Structured Review

New England Biolabs hogg1
AhR-dependent DNA strand breaks and 8-oxo-dGuo formation in Hepa cells-treated with B[ a ]P-7,8-dione. A , B[ a ]P-7,8-dione-mediated DNA strand breaks in Hepa cells. AhR-deficient Hepa1c1c12 cells, ARNT-deficient Hepa1c1c4, and their wild type Hepa1c1c7 cells were treated with 20 μ m B[ a ]P-7,8-dione for 6 h. The cells were harvested and used for the detection of DNA strand breaks by the <t>hOGG1-coupled</t> comet assay. Significant effects were observed at different incubation times and after hOGG1 treatment following B[ a ]P-7,8-dione treatment. Significant effects were also observed between AhR-deficient Hepa1c1c12 cells and ARNT-deficient Hepa 1c1c4 cells and their wild type Hepa 1c1c7 cells. *, p < 0.05. B , LC/MS detection of 8-oxo-dGuo in Hepa cells-treated with B[ a ]P-7,8-dione. Significant effects were observed again when AhR-deficient Hepa1c1c12 cells were compared with ARNT-deficient Hepa 1c1c4 cells and wild type Hepa 1c1c7 cells. *, p < 0.05. AU , arbitrary units.
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Images

1) Product Images from "Aryl Hydrocarbon Receptor Facilitates DNA Strand Breaks and 8-Oxo-2?-deoxyguanosine Formation by the Aldo-Keto Reductase Product Benzo[a]pyrene-7,8-dione"

Article Title: Aryl Hydrocarbon Receptor Facilitates DNA Strand Breaks and 8-Oxo-2?-deoxyguanosine Formation by the Aldo-Keto Reductase Product Benzo[a]pyrene-7,8-dione

Journal:

doi: 10.1074/jbc.M109.042143

AhR-dependent DNA strand breaks and 8-oxo-dGuo formation in Hepa cells-treated with B[ a ]P-7,8-dione. A , B[ a ]P-7,8-dione-mediated DNA strand breaks in Hepa cells. AhR-deficient Hepa1c1c12 cells, ARNT-deficient Hepa1c1c4, and their wild type Hepa1c1c7 cells were treated with 20 μ m B[ a ]P-7,8-dione for 6 h. The cells were harvested and used for the detection of DNA strand breaks by the hOGG1-coupled comet assay. Significant effects were observed at different incubation times and after hOGG1 treatment following B[ a ]P-7,8-dione treatment. Significant effects were also observed between AhR-deficient Hepa1c1c12 cells and ARNT-deficient Hepa 1c1c4 cells and their wild type Hepa 1c1c7 cells. *, p < 0.05. B , LC/MS detection of 8-oxo-dGuo in Hepa cells-treated with B[ a ]P-7,8-dione. Significant effects were observed again when AhR-deficient Hepa1c1c12 cells were compared with ARNT-deficient Hepa 1c1c4 cells and wild type Hepa 1c1c7 cells. *, p < 0.05. AU , arbitrary units.
Figure Legend Snippet: AhR-dependent DNA strand breaks and 8-oxo-dGuo formation in Hepa cells-treated with B[ a ]P-7,8-dione. A , B[ a ]P-7,8-dione-mediated DNA strand breaks in Hepa cells. AhR-deficient Hepa1c1c12 cells, ARNT-deficient Hepa1c1c4, and their wild type Hepa1c1c7 cells were treated with 20 μ m B[ a ]P-7,8-dione for 6 h. The cells were harvested and used for the detection of DNA strand breaks by the hOGG1-coupled comet assay. Significant effects were observed at different incubation times and after hOGG1 treatment following B[ a ]P-7,8-dione treatment. Significant effects were also observed between AhR-deficient Hepa1c1c12 cells and ARNT-deficient Hepa 1c1c4 cells and their wild type Hepa 1c1c7 cells. *, p < 0.05. B , LC/MS detection of 8-oxo-dGuo in Hepa cells-treated with B[ a ]P-7,8-dione. Significant effects were observed again when AhR-deficient Hepa1c1c12 cells were compared with ARNT-deficient Hepa 1c1c4 cells and wild type Hepa 1c1c7 cells. *, p < 0.05. AU , arbitrary units.

Techniques Used: Single Cell Gel Electrophoresis, Incubation, Liquid Chromatography, Mass Spectrometry

Analysis of hOGG1-dependent DNA strand breaks in both KBrO3 -treated Hepa and H358 cells. Three Hepa cell sublines and H358 cells were treated with 2.5 m m of potassium bromate for 3 h. The cells were harvested and used for the detection of DNA strand breaks by hOGG1-coupled comet assay. A , Hepa cells. B , H358 cells. AU , arbitrary units.
Figure Legend Snippet: Analysis of hOGG1-dependent DNA strand breaks in both KBrO3 -treated Hepa and H358 cells. Three Hepa cell sublines and H358 cells were treated with 2.5 m m of potassium bromate for 3 h. The cells were harvested and used for the detection of DNA strand breaks by hOGG1-coupled comet assay. A , Hepa cells. B , H358 cells. AU , arbitrary units.

Techniques Used: Single Cell Gel Electrophoresis

2) Product Images from "Oligo swapping method for in vitro DNA repair substrate containing a single DNA lesion at a specific site"

Article Title: Oligo swapping method for in vitro DNA repair substrate containing a single DNA lesion at a specific site

Journal: Genes and Environment

doi: 10.1186/s41021-018-0112-5

Preparation of DNA template (8-oxoG substrate) with 8-oxoG at a defined position. a Upper strand sequence containing 8-oxoG base and lower strand substrate containing original C base in pBS2/8-oxoG are shown diagrammatically. b Experimental procedure for purification of pBS2/8-oxoG using 8-oxoG oligo. c Identified DNA substrates (100 ng), pBS2/8-oxoG, were incubated with Fpg (2 units) or hOGG1 (0.16 units) at 37 °C for 30 min. Aliquots from the sample were run on 0.8% agarose gel and visualized by staining with EtBr. Lane 1, 1-kbp marker; lane 2, non-treatment; lane 3, Fpg-treatment; lane 4, hOGGI-treatment. Open circular DNA (OC), liner DNA (Lin), and covalently closed circular DNA (CCC) are indicated by arrows
Figure Legend Snippet: Preparation of DNA template (8-oxoG substrate) with 8-oxoG at a defined position. a Upper strand sequence containing 8-oxoG base and lower strand substrate containing original C base in pBS2/8-oxoG are shown diagrammatically. b Experimental procedure for purification of pBS2/8-oxoG using 8-oxoG oligo. c Identified DNA substrates (100 ng), pBS2/8-oxoG, were incubated with Fpg (2 units) or hOGG1 (0.16 units) at 37 °C for 30 min. Aliquots from the sample were run on 0.8% agarose gel and visualized by staining with EtBr. Lane 1, 1-kbp marker; lane 2, non-treatment; lane 3, Fpg-treatment; lane 4, hOGGI-treatment. Open circular DNA (OC), liner DNA (Lin), and covalently closed circular DNA (CCC) are indicated by arrows

Techniques Used: Sequencing, Purification, Incubation, Agarose Gel Electrophoresis, Staining, Marker, Countercurrent Chromatography

3) Product Images from "The function of cux1 in oxidative dna damage repair is needed to prevent premature senescence of mouse embryo fibroblasts"

Article Title: The function of cux1 in oxidative dna damage repair is needed to prevent premature senescence of mouse embryo fibroblasts

Journal: Oncotarget

doi:

Sodium borohydride trapping of OGG1 enzyme in the presence of CR1CR2 5′-end-labeled 32-mer duplex containing an 8-oxoG was incubated with hOGG1 and CR1CR2 or BSA at the indicated concentrations. After incubation at 37°C, 50 mM sodium borohydride was added. The reactions were pursued for another 5 min at 37°C. After termination of the reaction, the trapped complexes were separated from free substrate by 10% SDS-PAGE gel.
Figure Legend Snippet: Sodium borohydride trapping of OGG1 enzyme in the presence of CR1CR2 5′-end-labeled 32-mer duplex containing an 8-oxoG was incubated with hOGG1 and CR1CR2 or BSA at the indicated concentrations. After incubation at 37°C, 50 mM sodium borohydride was added. The reactions were pursued for another 5 min at 37°C. After termination of the reaction, the trapped complexes were separated from free substrate by 10% SDS-PAGE gel.

Techniques Used: Labeling, Incubation, SDS Page

4) Product Images from "The function of cux1 in oxidative dna damage repair is needed to prevent premature senescence of mouse embryo fibroblasts"

Article Title: The function of cux1 in oxidative dna damage repair is needed to prevent premature senescence of mouse embryo fibroblasts

Journal: Oncotarget

doi:

Sodium borohydride trapping of OGG1 enzyme in the presence of CR1CR2 5′-end-labeled 32-mer duplex containing an 8-oxoG was incubated with hOGG1 and CR1CR2 or BSA at the indicated concentrations. After incubation at 37°C, 50 mM sodium borohydride was added. The reactions were pursued for another 5 min at 37°C. After termination of the reaction, the trapped complexes were separated from free substrate by 10% SDS-PAGE gel.
Figure Legend Snippet: Sodium borohydride trapping of OGG1 enzyme in the presence of CR1CR2 5′-end-labeled 32-mer duplex containing an 8-oxoG was incubated with hOGG1 and CR1CR2 or BSA at the indicated concentrations. After incubation at 37°C, 50 mM sodium borohydride was added. The reactions were pursued for another 5 min at 37°C. After termination of the reaction, the trapped complexes were separated from free substrate by 10% SDS-PAGE gel.

Techniques Used: Labeling, Incubation, SDS Page

Related Articles

Clone Assay:

Article Title: Special AT-rich Sequence-binding Protein 1 (SATB1) Functions as an Accessory Factor in Base Excision Repair
Article Snippet: 280 , 40544–40551 [ ] 9. .. Radicella J. P., Dherin C., Desmaze C., Fox M. S., and Boiteux S. (1997) Cloning and characterization of hOGG1, a human homolog of the OGG1 gene of Saccharomyces cerevisiae . .. Natl.

Article Title: CHD4 Has Oncogenic Functions in Initiating and Maintaining Epigenetic Suppression of Multiple Tumor Suppressor Genes
Article Snippet: EMBO J. .. [ ] [ ] Radicella JP, Dherin C, Desmaze C, Fox MS, Boiteux S. Cloning and characterization of hOGG1, a human homolog of the OGG1 gene of Saccharomyces cerevisiae . .. Proc Natl Acad Sci USA.

Centrifugation:

Article Title: CHD4 Has Oncogenic Functions in Initiating and Maintaining Epigenetic Suppression of Multiple Tumor Suppressor Genes
Article Snippet: The total nuclear pellet was resuspended in modified RIPA buffer (50 mM Tris PH 7.5, 100 mM NaCl, 3 mM EDTA, 0.5% NP-40, 50 mMNaF), sonicated for three cycles of 30 s using a BioruptorPicosonicator (Diagenode), rotated at 4 °C for 1 hr with 60mM spermine and 20mMspermidine to release chromatin bound proteins, sonicated for two cycles of 30 s, and cleared by high-speed centrifugation. .. Purified recombinant hCHD4 and hOGG1 (M0241, NEB) proteins were incubated in IP buffer (50 mM Tris-HCl pH 8.0, 100 mM NaCl, 5 mM MgCl2 , 1% NP-40) with or without 8-OHdG oligonucleotides (double strand) at 4 °C for overnight, followed by co-precipitation using anti-flag M2 beads (M8823, Sigma) or protein A/G agarose (sc-2003, Santa Cruz) using antibodies against Flag (ab49763, Abcam) or OGG1 (sc-376935, Santa Cruz).

Nucleic Acid Electrophoresis:

Article Title: Characterization of DNA glycosylase activity by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
Article Snippet: Paragraph title: Enzymatic reactions analyzed by gel electrophoresis ... UNG (uracil-DNA glycosylase, E. coli ), Fpg (formamidopyrimidine DNA glycosylase, E. coli ), Nth (Endonuclease III, E. coli ) and hOGG1 (human oxoguanine glycosylase 1) were purchased from New England Biolabs (Beverly, MA).

Synthesized:

Article Title: Aryl Hydrocarbon Receptor Facilitates DNA Strand Breaks and 8-Oxo-2?-deoxyguanosine Formation by the Aldo-Keto Reductase Product Benzo[a]pyrene-7,8-dione
Article Snippet: (±)-B[ a ]P-7,8-dione was synthesized according to published methods ( ). .. HiPerFect transfection reagent was acquired from Qiagen. hOGG1 was obtained from New England BioLabs Inc. (Beverly, MA).

Autoradiography:

Article Title: Apex1 can cleave complex clustered DNA lesions in cells
Article Snippet: Duplex substrate was diluted to 10 fmol/ µl using 10 mM Tris pH8, 50 mM NaCl, and 1 µl used in a 5 µl reaction with either 0.03 units endonuclease IV (Trevigen, Gaithersburg, MD), 0.5 units Fpg (NEB, Beverly, MA, USA), 0.05–0.2 units hApe1 (Trevigen, Gaithersburg, MD), 0.25 or 0.5 units hOgg1 (NEB, Beverly, MA, USA), or 100 or 200 ng nuclear extract in 45 mM HEPES, pH 7.8, 70 mM KCl, 1 mM DTT, 2.5 mM MgCl2 . .. Duplex substrate was diluted to 10 fmol/ µl using 10 mM Tris pH8, 50 mM NaCl, and 1 µl used in a 5 µl reaction with either 0.03 units endonuclease IV (Trevigen, Gaithersburg, MD), 0.5 units Fpg (NEB, Beverly, MA, USA), 0.05–0.2 units hApe1 (Trevigen, Gaithersburg, MD), 0.25 or 0.5 units hOgg1 (NEB, Beverly, MA, USA), or 100 or 200 ng nuclear extract in 45 mM HEPES, pH 7.8, 70 mM KCl, 1 mM DTT, 2.5 mM MgCl2 .

Electrophoresis:

Article Title: IL-13 Overexpression in Mouse Lungs Triggers Systemic Genotoxicity in Peripheral Blood
Article Snippet: After 20 minutes in the electrophoresis buffer at 4°C, the gel was run for 45 minutes at 300 mA, allowed to dry and then stained with SYBR Gold (Molecular Probes). .. To measure oxidative DNA damage, the comet assay was modified to include an incubation step with hOGG1 (New England Biolabs, Ipswich, MA).

Article Title: Effects of side-stream tobacco smoke and smoke extract on glutathione- and oxidative DNA damage repair-deficient mice and blood cells
Article Snippet: After 20 minutes in the electrophoresis buffer at 4°C, the gel was run for 45 minutes at 300 mA, allowed to dry and then stained with SYBR Gold (Molecular Probes). .. To measure oxidative DNA damage, the comet assay was modified to include an incubation step with hOGG1 (New England Biolabs, Ipswich, MA).

Article Title: Apex1 can cleave complex clustered DNA lesions in cells
Article Snippet: Duplex substrate was diluted to 10 fmol/ µl using 10 mM Tris pH8, 50 mM NaCl, and 1 µl used in a 5 µl reaction with either 0.03 units endonuclease IV (Trevigen, Gaithersburg, MD), 0.5 units Fpg (NEB, Beverly, MA, USA), 0.05–0.2 units hApe1 (Trevigen, Gaithersburg, MD), 0.25 or 0.5 units hOgg1 (NEB, Beverly, MA, USA), or 100 or 200 ng nuclear extract in 45 mM HEPES, pH 7.8, 70 mM KCl, 1 mM DTT, 2.5 mM MgCl2 . .. All reactions were incubated at 37°C for 1–60 minutes and stopped by the addition of 5 µl 95% formamide, 20 mM EDTA, 0.05% bromophenol blue, 0.05% xylene cyanol FF.

Incubation:

Article Title: The function of cux1 in oxidative dna damage repair is needed to prevent premature senescence of mouse embryo fibroblasts
Article Snippet: 50 nM of bacterially purified proteins were used in the reaction together with 60 ng of poly(dI-dC) as a nonspecific competitor DNA. .. 5′-end-labeled 32-mer duplex containing a 8-oxoG (50 nM) was incubated with hOGG1, and CR1CR2 or BSA at the indicated concentrations. .. After incubation at 37°C for 30 mins, 50 mM sodium borohydride was added and the reactions were pursued for another 15 min at 37°C.

Article Title: Special AT-rich Sequence-binding Protein 1 (SATB1) Functions as an Accessory Factor in Base Excision Repair
Article Snippet: The samples were washed five times and separated by SDS-PAGE, followed by immunoblotting with anti-His antibody (Sigma). .. 5′ end-labeled 32-mer duplex containing an 8-oxoG (50 n m ) was incubated with hOGG1 (New England Biolabs) and SATB1 or BSA at the indicated concentrations. .. After incubation at 37 °C for 30 min, 50 m m sodium borohydride was added, and the reactions were pursued for another 15 min at 37 °C.

Article Title: Characterization of DNA glycosylase activity by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
Article Snippet: UNG (uracil-DNA glycosylase, E. coli ), Fpg (formamidopyrimidine DNA glycosylase, E. coli ), Nth (Endonuclease III, E. coli ) and hOGG1 (human oxoguanine glycosylase 1) were purchased from New England Biolabs (Beverly, MA). .. MUG (mispaired uracil-DNA glycosylase, E. coli ) and TDG (thymine DNA glycosylase, Methanobacterium thermoautotropicum ) were obtained from Trevigen (Gaithersburg, MD). hSMUG1 (single-strand selective monofunctional uracil-DNA glycosylase, human) was cloned and purified by our lab as described previously [ ].

Article Title: Solid-state nanopore analysis of diverse DNA base modifications using a modular enzymatic labeling process
Article Snippet: A custom 40 nt oligonucleotide with a 5′ FAM (sequence: TCA CGA CTA GTG TTA ACA TGT GCA CCT Go CA GAA TGA GAA T, where Go is oxoG) was annealed to a complementary sequence by mixing both at an equimolar ratio, incubating in deionized water at 95°C for 10 minutes, and cooling to room temperature over 1 hour. .. To excise oxoG, a 30 μL aliquot was prepared containing 100 pmol of duplex, 6.5 U hOGG1 (New England Biolabs), 40 U EndoIV, 3 μg BSA, and incubated in 1X NEB2 buffer at 37°C for 1 hr. .. Next, 1.5 nmol of biotinylated dGTP (Perkin Elmer) and 0.12 U T4(exo-) were added to a final volume of 40 μL in 1X NEB2 buffer and the mixture was incubated at 37°C for 30 minutes.

Article Title: IL-13 Overexpression in Mouse Lungs Triggers Systemic Genotoxicity in Peripheral Blood
Article Snippet: Comet tail-moments were analyzed using CASP (Comet Assay Software Project, ). .. To measure oxidative DNA damage, the comet assay was modified to include an incubation step with hOGG1 (New England Biolabs, Ipswich, MA). .. As described previously, embedded cells were incubated with hOGG1 (1:300 in NEBuffer1 and BSA) at 37°C for 30 minutes following the lysis step [ ].

Article Title: Effects of side-stream tobacco smoke and smoke extract on glutathione- and oxidative DNA damage repair-deficient mice and blood cells
Article Snippet: Comet tail-moments were analyzed using CASP (Comet Assay Software Project, ). .. To measure oxidative DNA damage, the comet assay was modified to include an incubation step with hOGG1 (New England Biolabs, Ipswich, MA). .. As described previously, embedded cells were incubated with hOGG1 (1:300 in NEBuffer1 and BSA) at 37°C for 30 minutes following the lysis step ( ).

Article Title: Mycofumigation through production of the volatile DNA-methylating agent N-methyl-N-nitrosoisobutyramide by fungi in the genus Muscodor
Article Snippet: Controls included pUC19 samples that were either (i) untreated, (ii) incubated with a single DNA glycosylase, or (iii) incubated with APE1 alone. .. Nicked pUC19 controls were acquired by incubating pUC19 with Nt.BsmA1 in New England Biolabs Buffer 4 for 1 h at 37 °C. hAAG (10,000 units/ml), APE1 (10,000 units/ml), and hOGG1 (1600 units/ml) were purchased from New England Biolabs (Ipswich, MA).

Article Title: CHD4 Has Oncogenic Functions in Initiating and Maintaining Epigenetic Suppression of Multiple Tumor Suppressor Genes
Article Snippet: Complexes were eluted off the beads in loading buffer at 65 °C for 15 min. Recombinant Flag-tagged human CHD4 (hCHD4) protein was purified from HEK293 cells transfected with (full-length) Flag-hCHD4 plasmid. .. Purified recombinant hCHD4 and hOGG1 (M0241, NEB) proteins were incubated in IP buffer (50 mM Tris-HCl pH 8.0, 100 mM NaCl, 5 mM MgCl2 , 1% NP-40) with or without 8-OHdG oligonucleotides (double strand) at 4 °C for overnight, followed by co-precipitation using anti-flag M2 beads (M8823, Sigma) or protein A/G agarose (sc-2003, Santa Cruz) using antibodies against Flag (ab49763, Abcam) or OGG1 (sc-376935, Santa Cruz). .. The beads were washed five times using an IP buffer and the immunoprecipitated proteins were analysed by Western blotting.

Article Title: IL-13 Overexpression in Mouse Lungs Triggers Systemic Genotoxicity in Peripheral Blood
Article Snippet: To measure oxidative DNA damage, the comet assay was modified to include an incubation step with hOGG1 (New England Biolabs, Ipswich, MA). .. As described previously, embedded cells were incubated with hOGG1 (1:300 in NEBuffer1 and BSA) at 37°C for 30 minutes following the lysis step [ ]. .. Tail-moments were normalized to a control to account for inter-experimental variability.

Article Title: Effects of side-stream tobacco smoke and smoke extract on glutathione- and oxidative DNA damage repair-deficient mice and blood cells
Article Snippet: To measure oxidative DNA damage, the comet assay was modified to include an incubation step with hOGG1 (New England Biolabs, Ipswich, MA). .. As described previously, embedded cells were incubated with hOGG1 (1:300 in NEBuffer1 and BSA) at 37°C for 30 minutes following the lysis step ( ). .. Tail-moments were normalized to a control to account for inter-experimental variability.

Article Title: In Vitro Fluorogenic Real-time Assay of the Repair of Oxidative DNA Damage
Article Snippet: Fpg, hOGG1, Fpg reaction buffer (NEB buffer 1: 10 mM Bis-Tris-Propane-HCl, 10 mM MgCl2 , 1 mM dithiothreitol, pH 7.0 at 25 °C), hOGG1 reaction buffer (NEB buffer 4: 50 mM potassium acetate, 20 mM Tris-acetate, 10 mM magnesium acetate, 1 mM dithiothreitol, pH 7.9 at 25 °C), and BSA (10 mg/mL) were purchased from New England Biolabs. .. The fluorescence emission spectrum was measured before addition of probe to determine buffer fluorescence.

Article Title: Apex1 can cleave complex clustered DNA lesions in cells
Article Snippet: Duplex substrate was diluted to 10 fmol/ µl using 10 mM Tris pH8, 50 mM NaCl, and 1 µl used in a 5 µl reaction with either 0.03 units endonuclease IV (Trevigen, Gaithersburg, MD), 0.5 units Fpg (NEB, Beverly, MA, USA), 0.05–0.2 units hApe1 (Trevigen, Gaithersburg, MD), 0.25 or 0.5 units hOgg1 (NEB, Beverly, MA, USA), or 100 or 200 ng nuclear extract in 45 mM HEPES, pH 7.8, 70 mM KCl, 1 mM DTT, 2.5 mM MgCl2 . .. Duplex substrate was diluted to 10 fmol/ µl using 10 mM Tris pH8, 50 mM NaCl, and 1 µl used in a 5 µl reaction with either 0.03 units endonuclease IV (Trevigen, Gaithersburg, MD), 0.5 units Fpg (NEB, Beverly, MA, USA), 0.05–0.2 units hApe1 (Trevigen, Gaithersburg, MD), 0.25 or 0.5 units hOgg1 (NEB, Beverly, MA, USA), or 100 or 200 ng nuclear extract in 45 mM HEPES, pH 7.8, 70 mM KCl, 1 mM DTT, 2.5 mM MgCl2 .

Single Cell Gel Electrophoresis:

Article Title: IL-13 Overexpression in Mouse Lungs Triggers Systemic Genotoxicity in Peripheral Blood
Article Snippet: Comet tail-moments were analyzed using CASP (Comet Assay Software Project, ). .. To measure oxidative DNA damage, the comet assay was modified to include an incubation step with hOGG1 (New England Biolabs, Ipswich, MA). .. As described previously, embedded cells were incubated with hOGG1 (1:300 in NEBuffer1 and BSA) at 37°C for 30 minutes following the lysis step [ ].

Article Title: Effects of side-stream tobacco smoke and smoke extract on glutathione- and oxidative DNA damage repair-deficient mice and blood cells
Article Snippet: Comet tail-moments were analyzed using CASP (Comet Assay Software Project, ). .. To measure oxidative DNA damage, the comet assay was modified to include an incubation step with hOGG1 (New England Biolabs, Ipswich, MA). .. As described previously, embedded cells were incubated with hOGG1 (1:300 in NEBuffer1 and BSA) at 37°C for 30 minutes following the lysis step ( ).

Mass Spectrometry:

Article Title: CHD4 Has Oncogenic Functions in Initiating and Maintaining Epigenetic Suppression of Multiple Tumor Suppressor Genes
Article Snippet: EMBO J. .. [ ] [ ] Radicella JP, Dherin C, Desmaze C, Fox MS, Boiteux S. Cloning and characterization of hOGG1, a human homolog of the OGG1 gene of Saccharomyces cerevisiae . .. Proc Natl Acad Sci USA.

Modification:

Article Title: The function of cux1 in oxidative dna damage repair is needed to prevent premature senescence of mouse embryo fibroblasts
Article Snippet: Cleavage reactions with bacterially purified proteins were conducted using 50 nM hOGG1 (New England Biolabs, Ipswich, MA), and 50 nM of BSA or the indicated proteins, unless otherwise indicated, in 25 mM NaCl, 10 mM Tris (pH 7.5), 1 mM MgCl2 , 5 mM EDTA (pH 8.0), 5% glycerol, 1 mM of DTT and 1 pmol of 32 P-radiolabeled double-stranded oligonucleotides containing an 8-oxoG base ( ). .. Cleavage reactions with bacterially purified proteins were conducted using 50 nM hOGG1 (New England Biolabs, Ipswich, MA), and 50 nM of BSA or the indicated proteins, unless otherwise indicated, in 25 mM NaCl, 10 mM Tris (pH 7.5), 1 mM MgCl2 , 5 mM EDTA (pH 8.0), 5% glycerol, 1 mM of DTT and 1 pmol of 32 P-radiolabeled double-stranded oligonucleotides containing an 8-oxoG base ( ).

Article Title: Characterization of DNA glycosylase activity by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
Article Snippet: UNG (uracil-DNA glycosylase, E. coli ), Fpg (formamidopyrimidine DNA glycosylase, E. coli ), Nth (Endonuclease III, E. coli ) and hOGG1 (human oxoguanine glycosylase 1) were purchased from New England Biolabs (Beverly, MA). .. DNA substrates (500 fmol/reaction) were incubated with recombinant proteins (5 pmol/reaction, except for endoIII, which was at 500 fmol/reaction) for 2 hours at 37 °C in the reaction buffer depending on the enzyme buffer recommended by the manufacturer in 10 μl total volume.

Article Title: The DNA repair function of CUX1 contributes to radioresistance
Article Snippet: Cleavage reactions with bacterially purified proteins were conducted using 50 nM hOGG1 (New England Biolabs), and 200 nM of BSA, His-C1C2, His-C1 or His-C1-2Ala in 50 mM Tris (pH 7.1), 1 mM EDTA, and 20 mM KCl. .. In Figure , cleavage assay was performed in the presence of either vehicle (DMSO) or 10 μM of chemical molecules (Chembridge 5245457 and 5552704).

Article Title: IL-13 Overexpression in Mouse Lungs Triggers Systemic Genotoxicity in Peripheral Blood
Article Snippet: Comet tail-moments were analyzed using CASP (Comet Assay Software Project, ). .. To measure oxidative DNA damage, the comet assay was modified to include an incubation step with hOGG1 (New England Biolabs, Ipswich, MA). .. As described previously, embedded cells were incubated with hOGG1 (1:300 in NEBuffer1 and BSA) at 37°C for 30 minutes following the lysis step [ ].

Article Title: Effects of side-stream tobacco smoke and smoke extract on glutathione- and oxidative DNA damage repair-deficient mice and blood cells
Article Snippet: Comet tail-moments were analyzed using CASP (Comet Assay Software Project, ). .. To measure oxidative DNA damage, the comet assay was modified to include an incubation step with hOGG1 (New England Biolabs, Ipswich, MA). .. As described previously, embedded cells were incubated with hOGG1 (1:300 in NEBuffer1 and BSA) at 37°C for 30 minutes following the lysis step ( ).

Article Title: CHD4 Has Oncogenic Functions in Initiating and Maintaining Epigenetic Suppression of Multiple Tumor Suppressor Genes
Article Snippet: The total nuclear pellet was resuspended in modified RIPA buffer (50 mM Tris PH 7.5, 100 mM NaCl, 3 mM EDTA, 0.5% NP-40, 50 mMNaF), sonicated for three cycles of 30 s using a BioruptorPicosonicator (Diagenode), rotated at 4 °C for 1 hr with 60mM spermine and 20mMspermidine to release chromatin bound proteins, sonicated for two cycles of 30 s, and cleared by high-speed centrifugation. .. Purified recombinant hCHD4 and hOGG1 (M0241, NEB) proteins were incubated in IP buffer (50 mM Tris-HCl pH 8.0, 100 mM NaCl, 5 mM MgCl2 , 1% NP-40) with or without 8-OHdG oligonucleotides (double strand) at 4 °C for overnight, followed by co-precipitation using anti-flag M2 beads (M8823, Sigma) or protein A/G agarose (sc-2003, Santa Cruz) using antibodies against Flag (ab49763, Abcam) or OGG1 (sc-376935, Santa Cruz).

High Performance Liquid Chromatography:

Article Title: Aryl Hydrocarbon Receptor Facilitates DNA Strand Breaks and 8-Oxo-2?-deoxyguanosine Formation by the Aldo-Keto Reductase Product Benzo[a]pyrene-7,8-dione
Article Snippet: HiPerFect transfection reagent was acquired from Qiagen. hOGG1 was obtained from New England BioLabs Inc. (Beverly, MA). .. HiPerFect transfection reagent was acquired from Qiagen. hOGG1 was obtained from New England BioLabs Inc. (Beverly, MA).

Transfection:

Article Title: Aryl Hydrocarbon Receptor Facilitates DNA Strand Breaks and 8-Oxo-2?-deoxyguanosine Formation by the Aldo-Keto Reductase Product Benzo[a]pyrene-7,8-dione
Article Snippet: Cell culture media, reagents, and DNAzol BD were obtained from Invitrogen. .. HiPerFect transfection reagent was acquired from Qiagen. hOGG1 was obtained from New England BioLabs Inc. (Beverly, MA). .. Bovine pancreas DNase I was purchased from Calbiochem Co. (San Diego, CA), and phosphodiesterase I was acquired from Worthington (Lakewood, NJ).

Article Title: CHD4 Has Oncogenic Functions in Initiating and Maintaining Epigenetic Suppression of Multiple Tumor Suppressor Genes
Article Snippet: Complexes were eluted off the beads in loading buffer at 65 °C for 15 min. Recombinant Flag-tagged human CHD4 (hCHD4) protein was purified from HEK293 cells transfected with (full-length) Flag-hCHD4 plasmid. .. Purified recombinant hCHD4 and hOGG1 (M0241, NEB) proteins were incubated in IP buffer (50 mM Tris-HCl pH 8.0, 100 mM NaCl, 5 mM MgCl2 , 1% NP-40) with or without 8-OHdG oligonucleotides (double strand) at 4 °C for overnight, followed by co-precipitation using anti-flag M2 beads (M8823, Sigma) or protein A/G agarose (sc-2003, Santa Cruz) using antibodies against Flag (ab49763, Abcam) or OGG1 (sc-376935, Santa Cruz).

Cell Culture:

Article Title: Aryl Hydrocarbon Receptor Facilitates DNA Strand Breaks and 8-Oxo-2?-deoxyguanosine Formation by the Aldo-Keto Reductase Product Benzo[a]pyrene-7,8-dione
Article Snippet: Cell culture media, reagents, and DNAzol BD were obtained from Invitrogen. .. HiPerFect transfection reagent was acquired from Qiagen. hOGG1 was obtained from New England BioLabs Inc. (Beverly, MA).

other:

Article Title: Oligo swapping method for in vitro DNA repair substrate containing a single DNA lesion at a specific site
Article Snippet: Nt.Bbv CI nicking endonuclease, Eco NI, Fpg, hOGG1, UDG, APE1, and T5 exonuclease were purchased from New England Biolabs (Ipswich, MA, USA).

Imaging:

Article Title: Mycofumigation through production of the volatile DNA-methylating agent N-methyl-N-nitrosoisobutyramide by fungi in the genus Muscodor
Article Snippet: Samples were run on 1% agarose gels (Affymetrix) stained with ethidium bromide (Sigma) Gels were visualized with the Bio-Rad ChemiDoc MP imaging system. .. Nicked pUC19 controls were acquired by incubating pUC19 with Nt.BsmA1 in New England Biolabs Buffer 4 for 1 h at 37 °C. hAAG (10,000 units/ml), APE1 (10,000 units/ml), and hOGG1 (1600 units/ml) were purchased from New England Biolabs (Ipswich, MA).

Polymerase Chain Reaction:

Article Title: Solid-state nanopore analysis of diverse DNA base modifications using a modular enzymatic labeling process
Article Snippet: To excise oxoG, a 30 μL aliquot was prepared containing 100 pmol of duplex, 6.5 U hOGG1 (New England Biolabs), 40 U EndoIV, 3 μg BSA, and incubated in 1X NEB2 buffer at 37°C for 1 hr. .. Next, 1.5 nmol of biotinylated dGTP (Perkin Elmer) and 0.12 U T4(exo-) were added to a final volume of 40 μL in 1X NEB2 buffer and the mixture was incubated at 37°C for 30 minutes.

Sonication:

Article Title: CHD4 Has Oncogenic Functions in Initiating and Maintaining Epigenetic Suppression of Multiple Tumor Suppressor Genes
Article Snippet: The total nuclear pellet was resuspended in modified RIPA buffer (50 mM Tris PH 7.5, 100 mM NaCl, 3 mM EDTA, 0.5% NP-40, 50 mMNaF), sonicated for three cycles of 30 s using a BioruptorPicosonicator (Diagenode), rotated at 4 °C for 1 hr with 60mM spermine and 20mMspermidine to release chromatin bound proteins, sonicated for two cycles of 30 s, and cleared by high-speed centrifugation. .. Purified recombinant hCHD4 and hOGG1 (M0241, NEB) proteins were incubated in IP buffer (50 mM Tris-HCl pH 8.0, 100 mM NaCl, 5 mM MgCl2 , 1% NP-40) with or without 8-OHdG oligonucleotides (double strand) at 4 °C for overnight, followed by co-precipitation using anti-flag M2 beads (M8823, Sigma) or protein A/G agarose (sc-2003, Santa Cruz) using antibodies against Flag (ab49763, Abcam) or OGG1 (sc-376935, Santa Cruz).

Recombinant:

Article Title: Characterization of DNA glycosylase activity by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
Article Snippet: UNG (uracil-DNA glycosylase, E. coli ), Fpg (formamidopyrimidine DNA glycosylase, E. coli ), Nth (Endonuclease III, E. coli ) and hOGG1 (human oxoguanine glycosylase 1) were purchased from New England Biolabs (Beverly, MA). .. MUG (mispaired uracil-DNA glycosylase, E. coli ) and TDG (thymine DNA glycosylase, Methanobacterium thermoautotropicum ) were obtained from Trevigen (Gaithersburg, MD). hSMUG1 (single-strand selective monofunctional uracil-DNA glycosylase, human) was cloned and purified by our lab as described previously [ ].

Article Title: CHD4 Has Oncogenic Functions in Initiating and Maintaining Epigenetic Suppression of Multiple Tumor Suppressor Genes
Article Snippet: Complexes were eluted off the beads in loading buffer at 65 °C for 15 min. Recombinant Flag-tagged human CHD4 (hCHD4) protein was purified from HEK293 cells transfected with (full-length) Flag-hCHD4 plasmid. .. Purified recombinant hCHD4 and hOGG1 (M0241, NEB) proteins were incubated in IP buffer (50 mM Tris-HCl pH 8.0, 100 mM NaCl, 5 mM MgCl2 , 1% NP-40) with or without 8-OHdG oligonucleotides (double strand) at 4 °C for overnight, followed by co-precipitation using anti-flag M2 beads (M8823, Sigma) or protein A/G agarose (sc-2003, Santa Cruz) using antibodies against Flag (ab49763, Abcam) or OGG1 (sc-376935, Santa Cruz). .. The beads were washed five times using an IP buffer and the immunoprecipitated proteins were analysed by Western blotting.

Cleavage Assay:

Article Title: The function of cux1 in oxidative dna damage repair is needed to prevent premature senescence of mouse embryo fibroblasts
Article Snippet: Paragraph title: In vitro 8-oxoG cleavage assay ... Cleavage reactions with bacterially purified proteins were conducted using 50 nM hOGG1 (New England Biolabs, Ipswich, MA), and 50 nM of BSA or the indicated proteins, unless otherwise indicated, in 25 mM NaCl, 10 mM Tris (pH 7.5), 1 mM MgCl2 , 5 mM EDTA (pH 8.0), 5% glycerol, 1 mM of DTT and 1 pmol of 32 P-radiolabeled double-stranded oligonucleotides containing an 8-oxoG base ( ).

Article Title: The DNA repair function of CUX1 contributes to radioresistance
Article Snippet: Paragraph title: In vitro 8-oxoG fluorogenic cleavage assay ... Cleavage reactions with bacterially purified proteins were conducted using 50 nM hOGG1 (New England Biolabs), and 200 nM of BSA, His-C1C2, His-C1 or His-C1-2Ala in 50 mM Tris (pH 7.1), 1 mM EDTA, and 20 mM KCl.

MTT Assay:

Article Title: Dental methacrylates may exert genotoxic effects via the oxidative induction of DNA double strand breaks and the inhibition of their repair
Article Snippet: We used commonly recognized antioxidants, sodium ascorbate, a form of vitamin C and melatonin to assess the role of oxidative mechanisms in the induction of DSBs by the methacrylate monomers. .. HEMA (CAS 868-77-9), Bis-GMA (CAS 1565-94-2), gradisol and RNase A, low melting point (LMP) and normal melting point (NMP) agarose, phosphate buffered saline (PBS), DAPI (4′,6-diamidino-2-phenylindole), dimethyl sulfoxide (DMSO), fetal bovine serum (FBS), MTT, lectin, penicillin, streptomycin, sodium ascorbate, Bradford reagent were from Sigma Chemicals (St. Loius, MO, USA). hOGG1 was purchased from New England Biolabs (Herts, UK). .. Melatonin (5-methoxy-N -acetyltryptamine) was provided by R.J. Reiter of University of Texas Health Science Center.

Fluorescence:

Article Title: In Vitro Fluorogenic Real-time Assay of the Repair of Oxidative DNA Damage
Article Snippet: Paragraph title: Fluorescence analysis of in vitro enzymatic activity ... Fpg, hOGG1, Fpg reaction buffer (NEB buffer 1: 10 mM Bis-Tris-Propane-HCl, 10 mM MgCl2 , 1 mM dithiothreitol, pH 7.0 at 25 °C), hOGG1 reaction buffer (NEB buffer 4: 50 mM potassium acetate, 20 mM Tris-acetate, 10 mM magnesium acetate, 1 mM dithiothreitol, pH 7.9 at 25 °C), and BSA (10 mg/mL) were purchased from New England Biolabs.

Labeling:

Article Title: Solid-state nanopore analysis of diverse DNA base modifications using a modular enzymatic labeling process
Article Snippet: Paragraph title: OxoG labeling ... To excise oxoG, a 30 μL aliquot was prepared containing 100 pmol of duplex, 6.5 U hOGG1 (New England Biolabs), 40 U EndoIV, 3 μg BSA, and incubated in 1X NEB2 buffer at 37°C for 1 hr.

Article Title: Apex1 can cleave complex clustered DNA lesions in cells
Article Snippet: Duplex substrate was diluted to 10 fmol/ µl using 10 mM Tris pH8, 50 mM NaCl, and 1 µl used in a 5 µl reaction with either 0.03 units endonuclease IV (Trevigen, Gaithersburg, MD), 0.5 units Fpg (NEB, Beverly, MA, USA), 0.05–0.2 units hApe1 (Trevigen, Gaithersburg, MD), 0.25 or 0.5 units hOgg1 (NEB, Beverly, MA, USA), or 100 or 200 ng nuclear extract in 45 mM HEPES, pH 7.8, 70 mM KCl, 1 mM DTT, 2.5 mM MgCl2 . .. Duplex substrate was diluted to 10 fmol/ µl using 10 mM Tris pH8, 50 mM NaCl, and 1 µl used in a 5 µl reaction with either 0.03 units endonuclease IV (Trevigen, Gaithersburg, MD), 0.5 units Fpg (NEB, Beverly, MA, USA), 0.05–0.2 units hApe1 (Trevigen, Gaithersburg, MD), 0.25 or 0.5 units hOgg1 (NEB, Beverly, MA, USA), or 100 or 200 ng nuclear extract in 45 mM HEPES, pH 7.8, 70 mM KCl, 1 mM DTT, 2.5 mM MgCl2 .

Purification:

Article Title: The function of cux1 in oxidative dna damage repair is needed to prevent premature senescence of mouse embryo fibroblasts
Article Snippet: The samples were washed five times and separated by SDS-PAGE followed by immunoblotting with anti-OGG1 antibody. .. Cleavage reactions with bacterially purified proteins were conducted using 50 nM hOGG1 (New England Biolabs, Ipswich, MA), and 50 nM of BSA or the indicated proteins, unless otherwise indicated, in 25 mM NaCl, 10 mM Tris (pH 7.5), 1 mM MgCl2 , 5 mM EDTA (pH 8.0), 5% glycerol, 1 mM of DTT and 1 pmol of 32 P-radiolabeled double-stranded oligonucleotides containing an 8-oxoG base ( ). .. Note that when using his-tagged fusion proteins, it is important at the end of the purification to carry several buffer exchanges in order to reduce imidazole concentration.

Article Title: Solid-state nanopore analysis of diverse DNA base modifications using a modular enzymatic labeling process
Article Snippet: To excise oxoG, a 30 μL aliquot was prepared containing 100 pmol of duplex, 6.5 U hOGG1 (New England Biolabs), 40 U EndoIV, 3 μg BSA, and incubated in 1X NEB2 buffer at 37°C for 1 hr. .. Next, 1.5 nmol of biotinylated dGTP (Perkin Elmer) and 0.12 U T4(exo-) were added to a final volume of 40 μL in 1X NEB2 buffer and the mixture was incubated at 37°C for 30 minutes.

Article Title: The DNA repair function of CUX1 contributes to radioresistance
Article Snippet: Each time point was done in triplicate, and the averages ± standard deviations were calculated. .. Cleavage reactions with bacterially purified proteins were conducted using 50 nM hOGG1 (New England Biolabs), and 200 nM of BSA, His-C1C2, His-C1 or His-C1-2Ala in 50 mM Tris (pH 7.1), 1 mM EDTA, and 20 mM KCl. .. In Figure , cleavage assay was performed in the presence of either vehicle (DMSO) or 10 μM of chemical molecules (Chembridge 5245457 and 5552704).

Article Title: CHD4 Has Oncogenic Functions in Initiating and Maintaining Epigenetic Suppression of Multiple Tumor Suppressor Genes
Article Snippet: Complexes were eluted off the beads in loading buffer at 65 °C for 15 min. Recombinant Flag-tagged human CHD4 (hCHD4) protein was purified from HEK293 cells transfected with (full-length) Flag-hCHD4 plasmid. .. Purified recombinant hCHD4 and hOGG1 (M0241, NEB) proteins were incubated in IP buffer (50 mM Tris-HCl pH 8.0, 100 mM NaCl, 5 mM MgCl2 , 1% NP-40) with or without 8-OHdG oligonucleotides (double strand) at 4 °C for overnight, followed by co-precipitation using anti-flag M2 beads (M8823, Sigma) or protein A/G agarose (sc-2003, Santa Cruz) using antibodies against Flag (ab49763, Abcam) or OGG1 (sc-376935, Santa Cruz). .. The beads were washed five times using an IP buffer and the immunoprecipitated proteins were analysed by Western blotting.

Sequencing:

Article Title: Solid-state nanopore analysis of diverse DNA base modifications using a modular enzymatic labeling process
Article Snippet: A custom 40 nt oligonucleotide with a 5′ FAM (sequence: TCA CGA CTA GTG TTA ACA TGT GCA CCT Go CA GAA TGA GAA T, where Go is oxoG) was annealed to a complementary sequence by mixing both at an equimolar ratio, incubating in deionized water at 95°C for 10 minutes, and cooling to room temperature over 1 hour. .. To excise oxoG, a 30 μL aliquot was prepared containing 100 pmol of duplex, 6.5 U hOGG1 (New England Biolabs), 40 U EndoIV, 3 μg BSA, and incubated in 1X NEB2 buffer at 37°C for 1 hr.

Lysis:

Article Title: IL-13 Overexpression in Mouse Lungs Triggers Systemic Genotoxicity in Peripheral Blood
Article Snippet: The gel was immersed in lysis buffer (2.5 M NaCl, 0.1 M EDTA, 10 mM Tris, 1% Triton, and 10% DMSO), then alkaline electrophoresis buffer (0.3 M NaOH, 1 mM EDTA). .. To measure oxidative DNA damage, the comet assay was modified to include an incubation step with hOGG1 (New England Biolabs, Ipswich, MA).

Article Title: Effects of side-stream tobacco smoke and smoke extract on glutathione- and oxidative DNA damage repair-deficient mice and blood cells
Article Snippet: The gel was immerse in lysis buffer (2.5 M NaCl, 0.1 M EDTA, 10 mM Tris, 1% Triton, and 10% DMSO), then alkaline electrophoresis buffer (0.3 M NaOH, 1 mM EDTA). .. To measure oxidative DNA damage, the comet assay was modified to include an incubation step with hOGG1 (New England Biolabs, Ipswich, MA).

Article Title: IL-13 Overexpression in Mouse Lungs Triggers Systemic Genotoxicity in Peripheral Blood
Article Snippet: To measure oxidative DNA damage, the comet assay was modified to include an incubation step with hOGG1 (New England Biolabs, Ipswich, MA). .. As described previously, embedded cells were incubated with hOGG1 (1:300 in NEBuffer1 and BSA) at 37°C for 30 minutes following the lysis step [ ]. .. Tail-moments were normalized to a control to account for inter-experimental variability.

Article Title: Effects of side-stream tobacco smoke and smoke extract on glutathione- and oxidative DNA damage repair-deficient mice and blood cells
Article Snippet: To measure oxidative DNA damage, the comet assay was modified to include an incubation step with hOGG1 (New England Biolabs, Ipswich, MA). .. As described previously, embedded cells were incubated with hOGG1 (1:300 in NEBuffer1 and BSA) at 37°C for 30 minutes following the lysis step ( ). .. Tail-moments were normalized to a control to account for inter-experimental variability.

SDS Page:

Article Title: Special AT-rich Sequence-binding Protein 1 (SATB1) Functions as an Accessory Factor in Base Excision Repair
Article Snippet: 5′ end-labeled 32-mer duplex containing an 8-oxoG (50 n m ) was incubated with hOGG1 (New England Biolabs) and SATB1 or BSA at the indicated concentrations. .. 5′ end-labeled 32-mer duplex containing an 8-oxoG (50 n m ) was incubated with hOGG1 (New England Biolabs) and SATB1 or BSA at the indicated concentrations.

Plasmid Preparation:

Article Title: Mycofumigation through production of the volatile DNA-methylating agent N-methyl-N-nitrosoisobutyramide by fungi in the genus Muscodor
Article Snippet: 100 ng (4 μl) of the exposed pUC19 plasmid were incubated with a DNA glycosylase (hAAG or hOGG1) and APE1 for 1 h at 37 °C. .. Nicked pUC19 controls were acquired by incubating pUC19 with Nt.BsmA1 in New England Biolabs Buffer 4 for 1 h at 37 °C. hAAG (10,000 units/ml), APE1 (10,000 units/ml), and hOGG1 (1600 units/ml) were purchased from New England Biolabs (Ipswich, MA).

Article Title: CHD4 Has Oncogenic Functions in Initiating and Maintaining Epigenetic Suppression of Multiple Tumor Suppressor Genes
Article Snippet: Complexes were eluted off the beads in loading buffer at 65 °C for 15 min. Recombinant Flag-tagged human CHD4 (hCHD4) protein was purified from HEK293 cells transfected with (full-length) Flag-hCHD4 plasmid. .. Purified recombinant hCHD4 and hOGG1 (M0241, NEB) proteins were incubated in IP buffer (50 mM Tris-HCl pH 8.0, 100 mM NaCl, 5 mM MgCl2 , 1% NP-40) with or without 8-OHdG oligonucleotides (double strand) at 4 °C for overnight, followed by co-precipitation using anti-flag M2 beads (M8823, Sigma) or protein A/G agarose (sc-2003, Santa Cruz) using antibodies against Flag (ab49763, Abcam) or OGG1 (sc-376935, Santa Cruz).

Software:

Article Title: IL-13 Overexpression in Mouse Lungs Triggers Systemic Genotoxicity in Peripheral Blood
Article Snippet: Comet tail-moments were analyzed using CASP (Comet Assay Software Project, ). .. To measure oxidative DNA damage, the comet assay was modified to include an incubation step with hOGG1 (New England Biolabs, Ipswich, MA).

Article Title: Effects of side-stream tobacco smoke and smoke extract on glutathione- and oxidative DNA damage repair-deficient mice and blood cells
Article Snippet: Comet tail-moments were analyzed using CASP (Comet Assay Software Project, ). .. To measure oxidative DNA damage, the comet assay was modified to include an incubation step with hOGG1 (New England Biolabs, Ipswich, MA).

Negative Control:

Article Title: CHD4 Has Oncogenic Functions in Initiating and Maintaining Epigenetic Suppression of Multiple Tumor Suppressor Genes
Article Snippet: Purified recombinant hCHD4 and hOGG1 (M0241, NEB) proteins were incubated in IP buffer (50 mM Tris-HCl pH 8.0, 100 mM NaCl, 5 mM MgCl2 , 1% NP-40) with or without 8-OHdG oligonucleotides (double strand) at 4 °C for overnight, followed by co-precipitation using anti-flag M2 beads (M8823, Sigma) or protein A/G agarose (sc-2003, Santa Cruz) using antibodies against Flag (ab49763, Abcam) or OGG1 (sc-376935, Santa Cruz). .. The beads were washed five times using an IP buffer and the immunoprecipitated proteins were analysed by Western blotting.

In Vitro:

Article Title: The function of cux1 in oxidative dna damage repair is needed to prevent premature senescence of mouse embryo fibroblasts
Article Snippet: Paragraph title: In vitro 8-oxoG cleavage assay ... Cleavage reactions with bacterially purified proteins were conducted using 50 nM hOGG1 (New England Biolabs, Ipswich, MA), and 50 nM of BSA or the indicated proteins, unless otherwise indicated, in 25 mM NaCl, 10 mM Tris (pH 7.5), 1 mM MgCl2 , 5 mM EDTA (pH 8.0), 5% glycerol, 1 mM of DTT and 1 pmol of 32 P-radiolabeled double-stranded oligonucleotides containing an 8-oxoG base ( ).

Article Title: The DNA repair function of CUX1 contributes to radioresistance
Article Snippet: Paragraph title: In vitro 8-oxoG fluorogenic cleavage assay ... Cleavage reactions with bacterially purified proteins were conducted using 50 nM hOGG1 (New England Biolabs), and 200 nM of BSA, His-C1C2, His-C1 or His-C1-2Ala in 50 mM Tris (pH 7.1), 1 mM EDTA, and 20 mM KCl.

Article Title: In Vitro Fluorogenic Real-time Assay of the Repair of Oxidative DNA Damage
Article Snippet: Paragraph title: Fluorescence analysis of in vitro enzymatic activity ... Fpg, hOGG1, Fpg reaction buffer (NEB buffer 1: 10 mM Bis-Tris-Propane-HCl, 10 mM MgCl2 , 1 mM dithiothreitol, pH 7.0 at 25 °C), hOGG1 reaction buffer (NEB buffer 4: 50 mM potassium acetate, 20 mM Tris-acetate, 10 mM magnesium acetate, 1 mM dithiothreitol, pH 7.9 at 25 °C), and BSA (10 mg/mL) were purchased from New England Biolabs.

Article Title: Apex1 can cleave complex clustered DNA lesions in cells
Article Snippet: Paragraph title: 2.11 In vitro DNA damage cleavage assays ... Duplex substrate was diluted to 10 fmol/ µl using 10 mM Tris pH8, 50 mM NaCl, and 1 µl used in a 5 µl reaction with either 0.03 units endonuclease IV (Trevigen, Gaithersburg, MD), 0.5 units Fpg (NEB, Beverly, MA, USA), 0.05–0.2 units hApe1 (Trevigen, Gaithersburg, MD), 0.25 or 0.5 units hOgg1 (NEB, Beverly, MA, USA), or 100 or 200 ng nuclear extract in 45 mM HEPES, pH 7.8, 70 mM KCl, 1 mM DTT, 2.5 mM MgCl2 .

Enzymatic Assay:

Article Title: Mycofumigation through production of the volatile DNA-methylating agent N-methyl-N-nitrosoisobutyramide by fungi in the genus Muscodor
Article Snippet: Paragraph title: Enzymatic assay for DNA methylation ... Nicked pUC19 controls were acquired by incubating pUC19 with Nt.BsmA1 in New England Biolabs Buffer 4 for 1 h at 37 °C. hAAG (10,000 units/ml), APE1 (10,000 units/ml), and hOGG1 (1600 units/ml) were purchased from New England Biolabs (Ipswich, MA).

DNA Methylation Assay:

Article Title: Mycofumigation through production of the volatile DNA-methylating agent N-methyl-N-nitrosoisobutyramide by fungi in the genus Muscodor
Article Snippet: Paragraph title: Enzymatic assay for DNA methylation ... Nicked pUC19 controls were acquired by incubating pUC19 with Nt.BsmA1 in New England Biolabs Buffer 4 for 1 h at 37 °C. hAAG (10,000 units/ml), APE1 (10,000 units/ml), and hOGG1 (1600 units/ml) were purchased from New England Biolabs (Ipswich, MA).

Liquid Chromatography with Mass Spectroscopy:

Article Title: Aryl Hydrocarbon Receptor Facilitates DNA Strand Breaks and 8-Oxo-2?-deoxyguanosine Formation by the Aldo-Keto Reductase Product Benzo[a]pyrene-7,8-dione
Article Snippet: The purity and identity of all PAH metabolites were checked by LC/MS before use. .. HiPerFect transfection reagent was acquired from Qiagen. hOGG1 was obtained from New England BioLabs Inc. (Beverly, MA).

Staining:

Article Title: IL-13 Overexpression in Mouse Lungs Triggers Systemic Genotoxicity in Peripheral Blood
Article Snippet: After 20 minutes in the electrophoresis buffer at 4°C, the gel was run for 45 minutes at 300 mA, allowed to dry and then stained with SYBR Gold (Molecular Probes). .. To measure oxidative DNA damage, the comet assay was modified to include an incubation step with hOGG1 (New England Biolabs, Ipswich, MA).

Article Title: Effects of side-stream tobacco smoke and smoke extract on glutathione- and oxidative DNA damage repair-deficient mice and blood cells
Article Snippet: After 20 minutes in the electrophoresis buffer at 4°C, the gel was run for 45 minutes at 300 mA, allowed to dry and then stained with SYBR Gold (Molecular Probes). .. To measure oxidative DNA damage, the comet assay was modified to include an incubation step with hOGG1 (New England Biolabs, Ipswich, MA).

Article Title: Mycofumigation through production of the volatile DNA-methylating agent N-methyl-N-nitrosoisobutyramide by fungi in the genus Muscodor
Article Snippet: Samples were run on 1% agarose gels (Affymetrix) stained with ethidium bromide (Sigma) Gels were visualized with the Bio-Rad ChemiDoc MP imaging system. .. Nicked pUC19 controls were acquired by incubating pUC19 with Nt.BsmA1 in New England Biolabs Buffer 4 for 1 h at 37 °C. hAAG (10,000 units/ml), APE1 (10,000 units/ml), and hOGG1 (1600 units/ml) were purchased from New England Biolabs (Ipswich, MA).

Activity Assay:

Article Title: Special AT-rich Sequence-binding Protein 1 (SATB1) Functions as an Accessory Factor in Base Excision Repair
Article Snippet: 29 , 430–438 [ ] [ ] 17. .. Vidal A. E., Hickson I. D., Boiteux S., and Radicella J. P. (2001) Mechanism of stimulation of the DNA glycosylase activity of hOGG1 by the major human AP endonuclease: bypass of the AP lyase activity step . .. Nucleic Acids Res .

Article Title: In Vitro Fluorogenic Real-time Assay of the Repair of Oxidative DNA Damage
Article Snippet: Paragraph title: Fluorescence analysis of in vitro enzymatic activity ... Fpg, hOGG1, Fpg reaction buffer (NEB buffer 1: 10 mM Bis-Tris-Propane-HCl, 10 mM MgCl2 , 1 mM dithiothreitol, pH 7.0 at 25 °C), hOGG1 reaction buffer (NEB buffer 4: 50 mM potassium acetate, 20 mM Tris-acetate, 10 mM magnesium acetate, 1 mM dithiothreitol, pH 7.9 at 25 °C), and BSA (10 mg/mL) were purchased from New England Biolabs.

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  • 95
    New England Biolabs hogg1
    AhR-dependent DNA strand breaks and 8-oxo-dGuo formation in Hepa cells-treated with B[ a ]P-7,8-dione. A , B[ a ]P-7,8-dione-mediated DNA strand breaks in Hepa cells. AhR-deficient Hepa1c1c12 cells, ARNT-deficient Hepa1c1c4, and their wild type Hepa1c1c7 cells were treated with 20 μ m B[ a ]P-7,8-dione for 6 h. The cells were harvested and used for the detection of DNA strand breaks by the <t>hOGG1-coupled</t> comet assay. Significant effects were observed at different incubation times and after hOGG1 treatment following B[ a ]P-7,8-dione treatment. Significant effects were also observed between AhR-deficient Hepa1c1c12 cells and ARNT-deficient Hepa 1c1c4 cells and their wild type Hepa 1c1c7 cells. *, p < 0.05. B , LC/MS detection of 8-oxo-dGuo in Hepa cells-treated with B[ a ]P-7,8-dione. Significant effects were observed again when AhR-deficient Hepa1c1c12 cells were compared with ARNT-deficient Hepa 1c1c4 cells and wild type Hepa 1c1c7 cells. *, p < 0.05. AU , arbitrary units.
    Hogg1, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hogg1/product/New England Biolabs
    Average 95 stars, based on 3 article reviews
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    80
    New England Biolabs hogg1 enzyme
    DNA strand breaks (A), FPG- (B) and <t>hOGG1-sensitive</t> sites (C) in the liver of lean or obese Zucker rats. The results are presented as mean and SEM (n = 7–8 per group). *P
    Hogg1 Enzyme, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 80/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hogg1 enzyme/product/New England Biolabs
    Average 80 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    hogg1 enzyme - by Bioz Stars, 2019-12
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    Image Search Results


    AhR-dependent DNA strand breaks and 8-oxo-dGuo formation in Hepa cells-treated with B[ a ]P-7,8-dione. A , B[ a ]P-7,8-dione-mediated DNA strand breaks in Hepa cells. AhR-deficient Hepa1c1c12 cells, ARNT-deficient Hepa1c1c4, and their wild type Hepa1c1c7 cells were treated with 20 μ m B[ a ]P-7,8-dione for 6 h. The cells were harvested and used for the detection of DNA strand breaks by the hOGG1-coupled comet assay. Significant effects were observed at different incubation times and after hOGG1 treatment following B[ a ]P-7,8-dione treatment. Significant effects were also observed between AhR-deficient Hepa1c1c12 cells and ARNT-deficient Hepa 1c1c4 cells and their wild type Hepa 1c1c7 cells. *, p < 0.05. B , LC/MS detection of 8-oxo-dGuo in Hepa cells-treated with B[ a ]P-7,8-dione. Significant effects were observed again when AhR-deficient Hepa1c1c12 cells were compared with ARNT-deficient Hepa 1c1c4 cells and wild type Hepa 1c1c7 cells. *, p < 0.05. AU , arbitrary units.

    Journal:

    Article Title: Aryl Hydrocarbon Receptor Facilitates DNA Strand Breaks and 8-Oxo-2?-deoxyguanosine Formation by the Aldo-Keto Reductase Product Benzo[a]pyrene-7,8-dione

    doi: 10.1074/jbc.M109.042143

    Figure Lengend Snippet: AhR-dependent DNA strand breaks and 8-oxo-dGuo formation in Hepa cells-treated with B[ a ]P-7,8-dione. A , B[ a ]P-7,8-dione-mediated DNA strand breaks in Hepa cells. AhR-deficient Hepa1c1c12 cells, ARNT-deficient Hepa1c1c4, and their wild type Hepa1c1c7 cells were treated with 20 μ m B[ a ]P-7,8-dione for 6 h. The cells were harvested and used for the detection of DNA strand breaks by the hOGG1-coupled comet assay. Significant effects were observed at different incubation times and after hOGG1 treatment following B[ a ]P-7,8-dione treatment. Significant effects were also observed between AhR-deficient Hepa1c1c12 cells and ARNT-deficient Hepa 1c1c4 cells and their wild type Hepa 1c1c7 cells. *, p < 0.05. B , LC/MS detection of 8-oxo-dGuo in Hepa cells-treated with B[ a ]P-7,8-dione. Significant effects were observed again when AhR-deficient Hepa1c1c12 cells were compared with ARNT-deficient Hepa 1c1c4 cells and wild type Hepa 1c1c7 cells. *, p < 0.05. AU , arbitrary units.

    Article Snippet: HiPerFect transfection reagent was acquired from Qiagen. hOGG1 was obtained from New England BioLabs Inc. (Beverly, MA).

    Techniques: Single Cell Gel Electrophoresis, Incubation, Liquid Chromatography, Mass Spectrometry

    Analysis of hOGG1-dependent DNA strand breaks in both KBrO3 -treated Hepa and H358 cells. Three Hepa cell sublines and H358 cells were treated with 2.5 m m of potassium bromate for 3 h. The cells were harvested and used for the detection of DNA strand breaks by hOGG1-coupled comet assay. A , Hepa cells. B , H358 cells. AU , arbitrary units.

    Journal:

    Article Title: Aryl Hydrocarbon Receptor Facilitates DNA Strand Breaks and 8-Oxo-2?-deoxyguanosine Formation by the Aldo-Keto Reductase Product Benzo[a]pyrene-7,8-dione

    doi: 10.1074/jbc.M109.042143

    Figure Lengend Snippet: Analysis of hOGG1-dependent DNA strand breaks in both KBrO3 -treated Hepa and H358 cells. Three Hepa cell sublines and H358 cells were treated with 2.5 m m of potassium bromate for 3 h. The cells were harvested and used for the detection of DNA strand breaks by hOGG1-coupled comet assay. A , Hepa cells. B , H358 cells. AU , arbitrary units.

    Article Snippet: HiPerFect transfection reagent was acquired from Qiagen. hOGG1 was obtained from New England BioLabs Inc. (Beverly, MA).

    Techniques: Single Cell Gel Electrophoresis

    Preparation of DNA template (8-oxoG substrate) with 8-oxoG at a defined position. a Upper strand sequence containing 8-oxoG base and lower strand substrate containing original C base in pBS2/8-oxoG are shown diagrammatically. b Experimental procedure for purification of pBS2/8-oxoG using 8-oxoG oligo. c Identified DNA substrates (100 ng), pBS2/8-oxoG, were incubated with Fpg (2 units) or hOGG1 (0.16 units) at 37 °C for 30 min. Aliquots from the sample were run on 0.8% agarose gel and visualized by staining with EtBr. Lane 1, 1-kbp marker; lane 2, non-treatment; lane 3, Fpg-treatment; lane 4, hOGGI-treatment. Open circular DNA (OC), liner DNA (Lin), and covalently closed circular DNA (CCC) are indicated by arrows

    Journal: Genes and Environment

    Article Title: Oligo swapping method for in vitro DNA repair substrate containing a single DNA lesion at a specific site

    doi: 10.1186/s41021-018-0112-5

    Figure Lengend Snippet: Preparation of DNA template (8-oxoG substrate) with 8-oxoG at a defined position. a Upper strand sequence containing 8-oxoG base and lower strand substrate containing original C base in pBS2/8-oxoG are shown diagrammatically. b Experimental procedure for purification of pBS2/8-oxoG using 8-oxoG oligo. c Identified DNA substrates (100 ng), pBS2/8-oxoG, were incubated with Fpg (2 units) or hOGG1 (0.16 units) at 37 °C for 30 min. Aliquots from the sample were run on 0.8% agarose gel and visualized by staining with EtBr. Lane 1, 1-kbp marker; lane 2, non-treatment; lane 3, Fpg-treatment; lane 4, hOGGI-treatment. Open circular DNA (OC), liner DNA (Lin), and covalently closed circular DNA (CCC) are indicated by arrows

    Article Snippet: Nt.Bbv CI nicking endonuclease, Eco NI, Fpg, hOGG1, UDG, APE1, and T5 exonuclease were purchased from New England Biolabs (Ipswich, MA, USA).

    Techniques: Sequencing, Purification, Incubation, Agarose Gel Electrophoresis, Staining, Marker, Countercurrent Chromatography

    Sodium borohydride trapping of OGG1 enzyme in the presence of CR1CR2 5′-end-labeled 32-mer duplex containing an 8-oxoG was incubated with hOGG1 and CR1CR2 or BSA at the indicated concentrations. After incubation at 37°C, 50 mM sodium borohydride was added. The reactions were pursued for another 5 min at 37°C. After termination of the reaction, the trapped complexes were separated from free substrate by 10% SDS-PAGE gel.

    Journal: Oncotarget

    Article Title: The function of cux1 in oxidative dna damage repair is needed to prevent premature senescence of mouse embryo fibroblasts

    doi:

    Figure Lengend Snippet: Sodium borohydride trapping of OGG1 enzyme in the presence of CR1CR2 5′-end-labeled 32-mer duplex containing an 8-oxoG was incubated with hOGG1 and CR1CR2 or BSA at the indicated concentrations. After incubation at 37°C, 50 mM sodium borohydride was added. The reactions were pursued for another 5 min at 37°C. After termination of the reaction, the trapped complexes were separated from free substrate by 10% SDS-PAGE gel.

    Article Snippet: Cleavage reactions with bacterially purified proteins were conducted using 50 nM hOGG1 (New England Biolabs, Ipswich, MA), and 50 nM of BSA or the indicated proteins, unless otherwise indicated, in 25 mM NaCl, 10 mM Tris (pH 7.5), 1 mM MgCl2 , 5 mM EDTA (pH 8.0), 5% glycerol, 1 mM of DTT and 1 pmol of 32 P-radiolabeled double-stranded oligonucleotides containing an 8-oxoG base ( ).

    Techniques: Labeling, Incubation, SDS Page

    DNA strand breaks (A), FPG- (B) and hOGG1-sensitive sites (C) in the liver of lean or obese Zucker rats. The results are presented as mean and SEM (n = 7–8 per group). *P

    Journal: PLoS ONE

    Article Title: Hepatic Oxidative Stress, Genotoxicity and Vascular Dysfunction in Lean or Obese Zucker Rats

    doi: 10.1371/journal.pone.0118773

    Figure Lengend Snippet: DNA strand breaks (A), FPG- (B) and hOGG1-sensitive sites (C) in the liver of lean or obese Zucker rats. The results are presented as mean and SEM (n = 7–8 per group). *P

    Article Snippet: The FPG enzyme was a gift from Professor Andrew Collins (University of Oslo, Norway), and the hOGG1 enzyme was obtained from New England Biolabs (Ipswich, MA, USA).

    Techniques: