Mutability of DNA polymerase I: implications for the creation of mutant DNA polymerases

DNA polymerases of the Family A catalyze the addition of deoxynucleotides to a primer with high efficiency, processivity, and selectivity-properties that are critical to their function both in nature and in the laboratory. These polymerases tolerate many amino acid substitutions, even in regions that are evolutionarily conserved. This tolerance can be exploited to create DNA polymerases with novel properties and altered substrate specificities, using rational design and molecular evolution. These efforts have focused mainly on the Family A DNA polymerises -Taq, E. coli Pol I, and T7 - because they are widely utilized in biotechnology today. The redesign of polymerases often requires knowledge of the function of specific residues in the protein, including those located in six evolutionarily conserved regions. The most well characterized of these are motifs A and B, which regulate the fidelity of replication and the incorporation of nucleotide analogs such as dideoxynucleotides. Regions that remain to be more thoroughly characterized are motif C, which is critical for catalysis, and motifs 1, 2 and 6, all of which bind to DNA primer or template. Several recently identified mutants with abilities to incorporate nucleotides with bulky adducts have mutations that are not located within conserved regions and warrant further study. Analysis of these mutants will help advance our understanding of how DNA polymerases select bases with high fidelity.     

The HeLa cell protein TEF-1 binds specifically and cooperatively to two SV40 enhancer motifs of unrelated sequence

We have purified a protein (TEF-1) that specifically binds to two sequence unrelated motifs (GT-IIC and Sph) of the simian virus 40 (SV40) enhancer. TEF-1 binds cooperatively to templates containing tandem but not inverted or spaced repeats of its cognate motifs. This cooperative binding correlates with the ability of the tandem repeats to generate enhancer activity in vivo. In contrast, TEF-1 and a second SV40 enhancer binding protein, TEF-2, bind independently to templates containing the cognate motifs of both proteins (GT-I and either GT-IIC or Sph motifs) even though these motifs cooperate in enhancer activity in vivo. These results allow us to distinguish different classes of enhancer factors.     

Evidence for FUS6 as a component of the nuclear-localized COP9 complex in Arabidopsis.

The pleiotropic CONSTITUTIVE PHOTOMORPHOGENIC (COP), DEETIOLATED (DET), and FUSCA (FUS) loci are essential regulatory genes involved in the light control of seedling developmental patterns in Arabidopsis. Although COP1, DET1, COP9, and FUS6 (also called COP11) have been cloned, their biochemical activities and interactions remain elusive. We have recently suggested that multiple pleiotropic COP, DET, and FUS genes may encode subunits of a large regulatory complex. In this study, we generated specific antibodies against Arabidopsis FUS6 and show that accumulation of both COP9 and FUS6 is coordinated in the pleiotropic cop, det, and fus mutant backgrounds and in wild-type plants throughout development. Both COP9 and FUS6 cofractionated into identical high molecular mass fractions in an analytical gel filtration assay, and neither was found in its monomeric form. Moreover, antibodies raised against either COP9 or FUS6 selectively coimmunoprecipitated both proteins. We have also developed an Arabidopsis protoplast immunolocalization assay and demonstrated that the COP9 complex is localized in the nucleus and that its nuclear localization is not affected by light conditions or tissue types. The integrated genetic and biochemical results strongly support the conclusion that both COP9 and FUS6 are components of the nuclear-localized COP9 complex. Therefore, we have provided the strongest evidence for the conclusion that at least some of the pleiotropic COP, DET, and FUS loci act in the same signaling pathway.     

Large granular lymphocytes,Leu 7 reactivity and natural killer cell function in peripheral blood of patients with Hodgkin's disease

Summary The percentage and absolute number of lymphocytes and Leu 7⁺ cells were significantly lower in HD even in active stages. There was no significant difference in the percentage of LGL between the three groups (control, active HD, inactive HD), however, because of differences in counts of lymphocytes the absolute number of LGL was significantly lower in HD even in the active group than that in healthy controls. The absolute count of LGL and Leu 7⁺ cells in patients in remission was significantly higher than that in active HD. Natural cytotoxicity against K-562 cells was also significantly lower in active patients in comparison with controls, while the percentage of cytotoxicity was slightly but not significantly higher in patients in remission than that in the active group. A positive correlation was observed between all the three examined parameters both in controls and in patients with active and inactive HD.     

Development of pulmonary intravascular macrophage function in newborn lambs.

We sought to determine whether pulmonary intravascular macrophages are involved in pulmonary vascular sensitivity to intravenously injected particles in sheep. We estimated that newborn lambs have few of these macrophages at birth but develop a 10-fold greater density within 2 wk. Awake, chronically instrumented newborn lambs showed no change in pulmonary vascular driving pressure (pulmonary arterial minus left atrial pressure) after injection of either liposomes [2 +/- 3 (SD) cmH2O; n = 5] or Monastral blue particles (3 +/- 2 cmH2O; n = 6) and showed no net pulmonary production of thromboxane B2, the stable metabolite of the vasoconstrictor thromboxane A2. In contrast, five of those lambs 2 wk later showed both an increase in pulmonary vascular driving pressure after injection of liposomes and Monastral blue (20 +/- 16 and 25 +/- 15 cmH2O, respectively; P < 0.05) and net pulmonary production of thromboxane B2 (171 +/- 103 and 429 +/- 419 pg/ml plasma, respectively; P < 0.05). Older lambs (n = 5) had higher pulmonary uptakes than newborn lambs (n = 6) of radioactive liposomes (47 +/- 13 vs. 12 +/- 10%; P < 0.01) and Monastral blue (53 +/- 6 vs. 21 +/- 10%; P < 0.05). We conclude that pulmonary intravascular macrophages are responsible for the sensitivity of sheep to intravenous foreign particles and are essential for a cascade of processes leading to microvascular injury.     

A Rapid Protocol For Site-directed Mutagenesis and Gene Synthesis Using Synthetic Oligonucleotides

Abstract

DNA segments of 100 to 150 nucleotides in length have been assembled by overlapping synthetic oligonucleotides and cloned directly into the single stranded vector M13 without purification of the synthetic DNA segments prior to cloning.