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1

Inhibitors of DNA polymerase beta inhibit base excision repair

100%
Yoshida S., Ogawa A.
Polish Journal of Environmental Studies
|
1999
|
tom 08
|
nr 5
2

Characterization of the mitochondrial DNA polymerase from Saccharomyces cerevisiae

100%
Sen S., Mukhopadhyay S., Wetzel J., Biswas T. K.
Acta Biochimica Polonica
|
1994
|
tom 41
|
nr 1
The mitochondrial DNA (mtDNA) polymerase was isolated from a protease-deficient yeast strain (PY2), and purified about 3000 fold by a column chromatography on phosphocellulose, heparin-agarose, and single-stranded DNA cellulose. The purified polymerase was characterized with respect to optimal nucleotide concentration, template-primer specificity and sensitivity to some inhibitors. These results were compared with the nuclear DNA polymerase I activity. Both polymerases showed similar requirement of deoxynucleotide concentrations (Km < 1 uM), and highest activity with poly(dA-dT) template. However, the mtDNA polymerase was more sensitive to ddTTP, EtBr and Mn2+ inhibition in comparison to the nuclear DNA polymerase I. The mtDNA polymerase did not need ATP as an energy source for in vitro DNA synthesis. This mtDNA polymerase preparation also showed 3' -> 5' exonudease activity.
3

Butylphenyl-dGTP as a structural probe of B family DNA polymerases

100%
Stattel J. M., Wright G. E.
Postępy Biochemii
|
1995
|
tom 41
|
nr 5
4

Cloning and characterisation of the 5'part of the high molecular weight transcript of rat DNA polymerase beta

88%
Konopinski R., Nowak R., Siedlecki J. A.
Acta Biochimica Polonica
|
1995
|
tom 42
|
nr 2
A rat brain cDNA library has been constructed. Three identical clones of about 2.2 kb representing high molecular weight DNA polymerase p transcript were found. Sequencing proved our earlier suggestion that both high and low molecular weight DNA polymerase p transcripts have the same open reading frame and differ mainly at the 3' end. Because of that, alternative polyadenylation is discussed as a possible mechanism for tissue- and development-specific regulation of the DNA polymerase p gene expression.
5

Nucleotide probes of DNA polymerases

88%
Wright G. E.
Acta Biochimica Polonica
|
1996
|
tom 43
|
nr 1
The modified nucleotides, N2-(p-n-butylphenyl)dGTP and 2-(p-n-butylanilino) dATP and related compounds have been developed as inhibitor-probes of B family DNA polymerases. Synthetic approaches to these compounds are summarized. The nucleotides are potent, non-substrate inhibitors of DNA polymerase a. In contrast, they inhibit other members of the family with less potency but act as substrates for these enzymes. Modelling of the inhibitor: enzyme binding mechanism has been done based on the known structure of E. coli DNA polymerase I, and site-directed muta­genesis experiments to evaluate this mechanism are proposed.
6

Recombinant His-tagged DNA polymerase. II. Cloning and purification of Thermus aquaticus recombinant DNA polymerase [Stoffel fragment]

75%
Dabrowski S., Kur J.
Acta Biochimica Polonica
|
1998
|
tom 45
|
nr 3
The Stoffel DNA fragment, shortened by 12 bp from 5' end, coding for StoffelDNA polymerase (missing 4 amino acids at N-terminus of Stoffel amino-acids sequence) from the thermophilic Thermus aquaticus (strain YT-1) was amplified, cloned and expressed in Escherichia coli. The recombinant Stoffel fragment contained a polyhistidine tag at the N-terminus (21 additional amino acids) that allowed its single-step isolation by Ni2+ affinity chromatography. The enzyme was characterized and displayed high DNA polymerase activity and thermostability evidently higher than the native Tag DNA polymerase.
7

Role of the DNA polymerase III in mutagenesis in the yeast Saccharomyces cerevisiae

75%
Zaborowska D., Baranowska H., Zuk J.
Bulletin of the Polish Academy of Sciences. Biological Sciences
|
1994
|
tom 42
|
nr 1
8

Recombinant His-tagged DNA polymerase. I. Cloning, purification and partial characterization of Thermus thermophilus recombinant DNA polymerase

75%
Dabrowski S., Kur J.
Acta Biochimica Polonica
|
1998
|
tom 45
|
nr 3
The Tth DNA polymerase gene from the thermophilic Thermus thermophilus (strain HB8) was amplified, cloned and expressed in Escherichia coli. The recombinant DNA polymerase containing a polyhistidine tag at the N-terminus was isolated in a single step by Ni2+ affinity chromatography. The purified recombinant enzyme, showing high polymerase activity contained 43 additional amino-acid residues (including a cluster of six histidine residues inserted for purification of the recombinant protein by metal-affinity chromatography) at N-terminus. The applied overexpression system was very efficient giving 700000 u of DNA polymerase activity from 1 liter of induced culture. The enzyme was characterized and displayed high DNA polymerase and reverse transcriptase activities and high thermostability as compared to the native Tht DNA polymerase.
9

Repair of DNA alkylation damage

75%
Bouziane M., Miao F., Ye N., Holmquist G., Chyzak G., O'Connor T. R.
Acta Biochimica Polonica
|
1998
|
tom 45
|
nr 1
Alkylation damage of DNA is one of the major types of insults which cells must repair to remain viable. One way alkylation damaged ring nitrogens are repaired is via the Base Excision Repair (BER) pathway. Examination of mutants in both BER and Nucleotide Excision Repair show that there is actually an overlap of repair by these two pathways for the removal of cytotoxic lesions in Escherichia coli. The enzymes removing damaged bases in the first step in the BER pathway are DNA glycosylases. The coding sequences for a number of methylpurine-DNA glycosylases (MPG proteins) were cloned, and a comparison of the amino-acid sequences shows that there are some similarities between these proteins, but nonetheless, compared to other DNA glycosylases, MPG proteins are more divergent. MPG proteins have been purified to homogeneity and used to identify their substrates ranging from methylating agents to deamination products to oxidatively damaged bases. The ligation-mediated polymerase chain reaction has been used to study the formation of alkylation damage, and its repair in mammalian cells. We have studied DNA damage in the PGK1 gene for a series of DNA alkylating agents including N-methyl-N'-nitro-N-nitrosoguanidine, Mechlorethamine, and Chlorambucil and shown that the damage observed in the PGK1 (phosphoglycerate kinase 1) gene depends on the alkylating agent used. This report reviews the literature on the MPG proteins, DNA glycosylases removing 3-methyladenine, and the use of these enzymes to detect DNA damage at the nucleotide level.
10

Gemcitabine affects the detection of deoxyribonucleotides with a DNA polymerase elongation assay

75%
Van Moorsel C. J. A., Smid K., Pinedo H. M., Peters G. J.
Cellular and Molecular Biology Letters
|
1999
|
tom 04
|
nr 3
11

Involvement of the essential yeast DNA polymerases in induced gene conversion

75%
Halas A., Ciesielski A., Zuk J.
Acta Biochimica Polonica
|
1999
|
tom 46
|
nr 4
In the yeast Saccharomyces cerevisiae three different DNA polymerases α, δ and ε are involved in DNA replication. DNA polymerase α is responsible for initiation of DNA synthesis and polymerases δ and ε are required for elongation of DNA strand during replication. DNA polymerases δ and ε are also involved in DNA repair. In this work we studied the role of these three DNA polymerases in the process of recombinational synthesis. Using thermo-sensitive heteroallelic mutants in genes encoding DNA polymerases we studied their role in the process of induced gene conversion. Mutant strains were treated with mutagens, incubated under permissive or restrictive conditions and the numbers of convertants obtained were compared. A very high difference in the number of convertants between restrictive and permissive conditions was observed for polymerases α and δ, which suggests that these two polymerases play an important role in DNA synthesis during mitotic gene conversion. Marginal dependence of gene conversion on the activity of polymerase ε indicates that this DNA polymerase may be involved in this process but rather as an auxiliary enzyme.
12
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The expression of UVR3 and two putative photolyases, PHR2 and At4g25290, is regulated by light

63%
Sztatelman O., Labuz J., Banas A. K.
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
|
2013
|
tom 94
|
nr 3
13

Characterization of the protein gp1 from bacteriophage phiIN93

63%
Matsushita I., Yanase H.
Biological Letters
|
2011
|
tom 48
|
nr 1
14

Mutation in DNA polymerase gamma cause error prone DNA synthesis in human mitochondrial disorders

63%
Copeland W. C., Ponamarev M. V., Nguyen D., Kunkel T. A., Longley M. J.
Acta Biochimica Polonica
|
2003
|
tom 50
|
nr 1
This paper summarizes recent advances in understanding the links between the cell's ability to maintain integrity of its mitochondrial genome and mitochondrial ge­netic diseases. Human mitochondrial DNA is replicated by the two-subunit DNA polγ- merase γ (pol γ). We investigated the fidelity of DNA replication by pol γ with and with­out exonucleolytic proofreading and its p55 accessory subunit. Pol γ has high base substitution fidelity due to efficient base selection and exonucleolytic proofreading, but low frameshift fidelity when copying homopolymeric sequences longer than four nucleotides. Progressive external ophthalmoplegia (PEO) is a rare disease character­ized by the accumulation of large deletions in mitochondrial DNA. Recently, several mutations in the polymerase and exonuclease domains of the human pol γ have been shown to be associated with PEO. We are analyzing the effect of these mutations on the human pol γ enzyme. In particular, three autosomal dominant mutations alter amino acids located within polymerase motif B of pol γ. These residues are highly con­served among family A DNA polymerases, which include T7 DNA polymerase and E. coli pol I. These PEO mutations have been generated in pol γ to analyze their effects on overall polymerase function as well as the effects on the fidelity of DNA synthesis. One mutation in particular, Y955C, was found in several families throughout Europe, including one Belgian family and five unrelated Italian families. The Y955C mutant pol γ retains a wild-type catalytic rate but suffers a 45-fold decrease in apparent binding affinity for the incoming dNTP. The Y955C derivative is also much less accurate than is wild-type pol γ, with error rates for certain mismatches elevated by 10- to 100-fold. The error prone DNA synthesis observed for the Y955C pol γ is consistent with the accumulation of mtDNA mutations in patients with PEO. The effects of other pol γ mutations associated with PEO are discussed.
15

Modified substrates of DNA polymerases and design of antivirals

63%
Krayevsky A. A., Alexandrova L., Dyatkina N. B., Kukhanova M. K., Shirokova E. A.
Acta Biochimica Polonica
|
1996
|
tom 43
|
nr 1
The results obtained in our laboratory on investigating of substrate properties of a large number of compounds towards different DNA polymerases have been summarized. On the basis of systematic analysis a directed synthesis of nucleotides with antiviral properties was performed.
16

Some aspects of the SOS response system - A critical survey

63%
Janion C.
Acta Biochimica Polonica
|
2001
|
tom 48
|
nr 3
The SOS system and SOS mutagenesis are frequently studied, or exploited to obtain an increase in mutagenicity of bacteria. Here a short survey is made of the phenome­non of SOS response with special attention to latest and less discussed data, especially the induction of the SOS system in response to cell starvation or mutation of certain genes and the role of inducible DNA polymerases.
17

Mammalian DNA polymerases

63%
Siedlecki J. A., Nowak R.
Postępy Biochemii
|
1995
|
tom 41
|
nr 5
18

The essential DNA polymerases delta and epsilon are involved in repair of UV-damaged DNA in the yeast Saccharomyces cerevisiae

63%
Halas A., Policinska Z., Baranowska H., Jachymczyk W. J.
Acta Biochimica Polonica
|
1999
|
tom 46
|
nr 2
We have studied the ability of yeast DNA polymerases to carry out repair of lesions caused by UV irradiation in Saccharomyces cerevisiae. By the analysis of postirradiation relative molecular mass changes in cellular DNA of different DNA polymerases mutant strains, it was established that mutations in DNA polymerases δ and ε showed accumulation of single-strand breaks indicating defective repair. Mutations in other DNA polymerase genes exhibited no defects in DNA repair. Thus, the data obtained suggest that DNA polymerases δ and ε are both necessary for DNA replication and for repair of lesions caused by UV irradiation. The results are discussed in the light of current concepts concerning the specifity of DNA polymerases in DNA repair.
19

Effect of SOS-induced Pol II, Pol IV, and Pol V DNA polymerases on UV-induced mutagenesis and MFD repair in Escherichia coli cells

51%
Wrzesinski M., Nowosielska A., Nieminuszczy J., Grzesiuk E.
Acta Biochimica Polonica
|
2005
|
tom 52
|
nr 1
Irradiation of organisms with UV light produces genotoxic and mutagenic lesions in DNA. Replication through these lesions (translesion DNA synthesis, TSL) in Escherichia coli requires polymerase V (Pol V) and polymerase III (Pol III) holoenzyme. However, some evidence indicates that in the absence of Pol V, and with Pol III inactivated in its proofreading activity by the mutD5 mutation, efficient TSL takes place. The aim of this work was to estimate the involvement of SOS-inducible DNA polymerases, Pol II, Pol IV and Pol V, in UV mutagenesis and in mutation frequency decline (MFD), a mechanism of repair of UV-induced damage to DNA under conditions of arrested protein synthesis. Using the argE3→Arg+ reversion to prototrophy system in E. coli AB1157, we found that the umuDC-encoded Pol V is the only SOS-inducible polymerase required for UV mutagenesis, since in its absence the level of Arg+ revertants is extremely low and independent of Pol II and/or Pol IV. The low level of UV-induced Arg+ revertants observed in the AB1157mutD5DumuDC strain indicates that under conditions of disturbed proofreading activity of Pol III and lack of Pol V, UV-induced lesions are bypassed without inducing mutations. The presented results also indicate that Pol V may provide substrates for MFD repair; moreover, we suggest that only those DNA lesions which result from umuDC-directed UV mutagenesis are subject to MFD repair.
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