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:5.99.1.2 (topoisomerase)
9,166 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The interaction of DNA topoisomerase II with the long terminal repeat (LTR) of the Drosophila melanogaster 1731 retrotransposon was studied. The covalent binding of topoisomerase II to the LTR was strongly stimulated by different inhibitors of the enzyme 4'-demethylepipodophyllotoxin-9-(4,6-O-2-ethylidene-beta-D-glucopy ranoside (VP-16), 4'-(9-acridinylamino)methanesulfon-m-anisidine) (m-AMSA) and an ellipticine derivative. Enzyme-mediated DNA cleavage could be observed in the absence of inhibitors and was stimulated in their presence. Cleavage occurred predominantly at sites located within or at the boundary of alternating purine/pyrimidine tracts in agreement with previous observations [Spitzner, J. R., Chung, I. K. & Muller, M. T. (1990) Eukaryotic topoisomerase II preferentially cleaves alternating purine-pyrimidine repeats, Nucleic Acids Res. 18, 1-11]. In addition, all of the cleavage sites observed in the absence of inhibitor were located in the U3 region of the LTR. The site specificity of drug-induced cleavage was studied and the conformity of the cleavage sites with previously established consensus sequences was examined. Our results suggest that DNA topoisomerase II, through its ability to alter the degree of DNA supercoiling, might be involved in the control of different functions of the LTR.
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PMID:Analysis of the DNA topoisomerase-II-mediated cleavage of the long terminal repeat of Drosophila 1731 retrotransposon. 824 80

To gain further knowledge of the molecular features of topoisomerase II inhibitors required for drug-receptor complex formation, we investigated the conformational drug determinants of the sequence specificities of drug-stimulated DNA cleavage by computer-aided molecular modeling techniques. DNA sequence specificities of bisantrene, genistein, piroxantrone and ellipticinium were determined by using simian virus 40 DNA and compared to those of mitoxantrone, 4-demethoxydaunorubicin, VM-26 and mAMSA. DNA cleavage intensity patterns of bisantrene and mAMSA were virtually identical in sequencing gels, although these drugs are of distinct chemical classes. Genistein and ellipticinium showed drug-specific DNA cleavage intensity patterns with no apparent similarity to other drugs or to each other. From 54 to 72 drug-stimulated sites were sequenced, and local base sequence specificities were established by statistical analyses. In complete agreement with mAMSA requirements, bisantrene required an adenine at position +1. Ellipticinium required a thymine and excluded a cytosine at position -1. Genistein was the only drug showing base requirements (thymines) at both positions -1 and +1. Piroxantrone (structurally related to mitoxantrone) required a pyrimidine at position -1. Since the common sequence specificity of bisantrene and mAMSA could not be simply explained by the nature of some chemical substituents, a comparative molecular modeling analysis of the drugs was carried out based on their steric and electronic attributes. Energy-minimized structures of mAMSA and bisantrene were very similar, since their planar aromatic domains and pendant side-chains overlapped to a very good approximation. In contrast, their most stable conformations were different from other drug structures. In particular, the planar system and pendant sugar moiety of doxorubicin, which also required an adenine but at position -1, was not superimposed to the corresponding moieties of mAMSA and bisantrene even when considering computer-generated conformations with higher energy contents. The most stable conformations of the other drugs studied revealed specific three-dimensional motifs. Therefore, since in a simple model of drug action each spatial region has a single chemical-pharmacological function, these results suggest that bisantrene and mAMSA share common steric and electronic features that may constitute a specific pharmacophore. We suggest that the molecular properties of this pharmacophore may be critical determinant of the +1 position specificity shown by mAMSA and bisantrene.
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PMID:Conformational drug determinants of the sequence specificity of drug-stimulated topoisomerase II DNA cleavage. 830 85

The molecular mechanism of topoisomerase II trapping by antitumor drugs probably involves the formation of a ternary complex DNA-drug-topoisomerase II. Recent studies support the view that a drug molecule might be placed at the DNA cleavage site interacting with the two flanking base pairs and amino acid residues of the enzyme. In this work, the DNA sequence-dependent action of mitoxantrone on topoisomerase II DNA cleavage was investigated in SV40 DNA fragments and short oligonucleotides, in comparison to VM-26, 4-demethoxydaunorubicin, and mAMSA. Mitoxantrone and VM-26 had a much lower degree of selectivity than 4-demethoxydaunorubicin and mAMSA in stimulating DNA cleavage. DNA cleavage at sites that were always stimulated also by VM-26. In contrast, mitoxantrone and 4-demethoxydaunorubicin shared only 7% of cleavage sites, and about 70% of the 4-demethoxydaunorubicin-stimulated sites were also stimulated by VM-26. Unlike what is generally seen with anthracyclines, the structurally related drug, mitoxantrone, stimulated cleavage also at DNA sites observed without drugs. Local base preferences at the cleavage site as determined by statistical analysis showed that mitoxantrone preferentially cleaved the DNA at sites with a cytosine or a thymine at position-1. However, strong DNA cleavage stimulation by mitoxantrone was favored by specific base pairs at the next positions flanking the cleaved bond (positions -2 and +2) and at positions +8 and +9. Effects of base mutations on drug stimulation of DNA cleavage in short DNA oligonucleotides independently showed that a pyrimidine at position -1 is required for mitoxantrone action.(ABSTRACT TRUNCATED AT 250 WORDS)
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PMID:Similar sequence specificity of mitoxantrone and VM-26 stimulation of in vitro DNA cleavage by mammalian DNA topoisomerase II. 838 86

The Human Immunodeficiency Virus (HIV) integrates into host cellular DNA as a double strand DNA molecule. Here a previously studied HIV isolate was examined for binding and cleavage by topoisomerase II in vitro within the 5' LTR region and human flanking DNA. A cluster of strong binding and cleavage sites in the human sequences was located approximately 850 bp upstream from the integration site. This region maps to a locus consisting of a complex repeating element, and alternating purine/pyrimidine sequences. Topoisomerase II binding and cleavage sites were also located within the HIV 5' LTR, in particular a site overlying the DNA sequence coding for TAR, another inverted repeat element in the DNA.
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PMID:A cluster of strong topoisomerase II cleavage sites is located near an integrated human immunodeficiency virus. 839 47

The pattern of sites for cleavage mediated by topoisomerase II was determined in 830 kb of cloned DNA from the Drosophila X chromosome, with the objectives of comparing it with mapped structural and functional landmarks and examining if the correlations with such landmarks reported in individual loci can be generalized to a region approximately 100 times longer. The relative frequencies of topoisomerase II cleavage sites in 247 restriction fragments from 67 clones were quantified by hybridization with probes prepared from DNA fragments which abutted all cleavage sites in each clone, selected through the covalently bound topoisomerase II subunit; the specificity and quantitative nature of this method were demonstrated using a plasmid DNA model. The 12 restriction fragments with strong nuclear scaffold attachment (SAR) activity, of which seven possess autonomous replication (ARS) activity, show statistically strong coincidence or contiguity ( P </=0.11) with regions of high topoisomerase II cleavage site frequency. These regions show no correlation with repetitive sequence or A/T or C/G content and some extend over >10 kb; their sensitivity is therefore unlikely to be due to alternating purine-pyrimidine repeats or regions of Z conformation, which are preferred motifs. The hypothesis that they possess intrinsic curvature is consistent with the similarity of their length and spacing to regions of predicted curvature in the 315 kb DNA of Saccharomyces cerevisiae chromosome III and with the reported strong binding preference of topoisomerase II for curved DNA. The topoisomerase II cleavage pattern in this DNA further shows that its relationships to functional properties seen in individual loci, especially to MAR/SAR and ARS activity and to the restricted accessibility of DNA to topoisomerase II in vivo, can be generalized to much longer regions of the genome.
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PMID:Distribution of topoisomerase II-mediated cleavage sites and relation to structural and functional landmarks in 830 kb of Drosophila DNA. 915

The two-drug regimen consisting of a platinum compound (cisplatin or carboplatin) combined with either a vinca alkaloid or a podophyllotoxin has been considered by many to be the standard chemotherapy treatment for non-small cell lung cancer (NSCLC). Randomized trials with these regimens have demonstrated modest but statistically significant increases in survival for patients with stage IV disease compared to treatment with best supportive care, and especially for selected patients with stage III disease when combined with radiotherapy or surgery compared to these treatments alone. Recently, several new compounds with promising efficacy and acceptable toxicity profiles have been investigated for the treatment of NSCLC, including the taxanes paclitaxel and docetaxel, the novel pyrimidine analog gemcitabine, and the topoisomerase inhibitors irinotecan and topotecan. Small but significant improvements in response rates and survival have been achieved with two-drug combinations, which include several of these new agents combined with a platinum-based compound, in patients with advanced NSCLC. Modifications of dosing schedules and the use of premedication regimens have resulted in better efficacy and more manageable side effects with such combinations. These encouraging gains in patients with advanced NSCLC suggest a potentially greater impact in patients with early stage disease. Given the manageable toxicity profiles of many of these newer agents, various three-drug regimens may be feasible in the future.
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PMID:Overview of current and future chemotherapeutic agents in non-small cell lung cancer. 919 77

Lung cancer, which is the leading cause of cancer mortality, remains a significant health-care problem among men and women in the United States, despite an overall 20-year decline in the incidence of cigarette smoking. Non-small cell lung cancer (NSCLC) comprises 75 to 80% of all lung cancer cases. The metastatic nature of this disease has been responsible for the poor survival statistics reported to date and emphasizes the need for effective systemic treatment. Prior to 1993, attempts to identify new chemotherapeutic agents and combinations with activity against NSCLC met with little success. Recently, however, several new compounds and classes of compounds have offered some hope for at least small improvements in response and survival while being relatively well tolerated in patients with this disease. This article presents current findings for some of these agents, including the taxanes paclitaxel and docetaxel, the topoisomerase inhibitors irinotecan and topotecan, and the novel pyrimidine analogue gemcitabine. In addition, the University of Southern California/Norris Cancer Center experience with the combination of carboplatin and paclitaxel is presented.
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PMID:Experience with new chemotherapeutic agents in non-small cell lung cancer. 943 88

Amine-carboxyboranes with varying alkyl chain lengths were observed to be potent cytotoxic agents inhibiting the growth of a number of histological types of murine, rat, and human tumors. These agents preferentially reduced L1210 DNA synthesis with marked inhibition of the activities of regulatory enzymes of the purine pathway. Other enzyme activities which were marginally reduced were DNA polymerase alpha, ribonucleoside reductase, dihydrofolate reductase, t-RNA polymerase, and nucleoside kinases. Pyrimidine nucleotide pools were not reduced but DNA strand scission occurred after 24 h incubation with the agents. The amine-carboxyboranes were not DNA topoisomerase II inhibitors at 100 microM. The agents did not cause DNA protein linked breaks themselves; nevertheless, VP-16 [etoposide] induced DNA protein linked breaks were increased two fold in the presence of the agents suggesting synergistic effects. The amine-carboxyboranes decreased protein kinase C mediated phosphorylation of L1210 topoisomerase II protein, potentially decreasing its enzymatic catalytic activity. Thus, the amine-carboxyboranes did not function like VP-16 in affording cleavable products but were synergistic with VP-16 in causing DNA fragmentation. The agents were also additive with VP-16 in reducing tumor cell number, soft-agar colony growth and DNA synthesis and in producing DNA strand scission.
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PMID:Effects of alkyl amine carboxyboranes on L1210 DNA fragmentation and nucleic acid metabolism. 969 Dec 46

A 52 base pair alternating purine-pyrimidine (RY) repeat sequence lies in the 5' upstream region of the human beta-globin gene. The structural transition of a plasmid containing this repeat was analyzed by two-dimensional gel electrophoresis. These conformational studies indicate that the 52 bp RY repeat undergoes local transition from the right-handed B-DNA into a cruciform DNA under torsional stress and the transition initiates at a threshold level of negative supercoiling (-sigma = 0.042). The superhelicity-dependent S1 nuclease cleavage sites were mapped only within the RY repeat and no nicking was observed outside of the repeat. In view of the fact that DNA topoisomerase II is highly reactive towards RY repeat which can adopt unusual DNA conformation, we have investigated the effects of the superhelicity-dependent conformational transition of the 52 bp RY repeat on topoisomerase II cleavages. Cleavage reactions were performed on the pRYG plasmid with varying levels of negative superhelical densities ranging from 0 to -0.074. Under the low torsional stress, topoisomerase II cleavage activity at the RY repeat gradually increased with the increasing levels of negative superhelical densities. However, over a threshold level of negative supercoiling for cruciform conformation, the intensities of enzyme cleavage sites at the RY repeat were essentially identical. These results suggest that topoisomerase II can bind and cleave the cruciform structure in a dynamic process identical to duplex B-DNA.
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PMID:Topoisomerase II-mediated DNA cleavage on the cruciform structure formed within the 5'upstream region of the human beta-globin gene. 974 29

This report demonstrates that Gadd45, a p53-responsive stress protein, can facilitate topoisomerase relaxing and cleavage activity in the presence of core histones. A correlation between reduced expression of Gadd45 and increased resistance to topoisomerase I and topoisomerase II inhibitors in a variety of human cell lines was also found. Gadd45 could potentially mediate this effect by destabilizing histone-DNA interactions since it was found to interact directly with the four core histones. To evaluate this possibility, we investigated the effect of Gadd45 on preassembled mononucleosomes. Our data indicate that Gadd45 directly associates with mononucleosomes that have been altered by histone acetylation or UV radiation. This interaction resulted in increased DNase I accessibility on hyperacetylated mononucleosomes and substantial reduction of T4 endonuclease V accessibility to cyclobutane pyrimidine dimers on UV-irradiated mononucleosomes but not on naked DNA. Both histone acetylation and UV radiation are thought to destabilize the nucleosomal structure. Hence, these results imply that Gadd45 can recognize an altered chromatin state and modulate DNA accessibility to cellular proteins.
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PMID:Gadd45, a p53-responsive stress protein, modifies DNA accessibility on damaged chromatin. 1002 55


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