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DNA Polymerization (dna + polymerization)

Distribution by Scientific Domains

Chemistry	83%

Selected Abstracts

Controlling DNA Polymerization with a Switchable Aptamer

CHEMBIOCHEM, Issue 14 2007
Eike Friedrichs
Controllable biochemical reactions. DNA polymerization by Taq polymerase can be controlled by switching an aptamer for Taq Pol between a binding and a nonbinding form. [source]

Hypotonic buffer induces meiosis and formation of anucleate cytoplasmic islands in the egg of the two-spotted cricket Gryllus bimaculatus

DEVELOPMENT GROWTH & DIFFERENTIATION, Issue 2 2003
Isao Sarashina
In insects, egg activation is known to occur in vivo and independently of fertilization, but its mechanisms are poorly understood. To gain understanding of these mechanisms, an attempt was made to activate the egg of Gryllus bimaculatus in vitro. It was found that meiosis resumed and was completed in unfertilized eggs treated with hypotonic buffer. Early developmental processes in activated, unfertilized eggs were investigated and compared with those in fertilized eggs. Mitosis did not progress, resulting in formation of anucleate cytoplasmic islands (pseudoenergids). Development in the activated, unfertilized eggs stopped at this stage and both yolk subdivision and cellularization did not occur. To elucidate the role of the nucleus in the developmental process to the syncytial stage in fertilized eggs, eggs were treated with aphidicolin to inhibit DNA polymerization. It was found that pseudoenergids also formed in these aphidicolin-treated fertilized eggs. These results demonstrate that pseudoenergids can increase in number independently of nuclei, suggesting that the cytoplasm rather than the nucleus plays the primary role in development to the syncytial stage in G. bimaculatus. [source]

Probing nonnucleoside inhibitor-induced active-site distortion in HIV-1 reverse transcriptase by transient kinetic analyses

PROTEIN SCIENCE, Issue 8 2007
Qing Xia
Abstract Nonnucleoside reverse transcriptase inhibitors (NNRTI) are a group of structurally diverse compounds that bind to a single site in HIV-1 reverse transcriptase (RT), termed the NNRTI-binding pocket (NNRTI-BP). NNRTI binding to RT induces conformational changes in the enzyme that affect key elements of the polymerase active site and also the association between the two protein subunits. To determine which conformational changes contribute to the mechanism of inhibition of HIV-1 reverse transcription, we used transient kinetic analyses to probe the catalytic events that occur directly at the enzyme's polymerase active site when the NNRTI-BP was occupied by nevirapine, efavirenz, or delavirdine. Our results demonstrate that all NNRTI,RT,template/primer (NNRTI,RT,T/P) complexes displayed a metal-dependent increase in dNTP binding affinity (Kd) and a metal-independent decrease in the maximum rate of dNTP incorporation (kpol). The magnitude of the decrease in kpol was dependent on the NNRTI used in the assay: Efavirenz caused the largest decrease followed by delavirdine and then nevirapine. Analyses that were designed to probe direct effects on phosphodiester bond formation suggested that the NNRTI mediate their effects on the chemistry step of the DNA polymerization reaction via an indirect manner. Because each of the NNRTI analyzed in this study exerted largely similar phenotypic effects on single nucleotide addition reactions, whereas each of them are known to exert differential effects on RT dimerization, we conclude that the NNRTI effects on subunit association do not directly contribute to the kinetic mechanism of inhibition of DNA polymerization. [source]

Novel 3,-O-Fluorescently Modified Nucleotides for Reversible Termination of DNA Synthesis

CHEMBIOCHEM, Issue 1 2010
Taek-Soo Kim Dr.
Serving a double purpose: 3,- O -fluorophore-labeled dTTPs were synthesized and used as reversible terminators of DNA polymerization. Successful incorporation of nucleotides with a bulky 3,- O -fluorophore and detection of fluorescence for base calling can potentially be used to improve sequencing-by-synthesis technology. [source]

Controlling DNA Polymerization with a Switchable Aptamer

In vitro Ruthenation of Human Breast Cancer Suppressor Gene 1 (BRCA1) by the Antimetastasis Compound RAPTA-C and Its Analogue CarboRAPTA-C

CHEMISTRY & BIODIVERSITY, Issue 5 2010
Adisorn Ratanaphan
Abstract The interaction of two ruthenium,arene,1,3,5-triaza-7-phosphaadamantane compounds ([Ru(,6 - p -cymene)Cl2(pta)] and [Ru(,6 - p -cymene)(C6H6O4)(pta)], termed RAPTA-C (3) and carboRAPTA-C (4), resp.) with the DNA sequence of the human breast-cancer suppressor gene 1 (BRCA1) has been studied using a range of techniques that probe conformation, cross-linking, base specificity, restriction analysis, and in vitro inhibition of DNA polymerization. The study demonstrates that substitution of the two labile chloride ligands in 3 by the more stable cyclobutane-1,1-dicarboxylate ligand onto the RAPTA framework reduces the rate of reaction with DNA in a similar manner to the analogous Pt-based drug pair cisplatin (1) and carboplatin (2), suggesting that hydrolysis may be a prerequisite to DNA binding with the Ru compounds. Moreover, the rate of DNA interaction for 3 is in a similar range to that of 2, despite the fact that these compounds have a different therapeutic profile. The similar rates of reaction contrasting with the different modes of activity suggests that the RAPTA compounds may be clinically useful against cancer cells that have developed resistance to Pt-based therapies, particularly involving excision,repair mechanisms. [source]