• Journal of Microbiology and Biotechnology
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• v.8 no.6
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• pp.669-675
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• 1998

Taq DNA polymerase exhibits a sizable drawback compared to the other thermophilic DNA polymerases in that it demonstrates lower proof-reading activity due to the deficiency of 3'-5'exonuclease activity. A study was undertaken to improve the 3'-5' exonuclease activity in the PCR of Taq DNA polymerase. The three-dimensional structural alignment of the polymerase and 3'-5' exonuclease domains from the pol I family DNA polymerases explains why Taq DNA polymerase has just a background level of 3'-5'exonuclease activity. A comparison indicated that the two polymerase domains are very similar in primary and tertiary conformations, even though Taq DNA polymerase carries a much shorter 3'-5'exonuclease domain than that of E. coli DNA polymerase I. Those two polymerase domains were interchanged between Taq DNA polymerase and E. coli DNA polymerase I. The 3'-5' exonuclease domain from E. coli DNA polymerase I was separated and pasted into the polymerase domain of Taq DNA polymerase I, which resulted in a functional fusion-Stoffel fragment. The 3'-5'exonuclease activity of the fusion-Stoffel fragment increased up to 48% of the value of the Klenow fragment, while that of Taq DNA polymerase remained at 6.0% of the Klenow fragment.

• Microbiology and Biotechnology Letters
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• v.38 no.2
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• pp.158-162
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• 2010

The gene encoding N-terminally truncated Tod polymerase ($\Delta$Tod polymerase) from Thermus thermophilus HJ6 was expressed in Escherichia coli under the control of the lambda pR and pL tandem promoters on the expression vector pJLA503. The N-terminal domain (250 amino acids) of Tod polymerase was removed without significant effect on enzyme activity and stability, while no 5'$\rightarrow$3' exonuclease activity was detected. The $\Delta$Tod polymerase was verified to possess very efficient reverse transcriptase (RT) activity in the presence of $MgCl_2$. The cDNA can also be amplified in the polymerase chain reaction (PCR) with this mutant enzyme. The $\Delta$Tod polymerase was exhibited higher activity than the Taq polymerase in a one-step RT-PCR.

• The Microorganisms and Industry
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• v.16 no.3
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• pp.6-14
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• 1990

PRDI DNA polymerase is the smallest member of the family B DNA polymerase (Jung et al., 1987). This DNA polyerase is specified by bacteriophage PRDI which infects a wide variety of gram-negative bacteria(Mindich and Bamford, 1988). Because PRDI is highly amenable to genetic and biochemical manipulation, it is a convenient model system with which to study structure-function relationships of DNA polymerase molecules. To determine the functional roles of the highly conserved regions of the family B DNA polymerases, we have initiated site-directed mutagenesis with PRD1 DNA polymerase, and our results show that mutations at the conserved regions within PRD1 DNA polymerase inactivate polymerase complementing activity and catalytic activity.

• Journal of Microbiology and Biotechnology
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• v.8 no.5
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• pp.471-477
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• 1998

Taq DNA polymerase from Thermus aquaticus is very useful in the polymerase chain reaction. Taq DNA polymerase is classified in the pol I family, represented by E. coli DNA polymerase I. The three-dimensional structural alignment of 3'-5'exonuclease domains from the pol I family DNA polymerases explains why Taq DNA polymerase does not carry out proofreading in polymerase chain reactions. Three sequence motifs, Exo I, II, and III, must exist to carry out 3'-5'exonuclease activity for proof- reading by a 3'-5'exonuclease reaction, but these are abolished in Taq DNA polymerase. The key catalytic module in 3'-5'exonuclease is two metal ions chelated by four active-site carboxylic amino acids. Taq DNA polymerase was mutagenized to construct the catalytic module in the active site. The circular dichroism technique supported the formation of the catalytic module, and the radioactive assay showed that the 3'-5'exonuclease activity doubled in the mutant Taq DNA polymerase.

• Journal of Microbiology and Biotechnology
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• v.14 no.5
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• pp.1022-1030
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• 2004

The gene encoding Aquifex pyrophilus (Apy) DNA polymerase was cloned and sequenced. The Apy DNA polymerase gene consists of 1,725 bp coding for a protein with 574 amino acid residues. The deduced amino acid sequence of Apy DNA. polymerase showed a high sequence homology to Escherichia coli DNA polymerase I-like DNA polymerases. It was deduced by amino acid sequence alignment that Apy DNA polymerase, like the Klenow fragment, has only the two domains, the $3'{\rightarrow}5'$ exonuclease domain and the $5'{\rightarrow}3'$ polymerase domain, containing the characteristic motifs. The Apy DNA polymerase gene was expressed under the control of T7lac promoter on the expression vector pET-22b(+) in E. coli. The expressed enzyme was purified by heat treatment, and Cibacron blue 3GA and $UNO^{TM}$ Q column chromatographies. The optimum pH of the purified enzyme was 7.5, and the optimal concentrations of KCl and $Mg^{2+}$ were 20 mM and 3 mM, respectively. Apy DNA polymerase contained a double strand-dependent $3'{\rightarrow}5'$ proofreading exonuclease activity, but lacked any detectable $5'{\rightarrow}3'$ exonuclease activity, which is consistent with its amino acid sequence. The somewhat lower thermostability of Apy DNA polymerase than the growth temperature of A. pyrophilus was analyzed by the comparison of amino acid composition and pressure effect.

• The Korean Journal of Zoology
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• v.22 no.4
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• pp.141-152
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• 1979

Feline leukemia virus DNA polymerase was purified by ion-exchange and nucleic acid affinity chromatographies. The enzyme consists of a single polypeptide chain of approximately 72, 000 molecular weight as determined by both of a glycerol density gradient centrifugation and SDS-polyacrylamide gel electrophoresis. The preferred divalent cation for DNA synthesis is $Mn^2+$ on a variety of template-primers, and its optimum concentration appears to be significantly lower than reported results of other mammalian type-C viral enzymes. The divalent cation requirement for maximum activity of RNase H is similar to those of DNA polymerase. Both DNA polymerase and RNase H activities appear to reside on the same molecule as demonstrated by the copurification of both activities through various purification steps. An additional RNase H without detectible polymerase activity was generated by a limited chymotrypsin digestion. This RNase H activity was inhibited equally effectively as RNase H in the intact reverse transcriptase by antisera prepared against reverse transcriptase of feline leukemia virus. Neutralization and binding test showed that antibody binding to reverse transcriptase molecule did not completely inhibit the polymerase activity.

• BMB Reports
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• v.33 no.2
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• pp.126-132
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• 2000

The hepadnaviruses replicate their nucleic acid through a reverse transcription step. The MBP-fused HBV polymerase was expressed in E. coli and purified by using amylase affinity column chromatography. The purified protein represented DNA-dependent DNA polymerase activity. In this report, the MBP-HBV polymerase was shown to lack 3'$\rightarrow$5' exonuclease activity, like other retroviral RTs. The ratio of the insertion efficiency for the wrong versus right vase pairs indicates the misinsertion frequency (f). The nucleotide insertion fidelity (1/f), observed with the MBP-HBV polymerase and HIV-1 RT, was between 60 and 54,000, and between 50 and 73,000, respectively, showing that they are in close range. A relatively efficient nucleotide incorporation by the MBP-HBV polymerase was observed with a specificity of three groups: (1) A : T, T : A>C : G, G : C (matched pairs), (2) A : C, C : A>G: T, T : G (purine-pyrimidine and pyrimidine-purine mispairs), and (3) C : C, A : A, G : G, T : T>T : C, C : T>A : G, G : A (purine-purine or pyrimidine-pyrimidine mispairs), and their order is (1)>(2)>(3). The data from the nucleotide insertion fidelity by the MBP-HBV polymerase suggest that the HBV polymerase may be as error-prone as HIV-1 RT.

• BMB Reports
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• v.31 no.5
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• pp.498-502
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• 1998

HBV polymerase shares several regions of amino acid homology with other DNA-directed and RNA-directed polymerases. The amino acid residues $Asp^{429}$, $Gly^{518}$, $Asp^{551}$, $Lys^{585}$, and $Gly^{641}$ in the conserved motifs A, B', C, D, and E in the polymerase domain of HBV polymerase were mutated to alanine or histidine by in vitro site-directed mutagenesis. Those mutants were overexpressed, purified, and analyzed against DNA-dependent DNA polymerase activity and affinity for DNA binding. All those mutants did not show DNA-dependent DNA polymerase activities indicating that those five amino acid residues are all critical in DNA polymerase activity. South-Western analysis shows that amino acid residues $ASp^{429}$ and $ASp^{551}$ are essential to DNA binding, and $Gly^{318}$ and $Gly^{585}$ also affect DNA binding to a certain extent.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.20 no.2
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• pp.136-145
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• 1987

From the sea-urchin, Hemicentrotus pulcherrismus, we have purified by four column chromatographic steps for DNA polymerase $\alpha$ activity. The molecular weight of DNA polymerase u was determined to be around 137,000-138,000 by Sephadex G-200 gel filtration and SDS-polyacrylamide gel electrophoresis. The purified enzyme had the optimal activity at pH 7.4. This enzyme showed to be a function of the metal ion $K^+,\;Na^+$\;and\;Mg^{2+}$ employed as activators, the optimum $K^+$\;or\;Na^+ concentration were 20 mM or 25mM and the optimum $Mg^{2+}$ concentration was 10 mM. The enzyme activity was inhibited by N-ethyl-maleimide, aphidicolin, cytosine $\beta-D-arabinofuranoside$ 5'-triphoshate (ara CTP) and phosphonoacetic acid.

• Korean Journal of Microbiology
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• v.29 no.4
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• pp.209-214
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• 1991

The PRD1 DNA polymerase is a small multi-functional enzyme containing conserved amino acid sequences shared by family B DNA polymerases. Thus the PRD1 DNA polymerase provides an useful model system with which to study structure-functional relationships of DNA polymerase molecules. In order to investigate the functional and structural roles of the highly conserved amino acid sequences, we have introduced three mutations into a conserved amino acid of the PRD1 DNA polymerase. Genetic complememtation study indicated that each mutation inactivated DNA polymerase catalytic activity.