38 research outputs found
Reply to "Comment on 'Inflation with a graceful exit and entrance driven by Hawking radiation' "
No full textThe Comment [J. T. Firouzjaee, preceding Comment, Phys. Rev. D 89, 068301 (2014)] raises two points in regard to our paper [S. K. Modak and D. Singleton, Phys. Rev. D 86, 123515 (2012)]. The first is that one cannot use the tunneling picture to obtain the temperature and particle production rate in the Friedman-Robertson-Walker space-time. The second comment raised by Firouzjaee is that the Hawking-like radiation model for inflation presented in [Modak and Singleton; S. K. Modak and D. Singleton, Int. J. Mod. Phys. D 21, 1242020 (2012)] is inconsistent with the observed scalar and tensor perturbation spectrum. We show that the first comment is beside the point-we do not use the tunneling method in our papers [Modak and Singleton; Modak and Singleton]. The second criticism by Firouzjaee comes from the author evaluating quantities at different times-he evaluates the parameters of our model at the beginning of inflation and then compares this with the scalar and tensor perturbations evaluated at the horizon exit point.From Physical Review D, Vol.89(6), 68302, available online: http://dx.doi.org/10.1103/PhysRevD.89.068302. Copyright ©2014 by American Physical Society.Publisher version: https://doi.org/10.1103/PhysRevD.89.06830
The J-helix ofEscherichia coliDNA Polymerase I (Klenow Fragment) Regulates Polymerase and 3′– 5′-Exonuclease Functions
No full textCharacterızatıon of catalytıc carboxylate trıad ın non-replıcatıve dna polymerase III (pol E) of Geobacillus kaustophilus HTA
No full textSANDALLI, Cemal/0000-0002-1298-3687Three aspartic acid residues D378, D380 and D531 form the catalytic carboxylate triad in Geobacillus kaustophilus (Gka) DNA polymerase III alpha-subunit homolog, pol E. We cloned, expressed and purified wild type (WT), alanine (D -> A) and glutamate (D -> E) mutant enzymes of D378, D380 and D531. the WT and mutant enzymes were biochemically characterized for DNA binding, dNTP binding and catalytic activity in the presence of two metal ions (Mg2+ and Mn2+). the polymerase activity of all mutant enzymes was lost in the presence Mg2+, whereas D378E and D531E mutant enzymes showed about 35 and 60 percent activity, with Mn2+. D380E mutant enzyme did not show noticeable activity with either metal ions suggesting its absolute requirement in polymerase reaction. Kinetic characterization of individual mutant proteins showed that the template-primer binding affinity (K-D.DNA) did not change due to both D -> A or D -> E mutation. the K-M.dNTP for D378E and D531E increased by about 10- and 100-fold, compared to WT enzyme implicating the function of these residues in dNTP binding. Based on these results and the analysis of the available crystal structures of the homologous enzyme species in their apo and E. DNA. dNTP ternary complex forms, we conclude that D378 and D531 are mainly responsible for the binding of metal chelated substrate dNTP, while D380 is solely responsible for the chemical step of phosphodiester bond formation.TUBITAKTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK)This study was supported by a scholarship to C. Sandalli from TUBITAK
Photoaffinity labeling of DNA template-primer binding site in Escherichia coli DNA polymerase I. Identification of involved amino acids.
No full textSite directed mutagenesis of DNA polymerase I (Klenow) from Escherichia coli. The significance of Arg682 in catalysis
No full textMolecular modeling of the interactions between Escherichia coli DNA polymerase I and substrates
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Adenosine 5′-triphosphate (ATP)-mediated stimulation and suppression of DNA synthesis in lymphoid cells. II. Suppressive effect of ATP on murine T-cell functions
No full textThe suppressive effects of ATP on murine T-cell functions were studied. The suppressive effects of ATP as well as adenosine on the DNA synthesis of spleen cells are due to the presence of mature T-cells, because ATP has no suppressive effect on athymic nu/nu spleen cells. Further characterization of the cells which are responsible for ATP-mediated suppression of DNA synthesis revealed that the cells are nylon wool-adherent T-cells and PHA-reactive T-cells. In addition, the suppressive effects of ATP on both spontaneous and mitogen-induced proliferative responses are stronger than that of adenosine, and T-cells are more sensitive to ATP than B-cells. The observation that both ATP and adenosine have unique effects on T-cells compared to B-cells may contribute toward explaining why patients with severe combined immunodeficiency (SCID) associated with adenosine deaminase (ADA) deficiency have greater T-cell than B-cell abnormalities
Comparison of DIG-11-dUTP utilization by Geobacillus caldoxylosilyticus TK4, Mycobacterium tuberculosis and Escherichia coli DNA polymerases
No full textDNA polymerases are used for many applications and we comparatively investigated DNA synthesis activity of DNA polymerase I enzymes of Geobacilluscaldoxylosilyticus TK4, Escherichia coli and Mycobacterium tuberculosis with DIG-11-dUTP using synthetic DNA substrates. We showed that Gca polymerase I and Klenow Fragment (KF) used DIG-11-dUTP instead of dTTP almost at the same ratio, but more efficiently than Mtb polymerase I. We considered that Gca polymerase I could be efficiently used to label a DNA oligonucleotide either internally or at the 3?-terminus by DIG-11-dUTP for the generation of non-radioactive labeled DNA substrates at higher temperature than KF. All three polymerases could not elongate the primer terminus after adding ddNTPs into DNA that is characteristic for all known DNA polymerase I enzymes. © Springer Science+Business Media B.V. 2009.Karadeniz Teknik Üniversitesi: BAP-2005.111.004.1 Türkiye Bilimsel ve Teknolojik Araştirma Kurumu: TUBİTAK-105T216Acknowledgment This study was supported by grants from The Scientific and Technical Research Council of Turkey (TUBİTAK-105T216) and Karadeniz Technical University (BAP-2005.111.004.1) and a scholarship to C. Sandalli from TUBİTAK
Identification of a pharmacophore for nucleoside analog inhibitors directed at HIV‐1 reverse transcriptase
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