dna fragments  (Valiant)

 
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    Name:
    Deoxyribonucleic acid sodium salt
    Description:
    Deoxyribonucleic Acid Sodium Salt
    Catalog Number:
    02152275-cf
    Price:
    10.0
    Category:
    Nucleotides Peptides Nucleotides
    Applications:
    Substrate for development of DNA detection assays
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    Structured Review

    Valiant dna fragments
    MprA directly binds upstream regions of stress-responsive sigma factors. 32 P-labeled <t>DNA</t> from the sigB (A), sigE (B), and sigH (C) upstream regions were incubated with His-MprA∼P and used in <t>EMSAs.</t> Seven nanograms of labeled DNA was used in all binding reaction mixtures. Labeled DNA was incubated in the absence (lane 1) or presence (lanes 2 to 8) of 0.44 to 35.0 pmol wild-type His-MprA∼P. Binding specificity was determined by incubation of labeled DNA (lane 9) with 6 pmol His-MprA∼P in the absence (lane 10) or presence of a 150-fold excess of cold DNA from either the mprA upstream region (lane 11) or PPE19 upstream region (lane 12). Labeled DNA was also incubated with 14 pmol of the phosphorylation-deficient His-MprA(D48A) mutant (lane 13). F, free DNA; B, bound DNA.
    Deoxyribonucleic Acid Sodium Salt
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    Average 98 stars, based on 1 article reviews
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    Images

    1) Product Images from "MprAB Is a Stress-Responsive Two-Component System That Directly Regulates Expression of Sigma Factors SigB and SigE in Mycobacterium tuberculosis §"

    Article Title: MprAB Is a Stress-Responsive Two-Component System That Directly Regulates Expression of Sigma Factors SigB and SigE in Mycobacterium tuberculosis §

    Journal: Journal of Bacteriology

    doi: 10.1128/JB.188.6.2134-2143.2006

    MprA directly binds upstream regions of stress-responsive sigma factors. 32 P-labeled DNA from the sigB (A), sigE (B), and sigH (C) upstream regions were incubated with His-MprA∼P and used in EMSAs. Seven nanograms of labeled DNA was used in all binding reaction mixtures. Labeled DNA was incubated in the absence (lane 1) or presence (lanes 2 to 8) of 0.44 to 35.0 pmol wild-type His-MprA∼P. Binding specificity was determined by incubation of labeled DNA (lane 9) with 6 pmol His-MprA∼P in the absence (lane 10) or presence of a 150-fold excess of cold DNA from either the mprA upstream region (lane 11) or PPE19 upstream region (lane 12). Labeled DNA was also incubated with 14 pmol of the phosphorylation-deficient His-MprA(D48A) mutant (lane 13). F, free DNA; B, bound DNA.
    Figure Legend Snippet: MprA directly binds upstream regions of stress-responsive sigma factors. 32 P-labeled DNA from the sigB (A), sigE (B), and sigH (C) upstream regions were incubated with His-MprA∼P and used in EMSAs. Seven nanograms of labeled DNA was used in all binding reaction mixtures. Labeled DNA was incubated in the absence (lane 1) or presence (lanes 2 to 8) of 0.44 to 35.0 pmol wild-type His-MprA∼P. Binding specificity was determined by incubation of labeled DNA (lane 9) with 6 pmol His-MprA∼P in the absence (lane 10) or presence of a 150-fold excess of cold DNA from either the mprA upstream region (lane 11) or PPE19 upstream region (lane 12). Labeled DNA was also incubated with 14 pmol of the phosphorylation-deficient His-MprA(D48A) mutant (lane 13). F, free DNA; B, bound DNA.

    Techniques Used: Labeling, Incubation, Binding Assay, Mutagenesis

    DNase I footprints of sigB and sigE upstream regions. (A) 32 P-labeled DNA from the sigB and sigE upstream regions was incubated in the absence or presence of 1.3 to 260 pmol His-MprA∼P and treated with 0.2 units DNase I; arrowheads denote sites of DNase I hypersensitivity. (B) Protected regions (shaded areas) are depicted for both sigB (B) and sigE (C) upstream regions along with the known transcriptional start site (*) and −10 and −35 sites (solid lines). Putative 8-bp direct repeat motifs (dotted line) were determined by GCG analyses and were similar to those found upstream of mprA and pepD . Start and stop codons are depicted in capital letters.
    Figure Legend Snippet: DNase I footprints of sigB and sigE upstream regions. (A) 32 P-labeled DNA from the sigB and sigE upstream regions was incubated in the absence or presence of 1.3 to 260 pmol His-MprA∼P and treated with 0.2 units DNase I; arrowheads denote sites of DNase I hypersensitivity. (B) Protected regions (shaded areas) are depicted for both sigB (B) and sigE (C) upstream regions along with the known transcriptional start site (*) and −10 and −35 sites (solid lines). Putative 8-bp direct repeat motifs (dotted line) were determined by GCG analyses and were similar to those found upstream of mprA and pepD . Start and stop codons are depicted in capital letters.

    Techniques Used: Labeling, Incubation

    Binding to sigE ). (B) Probes were generated to distal (probes 1 and 3), proximal (probe 2), or distal and proximal (probes 4 and 5) repeats and used in EMSAs. Probes either contained wild-type sequences or carried nucleotide substitutions in the first subunit of the distal repeat motif. (C to G) Probe DNA (2.5 ng) was labeled with 32 P and used in all binding reaction mixtures. Labeled DNA was incubated in the absence (lane 1) or presence (lanes 2 to 8) of 0.44 to 35.0 pmol wild-type His-MprA∼P. F, free DNA; B, bound DNA.
    Figure Legend Snippet: Binding to sigE ). (B) Probes were generated to distal (probes 1 and 3), proximal (probe 2), or distal and proximal (probes 4 and 5) repeats and used in EMSAs. Probes either contained wild-type sequences or carried nucleotide substitutions in the first subunit of the distal repeat motif. (C to G) Probe DNA (2.5 ng) was labeled with 32 P and used in all binding reaction mixtures. Labeled DNA was incubated in the absence (lane 1) or presence (lanes 2 to 8) of 0.44 to 35.0 pmol wild-type His-MprA∼P. F, free DNA; B, bound DNA.

    Techniques Used: Binding Assay, Generated, Labeling, Incubation

    2) Product Images from "Chromatin and sequence features that define the fine and gross structure of genomic methylation patterns"

    Article Title: Chromatin and sequence features that define the fine and gross structure of genomic methylation patterns

    Journal: Genome Research

    doi: 10.1101/gr.101535.109

    High-resolution genome-wide methylation profiling and genome-wide DNA methylation trends. ( A ) Browser view of Methyl-MAPS data from the genomic region spanning the BIK gene. Individual mapped sequence reads are shown in the top raw data tracks. Red sequences were resistant to methylation-sensitive restriction endonucleases (RE) and are therefore methylated. Blue sequences were resistant to the methylation-dependent McrBC complex and are unmethylated. Tick marks in both tracks along the top of the figure and within each sequence indicate locations of individual RE and McrBC recognition sequences. Methylation data is also presented in a concise view, where each CpG is assigned a methylation score from the ratio of methylated to total (unmethylated and methylated) sequences covering each CpG site. The bulk of the BIK gene is methylated, while the CpG-rich promoter is unmethylated. ( B ) Methylation of the SVA retrotransposon in a repeat-rich region of chr 19. While the CpG density is comparable to that of the CpG island of the BIK gene shown in A , the SVA retrotransposon is densely methylated.
    Figure Legend Snippet: High-resolution genome-wide methylation profiling and genome-wide DNA methylation trends. ( A ) Browser view of Methyl-MAPS data from the genomic region spanning the BIK gene. Individual mapped sequence reads are shown in the top raw data tracks. Red sequences were resistant to methylation-sensitive restriction endonucleases (RE) and are therefore methylated. Blue sequences were resistant to the methylation-dependent McrBC complex and are unmethylated. Tick marks in both tracks along the top of the figure and within each sequence indicate locations of individual RE and McrBC recognition sequences. Methylation data is also presented in a concise view, where each CpG is assigned a methylation score from the ratio of methylated to total (unmethylated and methylated) sequences covering each CpG site. The bulk of the BIK gene is methylated, while the CpG-rich promoter is unmethylated. ( B ) Methylation of the SVA retrotransposon in a repeat-rich region of chr 19. While the CpG density is comparable to that of the CpG island of the BIK gene shown in A , the SVA retrotransposon is densely methylated.

    Techniques Used: Genome Wide, Methylation, DNA Methylation Assay, Sequencing

    3) Product Images from "Quantitative Proteomic Analysis of Chromatin Reveals that Ctf18 Acts in the DNA Replication Checkpoint *"

    Article Title: Quantitative Proteomic Analysis of Chromatin Reveals that Ctf18 Acts in the DNA Replication Checkpoint *

    Journal: Molecular & Cellular Proteomics : MCP

    doi: 10.1074/mcp.M110.005561

    Ctf18 acts in the DNA replication checkpoint response to HU. A , Two-dimensional gel analysis of EcoRI fragments containing ARS305 (early origin) and ARS1413 (late origin) in WT, ctf18 Δ and mrc1 Δ cells released into S phase in the presence of 200 m m HU for 90 min at 30 °C. Strains used are SHY201, TKY1, and TKY111. B , ctf18 Δ cells are defective in activating Rad53 in response to HU. Cells were arrested in G1 phase then released into S phase in the presence (upper panels) or absence (lower panels) of 200 m m HU at 25 °C. Cells were collected at the indicated time points and protein extracts prepared, followed by Western blotting to detect Rad53. Arrowhead indicates unmodified Rad53 and the bracket, phosphorylated forms of Rad53. Strains used are SHY201, TKY1, and TKY111. C , An experiment similar to that in B shows that Rad53 activation in ctf18 Δ depends on the DNA damage (Rad9-mediated) checkpoint. Strains are TKY130 and TKY131. D , Chromatin abnormalities in cells lacking the checkpoint mediator Mrc1 treated with HU. Plot shows log 2 ratios of all chromosome proteins identified and their summed peptide intensities. mrc1 Δ cells were labeled with [ 13 C 6 ]-Arg and [ 13 C 6 , 15 N 2 ]-Lys. Strains used are SHY201 and TKY111. E , Abnormalities in chromatin composition in HU-treated ctf18 Δ cells resemble those of HU-treated mrc1 Δ cells. Log 2 ratios of chromatin association for mrc1 Δ/WT in HU, plotted against log 2 ratios of chromatin association for ctf18 Δ/WT in HU.
    Figure Legend Snippet: Ctf18 acts in the DNA replication checkpoint response to HU. A , Two-dimensional gel analysis of EcoRI fragments containing ARS305 (early origin) and ARS1413 (late origin) in WT, ctf18 Δ and mrc1 Δ cells released into S phase in the presence of 200 m m HU for 90 min at 30 °C. Strains used are SHY201, TKY1, and TKY111. B , ctf18 Δ cells are defective in activating Rad53 in response to HU. Cells were arrested in G1 phase then released into S phase in the presence (upper panels) or absence (lower panels) of 200 m m HU at 25 °C. Cells were collected at the indicated time points and protein extracts prepared, followed by Western blotting to detect Rad53. Arrowhead indicates unmodified Rad53 and the bracket, phosphorylated forms of Rad53. Strains used are SHY201, TKY1, and TKY111. C , An experiment similar to that in B shows that Rad53 activation in ctf18 Δ depends on the DNA damage (Rad9-mediated) checkpoint. Strains are TKY130 and TKY131. D , Chromatin abnormalities in cells lacking the checkpoint mediator Mrc1 treated with HU. Plot shows log 2 ratios of all chromosome proteins identified and their summed peptide intensities. mrc1 Δ cells were labeled with [ 13 C 6 ]-Arg and [ 13 C 6 , 15 N 2 ]-Lys. Strains used are SHY201 and TKY111. E , Abnormalities in chromatin composition in HU-treated ctf18 Δ cells resemble those of HU-treated mrc1 Δ cells. Log 2 ratios of chromatin association for mrc1 Δ/WT in HU, plotted against log 2 ratios of chromatin association for ctf18 Δ/WT in HU.

    Techniques Used: Two-Dimensional Gel Electrophoresis, Western Blot, Activation Assay, Labeling

    Chromatin association of PCNA and the flap endonuclease Rad27, but not Cdc45, GINS, or Ctf4, was increased in cells lacking Elg1. A , Changes in chromatin composition in HU-treated elg1 Δ cells, compared with HU-treated wild-type. elg1 Δ cells were labeled with [ 13 C 6 ]-Arg and [ 13 C 6 , 15 N 2 ]-Lys. Strains used are SHY201 and TKY18. B , Increase in chromatin-bound PCNA in HU-treated elg1 Δ cells confirmed by Western blot analysis. Strains used are SHY201 and TKY18. C , Changes in chromatin composition in elg1 Δ cells during normal S phase. elg1 Δ cells were labeled with [ 13 C 6 ]-Arg and [ 13 C 6 , 15 N 2 ]-Lys. Strains used are SHY201 and TKY18. D , Cell cycle progression was analyzed by flow cytometry. Wild-type and elg1 Δ cells were synchronized by blocking with α-factor in G1 phase and release into medium without HU. Both cultures were harvested in mid-S phase, 27 min after release. Positions of cells with 1C and 2C DNA contents are indicated. E , Two-dimensional gel analysis of EcoRI fragments containing ARS305 and ARS1413 in elg1 Δ cells released into S phase in the presence of 200 m m HU for 90 min at 30 °C. Strain used is TKY18. F , Kinetics of R ad53 phosphorylation in elg1 Δ cells. Rad53 was detected as in Fig. 6 B .
    Figure Legend Snippet: Chromatin association of PCNA and the flap endonuclease Rad27, but not Cdc45, GINS, or Ctf4, was increased in cells lacking Elg1. A , Changes in chromatin composition in HU-treated elg1 Δ cells, compared with HU-treated wild-type. elg1 Δ cells were labeled with [ 13 C 6 ]-Arg and [ 13 C 6 , 15 N 2 ]-Lys. Strains used are SHY201 and TKY18. B , Increase in chromatin-bound PCNA in HU-treated elg1 Δ cells confirmed by Western blot analysis. Strains used are SHY201 and TKY18. C , Changes in chromatin composition in elg1 Δ cells during normal S phase. elg1 Δ cells were labeled with [ 13 C 6 ]-Arg and [ 13 C 6 , 15 N 2 ]-Lys. Strains used are SHY201 and TKY18. D , Cell cycle progression was analyzed by flow cytometry. Wild-type and elg1 Δ cells were synchronized by blocking with α-factor in G1 phase and release into medium without HU. Both cultures were harvested in mid-S phase, 27 min after release. Positions of cells with 1C and 2C DNA contents are indicated. E , Two-dimensional gel analysis of EcoRI fragments containing ARS305 and ARS1413 in elg1 Δ cells released into S phase in the presence of 200 m m HU for 90 min at 30 °C. Strain used is TKY18. F , Kinetics of R ad53 phosphorylation in elg1 Δ cells. Rad53 was detected as in Fig. 6 B .

    Techniques Used: Labeling, Western Blot, Flow Cytometry, Cytometry, Blocking Assay, Two-Dimensional Gel Electrophoresis

    Related Articles

    Purification:

    Article Title: The Photobacterium damselae subsp. damselae Hemolysins Damselysin and HlyA Are Encoded within a New Virulence Plasmid ▿
    Article Snippet: .. Genomic DNA of P. damselae subsp. damselae RM-71 was purified using a genome DNA kit (Qbiogene). .. DNA was partially digested with Sau3AI and ligated into the compatible BamHI site of alkaline phosphatase-treated SuperCos 1 cosmid vector (Stratagene).

    Article Title: Genome-wide analysis of the omega-3 fatty acid desaturase gene family in Gossypium
    Article Snippet: The high fidelity polymerase “Phusion” (New England Biolabs, Ipswich, MA) was used for amplification. .. PCR products were resolved on DNA gels and bands of expected size were extracted and purified using the GeneClean kit (MP Biomedicals, Santa Ana, CA) and ligated into appropriate plasmid vectors. .. In some cases, blunt-ended PCR products were subcloned into pZero-Blunt (Life Technologies, Carlsbad, CA), while in other cases, unique restrictions sites were added to the 5’ and 3’ ends of gene-specific primers to allow for directional subcloning into pUC19.

    Western Blot:

    Article Title: The MSP1 Gene Is Necessary to Restrict the Number of Cells Entering into Male and Female Sporogenesis and to Initiate Anther Wall Formation in Rice
    Article Snippet: Genomic DNAs of 53 R3 plants segregating the msp1 phenotype were isolated according to , digested with XbaI at 37°C for 6 h, electrophoresed on a 0.8% agarose gel, blotted onto a nylon membrane (Biodyne B; Pall Corp., Port Washington, NY), and prepared for DNA gel blot hybridization with a 1.6-kb BamHI-XhoI fragment of Tos17 ( ) as a probe. .. An ∼4.0-kb XbaI fragment tagged by Tos17 , which was linked completely to the msp1 phenotype in DNA gel blot analysis, was sliced out from the gel, eluted using the GENECLEAN II kit (Qbiogene, Carlsbad, CA), and inserted into pBluescript SK− (Stratagene). .. Genomic sequences flanking Tos17 were amplified by PCR with the primers M13-20 (5′-GTAAAACGACGGCCAGT-3′) in the vector and T17LTR4MR (5′-CTGTATAGTTGGCCCATGTCCAG-3′) in the long terminal repeat of the Tos17 retrotransposon.

    Polymerase Chain Reaction:

    Article Title: Genome-wide analysis of the omega-3 fatty acid desaturase gene family in Gossypium
    Article Snippet: The high fidelity polymerase “Phusion” (New England Biolabs, Ipswich, MA) was used for amplification. .. PCR products were resolved on DNA gels and bands of expected size were extracted and purified using the GeneClean kit (MP Biomedicals, Santa Ana, CA) and ligated into appropriate plasmid vectors. .. In some cases, blunt-ended PCR products were subcloned into pZero-Blunt (Life Technologies, Carlsbad, CA), while in other cases, unique restrictions sites were added to the 5’ and 3’ ends of gene-specific primers to allow for directional subcloning into pUC19.

    Article Title: Intrauterine growth restriction alters growth performance, plasma hormones, and small intestinal microbial communities in growing-finishing pigs
    Article Snippet: Concentration of plasma hormonesPlasma concentrations of gastrin, growth hormone (GH), ghrelin, glucagon, insulin-like growth factor-1 (IGF-1), insulin, leptin, pancreatic polypeptide (PP), peptide YY (PYY), and somatostatin (SS) were assayed using the Meimian ELISA kit (Suzhou Yutong Biotechnology Company, Suzhou, Jiangsu, China), as per the manufacturer’s instructions, and then read on a spectrophotometer (Biomate 5, Thermo Electron Corporation, Rochester, NY, USA). .. Microbiota DNA isolation and PCR amplificationTotal bacterial genomic DNA was extracted from intestinal samples using the Fast DNA SPIN extraction kit (MP Biomedicals, Santa Ana, CA, USA) following the manufacturer’s instructions, and stored at −20 °C until further analysis. .. The quantity and quality of the extracted DNA were assessed using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) and agarose gel electrophoresis, respectively.

    Plasmid Preparation:

    Article Title: Genome-wide analysis of the omega-3 fatty acid desaturase gene family in Gossypium
    Article Snippet: The high fidelity polymerase “Phusion” (New England Biolabs, Ipswich, MA) was used for amplification. .. PCR products were resolved on DNA gels and bands of expected size were extracted and purified using the GeneClean kit (MP Biomedicals, Santa Ana, CA) and ligated into appropriate plasmid vectors. .. In some cases, blunt-ended PCR products were subcloned into pZero-Blunt (Life Technologies, Carlsbad, CA), while in other cases, unique restrictions sites were added to the 5’ and 3’ ends of gene-specific primers to allow for directional subcloning into pUC19.

    Labeling:

    Article Title: COMBO-FISH Enables High Precision Localization Microscopy as a Prerequisite for Nanostructure Analysis of Genome Loci
    Article Snippet: In the next step, it was verified that the labeled chromosome is really chromosome 9. .. For this purpose, the lymphocyte specimens were subjected to another two-color experiment ( ) using the repetitive centromere 9 PNA COMBO-FISH probe labeled with OregonGreen 488® and a commercially available 9q subtelomere (9qtel) DNA standard FISH probe (MPbiomedicals, Montreal, Quebec, Canada) labeled with rhodamine. ..

    Fluorescence In Situ Hybridization:

    Article Title: COMBO-FISH Enables High Precision Localization Microscopy as a Prerequisite for Nanostructure Analysis of Genome Loci
    Article Snippet: In the next step, it was verified that the labeled chromosome is really chromosome 9. .. For this purpose, the lymphocyte specimens were subjected to another two-color experiment ( ) using the repetitive centromere 9 PNA COMBO-FISH probe labeled with OregonGreen 488® and a commercially available 9q subtelomere (9qtel) DNA standard FISH probe (MPbiomedicals, Montreal, Quebec, Canada) labeled with rhodamine. ..

    TaqMan Assay:

    Article Title: Expression of coordinately regulated defence response genes and analysis of their role in disease resistance in Medicago truncatula
    Article Snippet: Entire root systems from six plants were harvested at 1, 2, 4 and 6 dai and used for RNA extraction. .. To quantify the amount of P. medicaginis DNA in inoculated roots, total DNA of entire root systems was extracted using the Fast DNA Kit and FastPrep Instrument (MP Biomedicals, Solon, OH, USA) and used in a TaqMan assay as described previously ( ). .. To measure gene expression in healthy plant tissues, leaves, stems, petioles and roots were harvested from healthy 3‐week‐old plants; leaves and roots were also harvested from plants inoculated with pathogens as described above.

    DNA Extraction:

    Article Title: Telomeric transcripts stimulate telomere recombination to suppress senescence in cells lacking telomerase
    Article Snippet: The colonies from freshly dissected tetrads were inoculated directly into 10 mL of liquid yeast extract peptone dextrose (YEPD) medium and cultured to 3 × 108 cells. .. The cells were resuspended in DNA extraction buffer [2% (vol/vol) Triton X-100, 1% SDS, 200 mM NaCl, 10 mM EDTA, 10 mM Tris⋅HCl, pH 8.0, and 25 units of RNase inhibitor in 500 μL of buffer] and lysed by vortexing with glass beads using the FastPrep-24 system (MP Biomedicals). .. The extracted DNA was fragmented into ∼500 bp by using a cup horn sonicator (Qsonica Sonicator 4000), followed by treatment with 200 μg of proteinase K at 42 °C for 1 h to eliminate the proteins.

    Article Title: Intrauterine growth restriction alters growth performance, plasma hormones, and small intestinal microbial communities in growing-finishing pigs
    Article Snippet: Concentration of plasma hormonesPlasma concentrations of gastrin, growth hormone (GH), ghrelin, glucagon, insulin-like growth factor-1 (IGF-1), insulin, leptin, pancreatic polypeptide (PP), peptide YY (PYY), and somatostatin (SS) were assayed using the Meimian ELISA kit (Suzhou Yutong Biotechnology Company, Suzhou, Jiangsu, China), as per the manufacturer’s instructions, and then read on a spectrophotometer (Biomate 5, Thermo Electron Corporation, Rochester, NY, USA). .. Microbiota DNA isolation and PCR amplificationTotal bacterial genomic DNA was extracted from intestinal samples using the Fast DNA SPIN extraction kit (MP Biomedicals, Santa Ana, CA, USA) following the manufacturer’s instructions, and stored at −20 °C until further analysis. .. The quantity and quality of the extracted DNA were assessed using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) and agarose gel electrophoresis, respectively.

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    Valiant dna fragments
    MprA directly binds upstream regions of stress-responsive sigma factors. 32 P-labeled <t>DNA</t> from the sigB (A), sigE (B), and sigH (C) upstream regions were incubated with His-MprA∼P and used in <t>EMSAs.</t> Seven nanograms of labeled DNA was used in all binding reaction mixtures. Labeled DNA was incubated in the absence (lane 1) or presence (lanes 2 to 8) of 0.44 to 35.0 pmol wild-type His-MprA∼P. Binding specificity was determined by incubation of labeled DNA (lane 9) with 6 pmol His-MprA∼P in the absence (lane 10) or presence of a 150-fold excess of cold DNA from either the mprA upstream region (lane 11) or PPE19 upstream region (lane 12). Labeled DNA was also incubated with 14 pmol of the phosphorylation-deficient His-MprA(D48A) mutant (lane 13). F, free DNA; B, bound DNA.
    Dna Fragments, supplied by Valiant, used in various techniques. Bioz Stars score: 98/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dna fragments/product/Valiant
    Average 98 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    dna fragments - by Bioz Stars, 2021-03
    98/100 stars
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    MprA directly binds upstream regions of stress-responsive sigma factors. 32 P-labeled DNA from the sigB (A), sigE (B), and sigH (C) upstream regions were incubated with His-MprA∼P and used in EMSAs. Seven nanograms of labeled DNA was used in all binding reaction mixtures. Labeled DNA was incubated in the absence (lane 1) or presence (lanes 2 to 8) of 0.44 to 35.0 pmol wild-type His-MprA∼P. Binding specificity was determined by incubation of labeled DNA (lane 9) with 6 pmol His-MprA∼P in the absence (lane 10) or presence of a 150-fold excess of cold DNA from either the mprA upstream region (lane 11) or PPE19 upstream region (lane 12). Labeled DNA was also incubated with 14 pmol of the phosphorylation-deficient His-MprA(D48A) mutant (lane 13). F, free DNA; B, bound DNA.

    Journal: Journal of Bacteriology

    Article Title: MprAB Is a Stress-Responsive Two-Component System That Directly Regulates Expression of Sigma Factors SigB and SigE in Mycobacterium tuberculosis §

    doi: 10.1128/JB.188.6.2134-2143.2006

    Figure Lengend Snippet: MprA directly binds upstream regions of stress-responsive sigma factors. 32 P-labeled DNA from the sigB (A), sigE (B), and sigH (C) upstream regions were incubated with His-MprA∼P and used in EMSAs. Seven nanograms of labeled DNA was used in all binding reaction mixtures. Labeled DNA was incubated in the absence (lane 1) or presence (lanes 2 to 8) of 0.44 to 35.0 pmol wild-type His-MprA∼P. Binding specificity was determined by incubation of labeled DNA (lane 9) with 6 pmol His-MprA∼P in the absence (lane 10) or presence of a 150-fold excess of cold DNA from either the mprA upstream region (lane 11) or PPE19 upstream region (lane 12). Labeled DNA was also incubated with 14 pmol of the phosphorylation-deficient His-MprA(D48A) mutant (lane 13). F, free DNA; B, bound DNA.

    Article Snippet: For electrophoretic mobility shift assays (EMSAs), DNA fragments derived from the upstream regions of sigB , sigE , and sigH were amplified from the M. tuberculosis H37Rv genome or generated by annealing complementary single-stranded DNA oligonucleotides, end-labeled with [γ-32 P]ATP (MP Biomedicals) using T4 polynucleotide kinase, and incubated at room temperature for 20 min with His-MprA that had been previously phosphorylated in vitro with acetyl phosphate ( ).

    Techniques: Labeling, Incubation, Binding Assay, Mutagenesis

    DNase I footprints of sigB and sigE upstream regions. (A) 32 P-labeled DNA from the sigB and sigE upstream regions was incubated in the absence or presence of 1.3 to 260 pmol His-MprA∼P and treated with 0.2 units DNase I; arrowheads denote sites of DNase I hypersensitivity. (B) Protected regions (shaded areas) are depicted for both sigB (B) and sigE (C) upstream regions along with the known transcriptional start site (*) and −10 and −35 sites (solid lines). Putative 8-bp direct repeat motifs (dotted line) were determined by GCG analyses and were similar to those found upstream of mprA and pepD . Start and stop codons are depicted in capital letters.

    Journal: Journal of Bacteriology

    Article Title: MprAB Is a Stress-Responsive Two-Component System That Directly Regulates Expression of Sigma Factors SigB and SigE in Mycobacterium tuberculosis §

    doi: 10.1128/JB.188.6.2134-2143.2006

    Figure Lengend Snippet: DNase I footprints of sigB and sigE upstream regions. (A) 32 P-labeled DNA from the sigB and sigE upstream regions was incubated in the absence or presence of 1.3 to 260 pmol His-MprA∼P and treated with 0.2 units DNase I; arrowheads denote sites of DNase I hypersensitivity. (B) Protected regions (shaded areas) are depicted for both sigB (B) and sigE (C) upstream regions along with the known transcriptional start site (*) and −10 and −35 sites (solid lines). Putative 8-bp direct repeat motifs (dotted line) were determined by GCG analyses and were similar to those found upstream of mprA and pepD . Start and stop codons are depicted in capital letters.

    Article Snippet: For electrophoretic mobility shift assays (EMSAs), DNA fragments derived from the upstream regions of sigB , sigE , and sigH were amplified from the M. tuberculosis H37Rv genome or generated by annealing complementary single-stranded DNA oligonucleotides, end-labeled with [γ-32 P]ATP (MP Biomedicals) using T4 polynucleotide kinase, and incubated at room temperature for 20 min with His-MprA that had been previously phosphorylated in vitro with acetyl phosphate ( ).

    Techniques: Labeling, Incubation

    Binding to sigE ). (B) Probes were generated to distal (probes 1 and 3), proximal (probe 2), or distal and proximal (probes 4 and 5) repeats and used in EMSAs. Probes either contained wild-type sequences or carried nucleotide substitutions in the first subunit of the distal repeat motif. (C to G) Probe DNA (2.5 ng) was labeled with 32 P and used in all binding reaction mixtures. Labeled DNA was incubated in the absence (lane 1) or presence (lanes 2 to 8) of 0.44 to 35.0 pmol wild-type His-MprA∼P. F, free DNA; B, bound DNA.

    Journal: Journal of Bacteriology

    Article Title: MprAB Is a Stress-Responsive Two-Component System That Directly Regulates Expression of Sigma Factors SigB and SigE in Mycobacterium tuberculosis §

    doi: 10.1128/JB.188.6.2134-2143.2006

    Figure Lengend Snippet: Binding to sigE ). (B) Probes were generated to distal (probes 1 and 3), proximal (probe 2), or distal and proximal (probes 4 and 5) repeats and used in EMSAs. Probes either contained wild-type sequences or carried nucleotide substitutions in the first subunit of the distal repeat motif. (C to G) Probe DNA (2.5 ng) was labeled with 32 P and used in all binding reaction mixtures. Labeled DNA was incubated in the absence (lane 1) or presence (lanes 2 to 8) of 0.44 to 35.0 pmol wild-type His-MprA∼P. F, free DNA; B, bound DNA.

    Article Snippet: For electrophoretic mobility shift assays (EMSAs), DNA fragments derived from the upstream regions of sigB , sigE , and sigH were amplified from the M. tuberculosis H37Rv genome or generated by annealing complementary single-stranded DNA oligonucleotides, end-labeled with [γ-32 P]ATP (MP Biomedicals) using T4 polynucleotide kinase, and incubated at room temperature for 20 min with His-MprA that had been previously phosphorylated in vitro with acetyl phosphate ( ).

    Techniques: Binding Assay, Generated, Labeling, Incubation

    High-resolution genome-wide methylation profiling and genome-wide DNA methylation trends. ( A ) Browser view of Methyl-MAPS data from the genomic region spanning the BIK gene. Individual mapped sequence reads are shown in the top raw data tracks. Red sequences were resistant to methylation-sensitive restriction endonucleases (RE) and are therefore methylated. Blue sequences were resistant to the methylation-dependent McrBC complex and are unmethylated. Tick marks in both tracks along the top of the figure and within each sequence indicate locations of individual RE and McrBC recognition sequences. Methylation data is also presented in a concise view, where each CpG is assigned a methylation score from the ratio of methylated to total (unmethylated and methylated) sequences covering each CpG site. The bulk of the BIK gene is methylated, while the CpG-rich promoter is unmethylated. ( B ) Methylation of the SVA retrotransposon in a repeat-rich region of chr 19. While the CpG density is comparable to that of the CpG island of the BIK gene shown in A , the SVA retrotransposon is densely methylated.

    Journal: Genome Research

    Article Title: Chromatin and sequence features that define the fine and gross structure of genomic methylation patterns

    doi: 10.1101/gr.101535.109

    Figure Lengend Snippet: High-resolution genome-wide methylation profiling and genome-wide DNA methylation trends. ( A ) Browser view of Methyl-MAPS data from the genomic region spanning the BIK gene. Individual mapped sequence reads are shown in the top raw data tracks. Red sequences were resistant to methylation-sensitive restriction endonucleases (RE) and are therefore methylated. Blue sequences were resistant to the methylation-dependent McrBC complex and are unmethylated. Tick marks in both tracks along the top of the figure and within each sequence indicate locations of individual RE and McrBC recognition sequences. Methylation data is also presented in a concise view, where each CpG is assigned a methylation score from the ratio of methylated to total (unmethylated and methylated) sequences covering each CpG site. The bulk of the BIK gene is methylated, while the CpG-rich promoter is unmethylated. ( B ) Methylation of the SVA retrotransposon in a repeat-rich region of chr 19. While the CpG density is comparable to that of the CpG island of the BIK gene shown in A , the SVA retrotransposon is densely methylated.

    Article Snippet: DNA fragments were collected in several size fractions (McrBC: 0.8–2 kb, 2–5 kb, > 5 kb; RE: 0.8–1.5 kb, 1.5–3 kb, 3–6 kb, > 6 kb) and extracted using the GENECLEAN Glassmilk Spin Column Kit (MP Biomedicals).

    Techniques: Genome Wide, Methylation, DNA Methylation Assay, Sequencing

    Ctf18 acts in the DNA replication checkpoint response to HU. A , Two-dimensional gel analysis of EcoRI fragments containing ARS305 (early origin) and ARS1413 (late origin) in WT, ctf18 Δ and mrc1 Δ cells released into S phase in the presence of 200 m m HU for 90 min at 30 °C. Strains used are SHY201, TKY1, and TKY111. B , ctf18 Δ cells are defective in activating Rad53 in response to HU. Cells were arrested in G1 phase then released into S phase in the presence (upper panels) or absence (lower panels) of 200 m m HU at 25 °C. Cells were collected at the indicated time points and protein extracts prepared, followed by Western blotting to detect Rad53. Arrowhead indicates unmodified Rad53 and the bracket, phosphorylated forms of Rad53. Strains used are SHY201, TKY1, and TKY111. C , An experiment similar to that in B shows that Rad53 activation in ctf18 Δ depends on the DNA damage (Rad9-mediated) checkpoint. Strains are TKY130 and TKY131. D , Chromatin abnormalities in cells lacking the checkpoint mediator Mrc1 treated with HU. Plot shows log 2 ratios of all chromosome proteins identified and their summed peptide intensities. mrc1 Δ cells were labeled with [ 13 C 6 ]-Arg and [ 13 C 6 , 15 N 2 ]-Lys. Strains used are SHY201 and TKY111. E , Abnormalities in chromatin composition in HU-treated ctf18 Δ cells resemble those of HU-treated mrc1 Δ cells. Log 2 ratios of chromatin association for mrc1 Δ/WT in HU, plotted against log 2 ratios of chromatin association for ctf18 Δ/WT in HU.

    Journal: Molecular & Cellular Proteomics : MCP

    Article Title: Quantitative Proteomic Analysis of Chromatin Reveals that Ctf18 Acts in the DNA Replication Checkpoint *

    doi: 10.1074/mcp.M110.005561

    Figure Lengend Snippet: Ctf18 acts in the DNA replication checkpoint response to HU. A , Two-dimensional gel analysis of EcoRI fragments containing ARS305 (early origin) and ARS1413 (late origin) in WT, ctf18 Δ and mrc1 Δ cells released into S phase in the presence of 200 m m HU for 90 min at 30 °C. Strains used are SHY201, TKY1, and TKY111. B , ctf18 Δ cells are defective in activating Rad53 in response to HU. Cells were arrested in G1 phase then released into S phase in the presence (upper panels) or absence (lower panels) of 200 m m HU at 25 °C. Cells were collected at the indicated time points and protein extracts prepared, followed by Western blotting to detect Rad53. Arrowhead indicates unmodified Rad53 and the bracket, phosphorylated forms of Rad53. Strains used are SHY201, TKY1, and TKY111. C , An experiment similar to that in B shows that Rad53 activation in ctf18 Δ depends on the DNA damage (Rad9-mediated) checkpoint. Strains are TKY130 and TKY131. D , Chromatin abnormalities in cells lacking the checkpoint mediator Mrc1 treated with HU. Plot shows log 2 ratios of all chromosome proteins identified and their summed peptide intensities. mrc1 Δ cells were labeled with [ 13 C 6 ]-Arg and [ 13 C 6 , 15 N 2 ]-Lys. Strains used are SHY201 and TKY111. E , Abnormalities in chromatin composition in HU-treated ctf18 Δ cells resemble those of HU-treated mrc1 Δ cells. Log 2 ratios of chromatin association for mrc1 Δ/WT in HU, plotted against log 2 ratios of chromatin association for ctf18 Δ/WT in HU.

    Article Snippet: DNA fragments digested using EcoRI were separated by neutral/neutral two-dimensional agarose gel electrophoresis ( ) and transferred to Neutral membrane (Qbiogene, Illkirch, France) by capillary blotting.

    Techniques: Two-Dimensional Gel Electrophoresis, Western Blot, Activation Assay, Labeling

    Chromatin association of PCNA and the flap endonuclease Rad27, but not Cdc45, GINS, or Ctf4, was increased in cells lacking Elg1. A , Changes in chromatin composition in HU-treated elg1 Δ cells, compared with HU-treated wild-type. elg1 Δ cells were labeled with [ 13 C 6 ]-Arg and [ 13 C 6 , 15 N 2 ]-Lys. Strains used are SHY201 and TKY18. B , Increase in chromatin-bound PCNA in HU-treated elg1 Δ cells confirmed by Western blot analysis. Strains used are SHY201 and TKY18. C , Changes in chromatin composition in elg1 Δ cells during normal S phase. elg1 Δ cells were labeled with [ 13 C 6 ]-Arg and [ 13 C 6 , 15 N 2 ]-Lys. Strains used are SHY201 and TKY18. D , Cell cycle progression was analyzed by flow cytometry. Wild-type and elg1 Δ cells were synchronized by blocking with α-factor in G1 phase and release into medium without HU. Both cultures were harvested in mid-S phase, 27 min after release. Positions of cells with 1C and 2C DNA contents are indicated. E , Two-dimensional gel analysis of EcoRI fragments containing ARS305 and ARS1413 in elg1 Δ cells released into S phase in the presence of 200 m m HU for 90 min at 30 °C. Strain used is TKY18. F , Kinetics of R ad53 phosphorylation in elg1 Δ cells. Rad53 was detected as in Fig. 6 B .

    Journal: Molecular & Cellular Proteomics : MCP

    Article Title: Quantitative Proteomic Analysis of Chromatin Reveals that Ctf18 Acts in the DNA Replication Checkpoint *

    doi: 10.1074/mcp.M110.005561

    Figure Lengend Snippet: Chromatin association of PCNA and the flap endonuclease Rad27, but not Cdc45, GINS, or Ctf4, was increased in cells lacking Elg1. A , Changes in chromatin composition in HU-treated elg1 Δ cells, compared with HU-treated wild-type. elg1 Δ cells were labeled with [ 13 C 6 ]-Arg and [ 13 C 6 , 15 N 2 ]-Lys. Strains used are SHY201 and TKY18. B , Increase in chromatin-bound PCNA in HU-treated elg1 Δ cells confirmed by Western blot analysis. Strains used are SHY201 and TKY18. C , Changes in chromatin composition in elg1 Δ cells during normal S phase. elg1 Δ cells were labeled with [ 13 C 6 ]-Arg and [ 13 C 6 , 15 N 2 ]-Lys. Strains used are SHY201 and TKY18. D , Cell cycle progression was analyzed by flow cytometry. Wild-type and elg1 Δ cells were synchronized by blocking with α-factor in G1 phase and release into medium without HU. Both cultures were harvested in mid-S phase, 27 min after release. Positions of cells with 1C and 2C DNA contents are indicated. E , Two-dimensional gel analysis of EcoRI fragments containing ARS305 and ARS1413 in elg1 Δ cells released into S phase in the presence of 200 m m HU for 90 min at 30 °C. Strain used is TKY18. F , Kinetics of R ad53 phosphorylation in elg1 Δ cells. Rad53 was detected as in Fig. 6 B .

    Article Snippet: DNA fragments digested using EcoRI were separated by neutral/neutral two-dimensional agarose gel electrophoresis ( ) and transferred to Neutral membrane (Qbiogene, Illkirch, France) by capillary blotting.

    Techniques: Labeling, Western Blot, Flow Cytometry, Cytometry, Blocking Assay, Two-Dimensional Gel Electrophoresis

    Telomere fusion junction sequence analysis from breast tumor tissue. ( A ) Summary of telomere fusion junction sequence analysis using TAR fusion PCR. Fusion chromosomes, chromosomes involved in fusion junction. Source of telomeric DNA, chromosome presumed

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    Article Title: Telomere fusions in early human breast carcinoma

    doi: 10.1073/pnas.1120062109

    Figure Lengend Snippet: Telomere fusion junction sequence analysis from breast tumor tissue. ( A ) Summary of telomere fusion junction sequence analysis using TAR fusion PCR. Fusion chromosomes, chromosomes involved in fusion junction. Source of telomeric DNA, chromosome presumed

    Article Snippet: DNA samples were purified from either PCR reactions or gel-purified DNA fragments using the GENECLEAN Turbo Kit (MP Biomedicals).

    Techniques: Sequencing, Polymerase Chain Reaction

    Strategy for the detection of telomere fusions using TAR fusion PCR. ( A ) annealing within TAR1 regions adjacent to telomeric DNA sequences. The fusion junctions

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    Article Title: Telomere fusions in early human breast carcinoma

    doi: 10.1073/pnas.1120062109

    Figure Lengend Snippet: Strategy for the detection of telomere fusions using TAR fusion PCR. ( A ) annealing within TAR1 regions adjacent to telomeric DNA sequences. The fusion junctions

    Article Snippet: DNA samples were purified from either PCR reactions or gel-purified DNA fragments using the GENECLEAN Turbo Kit (MP Biomedicals).

    Techniques: Polymerase Chain Reaction