c2h2 zinc fingers as dna binding domains
Báo cáo khoa học: Common mode of DNA binding to cold shock domains Crystal structure of hexathymidine bound to the domain-swapped form of a major cold shock protein from Bacillus caldolyticus pot
... Preferential binding of different pyrimidine-based oligonucleotides to Bc-Csp It has been shown that homologous Bs-CspB has a general binding preference for polypyrimidines over polypurines, and its binding ... CT5) the decrease in affinity was significantly stronger: When C was introduced at these positions the KD increased 93- or 11-fold By contrast, at position (Table 2, CT2, CT3) C was preferred slightly ... nucleobase interaction subsites suggest that both Bc-Csp and Bs-CspB share identical ligand -binding interfaces (Fig 8), whereas differences in binding involving subsites and 7, as well as the...
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Báo cáo khoa học: Domains of ERRcthat mediate homodimerization and interaction with factors stimulating DNA binding potx
... the serum, binding was performed in the presence or absence of the preimmune serum Again, an increase of binding was observed; however, as expected, this was mainly due to an increase of the ... Previously, ERRc was reported to bind as a monomer to DNA [28] However, a recent report assumes that ERRc binds also as a dimer to DNA [35] For ERRa and ERRb, monomeric and dimeric binding has been demonstrated ... repeat with a spacing of three base pairs, the classical estrogen response element DNA binding of C-terminal deletion mutants Fig ERRc binds as a homodimer to DNA Binding of the full-length ERRc...
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Tài liệu Báo cáo khoa học: TransLISA, a novel quantitative, nonradioactive assay for transcription factor DNA-binding analyses pdf
... DNA pull-down assay to measure nuclear receptor DNA binding in solution BioTechniques 45, 445–448 Galas D & Schmitz A (1978) DNAse footprinting: a simple method for the detection of protein DNA ... amounts of radioactive and other waste Recently, Iwasaki et al [7] described a A B EMSA HSE liquid chemiluminescent DNA pull-down assay The method measures DNA binding of transcription factors, ... These experiments thus confirm that the assay specifically measures HSF1 DNA- binding activity Analytical range and precision The analytical range of the assay was evaluated using known concentrations...
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Tài liệu Báo cáo khoa học: DNA modification with cisplatin affects sequence-specific DNA binding of p53 and p73 proteins in a target site-dependent manner pptx
... p53 sequence-nonspecific DNA binding due to DNA cis-platination was observed [33–36] On the other hand, the same DNA treatment resulted in inhibition of p53 sequence-specific binding [31,32] An analogous ... individual p53DBSs at the same degree of global DNA cis-platination differed significantly The steepest decrease in p53 DNA binding with degree of DNA modification was exhibited by the mdm2 target The R53 ... and 53% of the p53 -binding capacity at rb ¼ 0.02, respectively (Fig 3A) Increasing the DNA modification degree to rb ¼ 0.04 resulted in a decrease of p53–p21 binding to 42%, whereas the PGM1 site...
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Tài liệu Báo cáo khoa học: Roles of the human Rad51 L1 and L2 loops in DNA binding doc
... (v ⁄ v) glycerol, and the flow rate was 0.5 mLÆmin)1 CD measurements DNAs The /X174 phage ssDNA and dsDNA used in the DNA binding and ATPase assays were purchased from New England Biolabs (Ipswich, ... of ssDNA or dsDNA In the ssDNA-dependent reaction, the /X174 circular ssDNA (20 lm) was used as a substrate In the dsDNA-dependent reaction, the /X174 RF I DNA (20 lm) (supercoiled dsDNA) was used ... exhibit DNA- dependent ATPase activity (Fig 2E) Neither ssDNA nor dsDNA induced the ATPase activity of Rad51-Y232A, while the ATPase activity of HsRad51 was stimulated by ssDNA and dsDNA (Fig...
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Tài liệu Báo cáo khoa học: Steady-state and time-resolved fluorescence studies of conformational changes induced by cyclic AMP and DNA binding to cyclic AMP receptor protein from Escherichia coli ppt
... nanosecond ash lamp nF 900 from Edinburgh Instruments was used as a light source (e) In the case of anisotropy measurements, (f) Glan Thompson prism polarizers were also used All measurements ... transfer measurements In the CRPW13F(cAMP)2 complex, the concentration of cAMP was 200 lM, whereas in the case of CRPW13F(cAMP)4 the concentration of cAMP was mM The molar ratio CRP to DNA in the ... uorescence intensity, increasing it by % 3.4% A pronounced increase in the Trp85 uorescence intensity was ể FEBS 2003 Conformational changes induced by cAMP and DNA binding to CRP (Eur J Biochem...
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Báo cáo khoa học: Roles of conserved arginines in ATP-binding domains of AAA+ chaperone ClpB from Thermus thermophilus pptx
... hexamers, as indicated Measurement of nucleotide binding Mant-ADP, a fluorescent nucleotide analog, was purchased from Invitrogen (Carlsbad, CA, USA) Nucleotide binding was detected as described ... stearothermophilus was purchased from Unitika (Tokyo, Japan), a-glucosidase from B stearothermophilus, a-casein, and j-casein from Sigma (St Louis, MO, USA), and rabbit pyruvate kinase and hog lactate ... All measurements were performed at 55 °C Fluorescence measurements were performed with a FP-6500 fluorometer (Jasco, Tokyo, Japan) The excita- Measurement of threading activity FITC was purchased...
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Báo cáo khoa học: Starch-binding domains in the CBM45 family – low-affinity domains from glucan, water dikinase and a-amylase involved in plastidial starch metabolism pptx
... the unbound fraction was subsequently measured A one-site binding model was fitted to the binding isotherm (Fig 5), resulting in a Kd value of 36 ± 6.8 mgÆmL)1 and maximum binding capacity (Bmax) ... several different CBM families, and starch and ⁄ or a-glucan binding has been demonstrated in a number of cases [20–26] Starch binding in the plastidial system is influenced by potential regulatory mechanisms ... representatives of the two classes of enzyme carrying CBM45-type domains, the Solanum tuberosum a-glucan, water dikinase (StGWD) and the A thaliana plastidial a-amylase (AtAMY3), suggesting that...
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Báo cáo khoa học: Analysis of DNA-binding sites on Mhr1, a yeast mitochondrial ATP-independent homologous pairing protein potx
... Mg2+-dependent DNAbinding activity of Mhr1, as Mg2+ increased the DNAbinding activity of Mhr1 The enhanced DNA- binding activity could be due to the shielding of negative charges around the Mhr1 DNA interface ... compilation ª 2010 FEBS T Masuda et al DNA- binding sites of Mhr1 Table DNA- binding activity of the Mhr1 variants N, DNA- binding activity is comparable to that of the wild type; +, DNA- binding activity ... defects in DNA binding (Fig 5A), although their DNA- binding activities were not completely lost We also examined the DNA- binding activity of Mhr1 in the absence of Mg2+, because the DNAbinding activities...
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Báo cáo khoa học: Physicochemical properties and distinct DNA binding capacity of the repressor of temperate Staphylococcus aureus phage /11 doc
... of O DNA by Taq polymerase using pSAU1201 DNA or /11 DNA as a template and the oligonucleotides pHC1 and labeled pHC2 as primers The resulting DNA fragment was purified from an agarose gel DNase ... Synthesis of O1 DNA Synthesis of O2 and O1O2 DNAs Synthesis of O2 DNA Synthesis of O3 DNA Synthesis of O3 DNA Synthesis of S aureus cspC DNA Synthesis of S aureus cspC DNA (Fig 2A) was synthesized ... DNA was also treated directly with DMS as above in the absence of CI and the recovered DNA was used as a control The gunaine-specific ladder DNAs, prepared from both control and experimental DNAs...
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Báo cáo khoa học: Activator-binding domains of the SWI ⁄ SNF chromatin remodeling complex characterized in vitro are required for its recruitment to promoters in vivo pot
... activator -binding domains The in vivo validation of the Swi1 and Snf5 activator -binding domains is also of interest in relation to the twostep binding mechanism between Gal4 and Swi1 that has been ... genes as well as GAL genes that have little or no requirement for SWI ⁄ SNF SWI ⁄ SNF dependence was associated with a class of highly inducible GAL genes (GAL1, GAL10, GAL2 and GAL7), whereas genes ... The existence of two activator -binding domains might be an adaptation to the fact that activators generally bind DNA as dimers, with the result that two activation domains are available to recruit...
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Báo cáo khoa học: DNA-binding characteristics of the regulator SenR in response to phosphorylation by the sensor histidine autokinase SenS from Streptomyces reticuli doc
... exact DNA- binding site(s) within up-furS1 and up-hbpS1, DNaseI footprinting experiTable Relative binding affinity of wild-type and mutated SenR proteins for 32P-labeled DNA- fragments EMSAs were ... helix–turn–helix DNA- binding domains of SenR and ChrA share 61% amino acid identity (data not shown) The designed SenRD60 and SenRD65A proteins showed reduced DNA- binding affinity for up-furS as well as for ... plasmids pWKB1 [16] and pQS1H199A were used as DNA templates Each PCR product was digested with EcoRI and PstI and ligated with EcoRI–PstIdigested pASK-IBA7 The resulting construct pASKS2 or pASKS2H199A...
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Báo cáo khóa học: FRET evidence for a conformational change in TFIIB upon TBP-DNA binding pptx
... the QIAfilter plasmid Giga kit (Qiagen) The plasmid DNA was cut by BamHI and EcoRI, phenol/chloroform extracted and precipitated After washing with 70% ethanol, the DNA pellet was dissolved in ... Protocol #PT2040-1) as well as the fluorescence intensity at 526 nm when excited at 514 nm The concentration of TBP was determined by Bradford assay (Bio-Rad) The concentration of DNA was determined ... This change was not observed when CYIIB was mixed with TBP alone or with DNA alone Furthermore, when TBP–AdML was added to a : mixture of ECFP– TFIIB and EYFP (Fig 3B), no ratio change was observed...
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Báo cáo khoa học: Akt-dependent phosphorylation negatively regulates the transcriptional activity of dHAND by inhibiting the DNA binding activity pdf
... protein kinase, protein kinase C and casein kinase II [36–42] The activation of cAMP-dependent protein kinase or protein kinase C can inhibit muscle differentiation, whereas casein kinase II stimulates ... mimicking mutants As shown in Fig 8C, dHAND-Asp-X and -Asp almost lost their DNA binding activity These results indicated that the phosphorylation of Thr102, Thr112, and Ser114 inhibited DNA binding activity ... dHAND and reporter plasmid containing the luciferase gene, whose expression was driven by five Gal4 binding sites, were transfected to C2C12 cells, and luciferase assay was performed Fold activation...
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Báo cáo khoa học: Characterization of HbpR binding by site-directed mutagenesis of its DNA-binding site and by deletion of the effector domain pot
... behaved like the wildtype operator as far as the UAS C-1 region was concerned (Fig 4) Binding to the UAS C-2 region (in which the mutations had been placed), was impaired both at the 3¢ end of ... (B) DNaseI footprinting analysis of CBP–HbpR and CBP–DA-HbpR binding to the UASs C-1 ⁄ C-2 region A 229 bp 32P-end-labelled fragment containing the UAS C-1 ⁄ C-2 was incubated with increasing ... shift assays (EMSAs) with mutated operator fragments and calmodulin -binding protein (CBP)–HbpR, and representation of the calculation of the half -binding concentration (A) EMSAs performed with DNA...
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Báo cáo khoa học: A new clan of CBM families based on bioinformatics of starch-binding domains from families CBM20 and CBM21 potx
... gmyAspaw glucoamylase gmyAspfi glucoamylase gmyAspka glucoamylase gmyAspni glucoamylase gmyAspor glucoamylase gmyAspsh glucoamylase gmyAspte glucoamylase gmyCorro glucoamylase gmyHorre glucoamylase ... CGTase cgtBacsp7 CGTase cgtBacsp3 CGTase cgtBacsp63 CGTase cgtBacsp6 CGTase cgtBacspB CGTase cgtBacspD CGTase cgtBacspE CGTase cgtBacspK CGTase cgtBacst CGTase cgtGeost CGTase cgtKlepn CGTase ... transferase cgtBacag CGTase cgtBacbr CGTase cgtBacci2 CGTase cgtBacci8 CGTase cgtBacciA CGTase cgtBaccl CGTase cgtBacli CGTase cgtBacma1 CGTase cgtBacma2 CGTase cgtBacoh CGTase cgtBacsp0 CGTase cgtBacsp1...
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Báo cáo khoa học: Transcription termination at the mouse mitochondrial H-strand promoter distal site requires an A/T rich sequence motif and sequence specific DNA binding proteins pptx
... D-TERM DNAs As shown in Figs D-TERM DNA specifically 1134 V Camasamudram et al (Eur J Biochem 270) Ó FEBS 2003 Fig Protein binding specificity and protein contact sites of the D-Term DNA (A) DNAse ... are important for protein binding to D-TERM DNA The binding specificity of D-TERM DNA and also the possible protein DNA contact sites were further investigated using DNAse1 footprinting and methylation ... proteins binding to the D-TERM DNA sequence UV-induced DNA cross-linking was carried out to investigate the size and complexity of mt proteins binding to the D-TERM DNA 32P-labelled photo-sensitive DNA...
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Báo cáo khoa học: Molecular dynamics of the DNA-binding domain of the papillomavirus E2 transcriptional regulator uncover differential properties for DNA target accommodation pdf
... facilitating DNA binding In this protein, a certain degree of plasticity is also shown by the DNA- binding helices a1, which, in their central part, partially lose secondary structure, as indicated ... N-terminal DBD has a role in domain stability and DNA binding [21] FEBS Journal 274 (2007) 2385–2395 ª 2007 The Authors Journal compilation ª 2007 FEBS 2387 Papillomavirus E2 DNA- binding domain ... connecting helix a2 and strand b4 This residue may have a role in DNA binding, as a single mutation of Lys349 to alanine weakens the DNA binding of the HPV-16 E2 C-terminal domain by 1.0 kcalÆmol)1...
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Báo cáo Y học: S-Decyl-glutathione nonspecifically stimulates the ATPase activity of the nucleotide-binding domains of the human multidrug resistance-associated protein, MRP1 (ABCC1) ppt
... nucleotide -binding domains (NBDs) of MRP1, and in search of a putative interaction of these NBDs with allocrites, we have overproduced these domains as glutathione-S-transferase or maltose binding ... Cloning of the nucleotide -binding domains of MRP DNA coding for the first nucleotide -binding domain (NBD1) of human MRP1 (residues Lys614–Lys959) was amplified by PCR from plasmid pJ3W (kindly donated ... X-100] was added After on ice, 75 lL of 34% (w/v) citric acid was added, and the plate was incubated for 30 at room temperature Subsequently, the D650 was measured in an ELISA plate reader As a...
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Báo cáo Y học: Ligand-induced heterodimerization between the ligand binding domains of the Drosophila ecdysteroid receptor and ultraspiracle docx
... own DNA binding domain can form heterodimers in vivo Yeast cells cotransfected with plasmids expressing these fragment types in the form of fusion proteins with GAL4 activation and DNA binding domains, ... proteins as used for the two-hybrid experiments, employing [3H] ponasterone A as a probe Extract of yeast cells expressing only GBD–USP(172–508) did not bind [3H]ponasterone A as its binding level ... lacking their DNA binding domains are able to heterodimerize in vivo as well as in vitro This heterodimerization obviously did not depend on a coordinated binding to a bipartite motif in DNA Thus,...
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