Structured Review

Thermo Fisher dnase i
Effects of noncomplementary dNTPs on <t>DNase</t> I footprints and stable complex formation by HIV-1 RT
Dnase I, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 46 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Images

1) Product Images from "Stable Complexes Formed by HIV-1 Reverse Transcriptase at Distinct Positions on the Primer-Template Controlled by Binding Deoxynucleoside Triphosphates or Foscarnet"

Article Title: Stable Complexes Formed by HIV-1 Reverse Transcriptase at Distinct Positions on the Primer-Template Controlled by Binding Deoxynucleoside Triphosphates or Foscarnet

Journal:

doi: 10.1016/j.jmb.2007.03.006

Effects of noncomplementary dNTPs on DNase I footprints and stable complex formation by HIV-1 RT
Figure Legend Snippet: Effects of noncomplementary dNTPs on DNase I footprints and stable complex formation by HIV-1 RT

Techniques Used:

Effects of foscarnet on DNase I protection and stable complex formation by HIV-1 RT
Figure Legend Snippet: Effects of foscarnet on DNase I protection and stable complex formation by HIV-1 RT

Techniques Used:

DNase I protection on P/Ts terminated with dT analogues
Figure Legend Snippet: DNase I protection on P/Ts terminated with dT analogues

Techniques Used:

Effects of the next complementary dNTP on DNase I protection and stable complex formation by HIV-1 RT
Figure Legend Snippet: Effects of the next complementary dNTP on DNase I protection and stable complex formation by HIV-1 RT

Techniques Used:

2) Product Images from "Complete, gene-specific siRNA libraries: Production and expression in mammalian cells"

Article Title: Complete, gene-specific siRNA libraries: Production and expression in mammalian cells

Journal:

doi: 10.1261/rna.7285805

Preparation of gene-specific siRNA libraries by DNase I fragmentation of double-stranded DNA. ( A ) The general scheme. The double-stranded DNA target is digested by DNase I in the presence of Mn 2+ ions, and the fraction containing 20–30-bp fragments
Figure Legend Snippet: Preparation of gene-specific siRNA libraries by DNase I fragmentation of double-stranded DNA. ( A ) The general scheme. The double-stranded DNA target is digested by DNase I in the presence of Mn 2+ ions, and the fraction containing 20–30-bp fragments

Techniques Used:

Silencing ability of species randomly selected from the DsRed-specific siRNA library produced by the DNase I method. ( A ) Randomly chosen clones were cotransfected with DsRed expression vector into 293FT cells with Lipofectamine 2000 (Invitrogen). DsRed
Figure Legend Snippet: Silencing ability of species randomly selected from the DsRed-specific siRNA library produced by the DNase I method. ( A ) Randomly chosen clones were cotransfected with DsRed expression vector into 293FT cells with Lipofectamine 2000 (Invitrogen). DsRed

Techniques Used: Produced, Clone Assay, Expressing, Plasmid Preparation

3) Product Images from "Transcription and Activity of Digestive Enzymes of Nezara viridula Maintained on Different Plant Diets"

Article Title: Transcription and Activity of Digestive Enzymes of Nezara viridula Maintained on Different Plant Diets

Journal: Frontiers in Physiology

doi: 10.3389/fphys.2019.01553

Nuclease activity is comparable between corresponding tissues from corn and green bean diet. DNase I and RNase A were used as positive control enzymes for DNA substrate and RNA and dsRNA substrates, respectively. Differences in nuclease activity between corresponding tissue extracts from each diet with each substrate were determined by a t -test with Bonferroni correction of α = 0.5. Error bars represent SEM of three biological replicates.
Figure Legend Snippet: Nuclease activity is comparable between corresponding tissues from corn and green bean diet. DNase I and RNase A were used as positive control enzymes for DNA substrate and RNA and dsRNA substrates, respectively. Differences in nuclease activity between corresponding tissue extracts from each diet with each substrate were determined by a t -test with Bonferroni correction of α = 0.5. Error bars represent SEM of three biological replicates.

Techniques Used: Activity Assay, Positive Control

4) Product Images from "Crystal Structure of the Regulatory Domain of MexT, a Transcriptional Activator of the MexEF-OprN Efflux Pump in Pseudomonas aeruginosa"

Article Title: Crystal Structure of the Regulatory Domain of MexT, a Transcriptional Activator of the MexEF-OprN Efflux Pump in Pseudomonas aeruginosa

Journal: Molecules and Cells

doi: 10.14348/molcells.2019.0168

MexT binding sequences identified by DNase I footprinting (A) A 630-bp DNA fragment containing the mexT - mexE intergenic region was labeled with 6-fluorescein amidite and then used as a DNA probe. The fluorescence-labeled DNA probe (400 ng) was incubated without or with 200 ng of purified FL MexT. The regions protected by MexT are indicated by red squares (MexT binding site I and II). Nucleotide numbers shown are the relative positions when the transcription start site mexE is designated as +1. (B) Comparison of the MexT-binding sequences. The two putative MexT-binding sequences in the mexEF - oprN regulatory region are shown at the top. The MexT-binding sequences from other promoters of MexT regulons are aligned below. Nucleotides in bold and underlined represent a partially conserved palindromic sequence, suggesting the potential consensus MexT-binding sequence, ATCA (N) 7 CGAT .
Figure Legend Snippet: MexT binding sequences identified by DNase I footprinting (A) A 630-bp DNA fragment containing the mexT - mexE intergenic region was labeled with 6-fluorescein amidite and then used as a DNA probe. The fluorescence-labeled DNA probe (400 ng) was incubated without or with 200 ng of purified FL MexT. The regions protected by MexT are indicated by red squares (MexT binding site I and II). Nucleotide numbers shown are the relative positions when the transcription start site mexE is designated as +1. (B) Comparison of the MexT-binding sequences. The two putative MexT-binding sequences in the mexEF - oprN regulatory region are shown at the top. The MexT-binding sequences from other promoters of MexT regulons are aligned below. Nucleotides in bold and underlined represent a partially conserved palindromic sequence, suggesting the potential consensus MexT-binding sequence, ATCA (N) 7 CGAT .

Techniques Used: Binding Assay, Footprinting, Labeling, Fluorescence, Incubation, Purification, Sequencing

5) Product Images from "Systematic Comparison and Validation of Quantitative Real-Time PCR Methods for the Quantitation of Adeno-Associated Viral Products"

Article Title: Systematic Comparison and Validation of Quantitative Real-Time PCR Methods for the Quantitation of Adeno-Associated Viral Products

Journal: Human Gene Therapy Methods

doi: 10.1089/hgtb.2015.013

Effects of enzymatic treatments on qPCR analysis. A lentiviral vector plasmid carrying the SV40 sequence was used to spike crude ( left ) and HPLC-purified ( middle ) AAV8 samples and AAV2 ( right ) samples before HPLC purification at a vector concentration of 6.25×10 13 copies/ml; qPCR analysis was performed, targeting spike-specific SV40 (hatched columns) and vector-specific sequences in AAV8 (gray columns) and AAV2 (cross-hatched columns); DNA copy number was determined on the basis of calibration curves generated from circular plasmid DNA standards. NT, no treatment; DT, treatment with Benzonase and DNase I; DT/PK, treatment with Benzonase and DNase I followed by proteinase K. Mean data are shown ( n =3). Asterisks indicate statistical significance between crude and purified samples, where * p
Figure Legend Snippet: Effects of enzymatic treatments on qPCR analysis. A lentiviral vector plasmid carrying the SV40 sequence was used to spike crude ( left ) and HPLC-purified ( middle ) AAV8 samples and AAV2 ( right ) samples before HPLC purification at a vector concentration of 6.25×10 13 copies/ml; qPCR analysis was performed, targeting spike-specific SV40 (hatched columns) and vector-specific sequences in AAV8 (gray columns) and AAV2 (cross-hatched columns); DNA copy number was determined on the basis of calibration curves generated from circular plasmid DNA standards. NT, no treatment; DT, treatment with Benzonase and DNase I; DT/PK, treatment with Benzonase and DNase I followed by proteinase K. Mean data are shown ( n =3). Asterisks indicate statistical significance between crude and purified samples, where * p

Techniques Used: Real-time Polymerase Chain Reaction, Plasmid Preparation, Sequencing, High Performance Liquid Chromatography, Purification, Concentration Assay, Generated

6) Product Images from "Poly(ADP-ribose)-dependent chromatin unfolding facilitates the association of DNA-binding proteins with DNA at sites of damage"

Article Title: Poly(ADP-ribose)-dependent chromatin unfolding facilitates the association of DNA-binding proteins with DNA at sites of damage

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkz820

The accessibility of DNase I at sites of micropore irradiation is regulated by PAR-signaling. ( A ) Schematic representation of micropore irradiation assay. Cells are labeled with BrdU to photosensitize the DNA. After micropore irradiation (100 J/m 2 of UVC light) and fixation, chromatin is digested by DNase I. The generated free DNA-ends are labeled with IdU by Terminal Deoxynucleotidyl Transferase (TdT) and visualized by immunofluorescence. ( B ) Representative images of the IdU-signal 30 minutes post-micropore-irradiation to analyze the chromatin accessibility to DNase I in the presence or absence of PARP inhibitor (Olaparib). The microirradiation sites are visualized with anti-γH2AX and anti-rabbit Alexa Fluor 555 antibodies. The free DNA-ends are visualized by anti-IdU and anti-mouse Alexa Fluor 488 antibodies. Scale bar = 10 μm. ( C ) Quantification of the IdU-signal intensity in the presence or absence of PARP inhibitor (PARPi). The irradiated areas are segmented by γH2AX signal in Hoechst positive nuclei and the average signal intensities of the background-subtracted IdU channel are measured. These average signal intensities are divided by the signal intensities of the corresponding nuclei and plotted.
Figure Legend Snippet: The accessibility of DNase I at sites of micropore irradiation is regulated by PAR-signaling. ( A ) Schematic representation of micropore irradiation assay. Cells are labeled with BrdU to photosensitize the DNA. After micropore irradiation (100 J/m 2 of UVC light) and fixation, chromatin is digested by DNase I. The generated free DNA-ends are labeled with IdU by Terminal Deoxynucleotidyl Transferase (TdT) and visualized by immunofluorescence. ( B ) Representative images of the IdU-signal 30 minutes post-micropore-irradiation to analyze the chromatin accessibility to DNase I in the presence or absence of PARP inhibitor (Olaparib). The microirradiation sites are visualized with anti-γH2AX and anti-rabbit Alexa Fluor 555 antibodies. The free DNA-ends are visualized by anti-IdU and anti-mouse Alexa Fluor 488 antibodies. Scale bar = 10 μm. ( C ) Quantification of the IdU-signal intensity in the presence or absence of PARP inhibitor (PARPi). The irradiated areas are segmented by γH2AX signal in Hoechst positive nuclei and the average signal intensities of the background-subtracted IdU channel are measured. These average signal intensities are divided by the signal intensities of the corresponding nuclei and plotted.

Techniques Used: Irradiation, Labeling, Generated, Immunofluorescence

7) Product Images from "Transcription and Activity of Digestive Enzymes of Nezara viridula Maintained on Different Plant Diets"

Article Title: Transcription and Activity of Digestive Enzymes of Nezara viridula Maintained on Different Plant Diets

Journal: Frontiers in Physiology

doi: 10.3389/fphys.2019.01553

Nuclease activity is comparable between corresponding tissues from corn and green bean diet. DNase I and RNase A were used as positive control enzymes for DNA substrate and RNA and dsRNA substrates, respectively. Differences in nuclease activity between corresponding tissue extracts from each diet with each substrate were determined by a t -test with Bonferroni correction of α = 0.5. Error bars represent SEM of three biological replicates.
Figure Legend Snippet: Nuclease activity is comparable between corresponding tissues from corn and green bean diet. DNase I and RNase A were used as positive control enzymes for DNA substrate and RNA and dsRNA substrates, respectively. Differences in nuclease activity between corresponding tissue extracts from each diet with each substrate were determined by a t -test with Bonferroni correction of α = 0.5. Error bars represent SEM of three biological replicates.

Techniques Used: Activity Assay, Positive Control

8) Product Images from "Epitope mapping using mRNA display and a unidirectional nested deletion library"

Article Title: Epitope mapping using mRNA display and a unidirectional nested deletion library

Journal:

doi: 10.1093/protein/gzi038

Construction of a unidirectional nested deletion library. ( A ) cDNA library reverse transcribed with dUTP is partially digested with DNase I. A randomly-primed fill-in reaction is performed with degenerate DNA hexamers containing a constant 5’
Figure Legend Snippet: Construction of a unidirectional nested deletion library. ( A ) cDNA library reverse transcribed with dUTP is partially digested with DNase I. A randomly-primed fill-in reaction is performed with degenerate DNA hexamers containing a constant 5’

Techniques Used: cDNA Library Assay

9) Product Images from "Complete, gene-specific siRNA libraries: Production and expression in mammalian cells"

Article Title: Complete, gene-specific siRNA libraries: Production and expression in mammalian cells

Journal:

doi: 10.1261/rna.7285805

Preparation of gene-specific siRNA libraries by DNase I fragmentation of double-stranded DNA. ( A ) The general scheme. The double-stranded DNA target is digested by DNase I in the presence of Mn 2+ ions, and the fraction containing 20–30-bp fragments
Figure Legend Snippet: Preparation of gene-specific siRNA libraries by DNase I fragmentation of double-stranded DNA. ( A ) The general scheme. The double-stranded DNA target is digested by DNase I in the presence of Mn 2+ ions, and the fraction containing 20–30-bp fragments

Techniques Used:

Silencing ability of species randomly selected from the DsRed-specific siRNA library produced by the DNase I method. ( A ) Randomly chosen clones were cotransfected with DsRed expression vector into 293FT cells with Lipofectamine 2000 (Invitrogen). DsRed
Figure Legend Snippet: Silencing ability of species randomly selected from the DsRed-specific siRNA library produced by the DNase I method. ( A ) Randomly chosen clones were cotransfected with DsRed expression vector into 293FT cells with Lipofectamine 2000 (Invitrogen). DsRed

Techniques Used: Produced, Clone Assay, Expressing, Plasmid Preparation

10) Product Images from "Poly(ADP-ribose)-dependent chromatin unfolding facilitates the association of DNA-binding proteins with DNA at sites of damage"

Article Title: Poly(ADP-ribose)-dependent chromatin unfolding facilitates the association of DNA-binding proteins with DNA at sites of damage

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkz820

The accessibility of DNase I at sites of micropore irradiation is regulated by PAR-signaling. ( A ) Schematic representation of micropore irradiation assay. Cells are labeled with BrdU to photosensitize the DNA. After micropore irradiation (100 J/m 2 of UVC light) and fixation, chromatin is digested by DNase I. The generated free DNA-ends are labeled with IdU by Terminal Deoxynucleotidyl Transferase (TdT) and visualized by immunofluorescence. ( B ) Representative images of the IdU-signal 30 minutes post-micropore-irradiation to analyze the chromatin accessibility to DNase I in the presence or absence of PARP inhibitor (Olaparib). The microirradiation sites are visualized with anti-γH2AX and anti-rabbit Alexa Fluor 555 antibodies. The free DNA-ends are visualized by anti-IdU and anti-mouse Alexa Fluor 488 antibodies. Scale bar = 10 μm. ( C ) Quantification of the IdU-signal intensity in the presence or absence of PARP inhibitor (PARPi). The irradiated areas are segmented by γH2AX signal in Hoechst positive nuclei and the average signal intensities of the background-subtracted IdU channel are measured. These average signal intensities are divided by the signal intensities of the corresponding nuclei and plotted.
Figure Legend Snippet: The accessibility of DNase I at sites of micropore irradiation is regulated by PAR-signaling. ( A ) Schematic representation of micropore irradiation assay. Cells are labeled with BrdU to photosensitize the DNA. After micropore irradiation (100 J/m 2 of UVC light) and fixation, chromatin is digested by DNase I. The generated free DNA-ends are labeled with IdU by Terminal Deoxynucleotidyl Transferase (TdT) and visualized by immunofluorescence. ( B ) Representative images of the IdU-signal 30 minutes post-micropore-irradiation to analyze the chromatin accessibility to DNase I in the presence or absence of PARP inhibitor (Olaparib). The microirradiation sites are visualized with anti-γH2AX and anti-rabbit Alexa Fluor 555 antibodies. The free DNA-ends are visualized by anti-IdU and anti-mouse Alexa Fluor 488 antibodies. Scale bar = 10 μm. ( C ) Quantification of the IdU-signal intensity in the presence or absence of PARP inhibitor (PARPi). The irradiated areas are segmented by γH2AX signal in Hoechst positive nuclei and the average signal intensities of the background-subtracted IdU channel are measured. These average signal intensities are divided by the signal intensities of the corresponding nuclei and plotted.

Techniques Used: Irradiation, Labeling, Generated, Immunofluorescence

11) Product Images from "Benchmarking protocols for the metagenomic analysis of stream biofilm viromes"

Article Title: Benchmarking protocols for the metagenomic analysis of stream biofilm viromes

Journal: PeerJ

doi: 10.7717/peerj.8187

Overview of methods for the extraction and purification of viruses from stream biofilms. First, phages are concentrated using either PEG precipitation or TFF. Different physico-chemical extraction procedures were then evaluated for their efficiency. Prior to DNase I digestion, centrifugation and filtration was used to remove cell debris from all samples. Finally, ultracentrifugation in sucrose or CsCl density gradients was used to purify viruses for downstream molecular analyses. Combinations of all protocols were evaluated for the recovery of VLPs and DNA yield.
Figure Legend Snippet: Overview of methods for the extraction and purification of viruses from stream biofilms. First, phages are concentrated using either PEG precipitation or TFF. Different physico-chemical extraction procedures were then evaluated for their efficiency. Prior to DNase I digestion, centrifugation and filtration was used to remove cell debris from all samples. Finally, ultracentrifugation in sucrose or CsCl density gradients was used to purify viruses for downstream molecular analyses. Combinations of all protocols were evaluated for the recovery of VLPs and DNA yield.

Techniques Used: Purification, Centrifugation, Filtration

12) Product Images from "Poly(ADP-ribose)-dependent chromatin unfolding facilitates the association of DNA-binding proteins with DNA at sites of damage"

Article Title: Poly(ADP-ribose)-dependent chromatin unfolding facilitates the association of DNA-binding proteins with DNA at sites of damage

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkz820

The accessibility of DNase I at sites of micropore irradiation is regulated by PAR-signaling. ( A ) Schematic representation of micropore irradiation assay. Cells are labeled with BrdU to photosensitize the DNA. After micropore irradiation (100 J/m 2 of UVC light) and fixation, chromatin is digested by DNase I. The generated free DNA-ends are labeled with IdU by Terminal Deoxynucleotidyl Transferase (TdT) and visualized by immunofluorescence. ( B ) Representative images of the IdU-signal 30 minutes post-micropore-irradiation to analyze the chromatin accessibility to DNase I in the presence or absence of PARP inhibitor (Olaparib). The microirradiation sites are visualized with anti-γH2AX and anti-rabbit Alexa Fluor 555 antibodies. The free DNA-ends are visualized by anti-IdU and anti-mouse Alexa Fluor 488 antibodies. Scale bar = 10 μm. ( C ) Quantification of the IdU-signal intensity in the presence or absence of PARP inhibitor (PARPi). The irradiated areas are segmented by γH2AX signal in Hoechst positive nuclei and the average signal intensities of the background-subtracted IdU channel are measured. These average signal intensities are divided by the signal intensities of the corresponding nuclei and plotted.
Figure Legend Snippet: The accessibility of DNase I at sites of micropore irradiation is regulated by PAR-signaling. ( A ) Schematic representation of micropore irradiation assay. Cells are labeled with BrdU to photosensitize the DNA. After micropore irradiation (100 J/m 2 of UVC light) and fixation, chromatin is digested by DNase I. The generated free DNA-ends are labeled with IdU by Terminal Deoxynucleotidyl Transferase (TdT) and visualized by immunofluorescence. ( B ) Representative images of the IdU-signal 30 minutes post-micropore-irradiation to analyze the chromatin accessibility to DNase I in the presence or absence of PARP inhibitor (Olaparib). The microirradiation sites are visualized with anti-γH2AX and anti-rabbit Alexa Fluor 555 antibodies. The free DNA-ends are visualized by anti-IdU and anti-mouse Alexa Fluor 488 antibodies. Scale bar = 10 μm. ( C ) Quantification of the IdU-signal intensity in the presence or absence of PARP inhibitor (PARPi). The irradiated areas are segmented by γH2AX signal in Hoechst positive nuclei and the average signal intensities of the background-subtracted IdU channel are measured. These average signal intensities are divided by the signal intensities of the corresponding nuclei and plotted.

Techniques Used: Irradiation, Labeling, Generated, Immunofluorescence

13) Product Images from "Poly(ADP-ribose)-dependent chromatin unfolding facilitates the association of DNA-binding proteins with DNA at sites of damage"

Article Title: Poly(ADP-ribose)-dependent chromatin unfolding facilitates the association of DNA-binding proteins with DNA at sites of damage

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkz820

The accessibility of DNase I at sites of micropore irradiation is regulated by PAR-signaling. ( A ) Schematic representation of micropore irradiation assay. Cells are labeled with BrdU to photosensitize the DNA. After micropore irradiation (100 J/m 2 of UVC light) and fixation, chromatin is digested by DNase I. The generated free DNA-ends are labeled with IdU by Terminal Deoxynucleotidyl Transferase (TdT) and visualized by immunofluorescence. ( B ) Representative images of the IdU-signal 30 minutes post-micropore-irradiation to analyze the chromatin accessibility to DNase I in the presence or absence of PARP inhibitor (Olaparib). The microirradiation sites are visualized with anti-γH2AX and anti-rabbit Alexa Fluor 555 antibodies. The free DNA-ends are visualized by anti-IdU and anti-mouse Alexa Fluor 488 antibodies. Scale bar = 10 μm. ( C ) Quantification of the IdU-signal intensity in the presence or absence of PARP inhibitor (PARPi). The irradiated areas are segmented by γH2AX signal in Hoechst positive nuclei and the average signal intensities of the background-subtracted IdU channel are measured. These average signal intensities are divided by the signal intensities of the corresponding nuclei and plotted.
Figure Legend Snippet: The accessibility of DNase I at sites of micropore irradiation is regulated by PAR-signaling. ( A ) Schematic representation of micropore irradiation assay. Cells are labeled with BrdU to photosensitize the DNA. After micropore irradiation (100 J/m 2 of UVC light) and fixation, chromatin is digested by DNase I. The generated free DNA-ends are labeled with IdU by Terminal Deoxynucleotidyl Transferase (TdT) and visualized by immunofluorescence. ( B ) Representative images of the IdU-signal 30 minutes post-micropore-irradiation to analyze the chromatin accessibility to DNase I in the presence or absence of PARP inhibitor (Olaparib). The microirradiation sites are visualized with anti-γH2AX and anti-rabbit Alexa Fluor 555 antibodies. The free DNA-ends are visualized by anti-IdU and anti-mouse Alexa Fluor 488 antibodies. Scale bar = 10 μm. ( C ) Quantification of the IdU-signal intensity in the presence or absence of PARP inhibitor (PARPi). The irradiated areas are segmented by γH2AX signal in Hoechst positive nuclei and the average signal intensities of the background-subtracted IdU channel are measured. These average signal intensities are divided by the signal intensities of the corresponding nuclei and plotted.

Techniques Used: Irradiation, Labeling, Generated, Immunofluorescence

14) Product Images from "Activation of the Human Contact System on Neutrophil Extracellular Traps"

Article Title: Activation of the Human Contact System on Neutrophil Extracellular Traps

Journal: Journal of Innate Immunity

doi: 10.1159/000203700

NET formation after stimulating the PMNs with M1 protein/fibrinogen complexes. a, b PMNs were incubated with M1 protein/fibrinogen complexes for 60 min and investigated by light and scanning electron microscopy. c , d For light microscopy, the PMNs were stained with DAPI. As a control, the stimulated cells were treated with 200 mU DNase I for 30 min. Arrowheads point to PMNs. Scale bar = 10 μm.
Figure Legend Snippet: NET formation after stimulating the PMNs with M1 protein/fibrinogen complexes. a, b PMNs were incubated with M1 protein/fibrinogen complexes for 60 min and investigated by light and scanning electron microscopy. c , d For light microscopy, the PMNs were stained with DAPI. As a control, the stimulated cells were treated with 200 mU DNase I for 30 min. Arrowheads point to PMNs. Scale bar = 10 μm.

Techniques Used: Incubation, Electron Microscopy, Light Microscopy, Staining

NET-DNA binds contact system proteins, which is followed by activation of the contact system. a Light and scanning electron microscopy of nonactivated PMNs and PMNs activated with 100 mU/ml GO for 60 min. As a control, PMNs were incubated with 200 mU DNase I for 30 min after activation. Scale bar = 10 μm. b Transmission electron microscopy of nonactivated PMNs as well as PMNs stimulated with 100 mU/ml GO and incubated with gold-labeled HK (small gold particles) and FXII (larger gold particles). Scale bar = 1 μm. A higher magnification of 2 areas (marked with * and **) showing the binding of gold-labeled contact factors to NETs is shown on the lower right (Scale bar = 100 nm). Arrowheads point to gold-labeled proteins. PMNs incubated with 200 mU DNase I after stimulation and before adding to gold-labeled proteins are shown on the lower left. c PK activity after incubation of GO- and IL-8-stimulated PMNs in human plasma. Results shown are a representative of at least 3 experiments with PMNs from 3 different donors.
Figure Legend Snippet: NET-DNA binds contact system proteins, which is followed by activation of the contact system. a Light and scanning electron microscopy of nonactivated PMNs and PMNs activated with 100 mU/ml GO for 60 min. As a control, PMNs were incubated with 200 mU DNase I for 30 min after activation. Scale bar = 10 μm. b Transmission electron microscopy of nonactivated PMNs as well as PMNs stimulated with 100 mU/ml GO and incubated with gold-labeled HK (small gold particles) and FXII (larger gold particles). Scale bar = 1 μm. A higher magnification of 2 areas (marked with * and **) showing the binding of gold-labeled contact factors to NETs is shown on the lower right (Scale bar = 100 nm). Arrowheads point to gold-labeled proteins. PMNs incubated with 200 mU DNase I after stimulation and before adding to gold-labeled proteins are shown on the lower left. c PK activity after incubation of GO- and IL-8-stimulated PMNs in human plasma. Results shown are a representative of at least 3 experiments with PMNs from 3 different donors.

Techniques Used: Activation Assay, Electron Microscopy, Incubation, Transmission Assay, Labeling, Binding Assay, Activity Assay

Purified DNA binds and activates the contact system. a Transmission electron microscopy of negative-stained DNA (yellow pseudo color) HK (red pseudo color), FXII (green pseudo color) or a mixture of all 3 molecules. b Measurement of PK activity after incubation of plasma with purified DNA (10 μg/ml). As a control, DNA was pretreated with 200 mU DNase I for 30 min at 37°C before incubating in plasma. c BK release after incubation of DNA (10 or 100 μg/ml) and the DNase I-pretreated controls in human plasma for 15 min at 37°C. All Data represent the mean + SD (n = 3) of 1 representative of 3 independently performed experiments. ** p
Figure Legend Snippet: Purified DNA binds and activates the contact system. a Transmission electron microscopy of negative-stained DNA (yellow pseudo color) HK (red pseudo color), FXII (green pseudo color) or a mixture of all 3 molecules. b Measurement of PK activity after incubation of plasma with purified DNA (10 μg/ml). As a control, DNA was pretreated with 200 mU DNase I for 30 min at 37°C before incubating in plasma. c BK release after incubation of DNA (10 or 100 μg/ml) and the DNase I-pretreated controls in human plasma for 15 min at 37°C. All Data represent the mean + SD (n = 3) of 1 representative of 3 independently performed experiments. ** p

Techniques Used: Purification, Transmission Assay, Electron Microscopy, Staining, Activity Assay, Incubation

15) Product Images from "The Scope for Thalassemia Gene Therapy by Disruption of Aberrant Regulatory Elements"

Article Title: The Scope for Thalassemia Gene Therapy by Disruption of Aberrant Regulatory Elements

Journal: Journal of Clinical Medicine

doi: 10.3390/jcm8111959

DARE-based correction in humanized transgenic MEL- HBB IVS  bulk cell populations.  HBB -specific designer nucleases were applied in comparison to  CCR5 -specific designer nucleases and the  GLOBE  gene addition vector as a negative and positive reference, respectively, for HBB induction. ( a ) The T7 endonuclease I assay depicting  HBB IVSI-110(G > A) -targeted disruption in TALEN- (R1/L1 or R1/L2) and RGN-edited cells relative to nuclease-free, pUC118-transfected negative controls (pUC118). ( b ) TIDE analysis depicting  HBB IVSI-110(G > A) -targeted disruption efficiencies of TALEN- (R1/L1 or R1/L2) and RGN-edited cells relative to pUC118. Same-size indels events (-10 deletions to +10 insertions) are scored as a percentage of the total number of events. Significance cutoff was the TIDE default ( p  value
Figure Legend Snippet: DARE-based correction in humanized transgenic MEL- HBB IVS bulk cell populations. HBB -specific designer nucleases were applied in comparison to CCR5 -specific designer nucleases and the GLOBE gene addition vector as a negative and positive reference, respectively, for HBB induction. ( a ) The T7 endonuclease I assay depicting HBB IVSI-110(G > A) -targeted disruption in TALEN- (R1/L1 or R1/L2) and RGN-edited cells relative to nuclease-free, pUC118-transfected negative controls (pUC118). ( b ) TIDE analysis depicting HBB IVSI-110(G > A) -targeted disruption efficiencies of TALEN- (R1/L1 or R1/L2) and RGN-edited cells relative to pUC118. Same-size indels events (-10 deletions to +10 insertions) are scored as a percentage of the total number of events. Significance cutoff was the TIDE default ( p value

Techniques Used: Transgenic Assay, Plasmid Preparation, T7EI Assay, Transfection

16) Product Images from "A genomic selection strategy to identify accessible and dimerization blocking targets in the 5?-UTR of HIV-1 RNA"

Article Title: A genomic selection strategy to identify accessible and dimerization blocking targets in the 5?-UTR of HIV-1 RNA

Journal:

doi: 10.1093/nar/gnh064

Construction of the RNA library. A pUC18 plasmid containing the HIV-1(LAI) leader sequence (+1–355) was digested partially with DNase I to create random fragments. A double-stranded oligonucleotide, containing a T7 promoter, a specific
Figure Legend Snippet: Construction of the RNA library. A pUC18 plasmid containing the HIV-1(LAI) leader sequence (+1–355) was digested partially with DNase I to create random fragments. A double-stranded oligonucleotide, containing a T7 promoter, a specific

Techniques Used: Plasmid Preparation, Sequencing

Related Articles

Amplification:

Article Title: Crystal Structure of the Regulatory Domain of MexT, a Transcriptional Activator of the MexEF-OprN Efflux Pump in Pseudomonas aeruginosa
Article Snippet: DNase I footprinting assay A DNA fragment of 630 bp (the mexT -mexT intergenic region [230 bp] + 200 bp upstream + 200 bp downstream) was amplified using polymerase chain reaction (PCR) from P. aeruginosa chromosomal DNA. .. Next, 0.04 units of DNase I (Fermentas) was added, and the reaction mixture (10 mM Tris [pH 8.0], 50 mM KCl, 8 mM MgCl2 , 50 ng/μl BSA, 5% glycerol) was incubated for 2 min at room temperature.

Article Title: Benchmarking protocols for the metagenomic analysis of stream biofilm viromes
Article Snippet: Purification To eliminate contaminating eukaryotic, prokaryotic and extracellular nucleic acids, DNase I at a final concentration of 2.5 U/µL (Life Technologies, Darmstadt, Germany) and Tris buffer (100 mM Tris pH 7.5, five mM CaCl2 and 25 mM MgCl2 ) were added to the clarified supernatant and incubated at 37 °C (2 h). .. PCR amplification was performed with a Biometra Thermal Cycler using Taq ALLin polymerase (Axon Lab, Baden, Switzerland) according to the manufacturer’s instructions with an initial enzyme activation step (95 °C for 2 min) followed by 30 cycles of denaturation (95 °C for 30 s) and hybridization (72 °C for 30 s) and a final elongation (72 °C for 10 min).

Positive Control:

Article Title: Transcription and Activity of Digestive Enzymes of Nezara viridula Maintained on Different Plant Diets
Article Snippet: .. Positive control reactions were prepared using 1 μl of 1 U/μl DNase I or 10 μg/μl RNaseA (ThermoFisher), according to substrate. ..

Synthesized:

Article Title: Epitope mapping using mRNA display and a unidirectional nested deletion library
Article Snippet: To generate the fragment-library, first-strand cDNA from a selected library was synthesized with dUTP instead of dTTP nucleotides (Superscript II). .. After RNase H treatment (Roche) to remove mRNA, the cDNA was purified by spin-column (QIAquick, Qiagen) and randomly digested with DNase I (0.25 U DNase I (Invitrogen) added to 30 pmol cDNA (~1.2 µM final) in ice-cold 1 × DNase I buffer (10 mM Tris-HCl, pH 7.4, 2.5 mM MgCl2 , and 0.1 mM CaCl2 )) at 15 °C for 10 min. DNase I was removed using DNase Removal Reagent (Ambion).

Electrophoresis:

Article Title: Stable Complexes Formed by HIV-1 Reverse Transcriptase at Distinct Positions on the Primer-Template Controlled by Binding Deoxynucleoside Triphosphates or Foscarnet
Article Snippet: After incubation on ice for 5 min, 0.03 U DNase I (USB corp.), in RB buffer, was added and the samples were incubated at room temperature for 3 min. .. The samples were reheated for 4 min at 90°C and separated by electrophoresis through a 20% denaturing (8M urea) polyacrylamide gel, at 2000 V for 3-4 h in TTE buffer (90 mM Tris-HCl, 30 mM taurine, 0.5 mM EDTA).

Incubation:

Article Title: Crystal Structure of the Regulatory Domain of MexT, a Transcriptional Activator of the MexEF-OprN Efflux Pump in Pseudomonas aeruginosa
Article Snippet: .. Next, 0.04 units of DNase I (Fermentas) was added, and the reaction mixture (10 mM Tris [pH 8.0], 50 mM KCl, 8 mM MgCl2 , 50 ng/μl BSA, 5% glycerol) was incubated for 2 min at room temperature. ..

Article Title: Stable Complexes Formed by HIV-1 Reverse Transcriptase at Distinct Positions on the Primer-Template Controlled by Binding Deoxynucleoside Triphosphates or Foscarnet
Article Snippet: .. After incubation on ice for 5 min, 0.03 U DNase I (USB corp.), in RB buffer, was added and the samples were incubated at room temperature for 3 min. ..

Article Title: Benchmarking protocols for the metagenomic analysis of stream biofilm viromes
Article Snippet: .. Purification To eliminate contaminating eukaryotic, prokaryotic and extracellular nucleic acids, DNase I at a final concentration of 2.5 U/µL (Life Technologies, Darmstadt, Germany) and Tris buffer (100 mM Tris pH 7.5, five mM CaCl2 and 25 mM MgCl2 ) were added to the clarified supernatant and incubated at 37 °C (2 h). .. To confirm the removal of contaminant DNA, polymerase chain reaction (PCR) targeting the 16S rRNA gene was performed using the universal primer pair 341f (5′-CCTACGGGNGGCWGCAG-3′) and 785r (5′-GACTACHVGGGTATCTAAKCC-3′) ( ).

Article Title: Transcription and Activity of Digestive Enzymes of Nezara viridula Maintained on Different Plant Diets
Article Snippet: Reactions were incubated for 30 min at 37°C and then stopped with 300 μl of chilled 10% trichloroacetic acid in nuclease-free water, with 20 μM sodium pyrophosphate. .. Positive control reactions were prepared using 1 μl of 1 U/μl DNase I or 10 μg/μl RNaseA (ThermoFisher), according to substrate.

Article Title: Systematic Comparison and Validation of Quantitative Real-Time PCR Methods for the Quantitation of Adeno-Associated Viral Products
Article Snippet: .. Method A used a treatment protocol incorporating incubation with DNase I and proteinase K, that is, 5 μl of vector was treated with 50 units of DNase I (Life Technologies/Thermo Fisher Scientific) at 37°C for 1 hr to remove residual plasmid DNA in vector samples. .. After the inactivation of DNase I at 65°C for 10 min, proteinase K (0.4 unit) was then added and incubated at 50°C for 1 hr to release vector DNA from AAV capsids before being inactivated at 95°C for 20 min.

Article Title: Transcription and Activity of Digestive Enzymes of Nezara viridula Maintained on Different Plant Diets
Article Snippet: .. DNase I (ThermoFisher) was added to samples and incubated at 37°C for 10 min. EDTA was added to 20 mM and incubated 10 min at 65°C. .. Reactions were cleaned by precipitating with 100 μl of isopropanol, 5 μl of sodium acetate 3 M pH 5.2, and 2.5 μl of RNA grade glycogen and incubated overnight at −20°C.

Activity Assay:

Article Title: Transcription and Activity of Digestive Enzymes of Nezara viridula Maintained on Different Plant Diets
Article Snippet: To monitor nuclease activity, we measured the absorbance due to the release of free nucleotides from nucleic acid substrates ( ). .. Positive control reactions were prepared using 1 μl of 1 U/μl DNase I or 10 μg/μl RNaseA (ThermoFisher), according to substrate.

Modification:

Article Title: Poly(ADP-ribose)-dependent chromatin unfolding facilitates the association of DNA-binding proteins with DNA at sites of damage
Article Snippet: Micropore irradiation assay A modified protocol previously described by Suzuki et al. was established to quantify PARylation induced chromatin relaxation at sites of microirradiation ( ). .. Cells were fixed with 3% PFA at different time points post-irradiation, washed with 0.5% Triton X-100 in PBS for 10 min and then treated with 0.005 U/μl DNase I (Thermo Fisher Scientific) for 5 min.

Hybridization:

Article Title: Benchmarking protocols for the metagenomic analysis of stream biofilm viromes
Article Snippet: Purification To eliminate contaminating eukaryotic, prokaryotic and extracellular nucleic acids, DNase I at a final concentration of 2.5 U/µL (Life Technologies, Darmstadt, Germany) and Tris buffer (100 mM Tris pH 7.5, five mM CaCl2 and 25 mM MgCl2 ) were added to the clarified supernatant and incubated at 37 °C (2 h). .. PCR amplification was performed with a Biometra Thermal Cycler using Taq ALLin polymerase (Axon Lab, Baden, Switzerland) according to the manufacturer’s instructions with an initial enzyme activation step (95 °C for 2 min) followed by 30 cycles of denaturation (95 °C for 30 s) and hybridization (72 °C for 30 s) and a final elongation (72 °C for 10 min).

High Performance Liquid Chromatography:

Article Title: Systematic Comparison and Validation of Quantitative Real-Time PCR Methods for the Quantitation of Adeno-Associated Viral Products
Article Snippet: Method A used a treatment protocol incorporating incubation with DNase I and proteinase K, that is, 5 μl of vector was treated with 50 units of DNase I (Life Technologies/Thermo Fisher Scientific) at 37°C for 1 hr to remove residual plasmid DNA in vector samples. .. To test the efficiency of DNase I and proteinase K treatments, replicates of a crude sample (before HPLC) and HPLC-purified AAV sample were spiked with 1.25×10 copies of the AAV-independent plasmid pRRLSIN.cPPT.PGK-GFP.WPRE (plasmid 12252; Addgene, Cambridge, MA) encoding lentiviral vector sequences.

Activation Assay:

Article Title: Benchmarking protocols for the metagenomic analysis of stream biofilm viromes
Article Snippet: Purification To eliminate contaminating eukaryotic, prokaryotic and extracellular nucleic acids, DNase I at a final concentration of 2.5 U/µL (Life Technologies, Darmstadt, Germany) and Tris buffer (100 mM Tris pH 7.5, five mM CaCl2 and 25 mM MgCl2 ) were added to the clarified supernatant and incubated at 37 °C (2 h). .. PCR amplification was performed with a Biometra Thermal Cycler using Taq ALLin polymerase (Axon Lab, Baden, Switzerland) according to the manufacturer’s instructions with an initial enzyme activation step (95 °C for 2 min) followed by 30 cycles of denaturation (95 °C for 30 s) and hybridization (72 °C for 30 s) and a final elongation (72 °C for 10 min).

Footprinting:

Article Title: Crystal Structure of the Regulatory Domain of MexT, a Transcriptional Activator of the MexEF-OprN Efflux Pump in Pseudomonas aeruginosa
Article Snippet: Paragraph title: DNase I footprinting assay ... Next, 0.04 units of DNase I (Fermentas) was added, and the reaction mixture (10 mM Tris [pH 8.0], 50 mM KCl, 8 mM MgCl2 , 50 ng/μl BSA, 5% glycerol) was incubated for 2 min at room temperature.

Cell Culture:

Article Title: Poly(ADP-ribose)-dependent chromatin unfolding facilitates the association of DNA-binding proteins with DNA at sites of damage
Article Snippet: U2OS cells were cultured as described above and labeled with 50 μM 5-bromo-2′-deoxyuridine (BrdU; Sigma) for 24 h followed by 1 h treatment with 10 μM Olaparib (Selleckchem) or were left untreated prior to UV irradiation. .. Cells were fixed with 3% PFA at different time points post-irradiation, washed with 0.5% Triton X-100 in PBS for 10 min and then treated with 0.005 U/μl DNase I (Thermo Fisher Scientific) for 5 min.

other:

Article Title: Poly(ADP-ribose)-dependent chromatin unfolding facilitates the association of DNA-binding proteins with DNA at sites of damage
Article Snippet: Increased accessibility to DNase I at sites of DNA damage is promoted by PAR-signaling The sensitivity of chromatin to nuclease digestion, such as DNase I that non specifically cleaves DNA, is broadly used in genomics to evaluate DNA accessibility ( , ).

Inverted Microscopy:

Article Title: Poly(ADP-ribose)-dependent chromatin unfolding facilitates the association of DNA-binding proteins with DNA at sites of damage
Article Snippet: Cells were fixed with 3% PFA at different time points post-irradiation, washed with 0.5% Triton X-100 in PBS for 10 min and then treated with 0.005 U/μl DNase I (Thermo Fisher Scientific) for 5 min. .. Primary antibodies were detected using Alexa Fluor 488 conjugated goat anti-mouse IgG (Invitrogen, A21422 at 1:1000) and Alexa Fluor 555 conjugated goat anti-rabbit IgG (Invitrogen, A21428 at 1:1000). z-stacks of images were acquired using a Visitron spinning disk confocal system (Visitron systems GmBH) equipped with Yokogawa CSU-W1 spinning disk unit, Olympus IX83 inverted microscope (60× oil objective, NA 1.42), Andor Zyla 4.2 Plus camera, with 405, 488 and 561 nm lasers.

Polymerase Chain Reaction:

Article Title: Benchmarking protocols for the metagenomic analysis of stream biofilm viromes
Article Snippet: Purification To eliminate contaminating eukaryotic, prokaryotic and extracellular nucleic acids, DNase I at a final concentration of 2.5 U/µL (Life Technologies, Darmstadt, Germany) and Tris buffer (100 mM Tris pH 7.5, five mM CaCl2 and 25 mM MgCl2 ) were added to the clarified supernatant and incubated at 37 °C (2 h). .. To confirm the removal of contaminant DNA, polymerase chain reaction (PCR) targeting the 16S rRNA gene was performed using the universal primer pair 341f (5′-CCTACGGGNGGCWGCAG-3′) and 785r (5′-GACTACHVGGGTATCTAAKCC-3′) ( ).

Article Title: Complete, gene-specific siRNA libraries: Production and expression in mammalian cells
Article Snippet: .. PCR-amplified cDNA encoding DsRed was subjected to partial digestion with DNase I in a buffer containing 1 mM MnCl2 , 50 mM Tris-HCl (pH 7.5), 0.5 μg/μL BSA, and 0.1–0.3 U/μg DNase I (Ambion) at 20°C for 1–10 min to generate small, blunt-ended DNA fragments (Fig. 2A ). .. Under these conditions DNase I displays little sequence specificity, cleaving all regions of the DNA (except the terminal nucleotides) at an equal rate ( ).

Radioactivity:

Article Title: Stable Complexes Formed by HIV-1 Reverse Transcriptase at Distinct Positions on the Primer-Template Controlled by Binding Deoxynucleoside Triphosphates or Foscarnet
Article Snippet: After incubation on ice for 5 min, 0.03 U DNase I (USB corp.), in RB buffer, was added and the samples were incubated at room temperature for 3 min. .. The gels were dried and the radioactivity visualized by exposure on X-ray film and quantified by phosphorimaging.

Isolation:

Article Title: Complete, gene-specific siRNA libraries: Production and expression in mammalian cells
Article Snippet: PCR-amplified cDNA encoding DsRed was subjected to partial digestion with DNase I in a buffer containing 1 mM MnCl2 , 50 mM Tris-HCl (pH 7.5), 0.5 μg/μL BSA, and 0.1–0.3 U/μg DNase I (Ambion) at 20°C for 1–10 min to generate small, blunt-ended DNA fragments (Fig. 2A ). .. Aliquots were collected at various time points and quenched with an equal volume of loading buffer (95% formamide, 10 mM EDTA, 0.1% SDS) and DNA fragments corresponding to 20–30 bp were isolated by native 15% polyacrylamide gel.

Labeling:

Article Title: Stable Complexes Formed by HIV-1 Reverse Transcriptase at Distinct Positions on the Primer-Template Controlled by Binding Deoxynucleoside Triphosphates or Foscarnet
Article Snippet: Five fmoles of labeled P/T was incubated with 200 fmoles RT and the indicated amounts of dNTP in 10 μl RB buffer for 15 min at 37°C. .. After incubation on ice for 5 min, 0.03 U DNase I (USB corp.), in RB buffer, was added and the samples were incubated at room temperature for 3 min.

Article Title: Poly(ADP-ribose)-dependent chromatin unfolding facilitates the association of DNA-binding proteins with DNA at sites of damage
Article Snippet: U2OS cells were cultured as described above and labeled with 50 μM 5-bromo-2′-deoxyuridine (BrdU; Sigma) for 24 h followed by 1 h treatment with 10 μM Olaparib (Selleckchem) or were left untreated prior to UV irradiation. .. Cells were fixed with 3% PFA at different time points post-irradiation, washed with 0.5% Triton X-100 in PBS for 10 min and then treated with 0.005 U/μl DNase I (Thermo Fisher Scientific) for 5 min.

Purification:

Article Title: Crystal Structure of the Regulatory Domain of MexT, a Transcriptional Activator of the MexEF-OprN Efflux Pump in Pseudomonas aeruginosa
Article Snippet: We mixed 400 ng of DNA and 200 ng of purified FL MexT for 30 min at room temperature. .. Next, 0.04 units of DNase I (Fermentas) was added, and the reaction mixture (10 mM Tris [pH 8.0], 50 mM KCl, 8 mM MgCl2 , 50 ng/μl BSA, 5% glycerol) was incubated for 2 min at room temperature.

Article Title: Benchmarking protocols for the metagenomic analysis of stream biofilm viromes
Article Snippet: .. Purification To eliminate contaminating eukaryotic, prokaryotic and extracellular nucleic acids, DNase I at a final concentration of 2.5 U/µL (Life Technologies, Darmstadt, Germany) and Tris buffer (100 mM Tris pH 7.5, five mM CaCl2 and 25 mM MgCl2 ) were added to the clarified supernatant and incubated at 37 °C (2 h). .. To confirm the removal of contaminant DNA, polymerase chain reaction (PCR) targeting the 16S rRNA gene was performed using the universal primer pair 341f (5′-CCTACGGGNGGCWGCAG-3′) and 785r (5′-GACTACHVGGGTATCTAAKCC-3′) ( ).

Article Title: Systematic Comparison and Validation of Quantitative Real-Time PCR Methods for the Quantitation of Adeno-Associated Viral Products
Article Snippet: Viral genome extraction Two methods were used to extract AAV vector DNA from purified AAV vectors. .. Method A used a treatment protocol incorporating incubation with DNase I and proteinase K, that is, 5 μl of vector was treated with 50 units of DNase I (Life Technologies/Thermo Fisher Scientific) at 37°C for 1 hr to remove residual plasmid DNA in vector samples.

Article Title: Epitope mapping using mRNA display and a unidirectional nested deletion library
Article Snippet: .. After RNase H treatment (Roche) to remove mRNA, the cDNA was purified by spin-column (QIAquick, Qiagen) and randomly digested with DNase I (0.25 U DNase I (Invitrogen) added to 30 pmol cDNA (~1.2 µM final) in ice-cold 1 × DNase I buffer (10 mM Tris-HCl, pH 7.4, 2.5 mM MgCl2 , and 0.1 mM CaCl2 )) at 15 °C for 10 min. DNase I was removed using DNase Removal Reagent (Ambion). .. A fill-in reaction (Sequenase v2.0, Amersham Biosciences) was performed according to the manufacturer’s instructions with 125 pmol of myc6-N6-FP (5’-ATC TCT GAA GAG GAC CTG NNN NNN) and 200 µM of each dNTP (~0.6 µM cDNA final).

Article Title: Transcription and Activity of Digestive Enzymes of Nezara viridula Maintained on Different Plant Diets
Article Snippet: Paragraph title: Extraction, Purification, and Sequencing of mRNA ... DNase I (ThermoFisher) was added to samples and incubated at 37°C for 10 min. EDTA was added to 20 mM and incubated 10 min at 65°C.

Sequencing:

Article Title: Complete, gene-specific siRNA libraries: Production and expression in mammalian cells
Article Snippet: PCR-amplified cDNA encoding DsRed was subjected to partial digestion with DNase I in a buffer containing 1 mM MnCl2 , 50 mM Tris-HCl (pH 7.5), 0.5 μg/μL BSA, and 0.1–0.3 U/μg DNase I (Ambion) at 20°C for 1–10 min to generate small, blunt-ended DNA fragments (Fig. 2A ). .. Under these conditions DNase I displays little sequence specificity, cleaving all regions of the DNA (except the terminal nucleotides) at an equal rate ( ).

Article Title: Transcription and Activity of Digestive Enzymes of Nezara viridula Maintained on Different Plant Diets
Article Snippet: Paragraph title: Extraction, Purification, and Sequencing of mRNA ... DNase I (ThermoFisher) was added to samples and incubated at 37°C for 10 min. EDTA was added to 20 mM and incubated 10 min at 65°C.

Staining:

Article Title: Benchmarking protocols for the metagenomic analysis of stream biofilm viromes
Article Snippet: Purification To eliminate contaminating eukaryotic, prokaryotic and extracellular nucleic acids, DNase I at a final concentration of 2.5 U/µL (Life Technologies, Darmstadt, Germany) and Tris buffer (100 mM Tris pH 7.5, five mM CaCl2 and 25 mM MgCl2 ) were added to the clarified supernatant and incubated at 37 °C (2 h). .. PCR products were visualized under UV light after migration on an agarose gel stained using GelRed (Biotium, Hayward, CA, USA).

Plasmid Preparation:

Article Title: Systematic Comparison and Validation of Quantitative Real-Time PCR Methods for the Quantitation of Adeno-Associated Viral Products
Article Snippet: .. Method A used a treatment protocol incorporating incubation with DNase I and proteinase K, that is, 5 μl of vector was treated with 50 units of DNase I (Life Technologies/Thermo Fisher Scientific) at 37°C for 1 hr to remove residual plasmid DNA in vector samples. .. After the inactivation of DNase I at 65°C for 10 min, proteinase K (0.4 unit) was then added and incubated at 50°C for 1 hr to release vector DNA from AAV capsids before being inactivated at 95°C for 20 min.

Software:

Article Title: Crystal Structure of the Regulatory Domain of MexT, a Transcriptional Activator of the MexEF-OprN Efflux Pump in Pseudomonas aeruginosa
Article Snippet: Next, 0.04 units of DNase I (Fermentas) was added, and the reaction mixture (10 mM Tris [pH 8.0], 50 mM KCl, 8 mM MgCl2 , 50 ng/μl BSA, 5% glycerol) was incubated for 2 min at room temperature. .. The size distribution was scanned using Peak Scanner software (ver.

Irradiation:

Article Title: Poly(ADP-ribose)-dependent chromatin unfolding facilitates the association of DNA-binding proteins with DNA at sites of damage
Article Snippet: Paragraph title: Micropore irradiation assay ... Cells were fixed with 3% PFA at different time points post-irradiation, washed with 0.5% Triton X-100 in PBS for 10 min and then treated with 0.005 U/μl DNase I (Thermo Fisher Scientific) for 5 min.

Agarose Gel Electrophoresis:

Article Title: Benchmarking protocols for the metagenomic analysis of stream biofilm viromes
Article Snippet: Purification To eliminate contaminating eukaryotic, prokaryotic and extracellular nucleic acids, DNase I at a final concentration of 2.5 U/µL (Life Technologies, Darmstadt, Germany) and Tris buffer (100 mM Tris pH 7.5, five mM CaCl2 and 25 mM MgCl2 ) were added to the clarified supernatant and incubated at 37 °C (2 h). .. PCR products were visualized under UV light after migration on an agarose gel stained using GelRed (Biotium, Hayward, CA, USA).

Article Title: Epitope mapping using mRNA display and a unidirectional nested deletion library
Article Snippet: After RNase H treatment (Roche) to remove mRNA, the cDNA was purified by spin-column (QIAquick, Qiagen) and randomly digested with DNase I (0.25 U DNase I (Invitrogen) added to 30 pmol cDNA (~1.2 µM final) in ice-cold 1 × DNase I buffer (10 mM Tris-HCl, pH 7.4, 2.5 mM MgCl2 , and 0.1 mM CaCl2 )) at 15 °C for 10 min. DNase I was removed using DNase Removal Reagent (Ambion). .. First-strand cDNA was digested with uracil-DNA glycosylase (UDG) and ssDNA > 50 bases was extracted with QiaEX II (Qiagen) from a 4% agarose gel ( ).

Concentration Assay:

Article Title: Benchmarking protocols for the metagenomic analysis of stream biofilm viromes
Article Snippet: .. Purification To eliminate contaminating eukaryotic, prokaryotic and extracellular nucleic acids, DNase I at a final concentration of 2.5 U/µL (Life Technologies, Darmstadt, Germany) and Tris buffer (100 mM Tris pH 7.5, five mM CaCl2 and 25 mM MgCl2 ) were added to the clarified supernatant and incubated at 37 °C (2 h). .. To confirm the removal of contaminant DNA, polymerase chain reaction (PCR) targeting the 16S rRNA gene was performed using the universal primer pair 341f (5′-CCTACGGGNGGCWGCAG-3′) and 785r (5′-GACTACHVGGGTATCTAAKCC-3′) ( ).

Article Title: Transcription and Activity of Digestive Enzymes of Nezara viridula Maintained on Different Plant Diets
Article Snippet: DNase I (ThermoFisher) was added to samples and incubated at 37°C for 10 min. EDTA was added to 20 mM and incubated 10 min at 65°C. .. The final pellet was resuspended in nuclease-free water, with concentration determined by Nanodrop.

Migration:

Article Title: Benchmarking protocols for the metagenomic analysis of stream biofilm viromes
Article Snippet: Purification To eliminate contaminating eukaryotic, prokaryotic and extracellular nucleic acids, DNase I at a final concentration of 2.5 U/µL (Life Technologies, Darmstadt, Germany) and Tris buffer (100 mM Tris pH 7.5, five mM CaCl2 and 25 mM MgCl2 ) were added to the clarified supernatant and incubated at 37 °C (2 h). .. PCR products were visualized under UV light after migration on an agarose gel stained using GelRed (Biotium, Hayward, CA, USA).

CTG Assay:

Article Title: Epitope mapping using mRNA display and a unidirectional nested deletion library
Article Snippet: After RNase H treatment (Roche) to remove mRNA, the cDNA was purified by spin-column (QIAquick, Qiagen) and randomly digested with DNase I (0.25 U DNase I (Invitrogen) added to 30 pmol cDNA (~1.2 µM final) in ice-cold 1 × DNase I buffer (10 mM Tris-HCl, pH 7.4, 2.5 mM MgCl2 , and 0.1 mM CaCl2 )) at 15 °C for 10 min. DNase I was removed using DNase Removal Reagent (Ambion). .. A fill-in reaction (Sequenase v2.0, Amersham Biosciences) was performed according to the manufacturer’s instructions with 125 pmol of myc6-N6-FP (5’-ATC TCT GAA GAG GAC CTG NNN NNN) and 200 µM of each dNTP (~0.6 µM cDNA final).

Lysis:

Article Title: Transcription and Activity of Digestive Enzymes of Nezara viridula Maintained on Different Plant Diets
Article Snippet: All RNAlater was removed from tissue samples, and then 600 μl of lysis buffer with β-mercaptoethanol was added. .. DNase I (ThermoFisher) was added to samples and incubated at 37°C for 10 min. EDTA was added to 20 mM and incubated 10 min at 65°C.

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  • 99
    Thermo Fisher dnase i
    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
    Dnase I, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 46 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 46 article reviews
    Price from $9.99 to $1999.99
    dnase i - by Bioz Stars, 2020-04
    99/100 stars
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    93
    Thermo Fisher human dnase i
    Enzymatic resistance of phosphorothioate-modified Au-TDNNs. (A, B) Fluorescence time graph depicting terminal-modified Au-TDNN and overall-modified Au-TDNN degradation by DNase I. (C, D) Fluorescence time graph depicting terminal-modified Au-TDNN and overall-modified Au-TDNN degradation by Exo III.
    Human Dnase I, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/human dnase i/product/Thermo Fisher
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    Price from $9.99 to $1999.99
    human dnase i - by Bioz Stars, 2020-04
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    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

    Agarose gel electrophoresis of CO 3 Ap/pDNA complexes at different concentrations of CO 3 Ap following DNase I treatment. Lane 1: 1 kb DNA ladder; Lane 2: 1 µ g super coiled pDNA; Lane 3: Naked pDNA; Lane 4: CO 3 Ap (4 µ L)/pDNA; Lane 5: CO 3 Ap (5 µ L)/pDNA; Lane 6: CO 3 Ap (6 µ L)/pDNA; Lane 7: CO 3 Ap (7 µ L)/pDNA; and Lane 8: CO 3 Ap (8 µ L)/pDNA. All the formulations were prepared in serum-free media and the respective formulations were run on 0.8% agarose gel for 45 min at 75 V.

    Journal: BioMed Research International

    Article Title: Gene Delivery Potential of Biofunctional Carbonate Apatite Nanoparticles in Lungs

    doi: 10.1155/2014/646787

    Figure Lengend Snippet: Agarose gel electrophoresis of CO 3 Ap/pDNA complexes at different concentrations of CO 3 Ap following DNase I treatment. Lane 1: 1 kb DNA ladder; Lane 2: 1 µ g super coiled pDNA; Lane 3: Naked pDNA; Lane 4: CO 3 Ap (4 µ L)/pDNA; Lane 5: CO 3 Ap (5 µ L)/pDNA; Lane 6: CO 3 Ap (6 µ L)/pDNA; Lane 7: CO 3 Ap (7 µ L)/pDNA; and Lane 8: CO 3 Ap (8 µ L)/pDNA. All the formulations were prepared in serum-free media and the respective formulations were run on 0.8% agarose gel for 45 min at 75 V.

    Article Snippet: To mimic the conducting airway system environment having a variety of nuclease activities, CO3 Ap/pDNA complexes prepared with different concentrations of CaCl2 were treated with DNase I.

    Techniques: Agarose Gel Electrophoresis

    Autorepression of graTA promoter by GraA. (A) β-Galactosidase activities measured in P. putida wild-type (WT) and graTA deletion strains carrying the transcriptional fusion of the graTA promoter with lacZ in plasmid p9TT1586. Bacteria were grown overnight in LB medium at 30°C. Data (means with 95% confidence intervals) of at least three independent experiments are presented. (B) Promoter region of graTA . The −10 and −35 elements of the promoter are boxed, the transcriptional start site is indicated by a black arrow, and the ATG of graT is underlined. Brackets indicate the regions protected by DNase I cleavage by binding of GraA, and the asterisk marks a hypersensitive cleavage site. The palindromic sequences of GraA binding site are designated by gray arrows. (C) DNase I footprint analysis for determining GraA and GraT-GraA binding sites in the graTA promoter region. Footprints on the upper strand of the promoter region are presented. Lane 0 represents the DNase I reaction carried out in the absence of TA proteins. Other lanes represent reactions which contain increasing amounts (in pmol) of either the GraA-His or the His-GraT+GraA complex. The line on the right designates the region of protection against DNase I cleavage, and the asterisk signifies a base which becomes hypersensitive to DNase I cleavage upon the formation of the DNA complex with TA protein.

    Journal: Journal of Bacteriology

    Article Title: A Moderate Toxin, GraT, Modulates Growth Rate and Stress Tolerance of Pseudomonas putida

    doi: 10.1128/JB.00851-13

    Figure Lengend Snippet: Autorepression of graTA promoter by GraA. (A) β-Galactosidase activities measured in P. putida wild-type (WT) and graTA deletion strains carrying the transcriptional fusion of the graTA promoter with lacZ in plasmid p9TT1586. Bacteria were grown overnight in LB medium at 30°C. Data (means with 95% confidence intervals) of at least three independent experiments are presented. (B) Promoter region of graTA . The −10 and −35 elements of the promoter are boxed, the transcriptional start site is indicated by a black arrow, and the ATG of graT is underlined. Brackets indicate the regions protected by DNase I cleavage by binding of GraA, and the asterisk marks a hypersensitive cleavage site. The palindromic sequences of GraA binding site are designated by gray arrows. (C) DNase I footprint analysis for determining GraA and GraT-GraA binding sites in the graTA promoter region. Footprints on the upper strand of the promoter region are presented. Lane 0 represents the DNase I reaction carried out in the absence of TA proteins. Other lanes represent reactions which contain increasing amounts (in pmol) of either the GraA-His or the His-GraT+GraA complex. The line on the right designates the region of protection against DNase I cleavage, and the asterisk signifies a base which becomes hypersensitive to DNase I cleavage upon the formation of the DNA complex with TA protein.

    Article Snippet: Proteins were allowed to bind to DNA during 30 min at room temperature before the start of digestion by DNase I (0.06 U; Thermo Scientific) for 3 min.

    Techniques: Plasmid Preparation, Binding Assay

    Enzymatic resistance of phosphorothioate-modified Au-TDNNs. (A, B) Fluorescence time graph depicting terminal-modified Au-TDNN and overall-modified Au-TDNN degradation by DNase I. (C, D) Fluorescence time graph depicting terminal-modified Au-TDNN and overall-modified Au-TDNN degradation by Exo III.

    Journal: Theranostics

    Article Title: High-Discrimination Factor Nanosensor Based on Tetrahedral DNA Nanostructures and Gold Nanoparticles for Detection of MiRNA-21 in Live Cells

    doi: 10.7150/thno.23852

    Figure Lengend Snippet: Enzymatic resistance of phosphorothioate-modified Au-TDNNs. (A, B) Fluorescence time graph depicting terminal-modified Au-TDNN and overall-modified Au-TDNN degradation by DNase I. (C, D) Fluorescence time graph depicting terminal-modified Au-TDNN and overall-modified Au-TDNN degradation by Exo III.

    Article Snippet: For both human DNase I (Thermo Scientific) and exonuclease III (New England Biolabs) digestion, a common concentration of 3 U/mL was used to digest 2 nM Au-TDNNs samples in PBS.

    Techniques: Modification, Fluorescence