uracil glycosylase inhibitor  (New England Biolabs)


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    Name:
    Uracil Glycosylase Inhibitor UGI
    Description:
    Uracil Glycosylase Inhibitor UGI 1 000 units
    Catalog Number:
    m0281l
    Price:
    293
    Size:
    1 000 units
    Category:
    Enzyme Inhibitors
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    Structured Review

    New England Biolabs uracil glycosylase inhibitor
    Uracil Glycosylase Inhibitor UGI
    Uracil Glycosylase Inhibitor UGI 1 000 units
    https://www.bioz.com/result/uracil glycosylase inhibitor/product/New England Biolabs
    Average 94 stars, based on 17 article reviews
    Price from $9.99 to $1999.99
    uracil glycosylase inhibitor - by Bioz Stars, 2020-08
    94/100 stars

    Images

    1) Product Images from "Human Base Excision Repair Creates a Bias Toward -1 Frameshift Mutations *"

    Article Title: Human Base Excision Repair Creates a Bias Toward -1 Frameshift Mutations *

    Journal: The Journal of Biological Chemistry

    doi: 10.1074/jbc.M110.118596

    Proposed single nucleotide deletion pathway catalyzed by BER enzymes. The pathway for AAG-initiated short-patch BER is shown on the left and the proposed pathway for single nucleotide deletion is shown on the right. X denotes a damaged nucleotide. Note that only the glycosylase and endonuclease reactions differ for the two pathways. After APE1 cleavage the 5′-dRP intermediate is chemically identical to the intermediate generated after single nucleotide incorporation in the short-patch BER pathway.
    Figure Legend Snippet: Proposed single nucleotide deletion pathway catalyzed by BER enzymes. The pathway for AAG-initiated short-patch BER is shown on the left and the proposed pathway for single nucleotide deletion is shown on the right. X denotes a damaged nucleotide. Note that only the glycosylase and endonuclease reactions differ for the two pathways. After APE1 cleavage the 5′-dRP intermediate is chemically identical to the intermediate generated after single nucleotide incorporation in the short-patch BER pathway.

    Techniques Used: Generated

    2) Product Images from "DIFFERENTIAL ROLE OF BASE EXCISION REPAIR PROTEINS IN MEDIATING CISPLATIN CYTOTOXICITY"

    Article Title: DIFFERENTIAL ROLE OF BASE EXCISION REPAIR PROTEINS IN MEDIATING CISPLATIN CYTOTOXICITY

    Journal: DNA repair

    doi: 10.1016/j.dnarep.2017.01.002

    Cisplatin cytotoxicity and effect on glycosylase activity (A) Colony survival assay in MDA-MB-231 cells following UNG and SMUG1 knockdown: shControl (open circles), shUNG (closed triangles), shSMUG1 (closed circles) and shUNG + shSMUG1 (open squares). Results are represented as mean ± SE from 3 independent experiments. Cells were transfected with shRNA directed against UNG and SMUG1. (B) Colony survival assay in MDA-MB-231 cells following MBD4 knockdown with shControl (open circles) and shMBD4 (closed triangles). shRNA transfected cells were treated with increasing doses of cisplatin and cytotoxicity. Results are represented as mean ± SE from 3 independent experiments. (C) In vitro glycosylase assay, DNA (5nM) was incubated with either pure enzyme or HeLa extract. Lane 1, undamaged DNA alone.; lane 2, undamaged DNA treated with UDG and APE1 to generate a 19 mer product; lane 3, undamaged DNA substrate treated with UDG, APE1 and 1 unit of UGI; lane 4, undamaged DNA incubated with HeLa extract; lane 5 reactions in which HeLa extract was preincubated with 1 unit of UGI before adding the undamaged DNA substrate. Lanes 6–10 follow the same set up as lanes 1–5, but with ICL DNA substrate. Both undamaged and ICL substrates contain a central uracil and a 3′ Cy3 label. M is a 21-nt marker.
    Figure Legend Snippet: Cisplatin cytotoxicity and effect on glycosylase activity (A) Colony survival assay in MDA-MB-231 cells following UNG and SMUG1 knockdown: shControl (open circles), shUNG (closed triangles), shSMUG1 (closed circles) and shUNG + shSMUG1 (open squares). Results are represented as mean ± SE from 3 independent experiments. Cells were transfected with shRNA directed against UNG and SMUG1. (B) Colony survival assay in MDA-MB-231 cells following MBD4 knockdown with shControl (open circles) and shMBD4 (closed triangles). shRNA transfected cells were treated with increasing doses of cisplatin and cytotoxicity. Results are represented as mean ± SE from 3 independent experiments. (C) In vitro glycosylase assay, DNA (5nM) was incubated with either pure enzyme or HeLa extract. Lane 1, undamaged DNA alone.; lane 2, undamaged DNA treated with UDG and APE1 to generate a 19 mer product; lane 3, undamaged DNA substrate treated with UDG, APE1 and 1 unit of UGI; lane 4, undamaged DNA incubated with HeLa extract; lane 5 reactions in which HeLa extract was preincubated with 1 unit of UGI before adding the undamaged DNA substrate. Lanes 6–10 follow the same set up as lanes 1–5, but with ICL DNA substrate. Both undamaged and ICL substrates contain a central uracil and a 3′ Cy3 label. M is a 21-nt marker.

    Techniques Used: Activity Assay, Clonogenic Cell Survival Assay, Multiple Displacement Amplification, Transfection, shRNA, In Vitro, Incubation, Marker

    3) Product Images from "Timing Facilitated Site Transfer of an Enzyme on DNA"

    Article Title: Timing Facilitated Site Transfer of an Enzyme on DNA

    Journal: Nature Chemical Biology

    doi: 10.1038/nchembio.764

    Facilitated site transfer by human uracil DNA glycosylase (hUNG). In all facilitated transfer assays the hUNG concentration is 5–20 pM and the DNA substrate concentration is 40 nM. (a) Facilitated site transfer of hUNG between two uracil sites on the same DNA strand separated by 10 bps (S10). Reactions in the absence and presence of 10 mM uracil are shown. Facilitated transfer is qualitatively indicated by an excess of double excision fragments (A and C) relative single site excision products (AB and BC). (b) Facilitated site transfer by hUNG between sites separated by 5 bp (S5) in the absence and presence of 10 mM uracil. (c) Observed probability of site transfer (P trans obs ) as a function of time and uracil concentration for the substrate with a 10 bp site separation. Linear extrapolation to the y axis provides the true transfer probability at zero time (P trans ). (d) P trans ′ as a function of increasing uracil for substrates with 5, 10 and 20 bp site spacings. Each data point represents an individual experiment as in panels a and b and the prime notation indicates correction for the efficiency of excision (see text). The non-linear least squares fits in (d) use a kinetic partitioning model that relates the dependence of the total transfer probability (P trans ′ = P slide ′ + P hop ′) to the uracil trap concentration ( Supplementary Methods ). Uncut gel images are shown in Supplementary Fig. 6 . Error bars represent the mean ± 1 s.d. of at least three independent trials.
    Figure Legend Snippet: Facilitated site transfer by human uracil DNA glycosylase (hUNG). In all facilitated transfer assays the hUNG concentration is 5–20 pM and the DNA substrate concentration is 40 nM. (a) Facilitated site transfer of hUNG between two uracil sites on the same DNA strand separated by 10 bps (S10). Reactions in the absence and presence of 10 mM uracil are shown. Facilitated transfer is qualitatively indicated by an excess of double excision fragments (A and C) relative single site excision products (AB and BC). (b) Facilitated site transfer by hUNG between sites separated by 5 bp (S5) in the absence and presence of 10 mM uracil. (c) Observed probability of site transfer (P trans obs ) as a function of time and uracil concentration for the substrate with a 10 bp site separation. Linear extrapolation to the y axis provides the true transfer probability at zero time (P trans ). (d) P trans ′ as a function of increasing uracil for substrates with 5, 10 and 20 bp site spacings. Each data point represents an individual experiment as in panels a and b and the prime notation indicates correction for the efficiency of excision (see text). The non-linear least squares fits in (d) use a kinetic partitioning model that relates the dependence of the total transfer probability (P trans ′ = P slide ′ + P hop ′) to the uracil trap concentration ( Supplementary Methods ). Uncut gel images are shown in Supplementary Fig. 6 . Error bars represent the mean ± 1 s.d. of at least three independent trials.

    Techniques Used: Concentration Assay

    Related Articles

    Concentration Assay:

    Article Title: Timing Facilitated Site Transfer of an Enzyme on DNA
    Article Snippet: .. At each time point 4 μl of the reaction mix was taken out and quenched with Uracil DNA Glycosylase Inhibitor (UGI) at a final concentration of 0.1 Units (New England Biolabs) or 50 nM final concentration of a highly potent duplex DNA inhibitor (2′-fluoro-2′-deoxyuridine paired with 4-methylindole in duplex DNA) , , both of which rapidly and efficiently quenched hUNG activity. ..

    Incubation:

    Article Title: Genomic Uracil Homeostasis during Normal B Cell Maturation and Loss of This Balance during B Cell Cancer Development
    Article Snippet: .. To assay uracil excision, 24 pmol of a 6-carboxyfluorescein (FAM)-labeled oligonucleotide (5′-ATTATTAUCCATTTATT) was incubated with extracts for 10 min at 37°C in a 20-μl total reaction mixture with 1 mM EDTA, 1 mM DTT, and 20 mM Tris-HCl (pH 8.0) with or without excess uracil DNA-glycosylase inhibitor (New England BioLabs). .. A single-stranded substrate was used in these assays to ensure that double-strand-specific glycosylases, including SMUG1, would not act on the uracil.

    Article Title: Ancient Fennoscandian genomes reveal origin and spread of Siberian ancestry in Europe
    Article Snippet: .. This again was followed by the addition of 200 U UGI (Uracil Glycosylase inhibitor, by NEB) and another identical incubation to stop the enzymatic excision of deaminated sites, as described in . .. For each library, a unique pair of eight-bp-long indexes was incorporated using a Pfu Turbo Cx Hotstart DNA Polymerase and a thermocycling program with the temperature profile as follows: initial denaturation (98 °C for 30 sec), cycle of denaturation/annealing/elongation (98 °C for 10 sec/ 60 °C for 20 sec/ 72 °C for 20 sec) and final extension at 72 °C for 10 min .

    Inhibition:

    Article Title: Human Base Excision Repair Creates a Bias Toward -1 Frameshift Mutations *
    Article Snippet: .. Inhibition of U-bulge glycosylase activity was achieved by addition of 0.02 units of uracil glycosylase inhibitor (New England Biolabs) to 0.4 mg/ml of HeLa WCE as described above. .. Inhibition of the glycosylase activity toward I-bulge and ϵA-bulge bulge DNA (10 n m ) was investigated by adding 100 n m unlabeled 25-mer competitor DNA that was either damaged (ϵA·T) or undamaged (A·T).

    Activity Assay:

    Article Title: Timing Facilitated Site Transfer of an Enzyme on DNA
    Article Snippet: .. At each time point 4 μl of the reaction mix was taken out and quenched with Uracil DNA Glycosylase Inhibitor (UGI) at a final concentration of 0.1 Units (New England Biolabs) or 50 nM final concentration of a highly potent duplex DNA inhibitor (2′-fluoro-2′-deoxyuridine paired with 4-methylindole in duplex DNA) , , both of which rapidly and efficiently quenched hUNG activity. ..

    Article Title: Human Base Excision Repair Creates a Bias Toward -1 Frameshift Mutations *
    Article Snippet: .. Inhibition of U-bulge glycosylase activity was achieved by addition of 0.02 units of uracil glycosylase inhibitor (New England Biolabs) to 0.4 mg/ml of HeLa WCE as described above. .. Inhibition of the glycosylase activity toward I-bulge and ϵA-bulge bulge DNA (10 n m ) was investigated by adding 100 n m unlabeled 25-mer competitor DNA that was either damaged (ϵA·T) or undamaged (A·T).

    other:

    Article Title: DIFFERENTIAL ROLE OF BASE EXCISION REPAIR PROTEINS IN MEDIATING CISPLATIN CYTOTOXICITY
    Article Snippet: Uracil DNA glycosylase from E. coli (UDG) 2,000 U/ml, human apurinic/apyridimic endonuclease (APE1) 10,000 U/ml, and Uracil Glycosylase inhibitor (UGI) 2,000 U/ml were from New England Biolabs.

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    New England Biolabs uracil glycosylase inhibitor
    Proposed single nucleotide deletion pathway catalyzed by BER enzymes. The pathway for AAG-initiated short-patch BER is shown on the left and the proposed pathway for single nucleotide deletion is shown on the right. X denotes a damaged nucleotide. Note that only the <t>glycosylase</t> and endonuclease reactions differ for the two pathways. After APE1 cleavage the 5′-dRP intermediate is chemically identical to the intermediate generated after single nucleotide incorporation in the short-patch BER pathway.
    Uracil Glycosylase Inhibitor, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/uracil glycosylase inhibitor/product/New England Biolabs
    Average 94 stars, based on 13 article reviews
    Price from $9.99 to $1999.99
    uracil glycosylase inhibitor - by Bioz Stars, 2020-08
    94/100 stars
      Buy from Supplier

    Image Search Results


    Proposed single nucleotide deletion pathway catalyzed by BER enzymes. The pathway for AAG-initiated short-patch BER is shown on the left and the proposed pathway for single nucleotide deletion is shown on the right. X denotes a damaged nucleotide. Note that only the glycosylase and endonuclease reactions differ for the two pathways. After APE1 cleavage the 5′-dRP intermediate is chemically identical to the intermediate generated after single nucleotide incorporation in the short-patch BER pathway.

    Journal: The Journal of Biological Chemistry

    Article Title: Human Base Excision Repair Creates a Bias Toward -1 Frameshift Mutations *

    doi: 10.1074/jbc.M110.118596

    Figure Lengend Snippet: Proposed single nucleotide deletion pathway catalyzed by BER enzymes. The pathway for AAG-initiated short-patch BER is shown on the left and the proposed pathway for single nucleotide deletion is shown on the right. X denotes a damaged nucleotide. Note that only the glycosylase and endonuclease reactions differ for the two pathways. After APE1 cleavage the 5′-dRP intermediate is chemically identical to the intermediate generated after single nucleotide incorporation in the short-patch BER pathway.

    Article Snippet: Inhibition of U-bulge glycosylase activity was achieved by addition of 0.02 units of uracil glycosylase inhibitor (New England Biolabs) to 0.4 mg/ml of HeLa WCE as described above.

    Techniques: Generated

    Cisplatin cytotoxicity and effect on glycosylase activity (A) Colony survival assay in MDA-MB-231 cells following UNG and SMUG1 knockdown: shControl (open circles), shUNG (closed triangles), shSMUG1 (closed circles) and shUNG + shSMUG1 (open squares). Results are represented as mean ± SE from 3 independent experiments. Cells were transfected with shRNA directed against UNG and SMUG1. (B) Colony survival assay in MDA-MB-231 cells following MBD4 knockdown with shControl (open circles) and shMBD4 (closed triangles). shRNA transfected cells were treated with increasing doses of cisplatin and cytotoxicity. Results are represented as mean ± SE from 3 independent experiments. (C) In vitro glycosylase assay, DNA (5nM) was incubated with either pure enzyme or HeLa extract. Lane 1, undamaged DNA alone.; lane 2, undamaged DNA treated with UDG and APE1 to generate a 19 mer product; lane 3, undamaged DNA substrate treated with UDG, APE1 and 1 unit of UGI; lane 4, undamaged DNA incubated with HeLa extract; lane 5 reactions in which HeLa extract was preincubated with 1 unit of UGI before adding the undamaged DNA substrate. Lanes 6–10 follow the same set up as lanes 1–5, but with ICL DNA substrate. Both undamaged and ICL substrates contain a central uracil and a 3′ Cy3 label. M is a 21-nt marker.

    Journal: DNA repair

    Article Title: DIFFERENTIAL ROLE OF BASE EXCISION REPAIR PROTEINS IN MEDIATING CISPLATIN CYTOTOXICITY

    doi: 10.1016/j.dnarep.2017.01.002

    Figure Lengend Snippet: Cisplatin cytotoxicity and effect on glycosylase activity (A) Colony survival assay in MDA-MB-231 cells following UNG and SMUG1 knockdown: shControl (open circles), shUNG (closed triangles), shSMUG1 (closed circles) and shUNG + shSMUG1 (open squares). Results are represented as mean ± SE from 3 independent experiments. Cells were transfected with shRNA directed against UNG and SMUG1. (B) Colony survival assay in MDA-MB-231 cells following MBD4 knockdown with shControl (open circles) and shMBD4 (closed triangles). shRNA transfected cells were treated with increasing doses of cisplatin and cytotoxicity. Results are represented as mean ± SE from 3 independent experiments. (C) In vitro glycosylase assay, DNA (5nM) was incubated with either pure enzyme or HeLa extract. Lane 1, undamaged DNA alone.; lane 2, undamaged DNA treated with UDG and APE1 to generate a 19 mer product; lane 3, undamaged DNA substrate treated with UDG, APE1 and 1 unit of UGI; lane 4, undamaged DNA incubated with HeLa extract; lane 5 reactions in which HeLa extract was preincubated with 1 unit of UGI before adding the undamaged DNA substrate. Lanes 6–10 follow the same set up as lanes 1–5, but with ICL DNA substrate. Both undamaged and ICL substrates contain a central uracil and a 3′ Cy3 label. M is a 21-nt marker.

    Article Snippet: Uracil DNA glycosylase from E. coli (UDG) 2,000 U/ml, human apurinic/apyridimic endonuclease (APE1) 10,000 U/ml, and Uracil Glycosylase inhibitor (UGI) 2,000 U/ml were from New England Biolabs.

    Techniques: Activity Assay, Clonogenic Cell Survival Assay, Multiple Displacement Amplification, Transfection, shRNA, In Vitro, Incubation, Marker

    Facilitated site transfer by human uracil DNA glycosylase (hUNG). In all facilitated transfer assays the hUNG concentration is 5–20 pM and the DNA substrate concentration is 40 nM. (a) Facilitated site transfer of hUNG between two uracil sites on the same DNA strand separated by 10 bps (S10). Reactions in the absence and presence of 10 mM uracil are shown. Facilitated transfer is qualitatively indicated by an excess of double excision fragments (A and C) relative single site excision products (AB and BC). (b) Facilitated site transfer by hUNG between sites separated by 5 bp (S5) in the absence and presence of 10 mM uracil. (c) Observed probability of site transfer (P trans obs ) as a function of time and uracil concentration for the substrate with a 10 bp site separation. Linear extrapolation to the y axis provides the true transfer probability at zero time (P trans ). (d) P trans ′ as a function of increasing uracil for substrates with 5, 10 and 20 bp site spacings. Each data point represents an individual experiment as in panels a and b and the prime notation indicates correction for the efficiency of excision (see text). The non-linear least squares fits in (d) use a kinetic partitioning model that relates the dependence of the total transfer probability (P trans ′ = P slide ′ + P hop ′) to the uracil trap concentration ( Supplementary Methods ). Uncut gel images are shown in Supplementary Fig. 6 . Error bars represent the mean ± 1 s.d. of at least three independent trials.

    Journal: Nature Chemical Biology

    Article Title: Timing Facilitated Site Transfer of an Enzyme on DNA

    doi: 10.1038/nchembio.764

    Figure Lengend Snippet: Facilitated site transfer by human uracil DNA glycosylase (hUNG). In all facilitated transfer assays the hUNG concentration is 5–20 pM and the DNA substrate concentration is 40 nM. (a) Facilitated site transfer of hUNG between two uracil sites on the same DNA strand separated by 10 bps (S10). Reactions in the absence and presence of 10 mM uracil are shown. Facilitated transfer is qualitatively indicated by an excess of double excision fragments (A and C) relative single site excision products (AB and BC). (b) Facilitated site transfer by hUNG between sites separated by 5 bp (S5) in the absence and presence of 10 mM uracil. (c) Observed probability of site transfer (P trans obs ) as a function of time and uracil concentration for the substrate with a 10 bp site separation. Linear extrapolation to the y axis provides the true transfer probability at zero time (P trans ). (d) P trans ′ as a function of increasing uracil for substrates with 5, 10 and 20 bp site spacings. Each data point represents an individual experiment as in panels a and b and the prime notation indicates correction for the efficiency of excision (see text). The non-linear least squares fits in (d) use a kinetic partitioning model that relates the dependence of the total transfer probability (P trans ′ = P slide ′ + P hop ′) to the uracil trap concentration ( Supplementary Methods ). Uncut gel images are shown in Supplementary Fig. 6 . Error bars represent the mean ± 1 s.d. of at least three independent trials.

    Article Snippet: At each time point 4 μl of the reaction mix was taken out and quenched with Uracil DNA Glycosylase Inhibitor (UGI) at a final concentration of 0.1 Units (New England Biolabs) or 50 nM final concentration of a highly potent duplex DNA inhibitor (2′-fluoro-2′-deoxyuridine paired with 4-methylindole in duplex DNA) , , both of which rapidly and efficiently quenched hUNG activity.

    Techniques: Concentration Assay