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TaKaRa dnaase i
Dnaase I, supplied by TaKaRa, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Real-time Polymerase Chain Reaction:

Article Title: Identification of the Cluster Control Region for the Protocadherin-? Genes Located beyond the Protocadherin-? Cluster *
Article Snippet: .. For qPCR analysis, 1 μg of total RNA was treated with DNase I (Takara) and reverse transcribed with random primers (Invitrogen) and SuperscriptIII reverse transcriptase (Invitrogen). qPCR was performed with the SYBR Green PCR Master Mix (Applied Biosystems) using ABI 7900HT (Applied Biosystems). .. The primer sequences used for qPCR are shown in .

Centrifugation:

Article Title: AHM1, a Novel Type of Nuclear Matrix-Localized, MAR Binding Protein with a Single AT Hook and a J Domain-Homologous Region
Article Snippet: The crude nuclei were collected by centrifugation and washed twice in the lysis buffer without Triton X-100. .. Briefly, nuclei were suspended in buffer A (50 mM Mes, 5 mM MgCl2 , 0.25 M sucrose, and 10% glycerol, pH 6.0) plus 1 mM PMSF and incubated at 12°C for 1 hr with DNase I (Takara Shuzo) at a final concentration of 50 μg/mL.

Amplification:

Article Title: Direct and Indirect Regulation of the ycnKJI Operon Involved in Copper Uptake through Two Transcriptional Repressors, YcnK and CsoR, in Bacillus subtilis
Article Snippet: Prior to PCR amplification, the 5′ terminus of only one of the primers was labeled with [γ-32 P]ATP using a Megalabel kit. .. The P ycnK probe (0.04 pmol), labeled at the 5′ end, was mixed with the YcnK protein to obtain a DNA-protein complex, which was then partially digested with DNase I (TaKaRa-bio) in 50 μl of a reaction mixture and subjected to urea-PAGE with sequencing ladders prepared using genomic DNA of strain 168 and the primer pair PycnKF/PycnKR.

Article Title: A Type Ib ParB Protein Involved in Plasmid Partitioning in a Gram-Positive Bacterium ▿
Article Snippet: DNA fragment parS-L was amplified by using primers Dpar3104 and Dpar3361 (Fig. ) and then cleaved by endonucleases BamHI or HindIII (Takara), and the sticky 5′ end was labeled with [α-32 P]dATP (Furui Biotech, Beijing, China) or [α-32 P]dCTP (Amersham Pharmacia Biotech, United Kingdom) by Klenow fragment (Takara). .. After incubation, DNase I (Takara) and 20 μl of the reaction buffer (10 mM MgCl2 and 5 mM CaCl2 ) were added.

Isolation:

Article Title: Identification of the Cluster Control Region for the Protocadherin-? Genes Located beyond the Protocadherin-? Cluster *
Article Snippet: Total RNA was isolated using TRIzol (Invitrogen), according to the supplier's recommendations. .. For qPCR analysis, 1 μg of total RNA was treated with DNase I (Takara) and reverse transcribed with random primers (Invitrogen) and SuperscriptIII reverse transcriptase (Invitrogen). qPCR was performed with the SYBR Green PCR Master Mix (Applied Biosystems) using ABI 7900HT (Applied Biosystems).

Article Title: Organic Peroxide-Sensing Repressor OhrR Regulates Organic Hydroperoxide Stress Resistance and Avermectin Production in Streptomyces avermitilis
Article Snippet: RNA was isolated from S. avermitilis mycelia grown in FM-I or YEME, using TRIzol reagent (Tiangen, China) as described previously ( ). .. The chromosomal DNA contamination of RNA samples was removed by adding DNase I (TaKaRa, Japan).

Article Title: AHM1, a Novel Type of Nuclear Matrix-Localized, MAR Binding Protein with a Single AT Hook and a J Domain-Homologous Region
Article Snippet: Paragraph title: Isolation of Nuclei and Nuclear Matrix ... Briefly, nuclei were suspended in buffer A (50 mM Mes, 5 mM MgCl2 , 0.25 M sucrose, and 10% glycerol, pH 6.0) plus 1 mM PMSF and incubated at 12°C for 1 hr with DNase I (Takara Shuzo) at a final concentration of 50 μg/mL.

Footprinting:

Article Title: Direct and Indirect Regulation of the ycnKJI Operon Involved in Copper Uptake through Two Transcriptional Repressors, YcnK and CsoR, in Bacillus subtilis
Article Snippet: Paragraph title: DNase I footprinting analysis. ... The P ycnK probe (0.04 pmol), labeled at the 5′ end, was mixed with the YcnK protein to obtain a DNA-protein complex, which was then partially digested with DNase I (TaKaRa-bio) in 50 μl of a reaction mixture and subjected to urea-PAGE with sequencing ladders prepared using genomic DNA of strain 168 and the primer pair PycnKF/PycnKR.

Article Title: A Type Ib ParB Protein Involved in Plasmid Partitioning in a Gram-Positive Bacterium ▿
Article Snippet: Paragraph title: DNase I footprinting assay. ... After incubation, DNase I (Takara) and 20 μl of the reaction buffer (10 mM MgCl2 and 5 mM CaCl2 ) were added.

Sequencing:

Article Title: A novel nucleoid protein of Escherichia coli induced under anaerobiotic growth conditions
Article Snippet: .. After brief treatment with DNase I, at least four protected regions were identified ( A), of which three (Dan-I, Dan-II and Dan-III) covered 14-bp-long sequences and one (Dan-IV) covered 29-bp sequence, suggesting that two molecules of Dan are associated with Dan-IV site, designated as Dan-IV-1 and Dan-IV-2 ( B). ..

Article Title: Direct and Indirect Regulation of the ycnKJI Operon Involved in Copper Uptake through Two Transcriptional Repressors, YcnK and CsoR, in Bacillus subtilis
Article Snippet: .. The P ycnK probe (0.04 pmol), labeled at the 5′ end, was mixed with the YcnK protein to obtain a DNA-protein complex, which was then partially digested with DNase I (TaKaRa-bio) in 50 μl of a reaction mixture and subjected to urea-PAGE with sequencing ladders prepared using genomic DNA of strain 168 and the primer pair PycnKF/PycnKR. .. Gel retardation analysis was performed essentially as described previously ( ).

Article Title: A Type Ib ParB Protein Involved in Plasmid Partitioning in a Gram-Positive Bacterium ▿
Article Snippet: After incubation, DNase I (Takara) and 20 μl of the reaction buffer (10 mM MgCl2 and 5 mM CaCl2 ) were added. .. The samples were run on a denatured, 8% polyacrylamide sequence gel.

Cell Culture:

Article Title: Role of the SaeRS two-component regulatory system in Staphylococcus epidermidis autolysis and biofilm formation
Article Snippet: .. Briefly, mid-exponential phase cells were diluted to OD600 = 0.1 in PBS and then incubated in wells (1 mL per well) of cell-culture polystyrene chambers (Nunc, Denmark) with DNase I (140 U/mL) for 2 h at 37°C. .. Detection of Aap expression Concentrations of lysostaphin-treated whole bacterial proteins from SE1457ΔsaeRS , SE1457, and SE1457saec were determined by the Bradford method.

Purification:

Article Title: AHM1, a Novel Type of Nuclear Matrix-Localized, MAR Binding Protein with a Single AT Hook and a J Domain-Homologous Region
Article Snippet: Further purification of nuclei by Percoll gradient centrifugation and preparation of the nuclear matrix with lithium diiodosalicylate (either with or without heat stabilization) were performed as described previously ( ). .. Briefly, nuclei were suspended in buffer A (50 mM Mes, 5 mM MgCl2 , 0.25 M sucrose, and 10% glycerol, pH 6.0) plus 1 mM PMSF and incubated at 12°C for 1 hr with DNase I (Takara Shuzo) at a final concentration of 50 μg/mL.

Article Title: A Type Ib ParB Protein Involved in Plasmid Partitioning in a Gram-Positive Bacterium ▿
Article Snippet: The DNA probe was incubated with the indicated amounts of the purified proteins in a final volume of 20 μl at 30°C for 30 min in buffer containing 15 mM Tris-Hcl (pH 7.6), 3 mM MgCl2 , 0.3 mM dithisthreitol, 50 nM KCl, 1 mM ATP, and 2% glycerol. .. After incubation, DNase I (Takara) and 20 μl of the reaction buffer (10 mM MgCl2 and 5 mM CaCl2 ) were added.

SYBR Green Assay:

Article Title: Identification of the Cluster Control Region for the Protocadherin-? Genes Located beyond the Protocadherin-? Cluster *
Article Snippet: .. For qPCR analysis, 1 μg of total RNA was treated with DNase I (Takara) and reverse transcribed with random primers (Invitrogen) and SuperscriptIII reverse transcriptase (Invitrogen). qPCR was performed with the SYBR Green PCR Master Mix (Applied Biosystems) using ABI 7900HT (Applied Biosystems). .. The primer sequences used for qPCR are shown in .

Article Title: Organic Peroxide-Sensing Repressor OhrR Regulates Organic Hydroperoxide Stress Resistance and Avermectin Production in Streptomyces avermitilis
Article Snippet: The chromosomal DNA contamination of RNA samples was removed by adding DNase I (TaKaRa, Japan). .. Each reaction system (20 μl) contains template cDNA, forward and reverse primers (each 300 nM) and 10 μl FastStart Universal SYBR Green Master (ROX).

Concentration Assay:

Article Title: AHM1, a Novel Type of Nuclear Matrix-Localized, MAR Binding Protein with a Single AT Hook and a J Domain-Homologous Region
Article Snippet: .. Briefly, nuclei were suspended in buffer A (50 mM Mes, 5 mM MgCl2 , 0.25 M sucrose, and 10% glycerol, pH 6.0) plus 1 mM PMSF and incubated at 12°C for 1 hr with DNase I (Takara Shuzo) at a final concentration of 50 μg/mL. ..

Incubation:

Article Title: Role of the SaeRS two-component regulatory system in Staphylococcus epidermidis autolysis and biofilm formation
Article Snippet: .. Briefly, mid-exponential phase cells were diluted to OD600 = 0.1 in PBS and then incubated in wells (1 mL per well) of cell-culture polystyrene chambers (Nunc, Denmark) with DNase I (140 U/mL) for 2 h at 37°C. .. Detection of Aap expression Concentrations of lysostaphin-treated whole bacterial proteins from SE1457ΔsaeRS , SE1457, and SE1457saec were determined by the Bradford method.

Article Title: AHM1, a Novel Type of Nuclear Matrix-Localized, MAR Binding Protein with a Single AT Hook and a J Domain-Homologous Region
Article Snippet: .. Briefly, nuclei were suspended in buffer A (50 mM Mes, 5 mM MgCl2 , 0.25 M sucrose, and 10% glycerol, pH 6.0) plus 1 mM PMSF and incubated at 12°C for 1 hr with DNase I (Takara Shuzo) at a final concentration of 50 μg/mL. ..

Article Title: A Type Ib ParB Protein Involved in Plasmid Partitioning in a Gram-Positive Bacterium ▿
Article Snippet: .. After incubation, DNase I (Takara) and 20 μl of the reaction buffer (10 mM MgCl2 and 5 mM CaCl2 ) were added. .. Incubation was continued for 3 min, and an equal volume of stop buffer (1% sodium dodecyl sulfate, 200 mM NaCl, and 20 mM EDTA) was added.

other:

Article Title: Discovery of Two Novel Viruses Expands the Diversity of Single-Stranded DNA and Single-Stranded RNA Viruses Infecting a Cosmopolitan Marine Diatom
Article Snippet: All bands were digested by treatment with DNase I but not by RNase A treatment, indicating that the viral genome is composed of DNA ( , lanes 3 and 4, respectively).

Article Title: Differentially Expressed Genes in the Cuticle and Hemolymph of the Silkworm, Bombyx mori, Injected with the Fungus Beauveria bassiana
Article Snippet: The RNA was treated with DNase I following the manufacturer' s instructions.

Article Title: Discovery of Two Novel Viruses Expands the Diversity of Single-Stranded DNA and Single-Stranded RNA Viruses Infecting a Cosmopolitan Marine Diatom
Article Snippet: The genome treated with DNase I remained undigested ( , lane 2); treatment with RNase A resulted in complete digestion ( , lane 3).

Article Title: Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression *Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression * S⃞
Article Snippet: As a control, it was shown that DNase I digested the homoduplex and the D-loop structure equally (supplemental Fig. S3 A ).

Article Title: Identification and characterization of DNA endonucleases in Plasmodium falciparum 3D7 clone
Article Snippet: The EEP domain exists in a large number of enzymes, including AP endonuclease, DNase I, inositol-polyphosphate 5-phosphatase and sphingomyelinase, and these enzymes participate in DNA metabolism processes and intracellular signalling [ , ].

Quantitative RT-PCR:

Article Title: Organic Peroxide-Sensing Repressor OhrR Regulates Organic Hydroperoxide Stress Resistance and Avermectin Production in Streptomyces avermitilis
Article Snippet: Paragraph title: RNA Preparation and Quantitative Real-Time RT-PCR Analysis (qRT-PCR) ... The chromosomal DNA contamination of RNA samples was removed by adding DNase I (TaKaRa, Japan).

Spectrophotometry:

Article Title: Organic Peroxide-Sensing Repressor OhrR Regulates Organic Hydroperoxide Stress Resistance and Avermectin Production in Streptomyces avermitilis
Article Snippet: The chromosomal DNA contamination of RNA samples was removed by adding DNase I (TaKaRa, Japan). .. The concentrations of RNA were measured by NanoVue Plus spectrophotometer (GE Healthcare).

Lysis:

Article Title: AHM1, a Novel Type of Nuclear Matrix-Localized, MAR Binding Protein with a Single AT Hook and a J Domain-Homologous Region
Article Snippet: The crude nuclei were collected by centrifugation and washed twice in the lysis buffer without Triton X-100. .. Briefly, nuclei were suspended in buffer A (50 mM Mes, 5 mM MgCl2 , 0.25 M sucrose, and 10% glycerol, pH 6.0) plus 1 mM PMSF and incubated at 12°C for 1 hr with DNase I (Takara Shuzo) at a final concentration of 50 μg/mL.

Polymerase Chain Reaction:

Article Title: Identification of the Cluster Control Region for the Protocadherin-? Genes Located beyond the Protocadherin-? Cluster *
Article Snippet: .. For qPCR analysis, 1 μg of total RNA was treated with DNase I (Takara) and reverse transcribed with random primers (Invitrogen) and SuperscriptIII reverse transcriptase (Invitrogen). qPCR was performed with the SYBR Green PCR Master Mix (Applied Biosystems) using ABI 7900HT (Applied Biosystems). .. The primer sequences used for qPCR are shown in .

Article Title: Direct and Indirect Regulation of the ycnKJI Operon Involved in Copper Uptake through Two Transcriptional Repressors, YcnK and CsoR, in Bacillus subtilis
Article Snippet: Prior to PCR amplification, the 5′ terminus of only one of the primers was labeled with [γ-32 P]ATP using a Megalabel kit. .. The P ycnK probe (0.04 pmol), labeled at the 5′ end, was mixed with the YcnK protein to obtain a DNA-protein complex, which was then partially digested with DNase I (TaKaRa-bio) in 50 μl of a reaction mixture and subjected to urea-PAGE with sequencing ladders prepared using genomic DNA of strain 168 and the primer pair PycnKF/PycnKR.

Labeling:

Article Title: Direct and Indirect Regulation of the ycnKJI Operon Involved in Copper Uptake through Two Transcriptional Repressors, YcnK and CsoR, in Bacillus subtilis
Article Snippet: .. The P ycnK probe (0.04 pmol), labeled at the 5′ end, was mixed with the YcnK protein to obtain a DNA-protein complex, which was then partially digested with DNase I (TaKaRa-bio) in 50 μl of a reaction mixture and subjected to urea-PAGE with sequencing ladders prepared using genomic DNA of strain 168 and the primer pair PycnKF/PycnKR. .. Gel retardation analysis was performed essentially as described previously ( ).

Article Title: A Type Ib ParB Protein Involved in Plasmid Partitioning in a Gram-Positive Bacterium ▿
Article Snippet: DNA fragment parS-L was amplified by using primers Dpar3104 and Dpar3361 (Fig. ) and then cleaved by endonucleases BamHI or HindIII (Takara), and the sticky 5′ end was labeled with [α-32 P]dATP (Furui Biotech, Beijing, China) or [α-32 P]dCTP (Amersham Pharmacia Biotech, United Kingdom) by Klenow fragment (Takara). .. After incubation, DNase I (Takara) and 20 μl of the reaction buffer (10 mM MgCl2 and 5 mM CaCl2 ) were added.

Gradient Centrifugation:

Article Title: AHM1, a Novel Type of Nuclear Matrix-Localized, MAR Binding Protein with a Single AT Hook and a J Domain-Homologous Region
Article Snippet: Further purification of nuclei by Percoll gradient centrifugation and preparation of the nuclear matrix with lithium diiodosalicylate (either with or without heat stabilization) were performed as described previously ( ). .. Briefly, nuclei were suspended in buffer A (50 mM Mes, 5 mM MgCl2 , 0.25 M sucrose, and 10% glycerol, pH 6.0) plus 1 mM PMSF and incubated at 12°C for 1 hr with DNase I (Takara Shuzo) at a final concentration of 50 μg/mL.

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    TaKaRa dnase i
    Variations in expression levels of fungus-responsive genes in the hemolymph of silkworms, Bombyx mori , infected with Beauveria bassiana . The third-day larvae of the fifth instar of Dazao strains were infected with B. bassiana . Total RNA was extracted from the hemolymph at the indicated time points after infection and subjected to <t>DNase</t> I treatment and reverse transcription. Two microliters of each 10-fold diluted first strand cDNA (20 ng) was analyzed in each real-time qPCR reaction. The reaction was performed with specific primers for amplifying each of the six genes. The relative expression level of each gene at each time point was normalized using the Ct values obtained for the Bm GAPDH amplifications run in the same plate. In each assay, the expression level is shown relative to the lowest expression level, which was set to one. All samples were tested in triplicate. The mean value ± SD was used for the analysis of the relative transcript levels for each time point using the △△Ct method. The B. bassiana injected and water-treated individuals are shown on the left (blue) and right (purple), respectively. A. Chemosensory protein 11; B. Muscle LIM protein isoform 1; C. Transferrin; D. Sex-specific storage-protein SP1 precursor; E. Arylphorin; F. Low molecular lipoprotein 30K pBmHPC-6 (Lp-c6); G. lysozyme; H. Moricin. High quality figures are available online.
    Dnase I, supplied by TaKaRa, used in various techniques. Bioz Stars score: 99/100, based on 580 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dnase i/product/TaKaRa
    Average 99 stars, based on 580 article reviews
    Price from $9.99 to $1999.99
    dnase i - by Bioz Stars, 2020-04
    99/100 stars
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    Variations in expression levels of fungus-responsive genes in the hemolymph of silkworms, Bombyx mori , infected with Beauveria bassiana . The third-day larvae of the fifth instar of Dazao strains were infected with B. bassiana . Total RNA was extracted from the hemolymph at the indicated time points after infection and subjected to DNase I treatment and reverse transcription. Two microliters of each 10-fold diluted first strand cDNA (20 ng) was analyzed in each real-time qPCR reaction. The reaction was performed with specific primers for amplifying each of the six genes. The relative expression level of each gene at each time point was normalized using the Ct values obtained for the Bm GAPDH amplifications run in the same plate. In each assay, the expression level is shown relative to the lowest expression level, which was set to one. All samples were tested in triplicate. The mean value ± SD was used for the analysis of the relative transcript levels for each time point using the △△Ct method. The B. bassiana injected and water-treated individuals are shown on the left (blue) and right (purple), respectively. A. Chemosensory protein 11; B. Muscle LIM protein isoform 1; C. Transferrin; D. Sex-specific storage-protein SP1 precursor; E. Arylphorin; F. Low molecular lipoprotein 30K pBmHPC-6 (Lp-c6); G. lysozyme; H. Moricin. High quality figures are available online.

    Journal: Journal of Insect Science

    Article Title: Differentially Expressed Genes in the Cuticle and Hemolymph of the Silkworm, Bombyx mori, Injected with the Fungus Beauveria bassiana

    doi: 10.1673/031.013.13801

    Figure Lengend Snippet: Variations in expression levels of fungus-responsive genes in the hemolymph of silkworms, Bombyx mori , infected with Beauveria bassiana . The third-day larvae of the fifth instar of Dazao strains were infected with B. bassiana . Total RNA was extracted from the hemolymph at the indicated time points after infection and subjected to DNase I treatment and reverse transcription. Two microliters of each 10-fold diluted first strand cDNA (20 ng) was analyzed in each real-time qPCR reaction. The reaction was performed with specific primers for amplifying each of the six genes. The relative expression level of each gene at each time point was normalized using the Ct values obtained for the Bm GAPDH amplifications run in the same plate. In each assay, the expression level is shown relative to the lowest expression level, which was set to one. All samples were tested in triplicate. The mean value ± SD was used for the analysis of the relative transcript levels for each time point using the △△Ct method. The B. bassiana injected and water-treated individuals are shown on the left (blue) and right (purple), respectively. A. Chemosensory protein 11; B. Muscle LIM protein isoform 1; C. Transferrin; D. Sex-specific storage-protein SP1 precursor; E. Arylphorin; F. Low molecular lipoprotein 30K pBmHPC-6 (Lp-c6); G. lysozyme; H. Moricin. High quality figures are available online.

    Article Snippet: The RNA was treated with DNase I following the manufacturer' s instructions.

    Techniques: Expressing, Infection, Real-time Polymerase Chain Reaction, Injection

    Identification of the Dan box sequence. (A) Fluorescent-labeled SELEX segment (1.0 pmol) from the dan-ttdA spacer was incubated in the absence or presence of increasing concentrations of purified Dan (10, 20 and 40 pmol from left to right) and then subjected to DNase-I foot-printing assays. Lanes A, T, G and C represent the respective sequence ladders. ( B ) Four Dan-binding sites were identified on the dan-ttdA spacer sequence. ( C ) The Dan-box sequence GTTAAT was predicted after sequence comparison of four Dan-binding sites. Similar sequences were identified among a total of 688 Dan-binding fragments selected by Genomic SELEX. Using this Dan-box sequence, a total of about 1860 sites were predicted to be present in the entire E. coli genome. ( D ) Logo representation of Dan-binding site derived from sequences in in silico analysis. Logos were generated using weblogo ( http://weblogo.berkeley.edu/ ).

    Journal: Nucleic Acids Research

    Article Title: A novel nucleoid protein of Escherichia coli induced under anaerobiotic growth conditions

    doi: 10.1093/nar/gkq077

    Figure Lengend Snippet: Identification of the Dan box sequence. (A) Fluorescent-labeled SELEX segment (1.0 pmol) from the dan-ttdA spacer was incubated in the absence or presence of increasing concentrations of purified Dan (10, 20 and 40 pmol from left to right) and then subjected to DNase-I foot-printing assays. Lanes A, T, G and C represent the respective sequence ladders. ( B ) Four Dan-binding sites were identified on the dan-ttdA spacer sequence. ( C ) The Dan-box sequence GTTAAT was predicted after sequence comparison of four Dan-binding sites. Similar sequences were identified among a total of 688 Dan-binding fragments selected by Genomic SELEX. Using this Dan-box sequence, a total of about 1860 sites were predicted to be present in the entire E. coli genome. ( D ) Logo representation of Dan-binding site derived from sequences in in silico analysis. Logos were generated using weblogo ( http://weblogo.berkeley.edu/ ).

    Article Snippet: After brief treatment with DNase I, at least four protected regions were identified ( A), of which three (Dan-I, Dan-II and Dan-III) covered 14-bp-long sequences and one (Dan-IV) covered 29-bp sequence, suggesting that two molecules of Dan are associated with Dan-IV site, designated as Dan-IV-1 and Dan-IV-2 ( B).

    Techniques: Sequencing, Labeling, Incubation, Purification, Binding Assay, Derivative Assay, In Silico, Generated

    DNase I footprinting assay of ohrR–ohrB2 intergenic region using His 6 -OhrR. (A) Fluorograms corresponding to control DNA and to protected reactions with 0.4 and 0.8 μM His 6 -OhrR. (B) Nucleotide sequences of ohrR–ohrB2 intergenic region. Non-shaded boxes: presumed –35 and –10 regions of ohrR and ohrB2 . Shaded boxes: regions protected by His 6 -OhrR. Underlining: OhrR motif (site a and site b). Gray bent arrows: translational start codons. Black bent arrows: TSSs. (C) Consensus sequence of OhrR motif.

    Journal: Frontiers in Microbiology

    Article Title: Organic Peroxide-Sensing Repressor OhrR Regulates Organic Hydroperoxide Stress Resistance and Avermectin Production in Streptomyces avermitilis

    doi: 10.3389/fmicb.2018.01398

    Figure Lengend Snippet: DNase I footprinting assay of ohrR–ohrB2 intergenic region using His 6 -OhrR. (A) Fluorograms corresponding to control DNA and to protected reactions with 0.4 and 0.8 μM His 6 -OhrR. (B) Nucleotide sequences of ohrR–ohrB2 intergenic region. Non-shaded boxes: presumed –35 and –10 regions of ohrR and ohrB2 . Shaded boxes: regions protected by His 6 -OhrR. Underlining: OhrR motif (site a and site b). Gray bent arrows: translational start codons. Black bent arrows: TSSs. (C) Consensus sequence of OhrR motif.

    Article Snippet: The chromosomal DNA contamination of RNA samples was removed by adding DNase I (TaKaRa, Japan).

    Techniques: Footprinting, Sequencing

    Identification of novel HS sites by DNase I hypersensitivity assay. A , schematic diagram of the DNase I hypersensitivity assay of the Pcdh- γ gene. Upper part , the large colored boxes , Pcdh- γ or Diap1 exons. The small red boxes indicate

    Journal: The Journal of Biological Chemistry

    Article Title: Identification of the Cluster Control Region for the Protocadherin-? Genes Located beyond the Protocadherin-? Cluster *

    doi: 10.1074/jbc.M111.245605

    Figure Lengend Snippet: Identification of novel HS sites by DNase I hypersensitivity assay. A , schematic diagram of the DNase I hypersensitivity assay of the Pcdh- γ gene. Upper part , the large colored boxes , Pcdh- γ or Diap1 exons. The small red boxes indicate

    Article Snippet: For qPCR analysis, 1 μg of total RNA was treated with DNase I (Takara) and reverse transcribed with random primers (Invitrogen) and SuperscriptIII reverse transcriptase (Invitrogen). qPCR was performed with the SYBR Green PCR Master Mix (Applied Biosystems) using ABI 7900HT (Applied Biosystems).

    Techniques: