dutp  (Thermo Fisher)


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    Structured Review

    Thermo Fisher dutp
    Progress of <t>dUTP</t> hydrolysis of WT and mutant Dut NM1 detected by 1 H-NMR. For each spectral overlay, the black spectrum is for free dUTP, while the red, blue, and green spectra were obtained at the indicated time points following enzyme addition. 1 H signal assignments for dUTP (black) and <t>dUMP</t> (blue) are indicated at the bottom. Asterisks indicate signals of residual imidazole.
    Dutp, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 37 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Images

    1) Product Images from "Derepression of SaPIbov1 is independent of φNM1 type 2 dUTPase activity and is inhibited by dUTP and dUMP"

    Article Title: Derepression of SaPIbov1 is independent of φNM1 type 2 dUTPase activity and is inhibited by dUTP and dUMP

    Journal: Journal of molecular biology

    doi: 10.1016/j.jmb.2017.04.001

    Progress of dUTP hydrolysis of WT and mutant Dut NM1 detected by 1 H-NMR. For each spectral overlay, the black spectrum is for free dUTP, while the red, blue, and green spectra were obtained at the indicated time points following enzyme addition. 1 H signal assignments for dUTP (black) and dUMP (blue) are indicated at the bottom. Asterisks indicate signals of residual imidazole.
    Figure Legend Snippet: Progress of dUTP hydrolysis of WT and mutant Dut NM1 detected by 1 H-NMR. For each spectral overlay, the black spectrum is for free dUTP, while the red, blue, and green spectra were obtained at the indicated time points following enzyme addition. 1 H signal assignments for dUTP (black) and dUMP (blue) are indicated at the bottom. Asterisks indicate signals of residual imidazole.

    Techniques Used: Mutagenesis, Nuclear Magnetic Resonance

    2) Product Images from "RNA structure analysis assisted by capillary electrophoresis"

    Article Title: RNA structure analysis assisted by capillary electrophoresis

    Journal: Nucleic Acids Research

    doi:

    Analysis of structurally heterogeneous BRCA1 Ex1a and transcript truncation to obtain a homogeneous structure. ( A ) Non-denaturing 10% polyacrylamide gel electrophoresis of 5′-end radiolabeled Ex1a transcript treated as follows: lane 1, dissolved in water and incubated at 20°C for 30 min; lane 2, heated to 75°C for 1 min (denaturation) and cooled slowly to 20°C (renaturation); lane 3, dissolved in the structure-probing buffer (10 mM Tris–HCl pH 7.2, 10 mM magnesium ions, 40 mM NaCl) and incubated at 20°C for 30 min; lane 4, dissolved as described for lane 3 and subjected to the denaturation/renaturation procedure; lane 5, dissolved as described for lane 3, carrier RNA added to a final concentration of 8 µM, and incubated at 20°C for 30 min; lane 6, carrier RNA added and subjected to denaturation/renaturation. ( B ) CE in non-denaturing conditions of Ex1a transcript fluorescently labeled at its 3′ end with TdT and: [R110]dUTP, [RG6]dUTP, [TAMRA]dUTP (shadowed peaks); TAMRA-500 internal standard (gray line). ( C ) CE in non-denaturing polymer at temperatures: 30, 45 and 60°C of Ex1a transcript end labeled with [R110]dUTP and Klenow fragment. ( D ) Non-denaturing 10% polyacrylamide gel electrophoresis of 5′-end radiolabeled Ex1a transcript (0.5 µM) (lane 1), and the same transcript hybridized with 18 nt of Rex1a oligodeoxynucleotide complementary to its 3′ end (lane 2). Hybridization of transcript (1 µM) with oligodeoxynucleotide (1 µM) was performed in 15 mM Tris–HCl (pH 7.2), 10 mM MgCl 2 , 1.5 mM DTT by heating the sample at 90°C for 1 min and fast cooling. Arrowhead indicates the position of hybrid migration. ( E ) CE in non-denaturing conditions of Ex1a102nt transcript labeled with TdT and [RG6]dUTP (gray line indicates ROX-500 internal standard).
    Figure Legend Snippet: Analysis of structurally heterogeneous BRCA1 Ex1a and transcript truncation to obtain a homogeneous structure. ( A ) Non-denaturing 10% polyacrylamide gel electrophoresis of 5′-end radiolabeled Ex1a transcript treated as follows: lane 1, dissolved in water and incubated at 20°C for 30 min; lane 2, heated to 75°C for 1 min (denaturation) and cooled slowly to 20°C (renaturation); lane 3, dissolved in the structure-probing buffer (10 mM Tris–HCl pH 7.2, 10 mM magnesium ions, 40 mM NaCl) and incubated at 20°C for 30 min; lane 4, dissolved as described for lane 3 and subjected to the denaturation/renaturation procedure; lane 5, dissolved as described for lane 3, carrier RNA added to a final concentration of 8 µM, and incubated at 20°C for 30 min; lane 6, carrier RNA added and subjected to denaturation/renaturation. ( B ) CE in non-denaturing conditions of Ex1a transcript fluorescently labeled at its 3′ end with TdT and: [R110]dUTP, [RG6]dUTP, [TAMRA]dUTP (shadowed peaks); TAMRA-500 internal standard (gray line). ( C ) CE in non-denaturing polymer at temperatures: 30, 45 and 60°C of Ex1a transcript end labeled with [R110]dUTP and Klenow fragment. ( D ) Non-denaturing 10% polyacrylamide gel electrophoresis of 5′-end radiolabeled Ex1a transcript (0.5 µM) (lane 1), and the same transcript hybridized with 18 nt of Rex1a oligodeoxynucleotide complementary to its 3′ end (lane 2). Hybridization of transcript (1 µM) with oligodeoxynucleotide (1 µM) was performed in 15 mM Tris–HCl (pH 7.2), 10 mM MgCl 2 , 1.5 mM DTT by heating the sample at 90°C for 1 min and fast cooling. Arrowhead indicates the position of hybrid migration. ( E ) CE in non-denaturing conditions of Ex1a102nt transcript labeled with TdT and [RG6]dUTP (gray line indicates ROX-500 internal standard).

    Techniques Used: Polyacrylamide Gel Electrophoresis, Incubation, Concentration Assay, Labeling, Hybridization, Migration

    Structure analysis of two BRCA1 transcripts: Ex1a-2 and Ex1b. ( A ) Non-denaturing 6% polyacrylamide gel electrophoresis of 5′-end radiolabeled Ex1b transcript treated as follows: lane 1, dissolved in the structure-probing buffer (10 mM Tris–HCl pH 7.2, 10 mM magnesium ions, 40 mM NaCl) and heated to 75°C for 1 min (denaturation) and cooled slowly to 20°C (renaturation); lane 2, treated as above but with carrier RNA added to a final concentration of 8 µM. ( B ) CE in non-denaturing conditions of Ex1b transcript fluorescently labeled at its 3′ end with TdT and [R110]dUTP (shadowed peak); ROX-500 internal standard (gray line). ( C and D ) As described in (A) and (B) but for Ex1a-2 transcript.
    Figure Legend Snippet: Structure analysis of two BRCA1 transcripts: Ex1a-2 and Ex1b. ( A ) Non-denaturing 6% polyacrylamide gel electrophoresis of 5′-end radiolabeled Ex1b transcript treated as follows: lane 1, dissolved in the structure-probing buffer (10 mM Tris–HCl pH 7.2, 10 mM magnesium ions, 40 mM NaCl) and heated to 75°C for 1 min (denaturation) and cooled slowly to 20°C (renaturation); lane 2, treated as above but with carrier RNA added to a final concentration of 8 µM. ( B ) CE in non-denaturing conditions of Ex1b transcript fluorescently labeled at its 3′ end with TdT and [R110]dUTP (shadowed peak); ROX-500 internal standard (gray line). ( C and D ) As described in (A) and (B) but for Ex1a-2 transcript.

    Techniques Used: Polyacrylamide Gel Electrophoresis, Concentration Assay, Labeling

    Efficiency of fluorescent 3′-end labeling of the BRCA1 transcripts. ( A ) Three rhodamine derivatives of dUTP used for 3′-end labeling of RNAs: [R110]dUTP (left), [RG6]dUTP (middle), [TAMRA]dUTP (right). The maximum emission wavelengths of fluorochromes used are 525, 549 and 572 nm for R110, RG6 and TAMRA, respectively. ( B ) CE in denaturing conditions of three BRCA1 transcripts: Ex1a47nt, Ex1b64nt and Ex1a-2, labeled with Klenow fragment and [R110]dUTP (top), [RG6]dUTP (middle) and [TAMRA]dUTP (bottom); TAMRA-500 or ROX-1000 internal standard (gray lines). ( C ) CE in denaturing conditions of three BRCA1 transcripts: Ex1a102nt, Ex1a and Ex1a-2, labeled with TdT and [R110]dUTP (top), [RG6]dUTP (middle), [TAMRA]dUTP (bottom). ( D ) Relative labeling efficiency of three different RNA molecules with three fluorescent dUTP derivatives using Klenow fragment. The shown labeling efficiency with [TAMRA]dUTP was multiplied by a factor of 4, as the emission intensity of this fluorochrome is four times lower than that for the other two rhodamine derivatives used. The data represent average values obtained in three independent experiments, and [R110]dUTP incorporation is taken as 100%. ( E ) As in (D), but using TdT to label five different RNAs.
    Figure Legend Snippet: Efficiency of fluorescent 3′-end labeling of the BRCA1 transcripts. ( A ) Three rhodamine derivatives of dUTP used for 3′-end labeling of RNAs: [R110]dUTP (left), [RG6]dUTP (middle), [TAMRA]dUTP (right). The maximum emission wavelengths of fluorochromes used are 525, 549 and 572 nm for R110, RG6 and TAMRA, respectively. ( B ) CE in denaturing conditions of three BRCA1 transcripts: Ex1a47nt, Ex1b64nt and Ex1a-2, labeled with Klenow fragment and [R110]dUTP (top), [RG6]dUTP (middle) and [TAMRA]dUTP (bottom); TAMRA-500 or ROX-1000 internal standard (gray lines). ( C ) CE in denaturing conditions of three BRCA1 transcripts: Ex1a102nt, Ex1a and Ex1a-2, labeled with TdT and [R110]dUTP (top), [RG6]dUTP (middle), [TAMRA]dUTP (bottom). ( D ) Relative labeling efficiency of three different RNA molecules with three fluorescent dUTP derivatives using Klenow fragment. The shown labeling efficiency with [TAMRA]dUTP was multiplied by a factor of 4, as the emission intensity of this fluorochrome is four times lower than that for the other two rhodamine derivatives used. The data represent average values obtained in three independent experiments, and [R110]dUTP incorporation is taken as 100%. ( E ) As in (D), but using TdT to label five different RNAs.

    Techniques Used: End Labeling, Labeling

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    Thermo Fisher terminal deoxynucleotidyl transferase dutp nick end labeling tunel assay kit
    CAV-1 prevents apoptotic cell death. (A) Signals of terminal <t>deoxynucleotidyl</t> <t>TUNEL-positive</t> cells (arrows) were higher in the HC group than in the NC and HCAV-1 groups. Green fluorescence was observed during TUNEL staining (Alexa Fluror 488 nm), and the nuclei were stained with Hoechst dye (blue). (B) Quantification of the TUNEL IHF stain in rabbit renal tissue per 400× fields for seven fields per animal, with six rabbits for each group. A significantly low number of TUNEL-positive cells were observed in the HCAV-1 group; * and † differ significantly for the NC and HC groups, respectively, at P
    Terminal Deoxynucleotidyl Transferase Dutp Nick End Labeling Tunel Assay Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 97/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher terminal deoxynucleotidyl transferase dutp nick end labeling staining sections
    Terminal <t>deoxynucleotidyl</t> transferase <t>dUTP</t> nick end labeling (TUNEL) staining in the neuroretina. TUNEL staining of retinal sections from pigs subject to retinal ischemia followed by 5, 12, or 20 h of reperfusion versus control (sham). Note that TUNEL-positive cells can be detected in retinas from ischemia-reperfusion eyes but are absent in retinas from sham-operated eyes. The number of TUNEL-labeled cells increases gradually with the duration of reperfusion. TUNEL-positive cells are observed throughout the retinal sections, including the outer nuclear layer (ONL), inner nuclear layer (INL), and ganglion cell layer (GCL). The bottom panels are enlargements of the inserts above.
    Terminal Deoxynucleotidyl Transferase Dutp Nick End Labeling Staining Sections, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    97
    Thermo Fisher terminal deoxynucleotidyl transferase mediated dutp nick end labeling assaymasson trichrome
    There was decreased proliferation but increased apoptosis in female arteriovenous fistulas (AVFs). A , Representative Ki‐67 (female, N=5; male, N=6) and terminal <t>deoxynucleotidyl</t> transferase‐mediated <t>dUTP</t> nick‐end labeling (TUNEL) (female, N=5; male, N=7) sections from female and male AVFs at day 28. Positive Ki‐67 staining was observed throughout the whole male outflow vein. The positive TUNEL staining was shown in the whole vessel wall of female outflow vein. B and C , There was a significant decrease in the average Ki‐67 staining but increased TUNEL staining in females compared with males at day 28. Two‐sample t test was performed. Significant differences between female and male are indicated. ** P
    Terminal Deoxynucleotidyl Transferase Mediated Dutp Nick End Labeling Assaymasson Trichrome, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 97/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher fluorescein 12 dutp solution
    Micrographs showing salt stress-treated rice root tissue subjected to TUNEL assay to assess in situ DNA fragmentation. Root tissue from 15-day old rice seedlings was subjected to salinity stress (200 mM NaCl) for 60 h followed by TUNEL assay as per the protocol described above. F: Fluorescein (green), PI: Propidium Iodide (red), DAPI: 4’,6-diamidino-2-phenylindole (blue). Samples were mounted on slides in a mountant (ProLong ® Gold Antifade with DAPI, Thermo Fisher Scientific) and the slides were examined under Nikon A1R (Nikon, Japan) confocal microscope using a 20x objective. NIS Elements AR software (Nikon, Japan) was used to acquire and process the images. DAPI and PI were used to stain DNA (both damaged and undamaged). Fluorescein fluorescence (green) is due to incorporation of <t>fluorescein-12-dUTP</t> during the TUNEL reaction and would correspond to the number of free DNA ends. Scale bars = 100 µm.
    Fluorescein 12 Dutp Solution, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    CAV-1 prevents apoptotic cell death. (A) Signals of terminal deoxynucleotidyl TUNEL-positive cells (arrows) were higher in the HC group than in the NC and HCAV-1 groups. Green fluorescence was observed during TUNEL staining (Alexa Fluror 488 nm), and the nuclei were stained with Hoechst dye (blue). (B) Quantification of the TUNEL IHF stain in rabbit renal tissue per 400× fields for seven fields per animal, with six rabbits for each group. A significantly low number of TUNEL-positive cells were observed in the HCAV-1 group; * and † differ significantly for the NC and HC groups, respectively, at P

    Journal: PLoS ONE

    Article Title: Caveolin-1 Expression Ameliorates Nephrotic Damage in a Rabbit Model of Cholesterol-Induced Hypercholesterolemia

    doi: 10.1371/journal.pone.0154210

    Figure Lengend Snippet: CAV-1 prevents apoptotic cell death. (A) Signals of terminal deoxynucleotidyl TUNEL-positive cells (arrows) were higher in the HC group than in the NC and HCAV-1 groups. Green fluorescence was observed during TUNEL staining (Alexa Fluror 488 nm), and the nuclei were stained with Hoechst dye (blue). (B) Quantification of the TUNEL IHF stain in rabbit renal tissue per 400× fields for seven fields per animal, with six rabbits for each group. A significantly low number of TUNEL-positive cells were observed in the HCAV-1 group; * and † differ significantly for the NC and HC groups, respectively, at P

    Article Snippet: After incubation, cell death was detected in renal sections by using a terminal deoxynucleotidyl transferase dUTP nick end-labeling (TUNEL) assay kit (Invitrogen) according to manufacturer instructions.

    Techniques: TUNEL Assay, Fluorescence, Staining, Immunohistofluorescence

    Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) staining in the neuroretina. TUNEL staining of retinal sections from pigs subject to retinal ischemia followed by 5, 12, or 20 h of reperfusion versus control (sham). Note that TUNEL-positive cells can be detected in retinas from ischemia-reperfusion eyes but are absent in retinas from sham-operated eyes. The number of TUNEL-labeled cells increases gradually with the duration of reperfusion. TUNEL-positive cells are observed throughout the retinal sections, including the outer nuclear layer (ONL), inner nuclear layer (INL), and ganglion cell layer (GCL). The bottom panels are enlargements of the inserts above.

    Journal: Molecular Vision

    Article Title: Mitogen-activated protein kinases in the porcine retinal arteries and neuroretina following retinal ischemia-reperfusion

    doi:

    Figure Lengend Snippet: Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) staining in the neuroretina. TUNEL staining of retinal sections from pigs subject to retinal ischemia followed by 5, 12, or 20 h of reperfusion versus control (sham). Note that TUNEL-positive cells can be detected in retinas from ischemia-reperfusion eyes but are absent in retinas from sham-operated eyes. The number of TUNEL-labeled cells increases gradually with the duration of reperfusion. TUNEL-positive cells are observed throughout the retinal sections, including the outer nuclear layer (ONL), inner nuclear layer (INL), and ganglion cell layer (GCL). The bottom panels are enlargements of the inserts above.

    Article Snippet: Terminal deoxynucleotidyl transferase dUTP nick end labeling staining Sections were washed with PBS (0.14 M NaCI, 0.01 M PO4 Buffer, 0.003 M KCI, pH 7.45; Invitrogen, Carlsbad, CA), followed by a series of incubations with 0.05 M Tris, pH 7.6, between washing.

    Techniques: TUNEL Assay, Staining, Labeling

    There was decreased proliferation but increased apoptosis in female arteriovenous fistulas (AVFs). A , Representative Ki‐67 (female, N=5; male, N=6) and terminal deoxynucleotidyl transferase‐mediated dUTP nick‐end labeling (TUNEL) (female, N=5; male, N=7) sections from female and male AVFs at day 28. Positive Ki‐67 staining was observed throughout the whole male outflow vein. The positive TUNEL staining was shown in the whole vessel wall of female outflow vein. B and C , There was a significant decrease in the average Ki‐67 staining but increased TUNEL staining in females compared with males at day 28. Two‐sample t test was performed. Significant differences between female and male are indicated. ** P

    Journal: Journal of the American Heart Association: Cardiovascular and Cerebrovascular Disease

    Article Title: Differences in Transforming Growth Factor‐β1/BMP7 Signaling and Venous Fibrosis Contribute to Female Sex Differences in Arteriovenous Fistulas

    doi: 10.1161/JAHA.120.017420

    Figure Lengend Snippet: There was decreased proliferation but increased apoptosis in female arteriovenous fistulas (AVFs). A , Representative Ki‐67 (female, N=5; male, N=6) and terminal deoxynucleotidyl transferase‐mediated dUTP nick‐end labeling (TUNEL) (female, N=5; male, N=7) sections from female and male AVFs at day 28. Positive Ki‐67 staining was observed throughout the whole male outflow vein. The positive TUNEL staining was shown in the whole vessel wall of female outflow vein. B and C , There was a significant decrease in the average Ki‐67 staining but increased TUNEL staining in females compared with males at day 28. Two‐sample t test was performed. Significant differences between female and male are indicated. ** P

    Article Snippet: Masson Trichrome Staining and Terminal Deoxynucleotidyl Transferase‐Mediated dUTP Nick‐End Labeling AssayMasson trichrome (Richard‐Allan Scientific, Kalamazoo, MI) and terminal deoxynucleotidyl transferase‐mediated dUTP nick‐end labeling (TUNEL) staining (TACS 2 TdT DAB In Situ Apoptosis Detection Kit; Trevigen Inc, Gaithersburg, MD) were performed on female and male outflow veins, according to the manufacturer's directions, to evaluate vascular fibrosis and apoptosis, respectively., , .

    Techniques: End Labeling, TUNEL Assay, Staining

    Micrographs showing salt stress-treated rice root tissue subjected to TUNEL assay to assess in situ DNA fragmentation. Root tissue from 15-day old rice seedlings was subjected to salinity stress (200 mM NaCl) for 60 h followed by TUNEL assay as per the protocol described above. F: Fluorescein (green), PI: Propidium Iodide (red), DAPI: 4’,6-diamidino-2-phenylindole (blue). Samples were mounted on slides in a mountant (ProLong ® Gold Antifade with DAPI, Thermo Fisher Scientific) and the slides were examined under Nikon A1R (Nikon, Japan) confocal microscope using a 20x objective. NIS Elements AR software (Nikon, Japan) was used to acquire and process the images. DAPI and PI were used to stain DNA (both damaged and undamaged). Fluorescein fluorescence (green) is due to incorporation of fluorescein-12-dUTP during the TUNEL reaction and would correspond to the number of free DNA ends. Scale bars = 100 µm.

    Journal: Bio-protocol

    Article Title: TUNEL Assay to Assess Extent of DNA Fragmentation and Programmed Cell Death in Root Cells under Various Stress Conditions

    doi: 10.21769/BioProtoc.2502

    Figure Lengend Snippet: Micrographs showing salt stress-treated rice root tissue subjected to TUNEL assay to assess in situ DNA fragmentation. Root tissue from 15-day old rice seedlings was subjected to salinity stress (200 mM NaCl) for 60 h followed by TUNEL assay as per the protocol described above. F: Fluorescein (green), PI: Propidium Iodide (red), DAPI: 4’,6-diamidino-2-phenylindole (blue). Samples were mounted on slides in a mountant (ProLong ® Gold Antifade with DAPI, Thermo Fisher Scientific) and the slides were examined under Nikon A1R (Nikon, Japan) confocal microscope using a 20x objective. NIS Elements AR software (Nikon, Japan) was used to acquire and process the images. DAPI and PI were used to stain DNA (both damaged and undamaged). Fluorescein fluorescence (green) is due to incorporation of fluorescein-12-dUTP during the TUNEL reaction and would correspond to the number of free DNA ends. Scale bars = 100 µm.

    Article Snippet: Fluorescein-12-dUTP* (Thermo Fisher Scientific, Thermo ScientificTM, catalog number: R0101). dATP* (Promega, catalog number: U1202).

    Techniques: TUNEL Assay, In Situ, Microscopy, Software, Staining, Fluorescence