Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: EC:2.7.7.6 (RNA polymerase)
 34,946 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The A-type lamins have been observed to colocalize with RNA splicing factors in speckles within the nucleus, in addition to their typical distribution at the nuclear periphery. To understand the functions of lamin speckles, the effects of transcriptional inhibitors known to modify RNA splicing factor compartments (SFCs) were examined. Treatment of HeLa cells with alpha-amanitin or 5,6-dichlorobenzimidazole riboside (DRB) inhibited RNA polymerase II (pol II) transcription and led to the enlargement of lamin speckles as well as SFCs. Removal of the reversible inhibitor DRB resulted in the reactivation of transcription and a rapid, synchronous redistribution of lamins and splicing factors to normal-sized speckles, indicating a close association between lamin speckles and SFCs. Conversely, the expression of NH2-terminally modified lamin A or C in HeLa cells brought about a loss of lamin speckles, depletion of SFCs, and down-regulation of pol II transcription without affecting the peripheral lamina. Our results suggest a unique role for lamin speckles in the spatial organization of RNA splicing factors and pol II transcription in the nucleus.
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PMID:Lamin A/C speckles mediate spatial organization of splicing factor compartments and RNA polymerase II transcription. 1247 87

A T7 RNA polymerase in which Tyr639 is mutated to Phe readily utilizes 2'-deoxy, 2'-NH2 and 2'-F NTPs as substrates and has been widely used to synthesize modified RNAs for a variety of applications. This mutant does not readily utilize NTPs with bulkier 2'-substituents, nor does it facilitate incorporation of NTPs with modifications at other positions. Introduction of a second mutation (H784A) into the Y639F background markedly enhances utilization of NTPs with bulky 2'-substituents (2'-OMe and 2'-N3), and may also enhance use of NTPs with modifications at other than the 2'-position. The Y639F/H784A double mutant may therefore be exceptionally useful for incorporation of a variety of non-canonical NMPs into RNA.
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PMID:A Y639F/H784A T7 RNA polymerase double mutant displays superior properties for synthesizing RNAs with non-canonical NTPs. 1249 Jul 29

The DNA binding and inhibition of transcription in vitro by neutral Rh(2)(mu-O(2)CCH(3))(4) and cationic cis-[Rh(2)(mu-O(2)CCH(3))(2)(phen)(2)](2+) complexes were investigated. The binding constants of the two complexes to calf-thymus DNA were estimated from absorption titrations to be 4.6 x 10(2) M(-)(1) and 1.7 x 10(4) M(-)(1) for Rh(2)(mu-O(2)CCH(3))(4) and cis-[Rh(2)(mu-O(2)CCH(3))(2)(phen)(2)](2+), respectively. The shift to higher energies of the low-energy absorption of the complexes upon addition of DNA is consistent with axial binding of the complexes to duplex DNA. The relative concentrations, [complex]/[DNA], of Rh(2)(mu-O(2)CCH(3))(4) and cis-[Rh(2)(mu-O(2)CCH(3))(2)(phen)(2)](2+) at which 50% of the transcription is inhibited (R(inh)(50)), are 0.0031 and 0.0011, respectively. These concentrations are significantly lower than that required for activated cisplatin, cis-[Pt(NH(3))(2)(H(2)O)(2)](2+), with R(inh)(50) = 0.0085 under similar experimental conditions. Upon incubation of cis-[Pt(NH(3))(2)(H(2)O)(2)](2+) with the template DNA prior to the addition of the enzyme and nucleobases necessary for the transcription reaction for 30 min at 37 degrees C, significantly lower concentrations of the complex were required to attain 50% inhibition. In contrast, similar incubation of the DNA with the dirhodium complexes did not result in better transcription inhibition. Experiments designed to elucidate the mechanism of the observed inhibition indicate that, unlike cis-[Pt(NH(3))(2)(H(2)O)(2)](2+), Rh(2)(mu-O(2)CCH(3))(4) and cis-[Rh(2)(mu-O(2)CCH(3))(2)(phen)(2)](2+) appear to interact directly with the enzyme T7-RNA polymerase as their mode of inhibition.
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PMID:Inhibition of transcription in vitro by anticancer active dirhodium(II) complexes. 1258 65

Transcription inhibition by DNA adducts of cisplatin is considered to be one of the major routes by which this anticancer drug kills cancer cells. Stalled RNA polymerases at platinum-DNA lesions evoke various cellular responses such as nucleotide excision repair, polymerase degradation, and apoptosis. T7 RNA polymerase and site-specifically platinated DNA templates immobilized on a solid support were used to study stalled transcription elongation complexes. In vitro transcription studies were performed in both a promoter-dependent and -independent manner. An elongation complex is strongly blocked by cisplatin 1,2-intrastrand d(GpG) and 1,3-intrastrand d(GpTpG) cross-links located on the template strand. Polymerase action is inhibited at multiple sites in the vicinity of the platinum lesion, the nature of which can be altered by the choice and concentration of NTPs. The [(1R,2R-diaminocyclohexane)Pt]2+ DNA adducts formed by oxaliplatin, which carries a stereochemically more demanding spectator ligand than the ammine groups in cisplatin, also strongly block the polymerase with measurable differences compared with cis-[(NH3)2Pt]2+ lesions. Elongation complexes stopped at sites of platinum damage were isolated and characterized. The stalled polymerase can be dissociated from the DNA by subsequent polymerases initiated from the same template. We also discovered that a polymerase stalled at the platinum-DNA lesion can resume transcription after the platinum adduct is chemically removed from the template.
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PMID:Multiple states of stalled T7 RNA polymerase at DNA lesions generated by platinum anticancer agents. 1453

Nitrogen limitation in Escherichia coli activates about 100 genes. Their expression requires the response regulator NtrC (also called nitrogen regulator I or NR(I)). Phosphorylation of the amino-terminal domain (NTD) of NtrC activates the neighboring central domain and leads to transcriptional activation from promoters that require sigma(54)-containing RNA polymerase. The NTD has five beta strands alternating with five alpha helices. Phosphorylation of aspartate 54 has been shown to reposition alpha helix 3 to beta strand 5 (the "3445 face") within the NTD. To further study the interactions between the amino-terminal and central domains, we isolated strains with alterations in the NTD that were able to grow on a poor nitrogen source in the absence of phosphorylation by the cognate sensor kinase. We identified strains with alterations located in the 3445 face and alpha helix 5. Both types of alterations stimulated central domain activities. The alpha helix 5 alterations differed from those in the 3445 face. They did not cause a large scale conformational change in the NTD, which is not necessary for transcriptional activation in these mutants. Yeast two-hybrid analysis indicated that substitutions in both alpha helix 5 and the 3445 face diminish the interaction between the NTD and the central domain. Our results suggest that alpha helix 5 of the NTD, in addition to the 3445 face, interacts with the central domain. We present a model of interdomain signal transduction that proposes different functions for alpha helix 5 and the 3445 face.
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PMID:Evidence for a second interaction between the regulatory amino-terminal and central output domains of the response regulator NtrC (nitrogen regulator I) in Escherichia coli. 1456 53

Fluorescent nucleic acid hybridization probes traditionally have been generated by enzymatic incorporation of dye-labeled nucleotides, even though incorporation efficiency is low and variable from dye to dye. Alternatively, 5-(3-aminoallyl)-2'-deoxyuridine 5'-triphosphate (aa-dUTP) is enzymatically incorporated to generate amine-modified DNA, which is then chemically labeled with an amine-reactive fluorescent dye. We optimized this latter two-step approach for maximal hybridization signal brightness using DNA probes labeled to varying degrees with different fluorescent dyes. Reverse transcriptase and DNA polymerase 1 efficiently incorporated aa-dUTP into DNA, and adjusting the aa-dUTP:dTTP ratio controlled the degree of substitution. With cDNA probes hybridized to dot blots, probes having approximately eight dyes per 100 bases gave the best sensitivity, irrespective of the dye label. alpha-Satellite probes generated by nick translation and hybridized to human chromosome spreads also showed that probes having approximately eight dyes per 100 bases provided the brightest overall signals. These data demonstrate that this labeling method generates highly sensitive DNA probes that are difficult to obtain by conventional direct incorporation approaches. The technique is inherently consistent and versatile by virtue of the efficient incorporation of primary amines and the reliable chemical labeling reaction.
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PMID:Fluorescent DNA hybridization probe preparation using amine modification and reactive dye coupling. 1474 Apr 93

The arginine deiminase system (ADS) is of critical importance in oral biofilm pH homeostasis and microbial ecology. The ADS consists of three enzymes. Arginine is hydrolyzed by AD (ArcA) to generate citrulline and ammonia. Citrulline is then converted to ornithine and carbamoylphosphate via ornithine carbamoyltransferase (ArcB). Finally, carbamate kinase (ArcC) transfers a phosphate from carbamoylphosphate to ADP, yielding ATP. Ammonia production from this pathway protects bacteria from lethal acidification, and ATP production provides a source of energy for the cells. The purpose of this study was to initiate a characterization of the arc operon of Streptococcus rattus, the least cariogenic and sole ADS-positive member of the mutans streptococci. Using an arcB gene fragment obtained by degenerate PCRs, the FA-1 arc operon was identified in subgenomic DNA libraries and sequence analysis was performed. Results showed that the genes encoding the AD pathway in S. rattus FA-1 are organized as an arcABCDT-adiR operon gene cluster, including the enzymes of the pathway, an arginine-ornithine antiporter (ArcD) and a putative regulatory protein (AdiR). The arcA transcriptional start site was identified by primer extension, and a sigma(70)-like promoter was mapped 5' to arcA. Reverse transcriptase PCR was used to establish that arcABCDT could be cotranscribed. Reporter gene fusions and AD assays demonstrated that the operon is regulated by substrate induction and catabolite repression, the latter apparently through a CcpA-dependent pathway.
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PMID:Characterization of the arginine deiminase operon of Streptococcus rattus FA-1. 1500 49

Doxorubicin (DOX), daunorubicin (DRB), epidoxorubicin (EDOX) and their analogues with a 3'-NH2 group in daunosamine form a covalent bond with a 2-NH2 group of guanine via a methylene group from formaldehyde (CH2O). It is assumed that a Schiff base type intermediate is formed between CH2O and the 3'-NH2 group in the reaction. This reaction is supposed to occur in the cell. New analogues of anthracyclines with formamidine functionality bound to C-3' of daunosamine and containing the bulky morpholine (DRBM, DOXM and EDOXM) or hexamethyleneimine rings attached are studied in our laboratory. These substituents decrease the association of the drugs to DNA and potentially hinder the formation of Schiff base-intermediates. Our experiments indicate that the formation of the covalent complexes by DRB, DOX and EDOX under these conditions is confirmed by a high enhancement (17-40x) of the inhibition of overall RNA synthesis by E. coli RNA polymerase on T7 DNA. DRBM and DOXM exhibit a lower enhancement of the inhibition by CH2O (7-13x). The other analogues show a 1.6-3x increase of inhibition. Hence, their covalent binding is lower than that of the parent compounds. These conclusions are confirmed by spectrophotometric estimations following removal of non-covalently associated drugs. Electrophoretic analysis of drug-DNA complexes formed in the presence of CH2O indicates that DRBM and DOXM as their parent compounds induce labile cross-links in DNA. Comparison of the results obtained at the subcellular level with cytotoxicity estimations indicates that there is a correlation between cytotoxicity of the anthracyclines on L1210 cells and transcriptional template activity of drug-DNA complexes formed in the presence of CH2O (r = 0.64; n = 9). These data confirm a notion that covalent attachment of anthracyclines to DNA is an essential event leading to cytotoxicity.
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PMID:Interactions of novel morpholine and hexamethylene derivatives of anthracycline antibiotics with DNA. 1554 Jun 9

During mRNA elongation, the SRI domain of the histone H3 methyltransferase Set2 binds to the phosphorylated carboxyl-terminal domain (CTD) of RNA polymerase II. The solution structure of the yeast Set2 SRI domain reveals a novel CTD-binding fold consisting of a left-handed three-helix bundle. NMR titration shows that the SRI domain binds an Ser2/Ser5-phosphorylated CTD peptide comprising two heptapeptide repeats and three flanking NH2-terminal residues, whereas a single CTD repeat is insufficient for binding. Residues that show strong chemical shift perturbations upon CTD binding cluster in two regions. Both CTD tyrosine side chains contact the SRI domain. One of the tyrosines binds in the region with the strongest chemical shift perturbations, formed by the two NH2-terminal helices. Unexpectedly, the SRI domain fold resembles the structure of an RNA polymerase-interacting domain in bacterial sigma factors (domain sigma2 in sigma70).
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PMID:Structure and carboxyl-terminal domain (CTD) binding of the Set2 SRI domain that couples histone H3 Lys36 methylation to transcription. 1628 74

The tethered RuII half-sandwich complexes [eta(6):eta(1)-C(6)H(5)(CH(2))(n)NH(2))RuCl(2)] 1 (n = 3) and 2 (n = 2) have been synthesized as potential bifunctional anticancer complexes, and their X-ray crystal structures have been determined. They hydrolyze rapidly in aqueous solution to give predominantly mono-aqua mono-chlorido species. Mono-9EtG adducts, where 9EtG = 9-ethylguanine, form rapidly, but the second 9EtG binds more slowly and more weakly. In the X-ray crystal structure of the di-9EtG adduct [(eta(6):eta(1)-C(6)H(5)(CH(2))(3)NH(2))Ru(9EtG)2](CF(3)SO(3))(2).H(2)O (8.H(2)O), one of the Ru-N7 bonds is significantly longer than the other (2.1588(18) vs 2.101(2) A). The bound guanine bases adopt a head-to-head configuration, stabilized by tether NH2 hydrogen bonding to C6O of 9EtG. The X-ray crystal structure of the dinitrato complex [(eta(6):eta(1)-C(6)H(5)(CH(2))(3)NH(2))Ru(NO(3))(2)] (3) showed both nitrates to be bound to ruthenium. This complex readily rutheniated calf thymus DNA but failed to produce stop sites on pSP73KB plasmid DNA during DNA transcription by an RNA polymerase. This suggested that only monofunctional DNA adducts formed, as did interstrand cross-linking assays. Also, the unwinding angle induced in negatively supercoiled DNA (9 +/- 1 degrees) was less than that induced by cisplatin (13 degrees). These findings may explain why complexes such as 1 and 2 exhibited low cytotoxicities (IC(50) values >100 microM) toward A2780 human ovarian cancer cells.
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PMID:Bifunctional amine-tethered ruthenium(II) arene complexes form monofunctional adducts on DNA. 1785 Jan 43


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