deoxyribonuclease i  (Thermo Fisher)


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    Name:
    DNase I
    Description:
    DNase I Deoxyribonuclease I digests single and double stranded DNA to oligodeoxyribonucleotides containing a 5 phosphate Ribonuclease has been reduced to non detectable levels ApplicationsDNase I is suitable for removing DNA from protein preparations nick translating DNA and generating random fragments for dideoxy sequencing NOTE for removing DNA from RNA preparations use Amplification Grade DNase I Cat No 18068 015 SourceDNase I is purified from bovine pancreas Specific activityThe specific activity of DNase I is typically in the range of 10 000 25 000 units mg
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    PCR & Real-Time PCR|Reverse Transcription
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    Proteins Enzymes Peptides
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    Structured Review

    Thermo Fisher deoxyribonuclease i
    Effect of NGF on actin polymerization and cell migration in aging GECs.  Young and aging GECs were treated with PBS or NGF (100 ng/mL) for 1 hour after pretreatment with Latrunculin B (0.5 μmol/L for 30 minutes), a specific inhibitor of actin polymerization. ( A ) Representative photomicrographs of young and aging GECs showing visualization of F-actin and G-actin by double staining using Alexa Green–conjugated phalloidin to detect F-actin and Alexa Red–conjugated DNase I to detect G-actin. NGF treatment induced formation of extensive F-actin stress fibers and an increased F:G actin ratio in young and aging GECs. Treatment with Latrunculin B inhibited NGF-induced F-actin polymerization. ( B ) NGF treatment significantly increased the migration rate in young and aging GECs, but this effect was abolished by treatment with Latrunculin B. Data are means ± SD (N = 6). The Student  t  test and 1-way analysis of variance with the Tukey multiple comparison tests were used to determine statistical significance between 2 or multiple groups, respectively.
    DNase I Deoxyribonuclease I digests single and double stranded DNA to oligodeoxyribonucleotides containing a 5 phosphate Ribonuclease has been reduced to non detectable levels ApplicationsDNase I is suitable for removing DNA from protein preparations nick translating DNA and generating random fragments for dideoxy sequencing NOTE for removing DNA from RNA preparations use Amplification Grade DNase I Cat No 18068 015 SourceDNase I is purified from bovine pancreas Specific activityThe specific activity of DNase I is typically in the range of 10 000 25 000 units mg
    https://www.bioz.com/result/deoxyribonuclease i/product/Thermo Fisher
    Average 99 stars, based on 70 article reviews
    Price from $9.99 to $1999.99
    deoxyribonuclease i - by Bioz Stars, 2020-08
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    Images

    1) Product Images from "Reduced NGF in Gastric Endothelial Cells Is One of the Main Causes of Impaired Angiogenesis in Aging Gastric Mucosa"

    Article Title: Reduced NGF in Gastric Endothelial Cells Is One of the Main Causes of Impaired Angiogenesis in Aging Gastric Mucosa

    Journal: Cellular and Molecular Gastroenterology and Hepatology

    doi: 10.1016/j.jcmgh.2018.05.003

    Effect of NGF on actin polymerization and cell migration in aging GECs.  Young and aging GECs were treated with PBS or NGF (100 ng/mL) for 1 hour after pretreatment with Latrunculin B (0.5 μmol/L for 30 minutes), a specific inhibitor of actin polymerization. ( A ) Representative photomicrographs of young and aging GECs showing visualization of F-actin and G-actin by double staining using Alexa Green–conjugated phalloidin to detect F-actin and Alexa Red–conjugated DNase I to detect G-actin. NGF treatment induced formation of extensive F-actin stress fibers and an increased F:G actin ratio in young and aging GECs. Treatment with Latrunculin B inhibited NGF-induced F-actin polymerization. ( B ) NGF treatment significantly increased the migration rate in young and aging GECs, but this effect was abolished by treatment with Latrunculin B. Data are means ± SD (N = 6). The Student  t  test and 1-way analysis of variance with the Tukey multiple comparison tests were used to determine statistical significance between 2 or multiple groups, respectively.
    Figure Legend Snippet: Effect of NGF on actin polymerization and cell migration in aging GECs. Young and aging GECs were treated with PBS or NGF (100 ng/mL) for 1 hour after pretreatment with Latrunculin B (0.5 μmol/L for 30 minutes), a specific inhibitor of actin polymerization. ( A ) Representative photomicrographs of young and aging GECs showing visualization of F-actin and G-actin by double staining using Alexa Green–conjugated phalloidin to detect F-actin and Alexa Red–conjugated DNase I to detect G-actin. NGF treatment induced formation of extensive F-actin stress fibers and an increased F:G actin ratio in young and aging GECs. Treatment with Latrunculin B inhibited NGF-induced F-actin polymerization. ( B ) NGF treatment significantly increased the migration rate in young and aging GECs, but this effect was abolished by treatment with Latrunculin B. Data are means ± SD (N = 6). The Student t test and 1-way analysis of variance with the Tukey multiple comparison tests were used to determine statistical significance between 2 or multiple groups, respectively.

    Techniques Used: Migration, Double Staining

    2) Product Images from "Chitosan/hyaluronic acid/plasmid-DNA nanoparticles encoding interleukin-1 receptor antagonist attenuate inflammation in synoviocytes induced by interleukin-1 beta"

    Article Title: Chitosan/hyaluronic acid/plasmid-DNA nanoparticles encoding interleukin-1 receptor antagonist attenuate inflammation in synoviocytes induced by interleukin-1 beta

    Journal: Journal of Materials Science. Materials in Medicine

    doi: 10.1007/s10856-018-6160-3

    Gel electrophoresis of CS/HA/pIL-1Ra nanoparticles. Lane a: normal naked pIL-1Ra; Lane b: CS/HA/pIL-1Ra nanoparticles; Lane c: naked pIL-1Ra digested by DNase I; Lane d: CS/HA/pIL-1Ra nanoparticles digested by DNase I; Lane e: CS/HA/pIL-1Ra nanoparticles digested by chitosanase
    Figure Legend Snippet: Gel electrophoresis of CS/HA/pIL-1Ra nanoparticles. Lane a: normal naked pIL-1Ra; Lane b: CS/HA/pIL-1Ra nanoparticles; Lane c: naked pIL-1Ra digested by DNase I; Lane d: CS/HA/pIL-1Ra nanoparticles digested by DNase I; Lane e: CS/HA/pIL-1Ra nanoparticles digested by chitosanase

    Techniques Used: Nucleic Acid Electrophoresis

    3) Product Images from "Role and regulation of Abelson tyrosine kinase in Crk-associated substrate/profilin-1 interaction and airway smooth muscle contraction"

    Article Title: Role and regulation of Abelson tyrosine kinase in Crk-associated substrate/profilin-1 interaction and airway smooth muscle contraction

    Journal: Respiratory Research

    doi: 10.1186/s12931-017-0709-4

    c-Abl knockout inhibits actin filament polymerization in response to ACh stimulation.  a  Mouse tracheal rings from c-Abl -lox  and c-Abl smko  mice were treated with acetylcholine (ACh) (100 μM, 5 min) or left untreated (UT). F/G-actin ratios were evaluated using the fractionation assay. Data are mean ± SE ( n  = 5).  b  Representative images illustrating the effects of c-Abl knockout on F/G-actin ratios. Sections of trachealis from c-Abl -lox  and c-Abl smko  mice were stained with DNase I (for G-actin) or phalloidin (for F-actin).  c  ACh-induced increases in F/G-actin ratios evaluated by fluorescent microscopy are reduced in c-Abl smko  mice ( n  = 4). * P
    Figure Legend Snippet: c-Abl knockout inhibits actin filament polymerization in response to ACh stimulation. a Mouse tracheal rings from c-Abl -lox and c-Abl smko mice were treated with acetylcholine (ACh) (100 μM, 5 min) or left untreated (UT). F/G-actin ratios were evaluated using the fractionation assay. Data are mean ± SE ( n  = 5). b Representative images illustrating the effects of c-Abl knockout on F/G-actin ratios. Sections of trachealis from c-Abl -lox and c-Abl smko mice were stained with DNase I (for G-actin) or phalloidin (for F-actin). c ACh-induced increases in F/G-actin ratios evaluated by fluorescent microscopy are reduced in c-Abl smko mice ( n  = 4). * P

    Techniques Used: Knock-Out, Mouse Assay, Fractionation, Staining, Microscopy

    4) Product Images from "Reduced NGF in Gastric Endothelial Cells Is One of the Main Causes of Impaired Angiogenesis in Aging Gastric Mucosa"

    Article Title: Reduced NGF in Gastric Endothelial Cells Is One of the Main Causes of Impaired Angiogenesis in Aging Gastric Mucosa

    Journal: Cellular and Molecular Gastroenterology and Hepatology

    doi: 10.1016/j.jcmgh.2018.05.003

    Effect of NGF on actin polymerization and cell migration in aging GECs.  Young and aging GECs were treated with PBS or NGF (100 ng/mL) for 1 hour after pretreatment with Latrunculin B (0.5 μmol/L for 30 minutes), a specific inhibitor of actin polymerization. ( A ) Representative photomicrographs of young and aging GECs showing visualization of F-actin and G-actin by double staining using Alexa Green–conjugated phalloidin to detect F-actin and Alexa Red–conjugated DNase I to detect G-actin. NGF treatment induced formation of extensive F-actin stress fibers and an increased F:G actin ratio in young and aging GECs. Treatment with Latrunculin B inhibited NGF-induced F-actin polymerization. ( B ) NGF treatment significantly increased the migration rate in young and aging GECs, but this effect was abolished by treatment with Latrunculin B. Data are means ± SD (N = 6). The Student  t  test and 1-way analysis of variance with the Tukey multiple comparison tests were used to determine statistical significance between 2 or multiple groups, respectively.
    Figure Legend Snippet: Effect of NGF on actin polymerization and cell migration in aging GECs. Young and aging GECs were treated with PBS or NGF (100 ng/mL) for 1 hour after pretreatment with Latrunculin B (0.5 μmol/L for 30 minutes), a specific inhibitor of actin polymerization. ( A ) Representative photomicrographs of young and aging GECs showing visualization of F-actin and G-actin by double staining using Alexa Green–conjugated phalloidin to detect F-actin and Alexa Red–conjugated DNase I to detect G-actin. NGF treatment induced formation of extensive F-actin stress fibers and an increased F:G actin ratio in young and aging GECs. Treatment with Latrunculin B inhibited NGF-induced F-actin polymerization. ( B ) NGF treatment significantly increased the migration rate in young and aging GECs, but this effect was abolished by treatment with Latrunculin B. Data are means ± SD (N = 6). The Student t test and 1-way analysis of variance with the Tukey multiple comparison tests were used to determine statistical significance between 2 or multiple groups, respectively.

    Techniques Used: Migration, Double Staining

    5) Product Images from "Efficient gene delivery system mediated by cis-aconitate-modified chitosan-g-stearic acid micelles"

    Article Title: Efficient gene delivery system mediated by cis-aconitate-modified chitosan-g-stearic acid micelles

    Journal: International Journal of Nanomedicine

    doi: 10.2147/IJN.S61103

    ( A ) Transmission electron micrographs of CSO-SA and CA-CSO-SA micelles. ( B ) Transmission electron micrographs of CSO-SA/pDNA and CA-CSO-SA/pDNA nanoparticles (at a weight ratio of 5). ( C ) Gel retardation analyses of CSO-SA/pDNA and CA-CSO-SA/pDNA nanocomplexes, where lanes 1–6 show weight ratios of 0, 0.2, 0.5, 1, 2, and 5, respectively. ( D ) DNase I protection assay, where lanes 1–6 represent naked pDNA, naked pDNA + DNase I, CSO-SA/pDNA, CSO-SA/pDNA + DNase I, CA-CSO-SA/pDNA, and CA-CSO-SA/pDNA + DNase I, respectively. Notes:  CSO-SA/pDNA and CA-CSO-SA/pDNA nanocomplexes prepared at a weight ratio of 2.5. After inactivation by DNase, heparin was added to disassemble the polyplexes. Abbreviations:  CA, cis-aconitate; SA, stearic acid; CSO, chitosan oligosaccharide; pDNA, plasmid DNA; w/w, weight ratio.
    Figure Legend Snippet: ( A ) Transmission electron micrographs of CSO-SA and CA-CSO-SA micelles. ( B ) Transmission electron micrographs of CSO-SA/pDNA and CA-CSO-SA/pDNA nanoparticles (at a weight ratio of 5). ( C ) Gel retardation analyses of CSO-SA/pDNA and CA-CSO-SA/pDNA nanocomplexes, where lanes 1–6 show weight ratios of 0, 0.2, 0.5, 1, 2, and 5, respectively. ( D ) DNase I protection assay, where lanes 1–6 represent naked pDNA, naked pDNA + DNase I, CSO-SA/pDNA, CSO-SA/pDNA + DNase I, CA-CSO-SA/pDNA, and CA-CSO-SA/pDNA + DNase I, respectively. Notes: CSO-SA/pDNA and CA-CSO-SA/pDNA nanocomplexes prepared at a weight ratio of 2.5. After inactivation by DNase, heparin was added to disassemble the polyplexes. Abbreviations: CA, cis-aconitate; SA, stearic acid; CSO, chitosan oligosaccharide; pDNA, plasmid DNA; w/w, weight ratio.

    Techniques Used: Transmission Assay, Electrophoretic Mobility Shift Assay, Plasmid Preparation

    6) Product Images from "The serpin gene family in Anopheles gambiae"

    Article Title: The serpin gene family in Anopheles gambiae

    Journal: Gene

    doi: 10.1016/j.gene.2009.04.013

    Expression profile of the A. gambiae serpins among developmental stages. Total RNA was isolated from mosquitoes, and deoxyribonuclease-I was used to remove genomic DNA. An equal amount of RNA was used to make cDNA, using the SuperScript first-strand cDNA
    Figure Legend Snippet: Expression profile of the A. gambiae serpins among developmental stages. Total RNA was isolated from mosquitoes, and deoxyribonuclease-I was used to remove genomic DNA. An equal amount of RNA was used to make cDNA, using the SuperScript first-strand cDNA

    Techniques Used: Expressing, Isolation

    7) Product Images from "Regulation of actin dynamics by WNT-5A: implications for human airway smooth muscle contraction"

    Article Title: Regulation of actin dynamics by WNT-5A: implications for human airway smooth muscle contraction

    Journal: Scientific Reports

    doi: 10.1038/srep30676

    Involvement of WNT-5A in the regulation of alpha smooth muscle actin. ( a ) Alpha smooth muscle actin, caveolin-1 and WNT-5A immunoblot of lysates from cultured human airway smooth muscle cells, normalised against GAPDH. Cell were grown to 50% confluence in serum-enriched (10% FBS) DMEM (serum-fed group) or grown to confluence and then serum-deprived in Ham’s F12 supplemented with ITS (serum-starved group) for 7 days. Cropped images are shown. Full-length blots are presented in  Supplementary Fig. 1 . α-SMA/GAPDH and caveolin-1/WNT-5A/GAPDH were derived from the same gel. Data represents four independent experiments. *vs serum-fed. ( b ) Airway smooth muscle actin immunoblot as performed in ( a ). Cells were treated with WNT-5A for 24 hours. Full-length blots are presented in  Supplementary Fig. 1 . Data represents three independent experiments. ( c ) Representative immunofluorescent images of a Phalloidin (F-actin, green) and DNAse I (G-actin, red) staining of airway smooth muscle cells exposed to WNT-5A (200 ng/mL) for 2 hours, and the corresponding quantification. White arrowhead points to filamentous actin. Dashed line represents a single cell boundary. Horizontal line represents the mean. Data is expressed as the mean ± SEM.
    Figure Legend Snippet: Involvement of WNT-5A in the regulation of alpha smooth muscle actin. ( a ) Alpha smooth muscle actin, caveolin-1 and WNT-5A immunoblot of lysates from cultured human airway smooth muscle cells, normalised against GAPDH. Cell were grown to 50% confluence in serum-enriched (10% FBS) DMEM (serum-fed group) or grown to confluence and then serum-deprived in Ham’s F12 supplemented with ITS (serum-starved group) for 7 days. Cropped images are shown. Full-length blots are presented in Supplementary Fig. 1 . α-SMA/GAPDH and caveolin-1/WNT-5A/GAPDH were derived from the same gel. Data represents four independent experiments. *vs serum-fed. ( b ) Airway smooth muscle actin immunoblot as performed in ( a ). Cells were treated with WNT-5A for 24 hours. Full-length blots are presented in Supplementary Fig. 1 . Data represents three independent experiments. ( c ) Representative immunofluorescent images of a Phalloidin (F-actin, green) and DNAse I (G-actin, red) staining of airway smooth muscle cells exposed to WNT-5A (200 ng/mL) for 2 hours, and the corresponding quantification. White arrowhead points to filamentous actin. Dashed line represents a single cell boundary. Horizontal line represents the mean. Data is expressed as the mean ± SEM.

    Techniques Used: Cell Culture, Derivative Assay, Staining

    WNT-5A mediates TGF-β1 induced actin polymerization. Representative immunofluorescent images of a Phalloidin (F-actin, green) and DNAse I (G-actin, red) staining of airway smooth muscle cells exposed to TGF-β1 (2 ng/mL) for 48 hours in the presence or absence of ( a ) latrunculin A (0.1 μM), or ( b ) WNT-5A-specific siRNA. White arrowhead points to filamentous actin. Dashed line represents a single cell boundary. Horizontal line represents the mean. ( c ) mRNA of airway smooth muscle cells pre-incubated with WNT-5A siRNA or control siRNA (30 pmol) for 36 hours was isolated and subjected to RT-qPCR. *vs control siRNA. Data represents three independent experiments. Data is expressed as the mean ± SEM.
    Figure Legend Snippet: WNT-5A mediates TGF-β1 induced actin polymerization. Representative immunofluorescent images of a Phalloidin (F-actin, green) and DNAse I (G-actin, red) staining of airway smooth muscle cells exposed to TGF-β1 (2 ng/mL) for 48 hours in the presence or absence of ( a ) latrunculin A (0.1 μM), or ( b ) WNT-5A-specific siRNA. White arrowhead points to filamentous actin. Dashed line represents a single cell boundary. Horizontal line represents the mean. ( c ) mRNA of airway smooth muscle cells pre-incubated with WNT-5A siRNA or control siRNA (30 pmol) for 36 hours was isolated and subjected to RT-qPCR. *vs control siRNA. Data represents three independent experiments. Data is expressed as the mean ± SEM.

    Techniques Used: Staining, Incubation, Isolation, Quantitative RT-PCR

    ROCK activation underlies WNT-5A-induced actin polymerisation. ( a ) Representative immunofluorescent images of a Phalloidin (F-actin, green) and DNAse I (G-actin, red) staining of airway smooth muscle cells exposed to WNT-5A (200 ng/mL) for 2 hours in the presence or absence of Y27632 (1.0 μM), and the corresponding quantification. White arrowhead points to filamentous actin. Dashed line represents a single cell boundary. Horizontal line represents the mean. ( b ) Organ-cultured bovine tracheal smooth muscle strips were pre-incubated with WNT-5A (500 ng/mL) and/or Y27632 (1.0 μM) for 48 hours and a cumulative dose-response curve to histamine for the maximum isometric tension was constructed. *vs Control, $ vs WNT-5A + Y27632. Data represents five independent experiments, each performed in duplicate. Data is expressed as the mean ± SEM.
    Figure Legend Snippet: ROCK activation underlies WNT-5A-induced actin polymerisation. ( a ) Representative immunofluorescent images of a Phalloidin (F-actin, green) and DNAse I (G-actin, red) staining of airway smooth muscle cells exposed to WNT-5A (200 ng/mL) for 2 hours in the presence or absence of Y27632 (1.0 μM), and the corresponding quantification. White arrowhead points to filamentous actin. Dashed line represents a single cell boundary. Horizontal line represents the mean. ( b ) Organ-cultured bovine tracheal smooth muscle strips were pre-incubated with WNT-5A (500 ng/mL) and/or Y27632 (1.0 μM) for 48 hours and a cumulative dose-response curve to histamine for the maximum isometric tension was constructed. *vs Control, $ vs WNT-5A + Y27632. Data represents five independent experiments, each performed in duplicate. Data is expressed as the mean ± SEM.

    Techniques Used: Activation Assay, Staining, Cell Culture, Incubation, Construct

    8) Product Images from "Chitosan/hyaluronic acid/plasmid-DNA nanoparticles encoding interleukin-1 receptor antagonist attenuate inflammation in synoviocytes induced by interleukin-1 beta"

    Article Title: Chitosan/hyaluronic acid/plasmid-DNA nanoparticles encoding interleukin-1 receptor antagonist attenuate inflammation in synoviocytes induced by interleukin-1 beta

    Journal: Journal of Materials Science. Materials in Medicine

    doi: 10.1007/s10856-018-6160-3

    Gel electrophoresis of CS/HA/pIL-1Ra nanoparticles. Lane a: normal naked pIL-1Ra; Lane b: CS/HA/pIL-1Ra nanoparticles; Lane c: naked pIL-1Ra digested by DNase I; Lane d: CS/HA/pIL-1Ra nanoparticles digested by DNase I; Lane e: CS/HA/pIL-1Ra nanoparticles digested by chitosanase
    Figure Legend Snippet: Gel electrophoresis of CS/HA/pIL-1Ra nanoparticles. Lane a: normal naked pIL-1Ra; Lane b: CS/HA/pIL-1Ra nanoparticles; Lane c: naked pIL-1Ra digested by DNase I; Lane d: CS/HA/pIL-1Ra nanoparticles digested by DNase I; Lane e: CS/HA/pIL-1Ra nanoparticles digested by chitosanase

    Techniques Used: Nucleic Acid Electrophoresis

    Related Articles

    Stability Assay:

    Article Title: Influence of phospholipid composition on cationic emulsions/DNA complexes: physicochemical properties, cytotoxicity, and transfection on Hep G2 cells
    Article Snippet: .. Stability assay To determine the stability of the cationic nanoemulsions/DNA plasmid complexes, they were submitted to a DNase I (Invitrogen) digestion assay. .. After formation of complexes at different charge ratios, as described above, they were incubated with 1 U DNase I at 37°C for 30 minutes.

    Synthesized:

    Article Title: Pleiotrophin Induces Transdifferentiation of Monocytes Into Functional Endothelial Cells
    Article Snippet: .. Extracted RNA was treated with DNase I (Ambion) in the presence of RNasin (Promega) to remove DNA contamination before cDNA synthesis. cDNA was synthesized with oligodeoxythymidylic acid primers (Boehringer Mannheim) and Superscript 11 reverse transcriptase (Life Technologies, Inc.). .. The cDNA primers and PCR conditions for the amplification of the endothelial cell markers are described in this supplement.

    Footprinting:

    Article Title: R2 retrotransposition on assembled nucleosomes depends on the translational position of the target site
    Article Snippet: .. In the case of the DNase I footprinting, after incubation with the R2 protein, the nucleosomes were treated with 0.2 U of DNase I (Ambion) for 3 min. ..

    Generated:

    Article Title: Dynamic metabolic exchange governs a marine algal-bacterial interaction
    Article Snippet: .. This section was revised and now includes the following details: “Positive controls were generated by pretreating cells with 15 U ml -1 DNase I (Thermo Fischer Scientific). ..

    Incubation:

    Article Title: The RofA Binding Site in Streptococcus pyogenes Is Utilized in Multiple Transcriptional Pathways
    Article Snippet: .. DNase I (0.01 U; Gibco-BRL) was added, and the incubation continued for 2 min at 25°C. ..

    Article Title: R2 retrotransposition on assembled nucleosomes depends on the translational position of the target site
    Article Snippet: .. In the case of the DNase I footprinting, after incubation with the R2 protein, the nucleosomes were treated with 0.2 U of DNase I (Ambion) for 3 min. ..

    Polymerase Chain Reaction:

    Article Title: Mapping three-dimensional genome architecture through in situ DNase Hi-C
    Article Snippet: .. Glycine (Sigma-Aldrich 50046) NEBuffer 2 (NEB B7002S) 10% (wt/vol) UltraPure SDS (Life Tech 15553-027) DNase I, RNase-free (supplied with MnCl2 and reaction buffer) (1 U/μL) (Thermo Scientific EN0525) RNase A, DNase and protease-free (10 mg/ml) (Thermo Scientific EN0531) Klenow Fragment (10 U/μL) (Thermo Scientific EP0052) Klenow Fragment (exo– ) (5 U/μL) (Thermo Scientific EP0422) T4 DNA Polymerase (5 U/μL) (Thermo Scientific EP0062) T4 DNA Ligase (5 U/μL) provided with 50% PEG-4000 (Thermo Scientific EL0012) T4 Polynucleotide Kinase (10 U/μL) (Thermo Scientific EK0032) 10X T4 DNA Ligase Buffer w/ATP (NEB B0202S) Agencourt AMPure XP (Beckman Coulter ) 2X HotStart PCR ReadyMix (KAPA KK2601) Fast DNA End Repair Kit (Thermo Scientific K0771) Proteinase K (Thermo Scientific EO0492) FastDigest® BamHI (Thermo Scientific FERFD0504) Dynabeads® MyOne™ Streptavidin C1 (Life Tech 65001) dNTP Set (100 mM 4x 0.25ml) (Thermo Scientific FERR0181) 100 bp DNA ladder (Thermo Scientific SM0243) GlycoBlue (Ambion AM9516) 3 M Sodium acetate (pH 5.2) (Cellgro 46-033-CI) Ethanol (Decon Labs Inc. 2716) CAUTION! .. Ethanol is flammable, and should be stored and handled under appropriate conditions Isopropanol (Sigma-Aldrich 437522) CAUTION!

    Plasmid Preparation:

    Article Title: Influence of phospholipid composition on cationic emulsions/DNA complexes: physicochemical properties, cytotoxicity, and transfection on Hep G2 cells
    Article Snippet: .. Stability assay To determine the stability of the cationic nanoemulsions/DNA plasmid complexes, they were submitted to a DNase I (Invitrogen) digestion assay. .. After formation of complexes at different charge ratios, as described above, they were incubated with 1 U DNase I at 37°C for 30 minutes.

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    Thermo Fisher dnase i
    Bacteria induce a unique algal death in aging co-cultures. ( a–d ) Images of cultures demonstrating the change in the culture color over time. ( e–h ) Phase contrast microscopy images. Arrow points to shed coccoliths. ( i–l ) Fluorescent images of chlorophyll and accessory pigments autofluorescence. ( m–p ) Fluorescent images of dead cells stained with Sytox green. Percentages indicate the number of dead cells counted in each population. For each value n  >  300 and the standard deviation between several analyzed fields was up to 20% of the indicated value. ( q–t ) Overlay of phase contrast microscopy images (grey) with fluorescent images of TUNEL assay (green) of cultures at day 20 (see Materials and methods). ( q ) Co-culture, ( r ) Axenic algal culture, ( s ) Positive control, cells were pretreated with DNase I, ( t ) Negative control, the terminal deoxynucleotidyl transferase enzyme (TdT) was replaced with distilled water. Percentages indicate the number of positively stained cells counted in each population. For each value n  >  300 and the standard deviation between several analyzed fields was up to 25% of the indicated value. Scale bar corresponds to 1 µm in e–p and 4 µm in q–t. DOI: http://dx.doi.org/10.7554/eLife.17473.009
    Dnase I, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 797 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dnase i/product/Thermo Fisher
    Average 99 stars, based on 797 article reviews
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    99
    Thermo Fisher dna digestion mix
    Overview of RT-RamDA and single-cell RamDA-seq. a Schematic diagram of RT-RamDA. 1. RT primers (oligo-dT and not-so-random primers) anneal to a RNA template. 2. Complementary <t>DNA</t> (cDNA) is synthesized by the RNA-dependent DNA polymerase activity of RNase H minus reverse transcriptase (RTase). 3. Endonuclease <t>(DNase</t> I) selectively nicks the cDNA of the RNA:cDNA hybrid strand. 4. The 3′ cDNA strand is displaced by the strand displacement activity of RTase mediated by the T4 gene 32 protein (gp32), starting from the nick randomly introduced by DNase I. cDNA is amplified as a displaced strand and protected by gp32 from DNase I. b Relative yield of cDNA molecules using RT-qPCR ( n = 4). Mouse ESC total RNA (10 pg) was used as a template, and 1/10 the amount of cDNA was used for qPCR. The relative yield was calculated by averaging the amplification efficiency of four mESC ( Nanog , Pou5f1 , Zfp42 , and Sox2 ) and three housekeeping ( Gnb2l1 , Atp5a1 , and Tubb5 ) genes using a conventional method (−) as a standard. c Schematic diagram of RamDA-seq and C1-RamDA-seq. For details, please refer to the Methods section. d Number of detected transcripts with twofold or lower expression changes against rdRNA-seq (count ≥ 10). For the boxplots in b and d , the center line, and lower and upper bounds of each box represent the median, and first and third quartiles, respectively. The lower (upper) whisker extends to smallest (largest) values no further than 1.5 × interquartile range (IQR) from the first (third) quartile. e Squared coefficient of variation of the read count. All conditions were adjusted, and 10 million reads were used in d and e . Transcripts were annotated by GENCODE gene annotation (vM9)
    Dna Digestion Mix, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dna digestion mix/product/Thermo Fisher
    Average 99 stars, based on 4 article reviews
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    Bacteria induce a unique algal death in aging co-cultures. ( a–d ) Images of cultures demonstrating the change in the culture color over time. ( e–h ) Phase contrast microscopy images. Arrow points to shed coccoliths. ( i–l ) Fluorescent images of chlorophyll and accessory pigments autofluorescence. ( m–p ) Fluorescent images of dead cells stained with Sytox green. Percentages indicate the number of dead cells counted in each population. For each value n  >  300 and the standard deviation between several analyzed fields was up to 20% of the indicated value. ( q–t ) Overlay of phase contrast microscopy images (grey) with fluorescent images of TUNEL assay (green) of cultures at day 20 (see Materials and methods). ( q ) Co-culture, ( r ) Axenic algal culture, ( s ) Positive control, cells were pretreated with DNase I, ( t ) Negative control, the terminal deoxynucleotidyl transferase enzyme (TdT) was replaced with distilled water. Percentages indicate the number of positively stained cells counted in each population. For each value n  >  300 and the standard deviation between several analyzed fields was up to 25% of the indicated value. Scale bar corresponds to 1 µm in e–p and 4 µm in q–t. DOI: http://dx.doi.org/10.7554/eLife.17473.009

    Journal: eLife

    Article Title: Dynamic metabolic exchange governs a marine algal-bacterial interaction

    doi: 10.7554/eLife.17473

    Figure Lengend Snippet: Bacteria induce a unique algal death in aging co-cultures. ( a–d ) Images of cultures demonstrating the change in the culture color over time. ( e–h ) Phase contrast microscopy images. Arrow points to shed coccoliths. ( i–l ) Fluorescent images of chlorophyll and accessory pigments autofluorescence. ( m–p ) Fluorescent images of dead cells stained with Sytox green. Percentages indicate the number of dead cells counted in each population. For each value n  >  300 and the standard deviation between several analyzed fields was up to 20% of the indicated value. ( q–t ) Overlay of phase contrast microscopy images (grey) with fluorescent images of TUNEL assay (green) of cultures at day 20 (see Materials and methods). ( q ) Co-culture, ( r ) Axenic algal culture, ( s ) Positive control, cells were pretreated with DNase I, ( t ) Negative control, the terminal deoxynucleotidyl transferase enzyme (TdT) was replaced with distilled water. Percentages indicate the number of positively stained cells counted in each population. For each value n  >  300 and the standard deviation between several analyzed fields was up to 25% of the indicated value. Scale bar corresponds to 1 µm in e–p and 4 µm in q–t. DOI: http://dx.doi.org/10.7554/eLife.17473.009

    Article Snippet: This section was revised and now includes the following details: “Positive controls were generated by pretreating cells with 15 U ml -1 DNase I (Thermo Fischer Scientific).

    Techniques: Microscopy, Staining, Standard Deviation, TUNEL Assay, Co-Culture Assay, Positive Control, Negative Control

    TLR9 signalling pathway, miR‐7 and Smad2 expressions in NET‐treated LFs. LFs were divided into control group, PMA group and PMA+DNase I group. A, Western blot assay showed that TLR9 protein level and phosphorylation levels of its downstream molecules p38, AKT and p65 were up‐regulated in PMA group, whereas PMA+DNase I decreased these expressions. B, miR‐7 expression level was down‐regulated in PMA group, whereas PMA+DNase I increased miR‐7 expression. C, Smad2 protein level was up‐regulated in PMA group, whereas PMA+DNase I inhibited Smad2 expression. ** P

    Journal: Journal of Cellular and Molecular Medicine

    Article Title: Neutrophil extracellular traps activate lung fibroblast to induce polymyositis‐related interstitial lung diseases via TLR9‐miR‐7‐Smad2 pathway, et al. Neutrophil extracellular traps activate lung fibroblast to induce polymyositis‐related interstitial lung diseases via TLR9‐miR‐7‐Smad2 pathway

    doi: 10.1111/jcmm.14858

    Figure Lengend Snippet: TLR9 signalling pathway, miR‐7 and Smad2 expressions in NET‐treated LFs. LFs were divided into control group, PMA group and PMA+DNase I group. A, Western blot assay showed that TLR9 protein level and phosphorylation levels of its downstream molecules p38, AKT and p65 were up‐regulated in PMA group, whereas PMA+DNase I decreased these expressions. B, miR‐7 expression level was down‐regulated in PMA group, whereas PMA+DNase I increased miR‐7 expression. C, Smad2 protein level was up‐regulated in PMA group, whereas PMA+DNase I inhibited Smad2 expression. ** P

    Article Snippet: We found PMA‐stimulated NET promoted mRNA levels of ACTA2 (α‐SMA gene), CCN2 (connective tissue growth factor gene, a profibrotic mediator) and ADAM12 (ADAM metallopeptidase domain 12, a fibrotic component) in LFs, whereas DNase I decreased these expressions, which indicated DNase I relieved PF (Figure B).

    Techniques: Western Blot, Expressing

    NETs accelerated the proliferation of LF and their differentiation into MF. LFs were divided into control group, PMA group and PMA+DNase I group. A, SYTOX Green nucleic acid stain showed that the nuclear membrane was fractured and DNA was released in PMA‐treated NET. B, qRT‐PCR assay detected mRNA levels of ACTA2 (α‐SMA gene), CCN2 (connective tissue growth factor) and ADAM12 (ADAM metallopeptidase domain 12) in control, PMA and PMA+DNase I groups. C, Western blot assay detected protein levels of α‐SMA and CCN2 in control, PMA and PMA+DNase I groups. D, PMA‐stimulated NET promoted the formation of collagen in LF, whereas the formation of collagen was reduced by DNase I. E‐F, The proliferation of LF was detected by MTT assay. G, The proliferation of LF was also detected by EdU experiment. H, The apoptosis of LF was detected by flow cytometry analysis. ** P

    Journal: Journal of Cellular and Molecular Medicine

    Article Title: Neutrophil extracellular traps activate lung fibroblast to induce polymyositis‐related interstitial lung diseases via TLR9‐miR‐7‐Smad2 pathway, et al. Neutrophil extracellular traps activate lung fibroblast to induce polymyositis‐related interstitial lung diseases via TLR9‐miR‐7‐Smad2 pathway

    doi: 10.1111/jcmm.14858

    Figure Lengend Snippet: NETs accelerated the proliferation of LF and their differentiation into MF. LFs were divided into control group, PMA group and PMA+DNase I group. A, SYTOX Green nucleic acid stain showed that the nuclear membrane was fractured and DNA was released in PMA‐treated NET. B, qRT‐PCR assay detected mRNA levels of ACTA2 (α‐SMA gene), CCN2 (connective tissue growth factor) and ADAM12 (ADAM metallopeptidase domain 12) in control, PMA and PMA+DNase I groups. C, Western blot assay detected protein levels of α‐SMA and CCN2 in control, PMA and PMA+DNase I groups. D, PMA‐stimulated NET promoted the formation of collagen in LF, whereas the formation of collagen was reduced by DNase I. E‐F, The proliferation of LF was detected by MTT assay. G, The proliferation of LF was also detected by EdU experiment. H, The apoptosis of LF was detected by flow cytometry analysis. ** P

    Article Snippet: We found PMA‐stimulated NET promoted mRNA levels of ACTA2 (α‐SMA gene), CCN2 (connective tissue growth factor gene, a profibrotic mediator) and ADAM12 (ADAM metallopeptidase domain 12, a fibrotic component) in LFs, whereas DNase I decreased these expressions, which indicated DNase I relieved PF (Figure B).

    Techniques: Staining, Quantitative RT-PCR, Western Blot, MTT Assay, Flow Cytometry

    ospR and ohr promoter analysis. (A) Primer extension analyses of gpx using total RNA extracted from Pseudomonas aeruginosa without and with 200 μM cumene hydroperoxide induction. The arrow indicates the transcription start site. The Sanger sequencing ladder to the left of the primer extension lanes was generated using the same primer used in the primer extension. The nucleotide sequences of the gpx (B) and ohr (C) promoter regions are shown. The putative −10 and −35 promoter regions, the transcription start site (+1), and the putative translation start codon are shown in bold. Locations, directions and names of oligonucleotides used in this study, i.e. BT462, BT214, BT484, and BT514, are indicated. The DNaseI-protected regions for OspR binding are boxed. Putative OspR binding sites and OhrR binding site are aligned with the predicted conserved sequences in shaded arrows. Dots indicate matched nucleotides.

    Journal: PLoS ONE

    Article Title: Regulation of Organic Hydroperoxide Stress Response by Two OhrR Homologs in Pseudomonas aeruginosa

    doi: 10.1371/journal.pone.0161982

    Figure Lengend Snippet: ospR and ohr promoter analysis. (A) Primer extension analyses of gpx using total RNA extracted from Pseudomonas aeruginosa without and with 200 μM cumene hydroperoxide induction. The arrow indicates the transcription start site. The Sanger sequencing ladder to the left of the primer extension lanes was generated using the same primer used in the primer extension. The nucleotide sequences of the gpx (B) and ohr (C) promoter regions are shown. The putative −10 and −35 promoter regions, the transcription start site (+1), and the putative translation start codon are shown in bold. Locations, directions and names of oligonucleotides used in this study, i.e. BT462, BT214, BT484, and BT514, are indicated. The DNaseI-protected regions for OspR binding are boxed. Putative OspR binding sites and OhrR binding site are aligned with the predicted conserved sequences in shaded arrows. Dots indicate matched nucleotides.

    Article Snippet: Briefly, contaminating DNA in the total RNA samples was hydrolyzed by the addition of DNaseI (Thermo Scientific) according to the manufacturer's instructions.

    Techniques: Sequencing, Generated, Binding Assay

    Overview of RT-RamDA and single-cell RamDA-seq. a Schematic diagram of RT-RamDA. 1. RT primers (oligo-dT and not-so-random primers) anneal to a RNA template. 2. Complementary DNA (cDNA) is synthesized by the RNA-dependent DNA polymerase activity of RNase H minus reverse transcriptase (RTase). 3. Endonuclease (DNase I) selectively nicks the cDNA of the RNA:cDNA hybrid strand. 4. The 3′ cDNA strand is displaced by the strand displacement activity of RTase mediated by the T4 gene 32 protein (gp32), starting from the nick randomly introduced by DNase I. cDNA is amplified as a displaced strand and protected by gp32 from DNase I. b Relative yield of cDNA molecules using RT-qPCR ( n = 4). Mouse ESC total RNA (10 pg) was used as a template, and 1/10 the amount of cDNA was used for qPCR. The relative yield was calculated by averaging the amplification efficiency of four mESC ( Nanog , Pou5f1 , Zfp42 , and Sox2 ) and three housekeeping ( Gnb2l1 , Atp5a1 , and Tubb5 ) genes using a conventional method (−) as a standard. c Schematic diagram of RamDA-seq and C1-RamDA-seq. For details, please refer to the Methods section. d Number of detected transcripts with twofold or lower expression changes against rdRNA-seq (count ≥ 10). For the boxplots in b and d , the center line, and lower and upper bounds of each box represent the median, and first and third quartiles, respectively. The lower (upper) whisker extends to smallest (largest) values no further than 1.5 × interquartile range (IQR) from the first (third) quartile. e Squared coefficient of variation of the read count. All conditions were adjusted, and 10 million reads were used in d and e . Transcripts were annotated by GENCODE gene annotation (vM9)

    Journal: Nature Communications

    Article Title: Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs

    doi: 10.1038/s41467-018-02866-0

    Figure Lengend Snippet: Overview of RT-RamDA and single-cell RamDA-seq. a Schematic diagram of RT-RamDA. 1. RT primers (oligo-dT and not-so-random primers) anneal to a RNA template. 2. Complementary DNA (cDNA) is synthesized by the RNA-dependent DNA polymerase activity of RNase H minus reverse transcriptase (RTase). 3. Endonuclease (DNase I) selectively nicks the cDNA of the RNA:cDNA hybrid strand. 4. The 3′ cDNA strand is displaced by the strand displacement activity of RTase mediated by the T4 gene 32 protein (gp32), starting from the nick randomly introduced by DNase I. cDNA is amplified as a displaced strand and protected by gp32 from DNase I. b Relative yield of cDNA molecules using RT-qPCR ( n = 4). Mouse ESC total RNA (10 pg) was used as a template, and 1/10 the amount of cDNA was used for qPCR. The relative yield was calculated by averaging the amplification efficiency of four mESC ( Nanog , Pou5f1 , Zfp42 , and Sox2 ) and three housekeeping ( Gnb2l1 , Atp5a1 , and Tubb5 ) genes using a conventional method (−) as a standard. c Schematic diagram of RamDA-seq and C1-RamDA-seq. For details, please refer to the Methods section. d Number of detected transcripts with twofold or lower expression changes against rdRNA-seq (count ≥ 10). For the boxplots in b and d , the center line, and lower and upper bounds of each box represent the median, and first and third quartiles, respectively. The lower (upper) whisker extends to smallest (largest) values no further than 1.5 × interquartile range (IQR) from the first (third) quartile. e Squared coefficient of variation of the read count. All conditions were adjusted, and 10 million reads were used in d and e . Transcripts were annotated by GENCODE gene annotation (vM9)

    Article Snippet: To eliminate genomic DNA contamination, 1 μL of genomic DNA digestion mix (0.5× PrimeScript Buffer, 0.2 U of DNase I Amplification Grade, 1: 5 000 000 ERCC RNA Spike-In Mix I (Thermo Fisher) in RNase-free water) was added to 1 μL of the denatured sample.

    Techniques: Synthesized, Activity Assay, Amplification, Quantitative RT-PCR, Real-time Polymerase Chain Reaction, Expressing, Whisker Assay