Inhibition of a novel subspecies of DNA polymerase alpha by 2'-deoxy-2'-azidoadenosine 5'-triphosphate

Optimization of Reporter Cells for Expression Profiling in a Microfluidic Device

The emergence of green fluorescence protein (GFP) technologies has enabled non-invasive monitoring of cell function and gene expression. GFP-based expression studies are typically performed in traditional single-dish or multi-well formats to monitor a small number of genes or conditions that do not lend well to scaling, high-throughput analysis, or single-cell measurements. We have recently developed a microfluidic device, the Living Cell Array (LCA), for monitoring GFP-based gene expression in a high-throughput manner. Here, we report the optimization of GFP reporter cell characteristics in this microfluidic device for gene expression profiling. A reporter cell line for the transcription factor NF-kappa B was generated and used as the model cell line. Reporter cells were seeded in the LCA and NF-kappa B activated by addition of the cytokine TNF-alpha . Our studies show that the fluorescence kinetics from the reporter cell line in response to both single and repeated TNF-alpha stimulation in the LCA is similar to that observed in standard tissue culture. In addition, our data also indicate that multiple expression waves can be reliably monitored from a small population of reporter cells. Using reporter cell line subcloning and cell cycle synchronization, we demonstrate that the kinetics and magnitude of induced fluorescence in the reporter cell lines can be further improved to maximize the fluorescence readout from reporter cell lines, thereby improving their applicability to live cell expression profiling. Our studies establish some of the important criteria to be considered when using reporter cell lines for dynamic expression profiling in microfluidic devices.

Deoxyribonucleotide analogs as inhibitors and substrates of DNA polymerases

Inhibitory and substrate properties of analogs of deoxyribonucleoside triphosphates toward DNA polymerases are reviewed. A general introduction is followed by a description of DNA polymerases and the reaction that they catalyze, and sites at which substrate analogs may inhibit them. Effects of modifications in the major family of compounds, nucleotide derivatives, at the base, sugar and triphosphate portions of the molecule, are summarized with respect to retention of substrate properties and generation of inhibitory properties. Structure-activity relationships and the basis of selectivity in the second family of compounds, deoxyribonucleotide mimics, are also presented. Conclusions are drawn regarding the structural basis of inhibitor selectivity and mechanism, relationship between in vitro and in vivo effects of inhibitors, and the promise of inhibitors as probes for study of active sites of DNA polymerases.

Eucaryotic primase

Eucaryotic primase, an enzyme that initiates de novo DNA replication, is tightly associated with polymerase alpha or yeast DNA polymerase I. It is probably a heterodimer of 5.6 +/- 0.1 S. The enzyme synthesizes oligoribonucleotides of about eight residues which are always initiated with a purine. In vitro the polymerase-primase complex initiates synthesis and pauses at preferred sites on natural single-stranded templates. The relative concentrations of ATP and GTP present in the reaction medium modulate the frequency of site recognition. Primase is strongly ATP-dependent in the presence of single-stranded DNA and of poly(dT). It also synthesizes oligo(rG) in the presence of poly(dC) very efficiently.

Size difference in catalytic polypeptides of two active forms of mouse DNA polymerase alpha and separation of the primase subunit from one form, DNA replicase

There are two active forms of DNA polymerase alpha in mouse cells. One form (DNA replicase) is a DNA polymerase associated with primase activity and the other form (7.3 S polymerase) has no primase activity (Yaugar, T., Kozu, T. and Seno, T. (1982) J. Biol. Chem. 257, 11121-11127). The primase activity was dissociated from partially purified DNA replicase by hydroxyapatite column chromatography in buffer containing dimethyl sulfoxide and ethylene glycol. Nearly homogeneous primase, consisting of a 58 kDa polypeptide was obtained by glycerol gradient sedimentation and DEAE-cellulose column chromatography. Experiments on the effect of proteinase treatment and measurement of the molecular weight of the catalytic polypeptide of DNA replicase after its dissociation from the primase polypeptide indicated that the primase is not part of the DNA polymerase molecule, but an independent protein associated with DNA polymerase alpha, and that the latter is a 115 kDa catalytic polypeptide. The other form of DNA polymerase alpha, 7.3 S polymerase, consists of a 72 kDa catalytic polypeptide. Thus, the two forms of mouse DNA polymerase alpha have partially, if not completely, different catalytic polypeptide structures, suggesting that the 7.3 S polymerase is not simply formed from DNA replicase by dissociation of the primase subunit.

DNA replication of single-stranded DNA of phage fd microinjected into Xenopus laevis eggs

Single-stranded circular DNA of phage fd was microinjected into Xenopus laevis eggs and DNA synthesis was analyzed after incubation. An efficient DNA synthesis occurred in the eggs: 2.7 ng of DNA was newly formed in an egg whose volume is approximately 900 nl during a 5-h incubation at 20 degrees C. The DNA synthesis was sensitive to aphidicolin, suggesting that DNA polymerase alpha participates in the synthesis. Agarose gel electrophoresis showed that full size of fd DNA is synthesized and that replicative form I of fd DNA is the major form of the newly produced DNAs. These results suggest that priming of DNA synthesis, elongation of DNA chain and ligation of DNA strands take place co-operatively in the egg with single-stranded DNA as a template.

2'-Fluoro-2'-deoxycytidine triphosphate as a substrate for RNA- and DNA-dependent DNA polymerases

The ability of the analog 2'-fluoro-2'-deoxycytidine triphosphate (dCflTP) to be used as a substrate in the reactions catalyzed by Xenopus laevis oocytes DNA polymerase alpha and AMV reverse transcriptase has been studied. The apparent Km values for dCTP and dCflTP, using activated DNA as templates, were 0.6 microM and 7 mM with DNA polymerase alpha and 0.14 microM and 7 microM with AMV reverse transcriptase, respectively. As observed with dCTP, aphidicolin was a noncompetitive inhibitor in the DNA polymerase alpha-catalyzed DNA synthesis; the Ki values were about 2 microM for both substrates. dCflTP can also be incorporated into DNA synthetized by other eukaryotic DNA polymerases and by reverse transcriptase with RNA as a template, both in the presence or absence of (dT)12 primer.

Mechanism of stimulation by a specific protein factor of de novo DNA synthesis by mouse DNA replicase with fd phage single stranded circular DNA

Mouse DNA replicase is a functional multienzyme complex consisting of DNA polymerase and DNA primase. The DNA and initiator RNA syntheses by DNA replicase with single stranded DNA as template are stimulated by a stimulating factor (T. Yagura, T. Kozu and T. Seno, 1982, J. Biochem. (Tokyo).91, 607-618). The action mechanism of the stimulating factor on this novel DNA synthesis with fd phage single stranded circular DNA as template was studied. The stimulating factor directly stimulated initiator RNA synthesis but did not change the length of either initiator RNA (8 to 10 nucleotides long) or the product DNA (300 to 1,000 nucleotides long). Kinetic studies and analysis of the products by neutral agarose gel electrophoresis show that the stimulating factor increased the affinity of DNA replicase for template DNA without changing the apparent Km values for deoxy- and ribonucleotide substrates. Thus, in combination with a sufficient amount of the stimulating factor, DNA replicase quantitatively converted the template DNA to the position of double-stranded circular replicative form II DNA, as shown by agarose gel electrophoresis.