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alui methyltransferase buffer  (New England Biolabs)


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    Structured Review

    New England Biolabs alui methyltransferase buffer
    A , Primary domain structure of SauUSI. B , Translocation directionality from displacement of the triplex forming oligonucleotides (TFO) using triplex gel electrophoresis assays with dimethylated DNA <t>(M.AluI)</t> or strand-specific hemimethylated DNA (M1/M2.BfuAI). C , Time-dependent triplex displacement from linear DNA with different hemimethylation – triplex distances measured using a stopped flow assay. Samples were mixed as indicated (cartoon) with Protein (P), DNA (D), ATP and heparin (Trap, where included). Rate determined in Supp. Fig. X . D , Role of upstream DNA in supporting translocation using a triplex gel electrophoresis assay with linear DNAs with different length of DNA upstream of a hemimethylated site. Data points are the average of 2 repeats with a line joining the points. ( inset ) AlphaFold3 model of a SauUSI dimer with one subunit binding a 41 bp hemimethylated DNA. E , Effect of ATP concentration on initiation measured using stopped flow triplex displacement ( left panel ) or on ATP hydrolysis rates measured using the phosphate binding protein (PBP, right panel ). Triplex assays were fitted to a plateau followed by a two-phase association (black line), with the amplitude of the fast phase giving the proportion of active translocating motors in the presence of excess K255A trap. The ATPase data was corrected for background ATPase activity and fitted by linear regression (black dotted line) to give rates that were adjusted by the active motor fraction . F , Comparison of the ATP dependence of the translocation rate ( k step ) and ATPase rate ( k ATP ). Lines are separate hyperbolic fits to the data (n = 2). Quoted parameters are the mean and standard errors.
    Alui Methyltransferase Buffer, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 93/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Images

    1) Product Images from "Individual Staphylococcus aureus SauUSI restriction endonuclease motors fragment methylated DNA"

    Article Title: Individual Staphylococcus aureus SauUSI restriction endonuclease motors fragment methylated DNA

    Journal: bioRxiv

    doi: 10.1101/2025.10.16.682607

    A , Primary domain structure of SauUSI. B , Translocation directionality from displacement of the triplex forming oligonucleotides (TFO) using triplex gel electrophoresis assays with dimethylated DNA (M.AluI) or strand-specific hemimethylated DNA (M1/M2.BfuAI). C , Time-dependent triplex displacement from linear DNA with different hemimethylation – triplex distances measured using a stopped flow assay. Samples were mixed as indicated (cartoon) with Protein (P), DNA (D), ATP and heparin (Trap, where included). Rate determined in Supp. Fig. X . D , Role of upstream DNA in supporting translocation using a triplex gel electrophoresis assay with linear DNAs with different length of DNA upstream of a hemimethylated site. Data points are the average of 2 repeats with a line joining the points. ( inset ) AlphaFold3 model of a SauUSI dimer with one subunit binding a 41 bp hemimethylated DNA. E , Effect of ATP concentration on initiation measured using stopped flow triplex displacement ( left panel ) or on ATP hydrolysis rates measured using the phosphate binding protein (PBP, right panel ). Triplex assays were fitted to a plateau followed by a two-phase association (black line), with the amplitude of the fast phase giving the proportion of active translocating motors in the presence of excess K255A trap. The ATPase data was corrected for background ATPase activity and fitted by linear regression (black dotted line) to give rates that were adjusted by the active motor fraction . F , Comparison of the ATP dependence of the translocation rate ( k step ) and ATPase rate ( k ATP ). Lines are separate hyperbolic fits to the data (n = 2). Quoted parameters are the mean and standard errors.
    Figure Legend Snippet: A , Primary domain structure of SauUSI. B , Translocation directionality from displacement of the triplex forming oligonucleotides (TFO) using triplex gel electrophoresis assays with dimethylated DNA (M.AluI) or strand-specific hemimethylated DNA (M1/M2.BfuAI). C , Time-dependent triplex displacement from linear DNA with different hemimethylation – triplex distances measured using a stopped flow assay. Samples were mixed as indicated (cartoon) with Protein (P), DNA (D), ATP and heparin (Trap, where included). Rate determined in Supp. Fig. X . D , Role of upstream DNA in supporting translocation using a triplex gel electrophoresis assay with linear DNAs with different length of DNA upstream of a hemimethylated site. Data points are the average of 2 repeats with a line joining the points. ( inset ) AlphaFold3 model of a SauUSI dimer with one subunit binding a 41 bp hemimethylated DNA. E , Effect of ATP concentration on initiation measured using stopped flow triplex displacement ( left panel ) or on ATP hydrolysis rates measured using the phosphate binding protein (PBP, right panel ). Triplex assays were fitted to a plateau followed by a two-phase association (black line), with the amplitude of the fast phase giving the proportion of active translocating motors in the presence of excess K255A trap. The ATPase data was corrected for background ATPase activity and fitted by linear regression (black dotted line) to give rates that were adjusted by the active motor fraction . F , Comparison of the ATP dependence of the translocation rate ( k step ) and ATPase rate ( k ATP ). Lines are separate hyperbolic fits to the data (n = 2). Quoted parameters are the mean and standard errors.

    Techniques Used: Translocation Assay, Nucleic Acid Electrophoresis, Binding Assay, Concentration Assay, Activity Assay, Comparison

    Related Articles

    Concentration Assay:

    Article Title: Cell cycle dynamics of lamina associated DNA
    Article Snippet: Unmethylated control plasmid was produced in dam − bacteria (New England BioLabs #C2925H) and methylation status was confirmed by DpnI and DpnII digestion. .. A concentration range (0.125, 0.5, 2 μL) of pA-Dam protein was incubated with 500 ng of unmethylated plasmid in 20 μL of 1x dam MethylTransferase buffer (New England BioLabs #M0222S) supplemented with 80 μM S-adenosylmethionine (SAM) for 30 minutes at 37°C. .. As a positive control, a concentration range (0.25, 1, 4, 16 units) of Dam enzyme was used (New England BioLabs #M0222S).

    Article Title: Cell cycle dynamics of lamina-associated DNA.
    Article Snippet: Unmethylated control plasmid was produced in dam bacteria (New England BioLabs #C2925H), and methylation status was confirmed by DpnI and DpnII digestion. .. A concentration range (0.125, 0.5, 2 ll) of pA-Dam protein was incubated with 500 ng of unmethylated plasmid in 20 ll of 1× dam MethylTransferase buffer (New England BioLabs #M0222S) supplemented with 80 lM Sadenosylmethionine (SAM) for 30 min at 37°C. .. As a positive control, a concentration range (0.25, 1, 4, 16 units) of Dam enzyme was used (New England BioLabs #M0222S).

    Article Title: Cell cycle dynamics of lamina‐associated DNA
    Article Snippet: Unmethylated control plasmid was produced in dam − bacteria (New England BioLabs #C2925H), and methylation status was confirmed by DpnI and DpnII digestion. .. A concentration range (0.125, 0.5, 2 μl) of pA‐Dam protein was incubated with 500 ng of unmethylated plasmid in 20 μl of 1× dam MethylTransferase buffer (New England BioLabs #M0222S) supplemented with 80 μM S‐adenosylmethionine (SAM) for 30 min at 37°C. .. As a positive control, a concentration range (0.25, 1, 4, 16 units) of Dam enzyme was used (New England BioLabs #M0222S).

    Incubation:

    Article Title: Cell cycle dynamics of lamina associated DNA
    Article Snippet: Unmethylated control plasmid was produced in dam − bacteria (New England BioLabs #C2925H) and methylation status was confirmed by DpnI and DpnII digestion. .. A concentration range (0.125, 0.5, 2 μL) of pA-Dam protein was incubated with 500 ng of unmethylated plasmid in 20 μL of 1x dam MethylTransferase buffer (New England BioLabs #M0222S) supplemented with 80 μM S-adenosylmethionine (SAM) for 30 minutes at 37°C. .. As a positive control, a concentration range (0.25, 1, 4, 16 units) of Dam enzyme was used (New England BioLabs #M0222S).

    Article Title: Dynamics of the Eukaryotic Replicative Helicase at Lagging-Strand Protein Barriers Support the Steric Exclusion Model
    Article Snippet: .. 5FdC-modified fork templates were mixed with HpaII methyltransferase (M.HpaII) in 1:4 DNA to protein molar ratio in methyltransferase buffer (50 mM Tris-HCl, pH 7.5, 0.5 mM 2-mercaptoethanol (β-ME), 10 mM EDTA, NEB) supplemented with 100 μM S-adenosylmethionine (NEB), and incubated at 37°C for 3 hours. ..

    Article Title: Molecular Basis for ATP-Hydrolysis-Driven DNA Translocation by the CMG Helicase of the Eukaryotic Replisome
    Article Snippet: .. M.HpaII (NEB) was crosslinked in methyltransferase buffer (50 mM Tris-HCl pH 7.5, 0.5 mM 2-mercaptoethanol, 10 mM EDTA, NEB) supplemented with 100 μM S-adenosylmethionine (NEB), and incubated at 37°C for 3 hours. ..

    Article Title: Cell cycle dynamics of lamina-associated DNA.
    Article Snippet: Unmethylated control plasmid was produced in dam bacteria (New England BioLabs #C2925H), and methylation status was confirmed by DpnI and DpnII digestion. .. A concentration range (0.125, 0.5, 2 ll) of pA-Dam protein was incubated with 500 ng of unmethylated plasmid in 20 ll of 1× dam MethylTransferase buffer (New England BioLabs #M0222S) supplemented with 80 lM Sadenosylmethionine (SAM) for 30 min at 37°C. .. As a positive control, a concentration range (0.25, 1, 4, 16 units) of Dam enzyme was used (New England BioLabs #M0222S).

    Article Title: Cell cycle dynamics of lamina‐associated DNA
    Article Snippet: Unmethylated control plasmid was produced in dam − bacteria (New England BioLabs #C2925H), and methylation status was confirmed by DpnI and DpnII digestion. .. A concentration range (0.125, 0.5, 2 μl) of pA‐Dam protein was incubated with 500 ng of unmethylated plasmid in 20 μl of 1× dam MethylTransferase buffer (New England BioLabs #M0222S) supplemented with 80 μM S‐adenosylmethionine (SAM) for 30 min at 37°C. .. As a positive control, a concentration range (0.25, 1, 4, 16 units) of Dam enzyme was used (New England BioLabs #M0222S).

    Article Title: Molecular Basis for ATP-Hydrolysis-Driven DNA Translocation by the CMG Helicase of the Eukaryotic Replisome
    Article Snippet: .. M.HpaII (NEB) was crosslinked in methyltransferase buffer (50 mM Tris-HCl pH 7.5, 0.5 mM 2-mercaptoethanol, 10 mM EDTA, NEB) supplemented with 100 μM S-adenosylmethionine (NEB), and incubated at 37°C for 5 hours. ..

    Plasmid Preparation:

    Article Title: Cell cycle dynamics of lamina associated DNA
    Article Snippet: Unmethylated control plasmid was produced in dam − bacteria (New England BioLabs #C2925H) and methylation status was confirmed by DpnI and DpnII digestion. .. A concentration range (0.125, 0.5, 2 μL) of pA-Dam protein was incubated with 500 ng of unmethylated plasmid in 20 μL of 1x dam MethylTransferase buffer (New England BioLabs #M0222S) supplemented with 80 μM S-adenosylmethionine (SAM) for 30 minutes at 37°C. .. As a positive control, a concentration range (0.25, 1, 4, 16 units) of Dam enzyme was used (New England BioLabs #M0222S).

    Article Title: Cell cycle dynamics of lamina-associated DNA.
    Article Snippet: Unmethylated control plasmid was produced in dam bacteria (New England BioLabs #C2925H), and methylation status was confirmed by DpnI and DpnII digestion. .. A concentration range (0.125, 0.5, 2 ll) of pA-Dam protein was incubated with 500 ng of unmethylated plasmid in 20 ll of 1× dam MethylTransferase buffer (New England BioLabs #M0222S) supplemented with 80 lM Sadenosylmethionine (SAM) for 30 min at 37°C. .. As a positive control, a concentration range (0.25, 1, 4, 16 units) of Dam enzyme was used (New England BioLabs #M0222S).

    Article Title: Cell cycle dynamics of lamina‐associated DNA
    Article Snippet: Unmethylated control plasmid was produced in dam − bacteria (New England BioLabs #C2925H), and methylation status was confirmed by DpnI and DpnII digestion. .. A concentration range (0.125, 0.5, 2 μl) of pA‐Dam protein was incubated with 500 ng of unmethylated plasmid in 20 μl of 1× dam MethylTransferase buffer (New England BioLabs #M0222S) supplemented with 80 μM S‐adenosylmethionine (SAM) for 30 min at 37°C. .. As a positive control, a concentration range (0.25, 1, 4, 16 units) of Dam enzyme was used (New England BioLabs #M0222S).

    DNA Methylation Assay:

    Article Title: De novo Identification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing
    Article Snippet: .. DNA methylation was performed in vitro by incubating DNA (60 ng/uL) with 1 uL of methyltransferase and 80uM S-adenosyl-L-methionine in 50 uL of aqueous solution containing the appropriate methyltransferase buffer (NEB Cutsmart Buffer was used for both the M.MpeI and M.TaqI). ..

    In Vitro:

    Article Title: De novo Identification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing
    Article Snippet: .. DNA methylation was performed in vitro by incubating DNA (60 ng/uL) with 1 uL of methyltransferase and 80uM S-adenosyl-L-methionine in 50 uL of aqueous solution containing the appropriate methyltransferase buffer (NEB Cutsmart Buffer was used for both the M.MpeI and M.TaqI). ..



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    A , Primary domain structure of SauUSI. B , Translocation directionality from displacement of the triplex forming oligonucleotides (TFO) using triplex gel electrophoresis assays with dimethylated DNA (M.AluI) or strand-specific hemimethylated DNA (M1/M2.BfuAI). C , Time-dependent triplex displacement from linear DNA with different hemimethylation – triplex distances measured using a stopped flow assay. Samples were mixed as indicated (cartoon) with Protein (P), DNA (D), ATP and heparin (Trap, where included). Rate determined in Supp. Fig. X . D , Role of upstream DNA in supporting translocation using a triplex gel electrophoresis assay with linear DNAs with different length of DNA upstream of a hemimethylated site. Data points are the average of 2 repeats with a line joining the points. ( inset ) AlphaFold3 model of a SauUSI dimer with one subunit binding a 41 bp hemimethylated DNA. E , Effect of ATP concentration on initiation measured using stopped flow triplex displacement ( left panel ) or on ATP hydrolysis rates measured using the phosphate binding protein (PBP, right panel ). Triplex assays were fitted to a plateau followed by a two-phase association (black line), with the amplitude of the fast phase giving the proportion of active translocating motors in the presence of excess K255A trap. The ATPase data was corrected for background ATPase activity and fitted by linear regression (black dotted line) to give rates that were adjusted by the active motor fraction . F , Comparison of the ATP dependence of the translocation rate ( k step ) and ATPase rate ( k ATP ). Lines are separate hyperbolic fits to the data (n = 2). Quoted parameters are the mean and standard errors.

    Journal: bioRxiv

    Article Title: Individual Staphylococcus aureus SauUSI restriction endonuclease motors fragment methylated DNA

    doi: 10.1101/2025.10.16.682607

    Figure Lengend Snippet: A , Primary domain structure of SauUSI. B , Translocation directionality from displacement of the triplex forming oligonucleotides (TFO) using triplex gel electrophoresis assays with dimethylated DNA (M.AluI) or strand-specific hemimethylated DNA (M1/M2.BfuAI). C , Time-dependent triplex displacement from linear DNA with different hemimethylation – triplex distances measured using a stopped flow assay. Samples were mixed as indicated (cartoon) with Protein (P), DNA (D), ATP and heparin (Trap, where included). Rate determined in Supp. Fig. X . D , Role of upstream DNA in supporting translocation using a triplex gel electrophoresis assay with linear DNAs with different length of DNA upstream of a hemimethylated site. Data points are the average of 2 repeats with a line joining the points. ( inset ) AlphaFold3 model of a SauUSI dimer with one subunit binding a 41 bp hemimethylated DNA. E , Effect of ATP concentration on initiation measured using stopped flow triplex displacement ( left panel ) or on ATP hydrolysis rates measured using the phosphate binding protein (PBP, right panel ). Triplex assays were fitted to a plateau followed by a two-phase association (black line), with the amplitude of the fast phase giving the proportion of active translocating motors in the presence of excess K255A trap. The ATPase data was corrected for background ATPase activity and fitted by linear regression (black dotted line) to give rates that were adjusted by the active motor fraction . F , Comparison of the ATP dependence of the translocation rate ( k step ) and ATPase rate ( k ATP ). Lines are separate hyperbolic fits to the data (n = 2). Quoted parameters are the mean and standard errors.

    Article Snippet: Methylation by M.AluI used equimolar methyltransferase to DNA with 640 μM S -adenosyl methionine (AdoMet) in AluI methyltransferase buffer (New England Biolabs, NEB).

    Techniques: Translocation Assay, Nucleic Acid Electrophoresis, Binding Assay, Concentration Assay, Activity Assay, Comparison