Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound   Target Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound

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Query: EC:2.7.7.7 (DNA polymerase)
17,007 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Pyridoxal phosphate modification of adenovirus DNA polymerase results in loss of DNA polymerase activity, whereas the 3' --> 5' exonuclease activity is unaffected. Inhibition by pyridoxal phosphate is time-dependent, displays saturation kinetics, and is reversible in the presence of excess primary amine unless the pyridoxal phosphate-enzyme adduct is first reduced with NaBH4. Thus, inhibition is the consequence of Schiff base formation between the aldehyde moiety of pyridoxal phosphate and primary amino groups on the enzyme. In addition to inhibiting DNA polymerase activity, pyridoxal phosphate also inhibited the ability of the enzyme to initiate viral DNA replication, by transfer of dCMP onto the preterminal protein. Neither template-primer nor dNTP protect against pyridoxal phosphate inhibition, but the combination of template-primer and complementary substrate dNTP protected both initiation and DNA polymerase activities. Thus, it is likely that both the dCMP transfer activity required for initiation and DNA polymerase activity are carried out at the same site of the enzyme.
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PMID:Pyridoxal 5'-phosphate inhibition of adenovirus DNA polymerase. 879 69

The activity of gemcitabine (dFdC), an effective agent against solid tumors, depends on the incorporation of its triphosphate into DNA. In vitro investigations demonstrated that, depending on the sequence of template DNA, polymerases may pause after incorporation of gemcitabine nucleotide at either the 3'-terminal or 3'-penultimate position. Proofreading enzymes such as 3'-->5' exonucleases, which are associated with DNA polymerases, can excise mismatched deoxynucleotides from DNA. To model this reaction, we evaluated excision of the gemcitabine nucleotide from oligodeoxynucleotide (19-mer) containing 3'-penultimate dFdC monophosphate (dFdCMP) or dCMP by the 3'-->5' exonuclease of the Klenow fragment. The rate of excision of the 3'-terminal deoxynucleotide was similar, with both primers resulting in formation of primers with terminal dCMP or dFdCMP. The primer containing dCMP was further excised, and by 40 min, more than 75% of total radioactivity was in excision products smaller than 18-mer. In contrast, most of the primers (90%) with terminal dFdCMP were unexcised. When primers terminated with either dFdCMP or dCMP were used as substrates, normal primer was hydrolyzed almost completely by 20 min; however, only 40% of primers containing dFdCMP had excision of dFdCMP molecule. Kinetic studies demonstrated that the enzyme had similar affinity for primers containing penultimate or terminal dFdCMP, but the apparent Vmax for excision was 4-5-fold greater for removal of a 3'-terminal deoxynucleotide than for cleavage of a dFdCMP molecule. Reaction conditions that permitted polymerization of one deoxynucleotide to primers containing either 3'-penultimate dCMP or dFdCMP were used to evaluate excision during DNA synthesis. The excised primers could not be extended because the reaction lacked the requisite deoxynucleotide triphosphate. After 5 min, more than one-half of the dCMP primers were extended, whereas only 15% had been excised. In comparison, 30% of the analogue-containing primers lost the terminal deoxynucleotide, with a proportional lower incidence of extension (30%). Lesser excision of dFdCMP-containing substrate was observed in reactions containing deoxynucleotide triphosphates required to make full-length products. Consistent with this result, in the absence of 3'-->5' exonuclease activity, both primers were extended similarly by the polymerization unit of the Klenow fragment. Taken together, these data demonstrate that dFdCMP residues are difficult to excise from DNA, and DNA polymerase can extend primers with 3'-dFdCMP. This results in the internal incorporation of dFdCMP into DNA, as observed in whole cells.
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PMID:Excision of 2',2'-difluorodeoxycytidine (gemcitabine) monophosphate residues from DNA. 881 40

Replication in vivo across unrepaired O6-methylguanine (m6dG) lesions by mammalian DNA polymerase beta (pol beta) during short patch repair may contribute to the cytotoxicity and mutagenesis of m6dG. We have employed in vitro steady state kinetic analysis to investigate the replication of oligonucleotide templates containing site-specific m6dG by human pol beta. Our results show that m6dG is a strong but not absolute block to replication by pol beta. pol beta exhibits mixed kinetic discrimination during overall replication across dG and m6dG. pol beta preferentially inserts dTMP rather than dCMP opposite m6dG. However, pol beta extends from the dC-m6dG base pair more efficiently than from the dT-m6dG base pair. This is in strong contrast to other polymerases such as the exonuclease-deficient Klenow fragment of Escherichia coli DNA polymerase I (exo-KF) that preferentially extends dT-m6dG by a factor of 10 over dC-m6dG. When both insertion and extension are considered, pol beta has a 15-fold overall preference for incorporation of the mutagenic substrate dTTP rather than the nonmutagenic substrate dCTP during replication across m6dG. This suggests that pol beta, in concert with the T:G-specific thymine DNA glycosylase, may be intricately involved in the futile cytotoxic repair induced by m6dG. Our results also suggest that replication across m6dG by pol beta may contribute to m6dG-induced G --> A transition mutations.
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PMID:Replication across O6-methylguanine by human DNA polymerase beta in vitro. Insights into the futile cytotoxic repair and mutagenesis of O6-methylguanine. 891 Apr 63

8-Methyl-2'-deoxyguanosine (8-MedG) was synthesized by reacting dG under the methyl radical generating system and incorporated into oligodeoxynucleotides using phosphoramidite techniques. The site-specifically modified oligodeoxynucleotide containing a single 8-MedG was then used as a template for primer extension reactions catalyzed by the 3' --> 5' exonuclease-free (exo-) Klenow fragment of Escherichia Coli DNA polymerase I and mammalian DNA polymerase alpha. Primer extension catalyzed by the exo- Klenow fragment readily passed the 8-MedG lesion in the template while that catalyzed by pol alpha was retarded opposite the lesion. The fully extended products formed during DNA synthesis were analyzed to quantify the miscoding specificities of 8-MedG. Both DNA polymerases incorporated primarily dCMP, the correct base opposite the lesion, along with small amounts of incorporation of dGMP and dAMP. In addition, two-base deletion was observed only when the exo- Klenow fragment was used. The thermodynamic stability of 8-MedG in the duplex was also studied. The duplex containing 8-MedG:dG was more thermally and thermodynamically stable than that of dG:dG. The duplex containing 8-MedG:dA was more thermodynamically stable than that of dG:dA. We conclude that 8-MedG is a miscoding lesion and capable of generating G --> C and G --> T transversions and deletion in cells.
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PMID:Synthesis, miscoding specificity, and thermodynamic stability of oligodeoxynucleotide containing 8-methyl-2'-deoxyguanosine. 895 Dec 29

DNA damage induced mutations arising during the course of translesion replication are likely to be an important contributory cause in the development of many cancers. In budding yeast, Saccharomyces cerevisiae, a good model system with which to investigate this process, mutagenesis is associated with the RAD6 repair pathway and depends on the functions of the REV1, REV3 and REV7 genes. The Rev3 and Rev7 proteins are subunits of a new type of DNA polymerase, called DNA polymerase zeta, that appears to carry out translesion replication, but no other repair, recombination or replication function. Pol zeta replicates past a T-T cyclobutane dimer with a higher efficiency than yeast pol alpha, is less prone than this enzyme to insert an incorrect nucleotide and is more efficient at elongating from a mismatched terminus. Rev1 protein is a terminal nucleotidyl transferase that inserts dCMP opposite template G, A and abasic sites. Types of mutations induced during translesion replication appear to depend largely on lesion structure, but the frequency and accuracy of bypass also depend on replication conditions. Inhibition of the activity or expression of pol zeta may be clinically useful for patients undergoing cancer therapy or for those with a familial predisposition to cancer.
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PMID:DNA polymerase zeta and the control of DNA damage induced mutagenesis in eukaryotes. 897 26

The miscoding properties of the model estrogen-derived DNA adducts, N2-[3-methoxyestra-1,3,5(10)-trien-6-yl]-2'-deoxyguanosine (dG-N2-3MeE) and N6-[3-methoxyestra-1,3,5(10)-trien-6-yl]-2'- deoxyadenosine (dA-N6-3MeE), have been explored, using an in vitro experimental system to quantify base substitutions and deletions. Site-specifically modified oligodeoxynucleotides containing a single dG-N2-3MeE or dA-N6-3MeE were prepared postsynthetically and used as templates in primer extension reactions catalyzed by Escherichia coli and mammalian DNA polymerases. When the 3'-->5' exonuclease free (exo-) Klenow fragment of DNA polymerase I was used, dG-N2-3MeE promoted mostly one- and two-base deletions, along with small amounts of incorporation of dAMP, dGMP, and dCMP opposite the lesion. dA-N6-3MeE promoted the incorporation of dTMP opposite the lesion as well as two-base deletions, accompanied by the incorporation of dAMP. Using pol alpha, primer extension reactions were blocked at dG-N2-3MeE; however, dA-N6-3MeE promoted preferential incorporation of dTMP opposite the lesion with small amounts of incorporation of dCMP and deletions. Primer extension reactions catalyzed by pol delta were blocked at these lesions. When pol beta was used, dG-N2-3MeE produced small amounts of incorporation of dAMP and deletions. dA-N6-3MeE promoted preferential incorporation of dTMP, along with incorporation of dCMP and two-base deletions. The miscoding specificities and frequencies varied depending on the DNA polymerase used. These results indicate that estrogen-DNA adducts have miscoding potential.
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PMID:Miscoding properties of model estrogen-DNA adducts in reactions catalyzed by mammalian and Escherichia coli DNA polymerases. 904 59

Site-specifically modified oligodeoxynucleotides containing a single natural abasic site or a chemically synthesized (tetrahydrofuran or deoxyribitol) model abasic site were used as templates for primer extension reactions catalyzed by the Klenow fragment of Escherichia coli DNA polymerase I or by calf thymus DNA polymerase alpha. Analysis of the fully extended products of these reactions indicated that both polymerases preferentially incorporate dAMP opposite the natural abasic site and tetrahydrofuran, while DNA templates containing the ring-opened deoxyribitol moiety block translesional synthesis, promoting sequence context-dependent deletions. The frequency of nucleotide insertion opposite the three types of abasic sites follows the order dAMP > dGMP > dCMP > dTMP. The frequency of chain extension was highest when dAMP was positioned opposite a natural abasic site. The frequency of translesional synthesis past abasic sites follows the order tetrahydrofuran > deoxyribose > deoxyribitol. The Klenow fragment promotes blunt end addition of dAMP; this reaction was much less efficient than insertion of dAMP opposite an abasic site. We conclude that the miscoding potential of a natural abasic site in vitro closely resembles that of its tetrahydrofuran analog. Ring-opened abasic sites favor deletions. Studies with polymerase alpha in vitro predict preferential incorporation of dAMP at abasic sites in mammalian cells.
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PMID:Translesional synthesis on DNA templates containing a single abasic site. A mechanistic study of the "A rule". 915 53

The mutagenic properties of 2-acetylaminofluorene-derived DNA adducts, including N-(deoxyguanosin-8-yl)-2-acetylaminofluorene, N-(deoxyguanosin-8-yl)-2-aminofluorene, N-(deoxyguanosin-N2-yl)-2-acetylaminofluorene, and several minor oxidation products have been explored, using site-specific techniques. Oligodeoxynucleotides containing a single AAF-derived DNA adduct were prepared by postsynthetic modification and used as templates in primer extension reactions catalyzed by bacterial and mammalian DNA polymerases. Base substitutions and deletions occurring during DNA synthesis were quantified. dG-C8-AAF promoted one- and two-base deletions and small amounts of incorporation of dCMP, dAMP, and/or dTMP opposite the lesion in reactions catalyzed by the 3'-->5' exonuclease-free Klenow fragment of DNA polymerase 1 (exo-) and polymerase alpha. dG-C8-AF did not miscode in reactions catalyzed by exo-; however, base misincorporation and deletions were observed in reactions with pol alpha. dG-N2-AAF promoted small amounts of dAMP incorporation in reactions catalyzed by exo-. The miscoding potential of minor oxidation products of dG-C8-AF was much higher than that of other adducts. Steady-state kinetics were used to measure frequencies of nucleotide insertion opposite the lesion and chain extension from the 3' terminus. Kinetic data were consistent with the results of primer extension studies. A mutation 'hot spot' was constructed and the influence of sequence context on the frequency of deletions generated by dG-C8-AAF was explored systematically in reactions catalyzed by exo-. Based on our results with aminofluorene DNA adducts, we propose a general mechanism for frameshift deletion mutagenesis. Site-specific methods also were used to establish the mutagenic potential of AAF-derived DNA adducts in mammalian cells. dG-C8-AAF and dG-C8-AF exhibited similar mutagenic specificities, predicting the occurrence of G-->T transversions and G-->A transitions in mammalian cells.
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PMID:Molecular mechanisms of mutagenesis by aromatic amines and amides. 920 40

5-Formyluracil (5-foU) is a major lesion of thymine produced in DNA by ionizing radiation and various chemical oxidants. To assess its biochemical effects on DNA replication, 22mer oligonucleotide templates containing an internal 5-foU at defined sites were synthesized by the phosphoramidite method and examined for ability to serve as a template for various DNA polymerases in vitro . Klenow fragments with and without 3'-->5'exonuclease of DNA polymerase I, Thermus thermophilus DNA polymerase (exonuclease-deficient) and Pyrococcus furiosus DNA polymerase (exonuclease-proficient) read through the site of 5-foU in the template. Primer extension assays revealed that the 5-foU directed not only incorporation of dAMP but also dCMP opposite the lesion during DNA synthesis. Misincorporation opposite 5-foU was unaffected by 3'-->5' exonuclease activity. DNA polymerases had different dissociation rates from a dCMP/T mispair and from a dCMP/5-foU mispair. The incorporation of an 'incorrect' nucleotide was dependent on the sequence context and DNA polymerase used. These results suggest that 5-foU produced in DNA has mutagenic potential leading to T-->G transversions during DNA synthesis.
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PMID:Replication of DNA templates containing 5-formyluracil, a major oxidative lesion of thymine in DNA. 932 44

The treatment of tamoxifen, widely used as adjuvant chemotherapy for breast cancer, increases significantly the risk of developing endometrial cancer. The miscoding properties of tamoxifen-derived DNA adducts, alpha-(N2-deoxyguanosinyl)tamoxifens (dG-N2-tamoxifen), have been explored, using an in vitro experimental system to quantify base substitutions and deletions. Site-specifically modified oligodeoxynucleotides containing an epimer of trans- and cis-forms of dG-N2-tamoxifens were prepared postsynthetically and used as templates in primer extension reactions catalyzed by mammalian DNA polymerases alpha, beta, and delta. Pol alpha catalyzed incorporation of dCMP and dAMP opposite all four stereoisomers of dG-N2-tamoxifen, accompanied by lesser amounts of dGMP. In contrast, pol delta catalyzed preferential incorporation of dCMP, a correct base, opposite the lesions; one of the trans-forms of dG-N2-tamoxifens only promoted incorporation of dTMP. Using pol beta, preferential incorporation of dCMP, along with small amounts of incorporation of dAMP and dGMP, was detected. One- and two base deletions were also observed with pol alpha and pol beta. The miscoding specificities and frequencies of dG-N2-tamoxifens varied depending on the DNA polymerase used. In addition, with pol alpha and pol beta, large amounts of 5-base deletions were preferentially formed at the cis-forms of dG-N2-tamoxifen, but not at the trans-forms of dG-N2-tamoxifen. We conclude that dG-N2-tamoxifen adducts have high miscoding potentials.
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PMID:Miscoding potential of tamoxifen-derived DNA adducts: alpha-(N2-deoxyguanosinyl)tamoxifen. 933 62


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