高产突变株.对突变株进行摇瓶发酵实验,最终选育出一株L-精氨酸产量较高且产酸性能比较稳定的突变菌株钝齿棒杆菌SYPA5-5-36.该菌株摇瓶发酵L-精氨酸产量可达35.85 g/L,比出发菌株提高了19.5％.因此,缺陷型菌株平板显色法可以用于快速、高效筛选高产L-精氨酸突变株.     

An ab Initio Algorithm for Low-Resolution 3-D Reconstructions from Cryoelectron Microscopy Images

A statistical method for determining low-resolution 3-D reconstructions of virus particles from cryoelectron microscope images by an ab initio algorithm is described. The method begins with a novel linear reconstruction method that generates a spherically symmetric reconstruction, which is followed by a nonlinear reconstruction method implementing an expectation-maximization procedure using the spherically symmetric reconstruction as an initial condition and resulting in a reconstruction with icosahedral symmetry. An important characteristic of the complete method is that very little need be known about the particle before the reconstruction is computed, in particular, only the type of symmetry and inner and outer radii. The method is demonstrated on synthetic cowpea mosaic virus data, and its robustness to 5% errors in the contrast transfer function, 5% errors in the location of the center of the particles in the images, and 5% distortion in the 3-D structure from which the images are derived is demonstrated numerically.     

A simple procedure for constructing 5'-amino-terminated oligodeoxynucleotides in aqueous solution.

A rapid method for the synthesis of oligodeoxynucleotides (ODNs) terminated by 5'-amino-5'-deoxythymidine is described. A 3'-phosphorylated ODN (the donor) is incubated in aqueous solution with 5'-amino- 5'-deoxythymidine in the presence of N-(3-dimethylaminopropyl)-N'-ethylcarbodiimide hydrochloride (EDC), extending the donor by one residue via a phosphoramidate bond. Template- directed ligation of the extended donor and an acceptor ODN, followed by acid hydrolysis, yields the acceptor ODN extended by a single 5'-amino-5'-deoxythymidine residue at its 5'terminus.     

A convenient sequencing method for 5'' protein-linked RNAs.

A convenient nucleotide sequencing method for 5' end protein-linked RNAs was developed. Genome of LSc, 2ab poliovirus, which has a protein (VPg) covalently linked to the 5' terminus, was labelled with 125I Bolton and Hunter reagent after proteinase K treatment. No sign of labelling of nucleotide moiety in the genome with the reagent was detected. A labelled oligo peptide-linked ribonuclease T1 fragment was obtained from the 5' end of the genome. Analysis of the complex by two dimensional gel electrophoresis after partial alkali digestion or by the nucleotide sequencing method of Donis-Keller et al. (1) revealed that LSc, 2ab strain genome had an identical 5' end structure to that of Mahoney strain genome, that is, VPg-pUpUpApApApApCpApGp. Our results have shown that this labelling method is useful for analysis of 5' end sequence of RNAs linked to protein at the 5' termini.     

Cyclic 3′,5′-nucleotide phosphodiesterase: A continuous titrimetric assay

A direct and continuous assay for cyclic 3′,5′-nucleotide phosphodiesterase has been developed. This method is based on the fact that the phosphate group of adenosine 3′,5′-phosphate has one titratable species whereas that of 5′-adenosine monophosphate has two. Hydrolysis of cyclic AMP to 5′-AMP by phosphodiesterase is accompanied by a stoichiometric generation of protons. The rate of addition of an alkaline solution to the reaction mixture to maintain a constant pH with a pH stat is thus stoichiometrically related to the rate of cyclic AMP hydrolysis. A reaction producing 10 mμmoles of H⁺ or more per minute in 1.5 ml of reaction mixture is accurately measured by this technique. Duplicates are usually within 5% of each other. Results obtained by the titrimetric method correlate well with those obtained by conventional methods. This technique has been successfully used to assay phosphodiesterase of bovine brain in the purified as well as the crude stage.     

A selective electrochemical method of glycosylation of 3β-hydroxy-Δ-steroids

A new electrochemical glycosylation method is presented. According to the method cholesterol and other 3β-hydroxy-Δ⁵-steroids can be selectively transformed to glycosides using non-activated sugars. The method is also useful for the synthesis of glycoconjugates with sugar linked to a steroid moiety by an ether bond.     

Interaction of the protein components of 5-oxoprolinase. Substrate-dependent enzyme complex formation

5-Oxo-L-prolinase from Pseudomonas putida is composed of two reversibly dissociable proteins: Component A catalyzes 5-oxoproline-dependent cleavage of ATP, but does not catalyze the decyclization of 5-oxoproline; Component B is required for the coupling of ATP cleavage to ring-opening of 5-oxoproline to form glutamate (Seddon, A. P., Li, L., and Meister, A. (1984) J. Biol. Chem. 259, 8091-8094). We describe here the purifications of Components A and B to apparent homogeneity and the interactions between these two proteins. The cellular content of Component B activity is significantly greater than that of Component A. By gel filtration, Component A is a hexamer; but in the presence of substrates, it is a dimer. Component B can exist as an aggregate, an octamer, or a tetramer, depending upon the conditions used. Gel filtration of a mixture of Components A and B in the presence of substrates gives a unique protein species that exhibits 5-oxoprolinase activity. The Mr of this Component A-Component B complex indicates that it probably has an A2-B2 structure. The molar ratio of Component A to Component B in the complex was determined to be 1:1 by the continuous variation method (Job). Titrations of each component by the other suggest that phosphorylated 5-oxoproline-bound Component A is the entity that interacts with Component B. These studies indicate that the binding of phosphorylated 5-oxoproline-bound Component A to Component B to form a complex proceeds by a cooperative type mechanism. This is supported by the observed shifts of the intersection points of the Job curves (see Appendix).     

Subcellular Distribution Studies of Diadenosine Polyphosphates—Ap4A and Ap5A—in Bovine Adrenal Medulla: Presence in Chromaffin Granules

Diadenosine tetraphosphate (Ap4A) and diadenosine pentaphosphate (Ap5A) have been identified in bovine adrenal medullary tissue using an HPLC method. The values obtained were 0.1 +/- 0.05 mumol/g of tissue for both compounds. The subcellular fraction where Ap4A and Ap5A were present in the highest concentration was chromaffin granules: 32 nmol/mg of protein for both compounds (approximately 6 mM intragranularly). This value was 30 times higher than in the cytosolic fraction. Enzymatic degradation of Ap4A and Ap5A, isolated from chromaffin granules, with phosphodiesterase produces AMP as the final product. The Ap4A and Ap5A obtained from this tissue were potent inhibitors of adenosine kinase. Their Ki values relative to adenosine were 0.3 and 2 microM for Ap4A and Ap5A, respectively. The cytosolic fraction also contains enzymatic activities that degrade Ap4A as well as Ap5A. These activities were measured by an HPLC method; the observed Km values were 10.5 +/- 0.5 and 13 +/- 1 microM for Ap4A and Ap5A, respectively.     

Structure of a cDNA for Ciona Cytochrome b(5) and the ubiquitous expression of mRNA in embryonic tissues

A cDNA clone for cytochrome b(5) was isolated from a cDNA library of an ascidian, Ciona savignyi, by a plaque hybridization method using a digoxigenin-labeled cDNA for the soluble form of human cytochrome b(5). The cDNA is composed of 5'- and 3'-noncoding sequences, and a 396-base pair coding sequence. The 3'-noncoding sequence contains polyadenylation signal sequences. The amino acid sequence of 132 residues deduced from the nucleotide sequence of the cDNA showed 61% identity and 82% similarity to the cytochrome b(5) of another ascidian species, Polyandrocarpa misakiensis, which we previously cloned. The amino-terminal hydrophilic domain of 98 residues contains well-conserved structures around two histidine residues for heme binding. A cDNA expression system was constructed to prepare a putative soluble form of Ciona cytochrome b(5). The recombinant soluble cytochrome b(5) showed an asymmetrical absorption spectrum at 560 nm as is shown by mammalian cytochromes b(5) upon reduction with NADH and NADH-cytochrome b(5) reductase. The recombinant Ciona cytochrome b(5) is reduced by NADH-cytochrome b(5) reductase with an apparent K(m) value of 3.3 microM. This value is similar to that of the cytochrome b(5) of Polyandrocarpa misakiensis. The expression of Ciona cytochrome b(5) mRNA during development was examined by an in situ hybridization method and ubiquitous expression in embryonic tissues was observed. The results indicate that cytochrome b(5) plays important roles in various metabolic processes during development.     

A sensitive radioenzymatic assay for (S)-5-formyltetrahydrofolate.

A highly sensitive, radioenzymatic method has been developed for the specific and quantitative estimation of (S)-5-formyltetrahydrofolate. This method is based on enzymatic cycling of the 5-formyl derivative to methylenetetrahydrofolate followed by entrapment into a stable ternary complex with thymidylate synthase and tritiated fluorodeoxyuridylate. Determination of bound radiolabeled ligand permits estimation of the original folate. The initial cycling step is catalyzed by the enzyme, methenyltetrahydrofolate synthetase, which is specific for the (S)-diastereomer of 5-formyltetrahydrofolate and generates a product which can be further cycled to tetrahydrofolate using either 10-formyltetrahydrofolate deacylase or glycinamide ribonucleotide transformylase. Tetrahydrofolate is ultimately converted to the entrapable methylene derivative in the presence of excess formaldehyde. Using this assay recovery of reference (S)-5-formyltetrahydrofolate was linear over the range 0.03-1.9 pmol with an average recovery of 83 +/- 2%. The method has been applied to estimation of plasma (S)-5-formyltetrahydrofolate from a volunteer who had been administered (R,S)-5-formyltetrahydrofolate. Where comparison was possible, estimation of plasma (S)-5-formyltetrahydrofolate by this one step ternary complex-based method yielded results that were very similar to those observed by Straw et al. (Cancer Res., 44, 3114, 1984) who used an HPLC-based method for separation of diastereomeric mixtures of reduced folates and microbiological growth dependence to determine (S)-5-formyltetrahydrofolate.     

New way to isolate simian virus 40 nucleoprotein complexes from infected cells: use of a thiol-specific reagent.

A new method for the isolation of simian virus 40 nucleoprotein complexes from nuclei of lytically infected cells is described. The method is based on the addition of a thiol-specific reagent, 5'5'-dithiobis(2-nitrobenzoic acid), to lysis and extraction buffers. By inhibiting an uncoating activity during simian virus 40 extraction, 5'5'-dithiobis (2-nitrobenzoic acid) allows the use of efficient extraction buffers, such as one containing Triton X-100 and EDTA, for the isolation of native simian virus 40 minichromosomes and virion-type structures. Use of the method is illustrated by following encapsidation of simian virus 40 minichromosomes in a pulse-chase experiment. Since 5'5'-dithiobis (2-nitrobenzoic acid) is an inhibitor of many different enzymes, the 5',5'-dithiobis (2-nitrobenzoic acid) extraction technique may be useful for the isolation of not only papovaviruses but also other viruses and possibly cellular chromatin.     

Cytofluorometric quantitation of 5-hydroxytryptamine in mast cells: an improved technique for the formaldehyde condensation reaction

A simple technique for the condensation of cellular 5-hydroxytryptamine (5-HT) with formaldehyde gas is described. The technique, which is especially suited for quantitative cytofluormetric studies, involves the generation of formaldehyde gas from dry paraformaldehyde in a closed reaction vessel with the addition of a measured quantity of water. The fluorescence yield of 5-HT was tested at various humidities. Optimal results were obtained with the addition of 100 mg water to a 1000 ml reaction vessel containing 6 g of dry paraformaldehyde. A major advantage of the method if the fact that the humidity during the reaction can be precisely controlled. The fluorescence yield of 5-HT, tested over a 50 day period showed excellent reproducibility. The stoichiometry of the reaction was tested by comparison of cytofluormetic data with that obtained by analysing the 5-HT content of pooled mast cells with an independent biochemical method. A highly satisfactory correlation (r = 0.96) was obtained within the range of 0.1 to 4 pg of 5-HT per cell. The limit of sensitivity of the cytofluorometric method was found to be of the order of 10(-13) g, and was determined by the fluorescence blank of the mast cells. This contributes to between 10 and 30 per cent of the total fluorescence emission from mast cells containing about 0.2 pg of 5-HT.     

High-performance liquid chromatographic measurement of 5,10-methylenetetrahydrofolate in liver.

The folate coenzyme 5,10-methylenetetrahydrofolate is an important folate metabolite which cannot be determined directly by HPLC near neutral pH because it dissociates to formaldehyde and tetrahydrofolate. A method for the determination of 5,10-methylenetetrahydrofolate in liver is described. This method involves (1) determination of liver 5-methyltetrahydrofolate; (2) chemical reduction of liver 5,10-methylenetetrahydrofolate (stabilized at pH 10) to 5-methyltetrahydrofolate; and (3) determination of total liver 5-methyltetrahydrofolate. Subtraction of (1) from (3) gives the concentration of 5,10-methylenetetrahydrofolate in liver.     

A simple method for the preparation of [beta-32P]purine nucleoside triphosphase.

A rapid, simple and inexpensive procedure is described for the preparation of purine ribo-and deoxyribonucleoside triphosphates specifically and highly radiolabeled with [32P]phosphate in the beta position. The method involves two successive enzymatic reactions: conversion of donor [gamma-32P]ATP in the presence of an excess of acceptor 5'-mononucleotide to the 5'-diphosphates by myokinase or guanosine 5'-monophosphate kinase followed by phosphorylation with pyruvate kinase to yield 5'-triphosphates.     

Simple and rapid enzymatic method for the synthesis of single-strand oligonucleotides containing trifluorothymidine

To investigate the mechanism of trifluorothymidine (TFT)-induced DNA damage, we developed an enzymatic method for the synthesis of single-strand oligonucleotides containing TFT-monophosphate residues. Sixteen-mer oligonucleotides and 14-mer 5'-phosphorylated oligonucleotides were annealed to the template of 25-mer, so as to empty one nucleotide site. TFT-triphosphate was incorporated into the site by DNA polymerase and then ligated to 5'-phosphorylated oligonucleotides by DNA ligase. The synthesized 31-mer oligonucleotides containing TFT residues were isolated from the 25-mer complementary template by denaturing polyacrylamide electrophoresis. Using these single-strand oligonucleotides containing TFT residues, the cleavage of TFT residues from DNA, using mismatch uracil-DNA glycosylase (MUG) of E.coli origin, was compared with that of 5-fluorouracil (5FU) and 5-bromodeoxyuridine (BrdU). The TFT/A pair was not cleaved by MUG, while the other pairs, namely, 5FU/A, 5FU/G, BrdU/A, BrdU/G, and TFT/G, were easily cleaved from each synthesized DNA. Thus, this method is useful for obtaining some site-specifically modified oligonucleotides.     

Rapid detection and enumeration of Naegleria fowleri in surface waters by solid-phase cytometry

A new method for the rapid and accurate detection of pathogenic Naegleria fowleri amoebae in surface environmental water was developed. The method is based on an immunofluorescent assay combined with detection by solid-phase cytometry. In this study we developed and compared two protocols using different reporter systems conjugated to antibodies. The monoclonal antibody Ac5D12 was conjugated with biotin and horseradish peroxidase, and the presence of cells was revealed with streptavidin conjugated to both R-phycoerythrin and cyanine Cy5 (RPE-Cy5) and tyramide-fluorescein isothiocyanate, respectively. The RPE-Cy5 protocol was the most efficient protocol and allowed the detection of both trophozoite and cyst forms in water. The direct counts obtained by this new method were not significantly different from those obtained by the traditional culture approach, and results were provided within 3 h. The sensitivity of the quantitative method is 200 cells per liter. The limit is due only to the filtration capacity of the membrane used.     

A General Assay Method for Nucleotide Pyrophosphorylases

A general assay method for nucleotide pyrophosphorylases has been investigated. The principle of the method is based on the measurement of consumption rate of 5-phosphoribosylpyrophosphate (PRPP) during the enzyme reaction. In the method, an enzyme preparation for sample was incubated in a reaction mixture containing a purine or pyrimidine base and PRPP for a certain time, and the amounts of PRPP before and after the reaction were determined. The amount of PRPP was determined by an enzymatic method using orotidine-5′-monophosphate (5′-OMP) pyrophosphorylase and 5′-OMP decarboxylase. Nucleotide pyrophosphorylase activity corresponding to each purine or pyrimidine base was determined from the amount of PRPP consumed per unit time.

The present method is generally applicable for determining activities of any kind of nucleotide pyrophosphorylases, and does not need any tedious separation procedure in all cases. Therefore, comparing with the conventional assay methods for nucleotide pyrophosphorylase activities, this method can be said to be much simpler and reliable. As an application of the present method, activities of several nucleotide pyrophosphorylases in Micrococcus glutamicus have been determined.