n 6 - Search Results


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  • 95
    Jena Bioscience n6 methyl datp
    Potential routes for cellular production and metabolism of <t>N6-methyl-dATP</t> and N6-methyl-ATP. N6-methyl-dATP and N6-methyl-ATP may be produced from N6-methyl-dAMP and N6-methyl-AMP formed upon DNA and RNA degradation, respectively. This may occur through the consecutive actions of adenylate kinase ( AK ) and nucleoside diphosphate kinase or through nonspecific methylation by S -adenosylmethionine ( SAM ), the N6-adenosine-methyltransferase METTL3 or N6-adenine–specific DNA methyltransferase 1 ( N6AMT1 ). N6-methyl-dATP and N6-methyl-ATP are hydrolyzed by MTH1 to their corresponding monophosphates and further metabolized by ADAL1 to dIMP and IMP that can then enter the nucleotide salvage pathway. Abbreviations used in the figure: NDPK , nucleoside diphosphate kinase; RNR, ribonucleotide reductase; METTL3, N6-adenosine methyltransferase; N6AMT1, N6-adenine-specific DNA methyltransferase 1.
    N6 Methyl Datp, supplied by Jena Bioscience, used in various techniques. Bioz Stars score: 95/100, based on 18 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    New England Biolabs lambda phage dna
    Potential routes for cellular production and metabolism of <t>N6-methyl-dATP</t> and N6-methyl-ATP. N6-methyl-dATP and N6-methyl-ATP may be produced from N6-methyl-dAMP and N6-methyl-AMP formed upon DNA and RNA degradation, respectively. This may occur through the consecutive actions of adenylate kinase ( AK ) and nucleoside diphosphate kinase or through nonspecific methylation by S -adenosylmethionine ( SAM ), the N6-adenosine-methyltransferase METTL3 or N6-adenine–specific DNA methyltransferase 1 ( N6AMT1 ). N6-methyl-dATP and N6-methyl-ATP are hydrolyzed by MTH1 to their corresponding monophosphates and further metabolized by ADAL1 to dIMP and IMP that can then enter the nucleotide salvage pathway. Abbreviations used in the figure: NDPK , nucleoside diphosphate kinase; RNR, ribonucleotide reductase; METTL3, N6-adenosine methyltransferase; N6AMT1, N6-adenine-specific DNA methyltransferase 1.
    Lambda Phage Dna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 179 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Millipore dibutyryl camp
    Proposed mechanism for intracellular zinc mobilization. Glucose induces <t>cAMP-PKA-dependent</t> intracellular zinc release and can be inhibited by the AC inhibitor MDL12330 or the PKA inhibitor myr-PKI. The cAMP analog, <t>dibutyryl</t> cAMP and PDE inhibitors, also induces intracellular zinc release. Extracellular Zn 2+ induces ER zinc efflux through a cAMP-PKA independent mechanism.
    Dibutyryl Camp, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 1835 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    New England Biolabs epimark n6 methyladenosine enrichment kit
    Proposed mechanism for intracellular zinc mobilization. Glucose induces <t>cAMP-PKA-dependent</t> intracellular zinc release and can be inhibited by the AC inhibitor MDL12330 or the PKA inhibitor myr-PKI. The cAMP analog, <t>dibutyryl</t> cAMP and PDE inhibitors, also induces intracellular zinc release. Extracellular Zn 2+ induces ER zinc efflux through a cAMP-PKA independent mechanism.
    Epimark N6 Methyladenosine Enrichment Kit, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 80 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    BIOLOG Life Science Institute n6 etheno adenosine
    Proposed mechanism for intracellular zinc mobilization. Glucose induces <t>cAMP-PKA-dependent</t> intracellular zinc release and can be inhibited by the AC inhibitor MDL12330 or the PKA inhibitor myr-PKI. The cAMP analog, <t>dibutyryl</t> cAMP and PDE inhibitors, also induces intracellular zinc release. Extracellular Zn 2+ induces ER zinc efflux through a cAMP-PKA independent mechanism.
    N6 Etheno Adenosine, supplied by BIOLOG Life Science Institute, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Millipore l n6
    Proposed mechanism for intracellular zinc mobilization. Glucose induces <t>cAMP-PKA-dependent</t> intracellular zinc release and can be inhibited by the AC inhibitor MDL12330 or the PKA inhibitor myr-PKI. The cAMP analog, <t>dibutyryl</t> cAMP and PDE inhibitors, also induces intracellular zinc release. Extracellular Zn 2+ induces ER zinc efflux through a cAMP-PKA independent mechanism.
    L N6, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 232 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Abcam anti n6 methyladenosine m6a antibody
    In silico and in vitro validation of Nanocompore. A: Position plots showing the median intensity (top) and dwell time (bottom) for simulated data generated by Nanocompore SimReads. Dashed vertical lines indicate modified positions, where a clear signal shift between unmodified (green) and modified (orange) reads can be seen. B: ROC curves obtained with the GMM method on in silico generated data. The different subplots indicate varying amounts of intensity and dwell time shifts from the unmodified model (from 1 to 4 standard deviations), whereas the different colors indicate varying fractions of modified reads in the generated data (from 10% to 100%). All the comparisons are against a fully unmodified reference dataset. C: Diagram depicting the experimental and signal processing workflow used to run Nanocompore on a synthetic RNA carrying an <t>N6-methyladenosine</t> residue. Briefly, the RNA sequence was obtained by ligating an oligo carrying an <t>m6A</t> residue at position 6 to a longer unmodified carrier obtained by IVT of the firefly luciferase gene. The data obtained by DRS was parsed to extract the signal from the 2 short regions corresponding to a “UGAGGACUGUA” with either an A or an m6A in the middle. D: Plot showing the Nanocompore p-values (-log 10 , y-axis. Tests: GMM+logit and KS) for the synthetically modified GGACU kmer and those surrounding it. E: Scatter plot showing the median signal intensity (x-axis) and scaled dwell time (log 10 , y-axis) for the synthetically modified kmer. The concentric lines show the kernel density estimates for the two samples.
    Anti N6 Methyladenosine M6a Antibody, supplied by Abcam, used in various techniques. Bioz Stars score: 92/100, based on 35 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Millipore n6 cyclopentyladenosine cpa
    In silico and in vitro validation of Nanocompore. A: Position plots showing the median intensity (top) and dwell time (bottom) for simulated data generated by Nanocompore SimReads. Dashed vertical lines indicate modified positions, where a clear signal shift between unmodified (green) and modified (orange) reads can be seen. B: ROC curves obtained with the GMM method on in silico generated data. The different subplots indicate varying amounts of intensity and dwell time shifts from the unmodified model (from 1 to 4 standard deviations), whereas the different colors indicate varying fractions of modified reads in the generated data (from 10% to 100%). All the comparisons are against a fully unmodified reference dataset. C: Diagram depicting the experimental and signal processing workflow used to run Nanocompore on a synthetic RNA carrying an <t>N6-methyladenosine</t> residue. Briefly, the RNA sequence was obtained by ligating an oligo carrying an <t>m6A</t> residue at position 6 to a longer unmodified carrier obtained by IVT of the firefly luciferase gene. The data obtained by DRS was parsed to extract the signal from the 2 short regions corresponding to a “UGAGGACUGUA” with either an A or an m6A in the middle. D: Plot showing the Nanocompore p-values (-log 10 , y-axis. Tests: GMM+logit and KS) for the synthetically modified GGACU kmer and those surrounding it. E: Scatter plot showing the median signal intensity (x-axis) and scaled dwell time (log 10 , y-axis) for the synthetically modified kmer. The concentric lines show the kernel density estimates for the two samples.
    N6 Cyclopentyladenosine Cpa, supplied by Millipore, used in various techniques. Bioz Stars score: 94/100, based on 26 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    BIOLOG Life Science Institute n6 etheno adenine
    In silico and in vitro validation of Nanocompore. A: Position plots showing the median intensity (top) and dwell time (bottom) for simulated data generated by Nanocompore SimReads. Dashed vertical lines indicate modified positions, where a clear signal shift between unmodified (green) and modified (orange) reads can be seen. B: ROC curves obtained with the GMM method on in silico generated data. The different subplots indicate varying amounts of intensity and dwell time shifts from the unmodified model (from 1 to 4 standard deviations), whereas the different colors indicate varying fractions of modified reads in the generated data (from 10% to 100%). All the comparisons are against a fully unmodified reference dataset. C: Diagram depicting the experimental and signal processing workflow used to run Nanocompore on a synthetic RNA carrying an <t>N6-methyladenosine</t> residue. Briefly, the RNA sequence was obtained by ligating an oligo carrying an <t>m6A</t> residue at position 6 to a longer unmodified carrier obtained by IVT of the firefly luciferase gene. The data obtained by DRS was parsed to extract the signal from the 2 short regions corresponding to a “UGAGGACUGUA” with either an A or an m6A in the middle. D: Plot showing the Nanocompore p-values (-log 10 , y-axis. Tests: GMM+logit and KS) for the synthetically modified GGACU kmer and those surrounding it. E: Scatter plot showing the median signal intensity (x-axis) and scaled dwell time (log 10 , y-axis) for the synthetically modified kmer. The concentric lines show the kernel density estimates for the two samples.
    N6 Etheno Adenine, supplied by BIOLOG Life Science Institute, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    ccpa  (Tocris)
    97
    Tocris ccpa
    In silico and in vitro validation of Nanocompore. A: Position plots showing the median intensity (top) and dwell time (bottom) for simulated data generated by Nanocompore SimReads. Dashed vertical lines indicate modified positions, where a clear signal shift between unmodified (green) and modified (orange) reads can be seen. B: ROC curves obtained with the GMM method on in silico generated data. The different subplots indicate varying amounts of intensity and dwell time shifts from the unmodified model (from 1 to 4 standard deviations), whereas the different colors indicate varying fractions of modified reads in the generated data (from 10% to 100%). All the comparisons are against a fully unmodified reference dataset. C: Diagram depicting the experimental and signal processing workflow used to run Nanocompore on a synthetic RNA carrying an <t>N6-methyladenosine</t> residue. Briefly, the RNA sequence was obtained by ligating an oligo carrying an <t>m6A</t> residue at position 6 to a longer unmodified carrier obtained by IVT of the firefly luciferase gene. The data obtained by DRS was parsed to extract the signal from the 2 short regions corresponding to a “UGAGGACUGUA” with either an A or an m6A in the middle. D: Plot showing the Nanocompore p-values (-log 10 , y-axis. Tests: GMM+logit and KS) for the synthetically modified GGACU kmer and those surrounding it. E: Scatter plot showing the median signal intensity (x-axis) and scaled dwell time (log 10 , y-axis) for the synthetically modified kmer. The concentric lines show the kernel density estimates for the two samples.
    Ccpa, supplied by Tocris, used in various techniques. Bioz Stars score: 97/100, based on 39 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher n 6 biotinamido hexyl 3 2 pyridyldithio propionamide biotin hpdp
    In silico and in vitro validation of Nanocompore. A: Position plots showing the median intensity (top) and dwell time (bottom) for simulated data generated by Nanocompore SimReads. Dashed vertical lines indicate modified positions, where a clear signal shift between unmodified (green) and modified (orange) reads can be seen. B: ROC curves obtained with the GMM method on in silico generated data. The different subplots indicate varying amounts of intensity and dwell time shifts from the unmodified model (from 1 to 4 standard deviations), whereas the different colors indicate varying fractions of modified reads in the generated data (from 10% to 100%). All the comparisons are against a fully unmodified reference dataset. C: Diagram depicting the experimental and signal processing workflow used to run Nanocompore on a synthetic RNA carrying an <t>N6-methyladenosine</t> residue. Briefly, the RNA sequence was obtained by ligating an oligo carrying an <t>m6A</t> residue at position 6 to a longer unmodified carrier obtained by IVT of the firefly luciferase gene. The data obtained by DRS was parsed to extract the signal from the 2 short regions corresponding to a “UGAGGACUGUA” with either an A or an m6A in the middle. D: Plot showing the Nanocompore p-values (-log 10 , y-axis. Tests: GMM+logit and KS) for the synthetically modified GGACU kmer and those surrounding it. E: Scatter plot showing the median signal intensity (x-axis) and scaled dwell time (log 10 , y-axis) for the synthetically modified kmer. The concentric lines show the kernel density estimates for the two samples.
    N 6 Biotinamido Hexyl 3 2 Pyridyldithio Propionamide Biotin Hpdp, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 31 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Millipore n6 benzyladenine
    In silico and in vitro validation of Nanocompore. A: Position plots showing the median intensity (top) and dwell time (bottom) for simulated data generated by Nanocompore SimReads. Dashed vertical lines indicate modified positions, where a clear signal shift between unmodified (green) and modified (orange) reads can be seen. B: ROC curves obtained with the GMM method on in silico generated data. The different subplots indicate varying amounts of intensity and dwell time shifts from the unmodified model (from 1 to 4 standard deviations), whereas the different colors indicate varying fractions of modified reads in the generated data (from 10% to 100%). All the comparisons are against a fully unmodified reference dataset. C: Diagram depicting the experimental and signal processing workflow used to run Nanocompore on a synthetic RNA carrying an <t>N6-methyladenosine</t> residue. Briefly, the RNA sequence was obtained by ligating an oligo carrying an <t>m6A</t> residue at position 6 to a longer unmodified carrier obtained by IVT of the firefly luciferase gene. The data obtained by DRS was parsed to extract the signal from the 2 short regions corresponding to a “UGAGGACUGUA” with either an A or an m6A in the middle. D: Plot showing the Nanocompore p-values (-log 10 , y-axis. Tests: GMM+logit and KS) for the synthetically modified GGACU kmer and those surrounding it. E: Scatter plot showing the median signal intensity (x-axis) and scaled dwell time (log 10 , y-axis) for the synthetically modified kmer. The concentric lines show the kernel density estimates for the two samples.
    N6 Benzyladenine, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 21 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher n 6 biotinamido hexyl 3 2 pyridyldithio propionamide
    In silico and in vitro validation of Nanocompore. A: Position plots showing the median intensity (top) and dwell time (bottom) for simulated data generated by Nanocompore SimReads. Dashed vertical lines indicate modified positions, where a clear signal shift between unmodified (green) and modified (orange) reads can be seen. B: ROC curves obtained with the GMM method on in silico generated data. The different subplots indicate varying amounts of intensity and dwell time shifts from the unmodified model (from 1 to 4 standard deviations), whereas the different colors indicate varying fractions of modified reads in the generated data (from 10% to 100%). All the comparisons are against a fully unmodified reference dataset. C: Diagram depicting the experimental and signal processing workflow used to run Nanocompore on a synthetic RNA carrying an <t>N6-methyladenosine</t> residue. Briefly, the RNA sequence was obtained by ligating an oligo carrying an <t>m6A</t> residue at position 6 to a longer unmodified carrier obtained by IVT of the firefly luciferase gene. The data obtained by DRS was parsed to extract the signal from the 2 short regions corresponding to a “UGAGGACUGUA” with either an A or an m6A in the middle. D: Plot showing the Nanocompore p-values (-log 10 , y-axis. Tests: GMM+logit and KS) for the synthetically modified GGACU kmer and those surrounding it. E: Scatter plot showing the median signal intensity (x-axis) and scaled dwell time (log 10 , y-axis) for the synthetically modified kmer. The concentric lines show the kernel density estimates for the two samples.
    N 6 Biotinamido Hexyl 3 2 Pyridyldithio Propionamide, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 80 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    97
    Millipore n 6 cyclohexyladenosine cha
    Effect of adenosine A 1 agonists on cardiac myocyte injury. Cultured ventricular myocytes were prepared, and extent of hypoxia-mediated myocyte injury was determined as described in METHODS. <t>CHA,</t> <t>N</t> 6 <t>-cyclohexyladenosine;</t> ADAC, adenosine amine congener. Adenosine A 1 -receptor agonists were added to medium at concentrations indicated in absence or presence of A 1 -receptor antagonist DPCPX during prolonged hypoxia. Percentage of cells killed was determined after hypoxic exposure and removal of A 1 -receptor agonists and antagonist. Data are means of 4 experiments. At 1 and 10 nM concentrations of A 1 agonists, percentages of myocytes killed were significantly lower than those obtained in presence of either of the 2 A 1 -agonist concentrations and DPCPX (1 μ M) ( P
    N 6 Cyclohexyladenosine Cha, supplied by Millipore, used in various techniques. Bioz Stars score: 97/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Enzo Biochem biotin n6 ddatp
    Effect of adenosine A 1 agonists on cardiac myocyte injury. Cultured ventricular myocytes were prepared, and extent of hypoxia-mediated myocyte injury was determined as described in METHODS. <t>CHA,</t> <t>N</t> 6 <t>-cyclohexyladenosine;</t> ADAC, adenosine amine congener. Adenosine A 1 -receptor agonists were added to medium at concentrations indicated in absence or presence of A 1 -receptor antagonist DPCPX during prolonged hypoxia. Percentage of cells killed was determined after hypoxic exposure and removal of A 1 -receptor agonists and antagonist. Data are means of 4 experiments. At 1 and 10 nM concentrations of A 1 agonists, percentages of myocytes killed were significantly lower than those obtained in presence of either of the 2 A 1 -agonist concentrations and DPCPX (1 μ M) ( P
    Biotin N6 Ddatp, supplied by Enzo Biochem, used in various techniques. Bioz Stars score: 92/100, based on 81 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Potential routes for cellular production and metabolism of N6-methyl-dATP and N6-methyl-ATP. N6-methyl-dATP and N6-methyl-ATP may be produced from N6-methyl-dAMP and N6-methyl-AMP formed upon DNA and RNA degradation, respectively. This may occur through the consecutive actions of adenylate kinase ( AK ) and nucleoside diphosphate kinase or through nonspecific methylation by S -adenosylmethionine ( SAM ), the N6-adenosine-methyltransferase METTL3 or N6-adenine–specific DNA methyltransferase 1 ( N6AMT1 ). N6-methyl-dATP and N6-methyl-ATP are hydrolyzed by MTH1 to their corresponding monophosphates and further metabolized by ADAL1 to dIMP and IMP that can then enter the nucleotide salvage pathway. Abbreviations used in the figure: NDPK , nucleoside diphosphate kinase; RNR, ribonucleotide reductase; METTL3, N6-adenosine methyltransferase; N6AMT1, N6-adenine-specific DNA methyltransferase 1.

    Journal: The Journal of Biological Chemistry

    Article Title: MutT homologue 1 (MTH1) removes N6-methyl-dATP from the dNTP pool

    doi: 10.1074/jbc.RA120.012636

    Figure Lengend Snippet: Potential routes for cellular production and metabolism of N6-methyl-dATP and N6-methyl-ATP. N6-methyl-dATP and N6-methyl-ATP may be produced from N6-methyl-dAMP and N6-methyl-AMP formed upon DNA and RNA degradation, respectively. This may occur through the consecutive actions of adenylate kinase ( AK ) and nucleoside diphosphate kinase or through nonspecific methylation by S -adenosylmethionine ( SAM ), the N6-adenosine-methyltransferase METTL3 or N6-adenine–specific DNA methyltransferase 1 ( N6AMT1 ). N6-methyl-dATP and N6-methyl-ATP are hydrolyzed by MTH1 to their corresponding monophosphates and further metabolized by ADAL1 to dIMP and IMP that can then enter the nucleotide salvage pathway. Abbreviations used in the figure: NDPK , nucleoside diphosphate kinase; RNR, ribonucleotide reductase; METTL3, N6-adenosine methyltransferase; N6AMT1, N6-adenine-specific DNA methyltransferase 1.

    Article Snippet: Determination of N6-methyl-dATP activity among NUDT1 enzymes from different species NUDT1 enzyme from human (hMTH1), dog (clNUDT1), pig (ssNUDT1), rat (rnNUDT1), mouse (mmNUDT1), zebrafish (zfNUDT1), A. thaliana (atNUDT1), and E. coli (E. coli MutT) (1.25 nm ) was incubated with 50 μm N6-methyl-dATP (Jena BioScience) in MTH1 reaction buffer (0.1 m Tris acetate, pH 7.5, 40 mm sodium chloride, 10 mm magnesium acetate), and 0.4 units/ml of PPase for 20 min at 22 °C in clear 384-well-plates, in quadruplicate.

    Techniques: Produced, Methylation

    MTH1 catalyzes the hydrolysis of N6-methyl-dATP. A, MTH1 catalyzes the hydrolysis of N6-methyl-dATP to N6-methyl-dAMP and PP i . B, time course hydrolysis of N6-methyl-dATP (1 m m ) catalyzed by MTH1 (20 n m ) was monitored by separation of reaction samples incubated 0–40 min at 22 °C on a Hypercarb column using HPLC coupled to MS. Reaction substrate and product was detected at 254 nm and the mass of the product N6-methyl-dAMP was clearly observed by mass detection. C, graph showing the fraction of N6-methyl-dATP and N6-methyl-dAMP in percent after various times of hydrolysis based on the respective area under the curve of the peaks in the corresponding HPLC chromatogram.

    Journal: The Journal of Biological Chemistry

    Article Title: MutT homologue 1 (MTH1) removes N6-methyl-dATP from the dNTP pool

    doi: 10.1074/jbc.RA120.012636

    Figure Lengend Snippet: MTH1 catalyzes the hydrolysis of N6-methyl-dATP. A, MTH1 catalyzes the hydrolysis of N6-methyl-dATP to N6-methyl-dAMP and PP i . B, time course hydrolysis of N6-methyl-dATP (1 m m ) catalyzed by MTH1 (20 n m ) was monitored by separation of reaction samples incubated 0–40 min at 22 °C on a Hypercarb column using HPLC coupled to MS. Reaction substrate and product was detected at 254 nm and the mass of the product N6-methyl-dAMP was clearly observed by mass detection. C, graph showing the fraction of N6-methyl-dATP and N6-methyl-dAMP in percent after various times of hydrolysis based on the respective area under the curve of the peaks in the corresponding HPLC chromatogram.

    Article Snippet: Determination of N6-methyl-dATP activity among NUDT1 enzymes from different species NUDT1 enzyme from human (hMTH1), dog (clNUDT1), pig (ssNUDT1), rat (rnNUDT1), mouse (mmNUDT1), zebrafish (zfNUDT1), A. thaliana (atNUDT1), and E. coli (E. coli MutT) (1.25 nm ) was incubated with 50 μm N6-methyl-dATP (Jena BioScience) in MTH1 reaction buffer (0.1 m Tris acetate, pH 7.5, 40 mm sodium chloride, 10 mm magnesium acetate), and 0.4 units/ml of PPase for 20 min at 22 °C in clear 384-well-plates, in quadruplicate.

    Techniques: Incubation, High Performance Liquid Chromatography

    Activity with N6-methyl-dATP is unique to MTH1 within human NUDIX subfamily. Activities of human NUDIX enzyme (MTH1, NUDT15, NUDT17, and NUDT18) were assayed with data points in quadruplicate with 50 μ m dATP or N6-methyl-dATP at 20 and 200 n m enzyme in MTH1 reaction buffer (pH 8.0). 0.2 units/ml of PPase was used to convert formed PP i to P i that was detected using malachite green reagent and measurement of absorbance at 630 nm. Graph shows mean ± S.D. from one experiment performed in triplicate.

    Journal: The Journal of Biological Chemistry

    Article Title: MutT homologue 1 (MTH1) removes N6-methyl-dATP from the dNTP pool

    doi: 10.1074/jbc.RA120.012636

    Figure Lengend Snippet: Activity with N6-methyl-dATP is unique to MTH1 within human NUDIX subfamily. Activities of human NUDIX enzyme (MTH1, NUDT15, NUDT17, and NUDT18) were assayed with data points in quadruplicate with 50 μ m dATP or N6-methyl-dATP at 20 and 200 n m enzyme in MTH1 reaction buffer (pH 8.0). 0.2 units/ml of PPase was used to convert formed PP i to P i that was detected using malachite green reagent and measurement of absorbance at 630 nm. Graph shows mean ± S.D. from one experiment performed in triplicate.

    Article Snippet: Determination of N6-methyl-dATP activity among NUDT1 enzymes from different species NUDT1 enzyme from human (hMTH1), dog (clNUDT1), pig (ssNUDT1), rat (rnNUDT1), mouse (mmNUDT1), zebrafish (zfNUDT1), A. thaliana (atNUDT1), and E. coli (E. coli MutT) (1.25 nm ) was incubated with 50 μm N6-methyl-dATP (Jena BioScience) in MTH1 reaction buffer (0.1 m Tris acetate, pH 7.5, 40 mm sodium chloride, 10 mm magnesium acetate), and 0.4 units/ml of PPase for 20 min at 22 °C in clear 384-well-plates, in quadruplicate.

    Techniques: Activity Assay

    Activity with N6-methyl-dATP is evolutionary conserved among vertebrates. MutT homologues (MTH1 and NUDT1) from different animal species as well as E. coli MutT and NUDT1 from the plant A. thaliana were screened for hydrolysis activity with N6-methyl-dATP. Enzyme (1.25 n m ) was incubated with 50 μ m N6-methyl-dATP in MTH1 reaction buffer (pH 7.5) with 0.4 units/ml of PPase for 20 min at 22 °C in triplicates. P i was detected using Biomol Green (Enzo Life Sciences). Absorbance at 630 nm was read after 20 min. A P i standard curve was included on the plate and used to convert the assay signal to produced PP i . Data are shown as hydrolyzed N6-methyl-dATP (μ m ) divided by concentration of NUDT1 enzyme (μ m ) per second. The graph shows the mean ± S.D. from an experiment performed in triplicate.

    Journal: The Journal of Biological Chemistry

    Article Title: MutT homologue 1 (MTH1) removes N6-methyl-dATP from the dNTP pool

    doi: 10.1074/jbc.RA120.012636

    Figure Lengend Snippet: Activity with N6-methyl-dATP is evolutionary conserved among vertebrates. MutT homologues (MTH1 and NUDT1) from different animal species as well as E. coli MutT and NUDT1 from the plant A. thaliana were screened for hydrolysis activity with N6-methyl-dATP. Enzyme (1.25 n m ) was incubated with 50 μ m N6-methyl-dATP in MTH1 reaction buffer (pH 7.5) with 0.4 units/ml of PPase for 20 min at 22 °C in triplicates. P i was detected using Biomol Green (Enzo Life Sciences). Absorbance at 630 nm was read after 20 min. A P i standard curve was included on the plate and used to convert the assay signal to produced PP i . Data are shown as hydrolyzed N6-methyl-dATP (μ m ) divided by concentration of NUDT1 enzyme (μ m ) per second. The graph shows the mean ± S.D. from an experiment performed in triplicate.

    Article Snippet: Determination of N6-methyl-dATP activity among NUDT1 enzymes from different species NUDT1 enzyme from human (hMTH1), dog (clNUDT1), pig (ssNUDT1), rat (rnNUDT1), mouse (mmNUDT1), zebrafish (zfNUDT1), A. thaliana (atNUDT1), and E. coli (E. coli MutT) (1.25 nm ) was incubated with 50 μm N6-methyl-dATP (Jena BioScience) in MTH1 reaction buffer (0.1 m Tris acetate, pH 7.5, 40 mm sodium chloride, 10 mm magnesium acetate), and 0.4 units/ml of PPase for 20 min at 22 °C in clear 384-well-plates, in quadruplicate.

    Techniques: Activity Assay, Incubation, Produced, Concentration Assay

    Kinetic characterization of MTH1-catalyzed hydrolysis of dATP, N6-methyl-dATP, N6-methyl-ATP, dGTP, and O6-methyl-dGTP. A, substrate saturation curves of MTH1 (1 n m ) were produced using MTH1 reaction buffer (pH 7.5). Initial rates were determined at dATP concentrations varied between 0 and 200 μ m and between 0 and 300 μ m for N6-methyl-dATP and N6-methyl-ATP, respectively, and for dGTP and O6-methyl-dGTP ( B ) using 0–300 and 0–200 μ m , respectively. Formed PP i was detected using PPiLight TM Inorganic Pyrophosphate Assay (Lonza) and the assay signal was converted to concentration of PP i by including a PP i standard curve on the assay plate.

    Journal: The Journal of Biological Chemistry

    Article Title: MutT homologue 1 (MTH1) removes N6-methyl-dATP from the dNTP pool

    doi: 10.1074/jbc.RA120.012636

    Figure Lengend Snippet: Kinetic characterization of MTH1-catalyzed hydrolysis of dATP, N6-methyl-dATP, N6-methyl-ATP, dGTP, and O6-methyl-dGTP. A, substrate saturation curves of MTH1 (1 n m ) were produced using MTH1 reaction buffer (pH 7.5). Initial rates were determined at dATP concentrations varied between 0 and 200 μ m and between 0 and 300 μ m for N6-methyl-dATP and N6-methyl-ATP, respectively, and for dGTP and O6-methyl-dGTP ( B ) using 0–300 and 0–200 μ m , respectively. Formed PP i was detected using PPiLight TM Inorganic Pyrophosphate Assay (Lonza) and the assay signal was converted to concentration of PP i by including a PP i standard curve on the assay plate.

    Article Snippet: Determination of N6-methyl-dATP activity among NUDT1 enzymes from different species NUDT1 enzyme from human (hMTH1), dog (clNUDT1), pig (ssNUDT1), rat (rnNUDT1), mouse (mmNUDT1), zebrafish (zfNUDT1), A. thaliana (atNUDT1), and E. coli (E. coli MutT) (1.25 nm ) was incubated with 50 μm N6-methyl-dATP (Jena BioScience) in MTH1 reaction buffer (0.1 m Tris acetate, pH 7.5, 40 mm sodium chloride, 10 mm magnesium acetate), and 0.4 units/ml of PPase for 20 min at 22 °C in clear 384-well-plates, in quadruplicate.

    Techniques: Produced, Pyrophosphate Assay, Concentration Assay

    MTH1 activity with N6-methyl-dATP and N6-methyl-ATP compared with dATP. Activity of 1 and 5 n m MTH1 was tested with 50 μ m N6-methyl-dATP, dATP, ATP, and N6-methyl-ATP in MTH1 reaction buffer (pH 8.0) at 22 °C. Reaction time was 30 min and 0.2 units/ml of PPase was used to generate P i from produced PP i . P i was detected by addition of malachite green reagent followed by measurement of the absorbance at 630 nm. Controls with PPase only was included and background signal was subtracted from the assay data. A P i standard curve was included on the plate enabling determination of the concentration of formed PP i . Graph shows mean ± S.D. from one experiment performed in quadruplicate.

    Journal: The Journal of Biological Chemistry

    Article Title: MutT homologue 1 (MTH1) removes N6-methyl-dATP from the dNTP pool

    doi: 10.1074/jbc.RA120.012636

    Figure Lengend Snippet: MTH1 activity with N6-methyl-dATP and N6-methyl-ATP compared with dATP. Activity of 1 and 5 n m MTH1 was tested with 50 μ m N6-methyl-dATP, dATP, ATP, and N6-methyl-ATP in MTH1 reaction buffer (pH 8.0) at 22 °C. Reaction time was 30 min and 0.2 units/ml of PPase was used to generate P i from produced PP i . P i was detected by addition of malachite green reagent followed by measurement of the absorbance at 630 nm. Controls with PPase only was included and background signal was subtracted from the assay data. A P i standard curve was included on the plate enabling determination of the concentration of formed PP i . Graph shows mean ± S.D. from one experiment performed in quadruplicate.

    Article Snippet: Determination of N6-methyl-dATP activity among NUDT1 enzymes from different species NUDT1 enzyme from human (hMTH1), dog (clNUDT1), pig (ssNUDT1), rat (rnNUDT1), mouse (mmNUDT1), zebrafish (zfNUDT1), A. thaliana (atNUDT1), and E. coli (E. coli MutT) (1.25 nm ) was incubated with 50 μm N6-methyl-dATP (Jena BioScience) in MTH1 reaction buffer (0.1 m Tris acetate, pH 7.5, 40 mm sodium chloride, 10 mm magnesium acetate), and 0.4 units/ml of PPase for 20 min at 22 °C in clear 384-well-plates, in quadruplicate.

    Techniques: Activity Assay, Produced, Concentration Assay

    Schematic representation of the recognition of nucleotides by hMTH1. Hydrogen bond interactions of ( A ) N6-methyl-dAMP (N6-metA), ( B ) 2-oxo-dATP (2-oxoA) ( 23 ), ( C ) O6-methyl-dGMP (O6-metG) ( 10 ), and ( D ) 8-oxo-dGMP (8-oxoG) ( 24 ). Hydrogen bonds are shown as dashed lines and bond distances are given in Angstroms (Å). Deprotonated aspartates, which act as hydrogen bond acceptors, are indicated by the minus sign , where this is unambiguous.

    Journal: The Journal of Biological Chemistry

    Article Title: MutT homologue 1 (MTH1) removes N6-methyl-dATP from the dNTP pool

    doi: 10.1074/jbc.RA120.012636

    Figure Lengend Snippet: Schematic representation of the recognition of nucleotides by hMTH1. Hydrogen bond interactions of ( A ) N6-methyl-dAMP (N6-metA), ( B ) 2-oxo-dATP (2-oxoA) ( 23 ), ( C ) O6-methyl-dGMP (O6-metG) ( 10 ), and ( D ) 8-oxo-dGMP (8-oxoG) ( 24 ). Hydrogen bonds are shown as dashed lines and bond distances are given in Angstroms (Å). Deprotonated aspartates, which act as hydrogen bond acceptors, are indicated by the minus sign , where this is unambiguous.

    Article Snippet: Determination of N6-methyl-dATP activity among NUDT1 enzymes from different species NUDT1 enzyme from human (hMTH1), dog (clNUDT1), pig (ssNUDT1), rat (rnNUDT1), mouse (mmNUDT1), zebrafish (zfNUDT1), A. thaliana (atNUDT1), and E. coli (E. coli MutT) (1.25 nm ) was incubated with 50 μm N6-methyl-dATP (Jena BioScience) in MTH1 reaction buffer (0.1 m Tris acetate, pH 7.5, 40 mm sodium chloride, 10 mm magnesium acetate), and 0.4 units/ml of PPase for 20 min at 22 °C in clear 384-well-plates, in quadruplicate.

    Techniques:

    N6-methyl-dATP is incorporated into DNA in an MTH1-dependent manner. DNA was extracted from zebrafish MTH1KO and MTH1WT embryos developed from fertilized zebrafish eggs microinjected with N6-methyl-dATP or left untreated. DNA was analyzed for N6-methyl-dA content using LC-MS/MS. N6-methyl-dA content was normalized to N6-methyldA levels in untreated MTH1KO and MTH1WT zebrafish embryos, respectively. N6-methyl-dATP microinjected MTH1KO zebrafish embryos display a 2-fold higher N6-methyl-dA level compared with untreated embryos, whereas N6-methyl-dA DNA levels in MTH1WT zebrafish did not differ between untreated and N6-methyl-dA–microinjected embryos. This suggests that N6-methyl-dATP is incorporated into DNA and incorporation can be prevented by MTH1. The graph shows mean ± S.D., n = 2.

    Journal: The Journal of Biological Chemistry

    Article Title: MutT homologue 1 (MTH1) removes N6-methyl-dATP from the dNTP pool

    doi: 10.1074/jbc.RA120.012636

    Figure Lengend Snippet: N6-methyl-dATP is incorporated into DNA in an MTH1-dependent manner. DNA was extracted from zebrafish MTH1KO and MTH1WT embryos developed from fertilized zebrafish eggs microinjected with N6-methyl-dATP or left untreated. DNA was analyzed for N6-methyl-dA content using LC-MS/MS. N6-methyl-dA content was normalized to N6-methyldA levels in untreated MTH1KO and MTH1WT zebrafish embryos, respectively. N6-methyl-dATP microinjected MTH1KO zebrafish embryos display a 2-fold higher N6-methyl-dA level compared with untreated embryos, whereas N6-methyl-dA DNA levels in MTH1WT zebrafish did not differ between untreated and N6-methyl-dA–microinjected embryos. This suggests that N6-methyl-dATP is incorporated into DNA and incorporation can be prevented by MTH1. The graph shows mean ± S.D., n = 2.

    Article Snippet: Determination of N6-methyl-dATP activity among NUDT1 enzymes from different species NUDT1 enzyme from human (hMTH1), dog (clNUDT1), pig (ssNUDT1), rat (rnNUDT1), mouse (mmNUDT1), zebrafish (zfNUDT1), A. thaliana (atNUDT1), and E. coli (E. coli MutT) (1.25 nm ) was incubated with 50 μm N6-methyl-dATP (Jena BioScience) in MTH1 reaction buffer (0.1 m Tris acetate, pH 7.5, 40 mm sodium chloride, 10 mm magnesium acetate), and 0.4 units/ml of PPase for 20 min at 22 °C in clear 384-well-plates, in quadruplicate.

    Techniques: Liquid Chromatography with Mass Spectroscopy

    Proposed mechanism for intracellular zinc mobilization. Glucose induces cAMP-PKA-dependent intracellular zinc release and can be inhibited by the AC inhibitor MDL12330 or the PKA inhibitor myr-PKI. The cAMP analog, dibutyryl cAMP and PDE inhibitors, also induces intracellular zinc release. Extracellular Zn 2+ induces ER zinc efflux through a cAMP-PKA independent mechanism.

    Journal: Frontiers in Microbiology

    Article Title: Cyclic AMP Pathway Activation and Extracellular Zinc Induce Rapid Intracellular Zinc Mobilization in Candida albicans

    doi: 10.3389/fmicb.2018.00502

    Figure Lengend Snippet: Proposed mechanism for intracellular zinc mobilization. Glucose induces cAMP-PKA-dependent intracellular zinc release and can be inhibited by the AC inhibitor MDL12330 or the PKA inhibitor myr-PKI. The cAMP analog, dibutyryl cAMP and PDE inhibitors, also induces intracellular zinc release. Extracellular Zn 2+ induces ER zinc efflux through a cAMP-PKA independent mechanism.

    Article Snippet: The following compounds were used: 25 μl of dithiothreitol (DTT, D0632, Sigma), theophylline (T1633, Sigma), caffeine (C8960, Sigma), dibutyryl cAMP (D0260, Sigma), MDL12330 (sc-3537, Santa Cruz,) or myristoylated PKI (14–22) (myr-PKI, sc-471154, Santa Cruz,).

    Techniques:

    In silico and in vitro validation of Nanocompore. A: Position plots showing the median intensity (top) and dwell time (bottom) for simulated data generated by Nanocompore SimReads. Dashed vertical lines indicate modified positions, where a clear signal shift between unmodified (green) and modified (orange) reads can be seen. B: ROC curves obtained with the GMM method on in silico generated data. The different subplots indicate varying amounts of intensity and dwell time shifts from the unmodified model (from 1 to 4 standard deviations), whereas the different colors indicate varying fractions of modified reads in the generated data (from 10% to 100%). All the comparisons are against a fully unmodified reference dataset. C: Diagram depicting the experimental and signal processing workflow used to run Nanocompore on a synthetic RNA carrying an N6-methyladenosine residue. Briefly, the RNA sequence was obtained by ligating an oligo carrying an m6A residue at position 6 to a longer unmodified carrier obtained by IVT of the firefly luciferase gene. The data obtained by DRS was parsed to extract the signal from the 2 short regions corresponding to a “UGAGGACUGUA” with either an A or an m6A in the middle. D: Plot showing the Nanocompore p-values (-log 10 , y-axis. Tests: GMM+logit and KS) for the synthetically modified GGACU kmer and those surrounding it. E: Scatter plot showing the median signal intensity (x-axis) and scaled dwell time (log 10 , y-axis) for the synthetically modified kmer. The concentric lines show the kernel density estimates for the two samples.

    Journal: bioRxiv

    Article Title: RNA modifications detection by comparative Nanopore direct RNA sequencing

    doi: 10.1101/843136

    Figure Lengend Snippet: In silico and in vitro validation of Nanocompore. A: Position plots showing the median intensity (top) and dwell time (bottom) for simulated data generated by Nanocompore SimReads. Dashed vertical lines indicate modified positions, where a clear signal shift between unmodified (green) and modified (orange) reads can be seen. B: ROC curves obtained with the GMM method on in silico generated data. The different subplots indicate varying amounts of intensity and dwell time shifts from the unmodified model (from 1 to 4 standard deviations), whereas the different colors indicate varying fractions of modified reads in the generated data (from 10% to 100%). All the comparisons are against a fully unmodified reference dataset. C: Diagram depicting the experimental and signal processing workflow used to run Nanocompore on a synthetic RNA carrying an N6-methyladenosine residue. Briefly, the RNA sequence was obtained by ligating an oligo carrying an m6A residue at position 6 to a longer unmodified carrier obtained by IVT of the firefly luciferase gene. The data obtained by DRS was parsed to extract the signal from the 2 short regions corresponding to a “UGAGGACUGUA” with either an A or an m6A in the middle. D: Plot showing the Nanocompore p-values (-log 10 , y-axis. Tests: GMM+logit and KS) for the synthetically modified GGACU kmer and those surrounding it. E: Scatter plot showing the median signal intensity (x-axis) and scaled dwell time (log 10 , y-axis) for the synthetically modified kmer. The concentric lines show the kernel density estimates for the two samples.

    Article Snippet: Fragmented RNA was then incubated with 2.5μg anti-m6A antibody (Abcam, ab151230) in IP buffer (50mM Tris-HCl pH 7.4, 100mM NaCl, 0.05% NP-40) at 4°C for 2 hours, in rotation.

    Techniques: In Silico, In Vitro, Generated, Modification, Sequencing, Luciferase

    Effect of adenosine A 1 agonists on cardiac myocyte injury. Cultured ventricular myocytes were prepared, and extent of hypoxia-mediated myocyte injury was determined as described in METHODS. CHA, N 6 -cyclohexyladenosine; ADAC, adenosine amine congener. Adenosine A 1 -receptor agonists were added to medium at concentrations indicated in absence or presence of A 1 -receptor antagonist DPCPX during prolonged hypoxia. Percentage of cells killed was determined after hypoxic exposure and removal of A 1 -receptor agonists and antagonist. Data are means of 4 experiments. At 1 and 10 nM concentrations of A 1 agonists, percentages of myocytes killed were significantly lower than those obtained in presence of either of the 2 A 1 -agonist concentrations and DPCPX (1 μ M) ( P

    Journal: The American journal of physiology

    Article Title: A novel cardioprotective function of adenosine A1 and A3 receptors during prolonged simulated ischemia

    doi:

    Figure Lengend Snippet: Effect of adenosine A 1 agonists on cardiac myocyte injury. Cultured ventricular myocytes were prepared, and extent of hypoxia-mediated myocyte injury was determined as described in METHODS. CHA, N 6 -cyclohexyladenosine; ADAC, adenosine amine congener. Adenosine A 1 -receptor agonists were added to medium at concentrations indicated in absence or presence of A 1 -receptor antagonist DPCPX during prolonged hypoxia. Percentage of cells killed was determined after hypoxic exposure and removal of A 1 -receptor agonists and antagonist. Data are means of 4 experiments. At 1 and 10 nM concentrations of A 1 agonists, percentages of myocytes killed were significantly lower than those obtained in presence of either of the 2 A 1 -agonist concentrations and DPCPX (1 μ M) ( P

    Article Snippet: The adenosine analogs 8-cyclopentyl-1,3-dipropylxanthine (DPCPX), 2-chloro- N 6 -cyclopentyladenosine (CCPA), and N 6 -cyclohexyladenosine (CHA) were from Research Biochemicals International (Natick, MA).

    Techniques: Cell Culture