fragmented dna Search Results


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  • 99
    Millipore dna fragment
    Nonradioactive EMSA of <t>Cra</t> and its binding site in aceBAK . EMSA experiment using 0.75 μM of the Cra site-containing <t>DNA</t> fragment and increasing concentrations of wild type Cra or the Cra mutant proteins in the presence of FBP ( a ) and the gray value of free DNA determined using Quantity one ( b ) and in the absence of FBP ( c ) and the gray value of free DNA determined using Quantity one ( d ). Lane 1, no protein; lane 2–5, 1, 2, 3, 4 μM Cra; lanes 6–9, 1, 2, 3, 4 μM Cra mutant (Tang1541); lanes 10–13, 1, 2, 3, 4 μM Cra mutant (Tang1544), respectively.
    Dna Fragment, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 4627 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dna fragment/product/Millipore
    Average 99 stars, based on 4627 article reviews
    Price from $9.99 to $1999.99
    dna fragment - by Bioz Stars, 2020-08
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    99
    Millipore dna fragments
    SNP analysis of centromeric domains. Sanger sequence traces from input ( above ) and CENP-A <t>immunoprecipitated</t> ( below ) samples from HSF-C, HSF-G, HSF-D and HSF-E. SNP coordinates are beneath traces. Stars indicate SNPs. For HSF-C, HSF-G, HSF-D-edge and HSF-E-edge, both nucleotides are present in input <t>DNA</t> while the immunoprecipitated DNA is enriched for one of the two nucleotides. For HSF-D centre and HSF-E centre, the two nucleotides are present in both input and CENP-A immunoprecipitated samples
    Dna Fragments, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 6230 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dna fragments/product/Millipore
    Average 99 stars, based on 6230 article reviews
    Price from $9.99 to $1999.99
    dna fragments - by Bioz Stars, 2020-08
    99/100 stars
      Buy from Supplier

    Image Search Results


    Nonradioactive EMSA of Cra and its binding site in aceBAK . EMSA experiment using 0.75 μM of the Cra site-containing DNA fragment and increasing concentrations of wild type Cra or the Cra mutant proteins in the presence of FBP ( a ) and the gray value of free DNA determined using Quantity one ( b ) and in the absence of FBP ( c ) and the gray value of free DNA determined using Quantity one ( d ). Lane 1, no protein; lane 2–5, 1, 2, 3, 4 μM Cra; lanes 6–9, 1, 2, 3, 4 μM Cra mutant (Tang1541); lanes 10–13, 1, 2, 3, 4 μM Cra mutant (Tang1544), respectively.

    Journal: Scientific Reports

    Article Title: Enhancing succinic acid biosynthesis in Escherichia coli by engineering its global transcription factor, catabolite repressor/activator (Cra)

    doi: 10.1038/srep36526

    Figure Lengend Snippet: Nonradioactive EMSA of Cra and its binding site in aceBAK . EMSA experiment using 0.75 μM of the Cra site-containing DNA fragment and increasing concentrations of wild type Cra or the Cra mutant proteins in the presence of FBP ( a ) and the gray value of free DNA determined using Quantity one ( b ) and in the absence of FBP ( c ) and the gray value of free DNA determined using Quantity one ( d ). Lane 1, no protein; lane 2–5, 1, 2, 3, 4 μM Cra; lanes 6–9, 1, 2, 3, 4 μM Cra mutant (Tang1541); lanes 10–13, 1, 2, 3, 4 μM Cra mutant (Tang1544), respectively.

    Article Snippet: Cra was incubated with the DNA fragment in the presence of 1 mM FBP (Sigma, 98% purity).

    Techniques: Binding Assay, Mutagenesis

    PBISe induces late stage apoptosis resulting in DNA fragmentation. Four different cell lines were used to demonstrate the late apoptotic process. ( a ) Skhep1; ( b ) HepG2; ( c ) C3A; ( d ) Huh-7. The cells were grown in 100 mm petridishes in 10% MEM, and then treated with different concentration of the drug for 48 h. Approximately 1 × 10 6 treated cells were suspended in 1X binding buffer. One-hundred microliters of suspended cells containing 1 × 10 5 cells were stained with 5 μL of FITC labeled annexin-V and 5 μL of Propidium iodide (PI) for 15 min at RT in dark. Apoptosis is measured by flow cytometry within one hour of staining. Graph showing the total apoptotic cell death from three quadrants representing the PI stained cells (early apoptotic), annexin-V staining (Late apoptotic) and double positive (early and late apoptotic). The p values are determined for all the indicated concentrations compared to control ( A ). As an indication of late stage apoptosis, PBISe induced DNA fragmentation of Skhep1, HepG2, C3A and Huh7 cell lines was performed by Tunnel assay. The cells are grown on the coverslip in a 6 well plate, treated with 10 μM conc. of PBISe for 48 h. The treated coverslips were fixed with paraformaldehyde followed by precooled ethanol and acetic acid. The coverslips were labeled with Apo tag red for Tunnel (red) and counterstained with DAPI nuclear stain (blue). The pictures were taken with Leica confocal microscopy ( B ).

    Journal: Pharmaceuticals

    Article Title: A Selenium Containing Inhibitor for the Treatment of Hepatocellular Cancer

    doi: 10.3390/ph9020018

    Figure Lengend Snippet: PBISe induces late stage apoptosis resulting in DNA fragmentation. Four different cell lines were used to demonstrate the late apoptotic process. ( a ) Skhep1; ( b ) HepG2; ( c ) C3A; ( d ) Huh-7. The cells were grown in 100 mm petridishes in 10% MEM, and then treated with different concentration of the drug for 48 h. Approximately 1 × 10 6 treated cells were suspended in 1X binding buffer. One-hundred microliters of suspended cells containing 1 × 10 5 cells were stained with 5 μL of FITC labeled annexin-V and 5 μL of Propidium iodide (PI) for 15 min at RT in dark. Apoptosis is measured by flow cytometry within one hour of staining. Graph showing the total apoptotic cell death from three quadrants representing the PI stained cells (early apoptotic), annexin-V staining (Late apoptotic) and double positive (early and late apoptotic). The p values are determined for all the indicated concentrations compared to control ( A ). As an indication of late stage apoptosis, PBISe induced DNA fragmentation of Skhep1, HepG2, C3A and Huh7 cell lines was performed by Tunnel assay. The cells are grown on the coverslip in a 6 well plate, treated with 10 μM conc. of PBISe for 48 h. The treated coverslips were fixed with paraformaldehyde followed by precooled ethanol and acetic acid. The coverslips were labeled with Apo tag red for Tunnel (red) and counterstained with DAPI nuclear stain (blue). The pictures were taken with Leica confocal microscopy ( B ).

    Article Snippet: Fragmented DNA of apoptotic cells was stained using an ApopTag Red in Situ Apoptosis Detection Kit according to the manufacturer’s instructions (Chemicon, Temecula, CA, USA) and visualized by fluorescence microscopy using appropriate filters.

    Techniques: Concentration Assay, Binding Assay, Staining, Labeling, Flow Cytometry, Cytometry, Confocal Microscopy

    Characterization of identified clones containing putative CepR-C 8 ]) to sequences in the genome of B. cepacia J2315. For those clones that showed a high degree of identity at the DNA level (see text), a region of the genome surrounding 2 kbp of each sequence was subsequently annotated. In the majority of the cases, it was possible to identify a homologue of a gene coding for a protein of known function. In such cases, the names of the respective genes are indicated inside of the putative ORFs (represented as thick gray arrows). A black arrow represents the size, position, and orientation of the identified insert in each clone (in scale with each clone). Within some genetic regions shown, hypothetical proteins of unknown function were found (here designated ORF). Such was the case with P67 (ORF represents what was probably a lysR family transcriptional regulator from R. solanacearum ), P80 (ORF represents a 4-hydroxybenzoate octaprenyl transferase from Xanthomonas axonopodis ), P114 (ORF1 represents a hypothetical protein from B. fungorum ; ORF2 represents a probable transcriptional regulator, PA1627, from P. aeruginosa ), P111 (ORF2 represents a short chain dehydrogenase-reductase from Pseudomonas putida , KT2440; ORF1 represents a hypothetical protein, PA1829, from P. aeruginosa ), P79 (ORF represents a protein of unknown function), P103 (ORF represents a protein of unknown function), P56 (ORF1 represents a probable efflux membrane protein from Mesorhizobium loti ; ORF2 represents a probable nucleoside triphosphate pyrophosphohydrolase from Agrobacterium tumefaciens ), P57 (ORF1 represents a probable porin transmembrane protein from R. solanacearum ; ORF2 represents a putative lipoprotein from R. solanacearum ), P105 (ORF represents a hypothetical protein from R. solanacearum ), and P135 (ORF1 represents a human RNA binding protein; ORF2 represents a putative small heat shock protein from R . solanacearum ). See text for details of all other ORFs mentioned.

    Journal: Journal of Bacteriology

    Article Title: Identification of Quorum-Sensing-Regulated Genes of Burkholderia cepacia

    doi: 10.1128/JB.185.21.6456-6462.2003

    Figure Lengend Snippet: Characterization of identified clones containing putative CepR-C 8 ]) to sequences in the genome of B. cepacia J2315. For those clones that showed a high degree of identity at the DNA level (see text), a region of the genome surrounding 2 kbp of each sequence was subsequently annotated. In the majority of the cases, it was possible to identify a homologue of a gene coding for a protein of known function. In such cases, the names of the respective genes are indicated inside of the putative ORFs (represented as thick gray arrows). A black arrow represents the size, position, and orientation of the identified insert in each clone (in scale with each clone). Within some genetic regions shown, hypothetical proteins of unknown function were found (here designated ORF). Such was the case with P67 (ORF represents what was probably a lysR family transcriptional regulator from R. solanacearum ), P80 (ORF represents a 4-hydroxybenzoate octaprenyl transferase from Xanthomonas axonopodis ), P114 (ORF1 represents a hypothetical protein from B. fungorum ; ORF2 represents a probable transcriptional regulator, PA1627, from P. aeruginosa ), P111 (ORF2 represents a short chain dehydrogenase-reductase from Pseudomonas putida , KT2440; ORF1 represents a hypothetical protein, PA1829, from P. aeruginosa ), P79 (ORF represents a protein of unknown function), P103 (ORF represents a protein of unknown function), P56 (ORF1 represents a probable efflux membrane protein from Mesorhizobium loti ; ORF2 represents a probable nucleoside triphosphate pyrophosphohydrolase from Agrobacterium tumefaciens ), P57 (ORF1 represents a probable porin transmembrane protein from R. solanacearum ; ORF2 represents a putative lipoprotein from R. solanacearum ), P105 (ORF represents a hypothetical protein from R. solanacearum ), and P135 (ORF1 represents a human RNA binding protein; ORF2 represents a putative small heat shock protein from R . solanacearum ). See text for details of all other ORFs mentioned.

    Article Snippet: DNA ligations between pSCR2 and the genomic restriction DNA fragments from B. cepacia (obtained using the restriction enzymes Nru I, Hae III, Hin cII, Alu I, and Sau 3AI independently) were transformed in E. coli DH5α and plated on selective medium containing 100 μg of ampicillin (Sigma-Aldrich)/ml, 20 μg of X-Gal (Sigma-Aldrich)/ml, and 100 nM C8 -HSL.

    Techniques: Clone Assay, Sequencing, RNA Binding Assay

    BAF complex preferentially binds and remodels H3K4me1 modified nucleosomes A) Purified Flag-BAF complex binding to H3K4 methylated-nucleosomes, western blotted with anti-FLAG antibody (M2). Pulldown repeated 3 times yielding the same result. B) Polyacrylamide gel showing representative (n=4) in vitro remodeling assay. After incubation with BAF complex, nucleosomes are slid to the end of the 216-bp DNA fragment resulting in a change in mobility in the gel. Top band is un-remodeled nucleosome, and lower four bands are slid nucleosomes with different positions away from 146-bp Widom601 binding sites in the middle. C) Quantification of nucleosome remodeling assays. Error bars, mean ±SD n=4 biological replicates, see Figure S4C . The reduced percentage of the top band is defined as remodeling efficiency.

    Journal: Nature genetics

    Article Title: Identification of H3K4me1-Associated Proteins at Mammalian Enhancers

    doi: 10.1038/s41588-017-0015-6

    Figure Lengend Snippet: BAF complex preferentially binds and remodels H3K4me1 modified nucleosomes A) Purified Flag-BAF complex binding to H3K4 methylated-nucleosomes, western blotted with anti-FLAG antibody (M2). Pulldown repeated 3 times yielding the same result. B) Polyacrylamide gel showing representative (n=4) in vitro remodeling assay. After incubation with BAF complex, nucleosomes are slid to the end of the 216-bp DNA fragment resulting in a change in mobility in the gel. Top band is un-remodeled nucleosome, and lower four bands are slid nucleosomes with different positions away from 146-bp Widom601 binding sites in the middle. C) Quantification of nucleosome remodeling assays. Error bars, mean ±SD n=4 biological replicates, see Figure S4C . The reduced percentage of the top band is defined as remodeling efficiency.

    Article Snippet: Cold mono-nucleosome (2 µM) was assembled using Xenopus laevis histones with unlabeled DNA fragment by the same method, which is then mixed with sonicated calf thymus DNA (1mg/ml, Sigma).

    Techniques: Modification, Purification, Binding Assay, Methylation, Western Blot, In Vitro, Incubation

    SNP analysis of centromeric domains. Sanger sequence traces from input ( above ) and CENP-A immunoprecipitated ( below ) samples from HSF-C, HSF-G, HSF-D and HSF-E. SNP coordinates are beneath traces. Stars indicate SNPs. For HSF-C, HSF-G, HSF-D-edge and HSF-E-edge, both nucleotides are present in input DNA while the immunoprecipitated DNA is enriched for one of the two nucleotides. For HSF-D centre and HSF-E centre, the two nucleotides are present in both input and CENP-A immunoprecipitated samples

    Journal: Chromosoma

    Article Title: Centromere sliding on a mammalian chromosome

    doi: 10.1007/s00412-014-0493-6

    Figure Lengend Snippet: SNP analysis of centromeric domains. Sanger sequence traces from input ( above ) and CENP-A immunoprecipitated ( below ) samples from HSF-C, HSF-G, HSF-D and HSF-E. SNP coordinates are beneath traces. Stars indicate SNPs. For HSF-C, HSF-G, HSF-D-edge and HSF-E-edge, both nucleotides are present in input DNA while the immunoprecipitated DNA is enriched for one of the two nucleotides. For HSF-D centre and HSF-E centre, the two nucleotides are present in both input and CENP-A immunoprecipitated samples

    Article Snippet: Both input and immunoprecipitated DNA fragments were purified and amplified using the whole genome amplification (WGA) kit (Sigma-Aldrich, St. Louis, USA).

    Techniques: Sequencing, Immunoprecipitation

    Variable position of the centromere of horse chromosome 11. a DNA obtained by chromatin immunoprecipitation. Using an anti-CENP-A antibody, from five different horse fibroblast cultures was hybridized to a tiling array covering the centromere region. Results are presented as the log2 ratio of the hybridization signals obtained with immunoprecipitated DNA versus input DNA; x -axis, genomic coordinates on ECA11. Positions of informative SNPs are indicated as black dots (a single nucleotide of the SNP is enriched in immunoprecipitated DNA), red dots (both SNP alleles are present in immunoprecipitated DNA) and blue carats (SNPs shown in Fig. 3 ). b Peak positions are represented as boxes . Epiallele identification was obtained by combining ChIP-on-chip, SNP (Fig. 3 ) and fibre FISH (Fig. 4 and Supplementary Table 2 ) results. Sequence coordinates refer to the horse EquCab2.0 (2007) sequence assembly, as reported by the UCSC genome browser ( http://genome.ucsc.edu ). Alleles are designated by the letter of the horse they derive from, followed by ‘1’ or ‘2’ to distinguish the two variants. In HSF-D and HSF-E, where a single broad peak was identified by ChIP-on-chip while two distinct centromeric domains were identified by fibre-FISH (Fig. 4 ) and SNP analysis (Fig. 3 and Supplementary Table 2 ), dotted lines represent the region of overlap of the two binding domains in the reference sequence. Therefore, at least seven different centromeric domains can be identified: Ba/Ea, Bb, Ca, Cb, Da/Eb, Db/Ga, Gb

    Journal: Chromosoma

    Article Title: Centromere sliding on a mammalian chromosome

    doi: 10.1007/s00412-014-0493-6

    Figure Lengend Snippet: Variable position of the centromere of horse chromosome 11. a DNA obtained by chromatin immunoprecipitation. Using an anti-CENP-A antibody, from five different horse fibroblast cultures was hybridized to a tiling array covering the centromere region. Results are presented as the log2 ratio of the hybridization signals obtained with immunoprecipitated DNA versus input DNA; x -axis, genomic coordinates on ECA11. Positions of informative SNPs are indicated as black dots (a single nucleotide of the SNP is enriched in immunoprecipitated DNA), red dots (both SNP alleles are present in immunoprecipitated DNA) and blue carats (SNPs shown in Fig. 3 ). b Peak positions are represented as boxes . Epiallele identification was obtained by combining ChIP-on-chip, SNP (Fig. 3 ) and fibre FISH (Fig. 4 and Supplementary Table 2 ) results. Sequence coordinates refer to the horse EquCab2.0 (2007) sequence assembly, as reported by the UCSC genome browser ( http://genome.ucsc.edu ). Alleles are designated by the letter of the horse they derive from, followed by ‘1’ or ‘2’ to distinguish the two variants. In HSF-D and HSF-E, where a single broad peak was identified by ChIP-on-chip while two distinct centromeric domains were identified by fibre-FISH (Fig. 4 ) and SNP analysis (Fig. 3 and Supplementary Table 2 ), dotted lines represent the region of overlap of the two binding domains in the reference sequence. Therefore, at least seven different centromeric domains can be identified: Ba/Ea, Bb, Ca, Cb, Da/Eb, Db/Ga, Gb

    Article Snippet: Both input and immunoprecipitated DNA fragments were purified and amplified using the whole genome amplification (WGA) kit (Sigma-Aldrich, St. Louis, USA).

    Techniques: Chromatin Immunoprecipitation, Hybridization, Immunoprecipitation, Fluorescence In Situ Hybridization, Sequencing, Binding Assay

    LMP2A or genistein inhibits BCR-induced tyrosine phosphorylation, DNA fragmentation, and cleavage PARP in Ramos cells. (A) Parental (P), vector control (V), and LMP2A-expressing (2A) Ramos cells (1 × 10 6 /ml) were treated without (control [−])

    Journal: Journal of Virology

    Article Title: Epstein-Barr Virus (EBV) Latent Membrane Protein 2A Regulates B-Cell Receptor-Induced Apoptosis and EBV Reactivation through Tyrosine Phosphorylation

    doi: 10.1128/JVI.79.13.8655-8660.2005

    Figure Lengend Snippet: LMP2A or genistein inhibits BCR-induced tyrosine phosphorylation, DNA fragmentation, and cleavage PARP in Ramos cells. (A) Parental (P), vector control (V), and LMP2A-expressing (2A) Ramos cells (1 × 10 6 /ml) were treated without (control [−])

    Article Snippet: To verify the DNA fragmentation and cleavage of PARP by BCR ligation were dependent on caspase activity in Ramos cells, cells were pretreated with zVAD-fmk (Calbiochem, La Jolla, CA), a broad caspase inhibitor and, as expected, DNA fragmentation and PARP cleavage were blocked by the addition of zVAD-fmk (Fig. and ).

    Techniques: Plasmid Preparation, Expressing

    LMP2A inhibits BCR-induced DNA fragmentation and cleavage of PARP in Ramos cells. (A) Cells were seeded at 3 × 10 5 cells/ml, and cells were treated without (control) or with 35 μg/ml anti-IgM antibody (αIgAb) for 24 h or 48 h.

    Journal: Journal of Virology

    Article Title: Epstein-Barr Virus (EBV) Latent Membrane Protein 2A Regulates B-Cell Receptor-Induced Apoptosis and EBV Reactivation through Tyrosine Phosphorylation

    doi: 10.1128/JVI.79.13.8655-8660.2005

    Figure Lengend Snippet: LMP2A inhibits BCR-induced DNA fragmentation and cleavage of PARP in Ramos cells. (A) Cells were seeded at 3 × 10 5 cells/ml, and cells were treated without (control) or with 35 μg/ml anti-IgM antibody (αIgAb) for 24 h or 48 h.

    Article Snippet: To verify the DNA fragmentation and cleavage of PARP by BCR ligation were dependent on caspase activity in Ramos cells, cells were pretreated with zVAD-fmk (Calbiochem, La Jolla, CA), a broad caspase inhibitor and, as expected, DNA fragmentation and PARP cleavage were blocked by the addition of zVAD-fmk (Fig. and ).

    Techniques:

    LMP2A or genistein blocks BCR-induced DNA fragmentation, cleavage of PARP, and EBV reactivation. (A) DNA fragmentation and evaluation of cleavage of PARP. Parental (P), vector control (V), and LMP2A-expressing (2A) Akata cells (5 × 10 5 /ml) were

    Journal: Journal of Virology

    Article Title: Epstein-Barr Virus (EBV) Latent Membrane Protein 2A Regulates B-Cell Receptor-Induced Apoptosis and EBV Reactivation through Tyrosine Phosphorylation

    doi: 10.1128/JVI.79.13.8655-8660.2005

    Figure Lengend Snippet: LMP2A or genistein blocks BCR-induced DNA fragmentation, cleavage of PARP, and EBV reactivation. (A) DNA fragmentation and evaluation of cleavage of PARP. Parental (P), vector control (V), and LMP2A-expressing (2A) Akata cells (5 × 10 5 /ml) were

    Article Snippet: To verify the DNA fragmentation and cleavage of PARP by BCR ligation were dependent on caspase activity in Ramos cells, cells were pretreated with zVAD-fmk (Calbiochem, La Jolla, CA), a broad caspase inhibitor and, as expected, DNA fragmentation and PARP cleavage were blocked by the addition of zVAD-fmk (Fig. and ).

    Techniques: Plasmid Preparation, Expressing