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)

The sequence of 29 nucleotides in the region preceding the initiation of the transcription of the Escherichia coli tyrosine tRNA gene has been determined. This is: (5') ---GGGGCGCATCATATCAAATGACGCGCCGC--- (3') (3') ---CCCCGCGTAGTATAGTTTACTGCGGCGGCG--- (5'). The general approach used for the sequence determination involved the DNA polymerase I-catalyzed elongation of suitable deoxyribopolynucleotide primers when hybridized to the 1-strand of phi80psuIII plus DNA at the appropriate site. Sequences of the newly grown oligonucleotide chains were determined by a combination of two-dimensional fingerprinting following partial exonucleolytic degradation, nearst neighbor analyses, and determination of pyrimidine tracts. Primer elongations were carried out in a controlled and stepwise manner and the newly grown oligonucleotide chains were kept short by incorporating the following features into the method: (a) the insertion of a ribonucleotide unit at or near the 3' terminus of the primers; (b) the use of a maximum of three nucleoside 5'-triphosphates in the first stage of the elongation reaction isolation of the elongated primer, and its reuse in a second step together with different sets of deoxy-nucleoside triphosphates; and (c) elongation of the primer using all of the four nucleoside triphosphates with one of the triphosphates being supplied in a limiting concentration.
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PMID:The nucleotide sequence in the promoter region of the fene for an Escherichia coli tyrosine transfer ribonucleic acid. 108 50

Exonuclease V (the recBC enzyme) of Escherichia coli can release pyrimidine dimers from ultraviolet-irradiated linear duplex DNA though it acts more slowly on irradiated DNA than on non-irradiated DAN. However, close circular lambda-dv DNA or phi X174 replicative form I DNA is not attacked by exonuclease V even though the DNA has been irradiated and treated with T4 endonuclease V to produce single-stranded breaks at the 5'-side of pyrimidine dimers. When irradiated circular DNA, previously nicked by T4 endonuclease V, is briefly exposed to elevated temperature, the DAN becomes susceptible to the action of exonuclease V, and pyrimidine dimers are selectively released. The increased susceptibility to exonuclease V may be resulted from locarized denaturation, or "fraying" of the 5'-termini at the nicks. The preferential release of pyrimidine dimers was observed when irradiated DNA, treated with T4 endonuclease V, was incubated with crude extracts of Escherichia coli. The activity was found in various strains defective in exonuclease V and/or DNA polymerase I.
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PMID:Action of exonuclease V (the recBC enzyme) on ultraviolet-irradiated DNA. 109 Dec 99

The changes in molecular weight of deoxyribonucleic acid (DNA) synthesized after ultraviolte irradiation of Escherichia coli WP28 uvrA, and strains additionally mutant at polA, exrA, recA, and exrA and polA loci, were examined by alkaline sucrose gradient centrifugation. In a repari=deficient uvrA recA strain, the frequency of breaks in newly synthesized DNA was equal to that for pyrimidine dimers in parental DNA. Measurements of the amounts and rates of postreplication repair of these breaks indicate that (i) repair is two to three times faster when DNA polymerase I is present, although (ii) almost all breaks are repaired regardless of DNA polymerase I activity. (iii) Increased ultraviolet doses lead to an increase in the proportion of breaks remaining unrepaired in uvrA recA, UVRA exrA, and uvrA exrA polA strains. The numbers of unrepaired breaks resemble the numbers expected if repair of one lesion is prevented by proximity of a second lesion.
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PMID:Genetic and kinetic evidence for different types of postreplication repair in Escherichia coli B. 109 49

The kinetic properties of Escherichia coli DNA polymerase I were simplified to those of a 1 deoxynucleotide substrate reaction by the use of polynucleotide templates. With poly(dA)-oligo(dT) as the template-primer complex, Mg2+ decreases the Km of the substrate dTTP but has little or no effect on the Km of the substrate Mg-dTTP, suggesting that multiple pathways involving the binding of Mg2+, dTTP, and Mg-dTTP are operative in forming the active complex. The Km of free Mg2+, extrapolated to zero concentration of substrate (830 = 62 muM), agrees within a factor of 2 with the dissociation constant of magnesium from 4 +/- 1 sites on the enzyme determined previously by binding studies (Slater, J.P., Tamir, I., Loeb, L.A., and Mildvan, A.S. (1972) J. Biol. Chem. 247, 6784-6794). The maximal turnover number with poly(dA) as template is 5.7 +/- 0.7 s-1. Changing the nature of the base in the polydeoxynucleotide template alters the maximal rate of polydeoxynucleotide synthesis by an overall factor of 31 with poly(dC) is greater than poly(dT) is greater than poly(dA) is greater than poly(dG), indicating that pyrimidine templates are copied faster than purine templates. Changing the sugar structure from poly(dA) to poly(rA) causes a 3-fold increase in the rate of template copying. A study of the kinetic effects of all noncomplementary deoxynucleotides with all deoxynucleotide templates, as well as with poly(rA)-oligo(dT), yields complex patterns of activation and inhibition requiring from 1 to 2 additional binding sites for the noncomplementary nucleotides. The kinetically determined affinities of the active site of the enzyme-template-primer complex for the complementary free nucleotide (as measured by Km) generally exceed those for the noncomplementary neuclotides (as measured by KI slope) by 1 or more than 3 orders of magnitude.
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PMID:Kinetic analysis of Escherichia coli deoxyribonucleic acid polymerase I. 110 40

From comparative studies between Escherichia coli PolA107 cells (lacking 5' in equilibrium 3' exonucleoytic activity associated with DNA polymerase I) and the isogenic wild-type strain, and between the purified DNA polymerase I preparations isolated from these strains, it can be concluded that the 5' in equilibrium 5' exonuclease is involved in excision of pyrimidine dimers in E. coli. Evidence is presented that the polA107 mutation is located on that part of the DNA polymerase I gene coding for the small fragment on which 5' in equilibrium 3' exonucleolytic activity is found.
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PMID:Involvement of Escherichia coli DNA polymerase-I-associated 5' in equilibrium 3' exonuclease in excision-repair of UV-damaged DNA. 110 28

Radiation sensitivity in the fungus Neurospora crassa is under the control of at least eight distinct loci and is also affected by cytoplasmic factors. Although radiation-sensitive mutants which affect inter- or intragenic meiotic recombination have not been isolated, mutants which are defective in the repair of pyrimidine dimers have been found. Evidence from both mutational and biochemical studies shows that Neurospora has an excision-repair system for pyrimidine dimers which is very similar to the one found in Escherichia coli. Wild-type strains excise dimers, but two mutants, uvs2 and upr1, are UV sensitive and excision defective. Like the E. coli excision-defective mutants, the Neurospora mutants show a greatly increased frequency of UV-induced mutation at low UV doses, and they do not affect recombination. However, they differ from the E. coli mutants in being significantly more sensitive to ionizing radiation than wild-type strains. A third mutant, uvs6, resembles the DNA polymerase-I-negative mutants of E. coli. It is sensitive to both UV and X-irradiation, has a wild-type pattern of UV-induced mutation, and increases spontaneous deletion frequencies. Its polymerases have not been examined. The high frequency of UV-induced mutation in excision-defective strains suggests that a "mutation prone" system of DNA repair exists in Neurospora. This is supported by the ppoperties of the uvs3 strain, which shows no UV-induced mutation. Like postreplication-repair-defective E. coli mutants, it is UV and ionizing radiation sensitive and sensitive to both monofunctional and bifunctional alkylating agents. This mutant is sterile. As expected, the double mutant uvs3 upr1 strain is much more sensitive to UV than either single-mutant strain. Two other loci, muc2 and gs6, may affect DNA repair. Mutations at the five remaining loci, uvs1, uvs4, uvs5, gs3, and gs20, lead to a constellation of properties unlike those of any DNA-repair-deficient E. coli mutant. The occurrence of these mutations could mean that other DNA repair systems exist in Neurospora, or, like the lon mutants of E. coli, they might indicate that cell sensitivity to radiation damage can be increases in other ways.
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PMID:Genetic control of radiation sensitivity and DNA repair in Neurospora. 110 73

Toluene-treated cells were used for examining excision of pyrimidine dimers in Escherichia coli strains W3110, DM845 (uvrA-), P3478 (polA-), and KS5064 (polAex1). Excision occurring in toluene-treated cells is rapid, adenosine 5'-triphosphate dependent, and requires the uvrA gene function. In strains lacking either the polymerizing or 5' leads to 3' exonucleolytic activity of deoxyribonucleic acid polymerase I, excision does occur. However, both in vivo and in vitro, the excision in such strains is initially slower than wild type.
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PMID:Excision of pyrimidine dimers in toluene-treated Escherichia coli. 110 6

Two mutants at the pyr I locus have been used to study the radiation sensitivity of pyrimidine auxotrophs of U. maydis. The mutant pry I-I has a reduced level of thymidine nucleotides, and this is a likely basis of the sensitivity. This strain is able to excise pyrimidine dimers from its DNA and is cross-sensitive to gamma-rays and nitrosoguanidine (NG) as well as to UV. A diploid heteroallelic at the pyr I locus was UV-sensitive but not deficient in UV-induced mitotic recombination. The results suggest that the UV sensitivity may be due to the failure of a repair DNA polymerase to fill post-excision single-strand gaps in the DNA. The mutant pyr I-I exhibits the property of UV recovery, and this is shown to be dependent on the presence of dimers in the DNA. A mechanism for UV recovery is proposed in which a repair system, possibly involving recombination, is induced by the UV irradiation.
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PMID:Radiation-sensitive pyrimidine auxotrophs of Ustilago maydis. II. A study of repair mechanisms and UV recovery in pyr I. 113 12

UV-induced pyrimidine dimers were excised from the DNA of wild-type and four mutant strains of Ustilago maydis. Excision was partially dose dependent. The kinetics of excision differed in recombination deficient strains (rec 1 and rec 2) from those found in a recombination proficient radiation-sensitive strain (uvs 3). At fluences above 100 J-m-2 excision was saturated in uvs 3 but not in rec 1 or rec 2. Fluences above 300 J-m-2 started to saturate excision in wild-type. pol1-1, a temperature-sensitive DNA polymerase mutant, was excision proficient at both the permissive (22 degree) and restrictive (32 degree) temperatures. Wild-type cells were observed to excise CC before CT or TT in high dose experiments.
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PMID:The excision of pyrimidine dimers from the DNA of mutant and wild-type strains of Ustilago. 115 59

The lowering of the viscosity of DNA solution was caused by the action of AsA or EA and facilitated in the presence of CU2+. However, the action of AsA-3-P was very weak. By sucrose density gradient centrifugation, it was observed that single- and double-strand scissions of DNA were provoked by AsA or EA and enhanced with Cu2+, while only a single-strand scission was caused by AsA-3-P and Cu2+. Similar action of AsA or AsA-3-P was also observed for RNA. Thus, the result indicates that the enediol group of AsA takes an essential part in the breakage of nucleic acids, and Cu2+ enhances the action. It was shown that Apu was mainly decomposed by AsA, whereas Apy not, suggesting that some pyrimidine cluster may be one of the regions attacked by AsA. During the reaction with DNA, the reducing activity of AsA decreased first to some extent and then increased, whereas the reducing activity of AsA-3-P was much lower than that of AsA and decreased steadily. The priming activity of DNA for DNA polymerase was changed after treatment with AsA according to the condition. It was enhanced when DNA was treated under mild conditions but decreased with severer action.
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PMID:Breaking action of ascorbic acid on nucleic acids. 121 77


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