Interaction of DNA methyltransferase with aminofluorene and N-acetylaminofluorene modified poly(dC-dG)

Poly(dC-dG) was reacted in vitro to yield templates containing similar amounts of aminofluorene (AF) or acetylaminofluorene (AAF) adducts. These modified poly(dC-dG) templates were tested in an in vitro DNA methylation system utilizing 1500-fold purified rat liver methyltransferase (DMase) to compare and quantitate the effects of these adducts on the kinetics of methylation and the interaction of DMase with such templates. Enzymatic methylation is severely impaired by arylamine adducts, with bound AF inhibiting more than AAF (relative Vmax 0.24 for AAF-poly(dC-dG) and 0.066 for AF-poly(dC-dG). The apparent km for the reaction is not appreciably altered by AAF modification: 10 microM for dCdG dinucleotide units, but it is threefold lower (3 microM) for AF-poly(dC-dG). In competition experiments it was demonstrated that a translocational block is imposed by the adducts. From differential salt inhibition assays and preincubation assays, no change in the ionic binding to the altered templates could be detected, which suggests that the enzyme interacts very strongly through hydrophobic interactions with the fluorene ring. Evidence that the fluorene ring is exposed is supported by circular dichroism spectra of the templates under the conditions of the assay, which indicated that the AF adducts do not appreciably change the normal B conformation of the template, while the template with 9.5% modification by AAF adducts adopted a Z form. These results suggest that the inhibitory effects of AAF and, in particular, AF upon DMase-catalyzed methylation reactions are not dependent upon helix conformation. Instead, they appear to depend upon DMase recognition of an altered dG base configuration, which is responsible for altered binding and methylation kinetics.     

A novel anticoagulant protein with high affinity to blood coagulation factor Va from Tegillarca granosa

A novel inhibitory protein against blood coagulation factor Va (FVa) was purified from muscle protein of granulated ark (Tegillarca granosa, order Arcoida, marine bivalvia) by consecutive FPLC method using anion exchange and gel permeation chromatography. In the results of ESIQTOF tandem mass analysis and database research, it was revealed that the purified T. granosa anticoagulant protein (TGAP) has 7.7 kDa of molecular mass and its partial sequence, HTHLQRAPHPNALGYHGK, has a high identity (64%) with serine/threonine kinase derived from Rhodopirellula baltica (order Planctomycetales, marine bacteria). TGAP could potently prolong thrombin time (TT), corresponding to inhibition of thrombin (FIIa) formation. Specific factor inhibitory assay showed that TGAP inhibits FVa among the major components of prothrombinase complex. In vitro assay for direct-binding affinity using surface plasmon resonance (SPR) spectrometer indicated that TGAP could be directly bound with FVa. In addition, the binding affinity of FVa to FII was decreased by addition of TGAP in dose-dependant manner (IC50 value = 77.9 nM). These results illustrated that TGAP might interact with a heavy chain of FVa (FVa(H)) bound to FII in prothrombin complex. The present study elucidated that non-cytotoxic T. granosa anticoagulant protein (TGAP) bound to FVa can prolong blood coagulation time by inhibiting conversion of FII to FIIa in blood coagulation cascade. In addition, TGAP did not significantly (P < 0.05) show fibrinolytic activity and cytotoxicity on venous endothelial cell line (ECV 304).     

A colorimetric assay for measuring the lysis of a plasma clot.

The present study describes a simple, quantitative assay for measuring the lysis of a plasma clot. The principle of the assay is based on the release of Coomassie brilliant blue R-250 dye from the clot. Thirty microliters of freshly prepared Coomassie brilliant blue R-250 (1 mg/ml) was added to 200 microliters of diluted human plasma (1:5). After mixing, 100 microliters of thrombin (2.5 NIH units/ml) were added to mediate a plasma clot. One milliliter of streptokinase (0.1 mg/ml) was used as a plasminogen activator to initiate clot lysis. During the course of lysis, 100 microliters of soluble material were transferred to microtiter wells and the absorbance at 540 nm was determined as a measure of clot lysis. This assay was used to measure clot lysis in 18 human plasma samples. The colorimetric method (X) developed in this report correlated well with that determined using a conventional 125I-fibrinogen method (Y): Y = 0.83X + 7.98 (r = 0.91).     

Direct solid phase radioimmunoassay for chicken lipoprotein lipase.

A direct, noncompetitive immunoassay for chicken lipoprotein lipase (LPL) was developed. Antibodies to LPL were purified by immunoadsorption chromatography of goat antisera on an LPL-Sepharose column. Purified anti-LPL immunoglobulins were coupled covalently to hydrophilic polyacrylamide beads by a carbodiimide reagent. An excess amount of these beads was incubated with the sample or the standard to be assayed. The amount of LPL immobilized by the beads was then detected by an excess amount of ¹²⁵I-labeled anti-LPL immunoglobulin. A linear relationship was obtained between the radioactivity bound and the amount of highly purified LPL used as a standard. The range of the assay was from 0.1-1.1 ng LPL. The assay was specific for chicken LPL and showed no cross-reactivity with liver lipase. It does not distinguish heat-inactivated from catalytically active enzyme species. This assay should be useful in studies of lipoprotein lipase where both catalytic activity and enzyme mass need to be quantitated.     

Supported Bilayers with Excess Membrane Reservoir: A Template for Reconstituting Membrane Budding and Fission

A complete mechanistic understanding of membrane-localized processes in vesicular transport, such as membrane budding and fission, requires their reconstitution with biochemically-defined components from a biochemically-defined substrate. Supported bilayers formed by vesicle fusion represent an attractive substrate for this purpose. However, conventional supported bilayers lack a sufficient membrane reservoir to recreate membrane budding and fission events. We describe the formation of supported bilayers with excess membrane reservoir (SUPER) templates from the fusion of liposomes containing negatively charged lipids on silica beads under high-ionic-strength conditions. Using a fluorescence microscopy-based assay to monitor early and late stages of supported bilayer formation, we show that an increase in ionic strength leads to an increase in the rates of liposome adsorption and subsequent fusion during formation of supported bilayers. The two rates, however, increase disproportionally, leading to accumulation of excess reservoir with an increase in ionic strength. SUPER templates allow the seamless application of microscopy-based assays to analyze membrane-localized processes together with sedimentation-based assays to isolate vesicular and nonvesicular products released from the membrane. The results presented here emphasize the general utility of these templates for analyzing vesicular and nonvesicular transport processes.     

Autographa californica nuclear polyhedrosis virus DNA polymerase: measurements of processivity and strand displacement

The DNA polymerase (DNApol) of Autographa californica nuclear polyhedrosis virus was purified to homogeneity from recombinant baculovirus-infected cells. DNApol was active in polymerase assays on singly primed M13 template, and full-length replicative form II product was synthesized at equimolar ratios of enzyme to template. The purified recombinant DNApol was shown to be processive by template challenge assay. Furthermore, DNApol was able to incorporate hundreds of nucleotides on an oligo(dT)-primed poly(dA) template with limiting amounts of polymerase. DNApol has moderate strand displacement activity, as it was active on nicked and gapped templates, and displaced a primer in a replication-dependent manner. Addition of saturating amounts of LEF-3, the viral single-stranded DNA-binding protein (SSB), increased the innate strand displacement ability of DNApol. However, when LEF-3 was added prior to the polymerase, it failed to stimulate DNApol replication on a singly primed M13 template because the helix-destabilizing activity of LEF-3 caused the primer to dissociate from the template. Escherichia coli SSB efficiently substituted for LEF-3 in the replication of a nicked template, suggesting that specific protein-protein interactions were not required for strand displacement in this assay.     

Molecular characterization of a dual inhibitory and mutagenic activity of 5-fluorouridine triphosphate on viral RNA synthesis. Implications for lethal mutagenesis

The basis for a dual inhibitory and mutagenic activity of 5-fluorouracil (5-FU) on foot-and-mouth disease virus (FMDV) RNA replication has been investigated with purified viral RNA-dependent RNA polymerase (3D) in vitro. 5-Fluorouridine triphosphate acted as a potent competitive inhibitor of VPg uridylylation, the initial step of viral replication. Peptide analysis by mass spectrometry has identified a VPg fragment containing 5-fluorouridine monophosphate (FUMP) covalently attached to Tyr3, the amino acid target of the uridylylation reaction. During RNA elongation, FUMP was incorporated in the place of UMP or CMP by FMDV 3D, using homopolymeric and heteropolymeric templates. Incorporation of FUMP did not prevent chain elongation, and, in some sequence contexts, it favored misincorporations at downstream positions. When present in the template, FUMP directed the incorporation of AMP and GMP, with ATP being a more effective substrate than GTP. The misincorporation of GMP was 17-fold faster opposite FU than opposite U in the template. These results in vitro are consistent with the mutational bias observed in the mutant spectra of 5-FU-treated FMDV populations. The dual mutagenic and inhibitory activity of 5-fluorouridine triphosphate may contribute to the effective extinction of FMDV by 5-FU through virus entry into error catastrophe.     

Fluorometric assay for tissue transglutaminase-mediated transamidation activity

Herein, we report the development of a direct discontinuous fluorometric transamidation assay for determining tissue transglutaminase (TG2) activity. In the assay reaction, TG2 catalyzes the formation of a biotin-fluorophore conjugate, using a fluorescent, high affinity γ-glutamyl donor substrate and a biotinylated amine as a γ-glutamyl acceptor substrate. After the reaction, the conjugate is fixed on streptavidin-coated beads and excess substrate is washed away, allowing the transamidation activity to be quantified by fluorescence measurement. This method was used to detect the activity of as little as 0.6 mU of purified TG2, and can be used for detection of activity from crude cellular lysates. Furthermore, this assay can be used for screening potential inhibitors and synthetic substrates, the latter of which was demonstrated herein.     

Magnetic, microplate-format plasmid isolation protocol for high-yield, sequencing-grade DNA

We have developed a rapid, microplate-format plasmid isolation procedure to purify sequencing-grade DNA templates for high-throughput DNA sequencing operations. A modified lysozyme/boiling method is used to produce a plasmid-containing supernatant that is then purified by iron bead capture. After binding, the beads are pelleted in a magnetic field, washed and the DNA eluted in water. The method yields up to 10 micrograms plasmid DNA from a 1-mL overnight culture in a deep-well microplate. The procedure is suitable for large-scale experiments, amenable to automation and does not require expensive reagents or equipment. The entire protocol can be completed in as little as 2 h, and one technician with a 96-well pipetting station can process up to 48 plates per day. This protocol is ideal for any high-throughput operation in which template quantity, quality and reproducibility are of primary importance.