atpase activation  (New England Biolabs)


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    PhiX174 Virion DNA
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    PhiX174 Virion DNA 250 ug
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    New England Biolabs atpase activation
    PhiX174 Virion DNA
    PhiX174 Virion DNA 250 ug
    https://www.bioz.com/result/atpase activation/product/New England Biolabs
    Average 93 stars, based on 1464 article reviews
    Price from $9.99 to $1999.99
    atpase activation - by Bioz Stars, 2020-11
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    Images

    1) Product Images from "The bacterial Mre11–Rad50 homolog SbcCD cleaves opposing strands of DNA by two chemically distinct nuclease reactions"

    Article Title: The bacterial Mre11–Rad50 homolog SbcCD cleaves opposing strands of DNA by two chemically distinct nuclease reactions

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gky878

    ATP hydrolysis stimulation and DNA binding of the SbcCD wt complex. ( A ) The ATP hydrolysis rate of SbcCD wt was measured in dependence to increasing plasmid DNA concentrations. Bacteriophage ΦX174 Plasmid DNA (5386 bp in length) was added as single-stranded, supercoiled, nicked or linear DNA. The data were fit to a Michaelis–Menten equation, error bars indicate the deviation from three replicates. ( B ) DNA stimulation of ATP hydrolysis by the nuclease-deficient SbcCD H84Q complex. The steady-state ATPase rates were measured at 37°C in the presence of 1 mM ATP, 5 mM MgCl 2 and 1 mM MnCl 2 . DNA with 20–60 bp in length was added as an activator. The data was fit to a Michaelis-Menten equation, error bars represent the standard deviation of three measurements. ( C ) DNA binding of SbcCD H84Q to 20–50 bp DNA was assayed in the presence of 1 mM ATP, 5 mM MgCl 2 and 1 mM MnCl 2 . DNA concentration was kept at 5 nM; the SbcCD H84Q concentration ranged from 2 to 1000 nM. Data points represent the change in fluorescence anisotropy and the data were fit to a 1 to 1 binding equation. Error bars represent the deviation from three independent experiments.
    Figure Legend Snippet: ATP hydrolysis stimulation and DNA binding of the SbcCD wt complex. ( A ) The ATP hydrolysis rate of SbcCD wt was measured in dependence to increasing plasmid DNA concentrations. Bacteriophage ΦX174 Plasmid DNA (5386 bp in length) was added as single-stranded, supercoiled, nicked or linear DNA. The data were fit to a Michaelis–Menten equation, error bars indicate the deviation from three replicates. ( B ) DNA stimulation of ATP hydrolysis by the nuclease-deficient SbcCD H84Q complex. The steady-state ATPase rates were measured at 37°C in the presence of 1 mM ATP, 5 mM MgCl 2 and 1 mM MnCl 2 . DNA with 20–60 bp in length was added as an activator. The data was fit to a Michaelis-Menten equation, error bars represent the standard deviation of three measurements. ( C ) DNA binding of SbcCD H84Q to 20–50 bp DNA was assayed in the presence of 1 mM ATP, 5 mM MgCl 2 and 1 mM MnCl 2 . DNA concentration was kept at 5 nM; the SbcCD H84Q concentration ranged from 2 to 1000 nM. Data points represent the change in fluorescence anisotropy and the data were fit to a 1 to 1 binding equation. Error bars represent the deviation from three independent experiments.

    Techniques Used: Binding Assay, Plasmid Preparation, Standard Deviation, Concentration Assay, Fluorescence

    2) Product Images from "The bacterial Mre11–Rad50 homolog SbcCD cleaves opposing strands of DNA by two chemically distinct nuclease reactions"

    Article Title: The bacterial Mre11–Rad50 homolog SbcCD cleaves opposing strands of DNA by two chemically distinct nuclease reactions

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gky878

    ATP hydrolysis stimulation and DNA binding of the SbcCD wt complex. ( A ) The ATP hydrolysis rate of SbcCD wt was measured in dependence to increasing plasmid DNA concentrations. Bacteriophage ΦX174 Plasmid DNA (5386 bp in length) was added as single-stranded, supercoiled, nicked or linear DNA. The data were fit to a Michaelis–Menten equation, error bars indicate the deviation from three replicates. ( B ) DNA stimulation of ATP hydrolysis by the nuclease-deficient SbcCD H84Q complex. The steady-state ATPase rates were measured at 37°C in the presence of 1 mM ATP, 5 mM MgCl 2 and 1 mM MnCl 2 . DNA with 20–60 bp in length was added as an activator. The data was fit to a Michaelis-Menten equation, error bars represent the standard deviation of three measurements. ( C ) DNA binding of SbcCD H84Q to 20–50 bp DNA was assayed in the presence of 1 mM ATP, 5 mM MgCl 2 and 1 mM MnCl 2 . DNA concentration was kept at 5 nM; the SbcCD H84Q concentration ranged from 2 to 1000 nM. Data points represent the change in fluorescence anisotropy and the data were fit to a 1 to 1 binding equation. Error bars represent the deviation from three independent experiments.
    Figure Legend Snippet: ATP hydrolysis stimulation and DNA binding of the SbcCD wt complex. ( A ) The ATP hydrolysis rate of SbcCD wt was measured in dependence to increasing plasmid DNA concentrations. Bacteriophage ΦX174 Plasmid DNA (5386 bp in length) was added as single-stranded, supercoiled, nicked or linear DNA. The data were fit to a Michaelis–Menten equation, error bars indicate the deviation from three replicates. ( B ) DNA stimulation of ATP hydrolysis by the nuclease-deficient SbcCD H84Q complex. The steady-state ATPase rates were measured at 37°C in the presence of 1 mM ATP, 5 mM MgCl 2 and 1 mM MnCl 2 . DNA with 20–60 bp in length was added as an activator. The data was fit to a Michaelis-Menten equation, error bars represent the standard deviation of three measurements. ( C ) DNA binding of SbcCD H84Q to 20–50 bp DNA was assayed in the presence of 1 mM ATP, 5 mM MgCl 2 and 1 mM MnCl 2 . DNA concentration was kept at 5 nM; the SbcCD H84Q concentration ranged from 2 to 1000 nM. Data points represent the change in fluorescence anisotropy and the data were fit to a 1 to 1 binding equation. Error bars represent the deviation from three independent experiments.

    Techniques Used: Binding Assay, Plasmid Preparation, Standard Deviation, Concentration Assay, Fluorescence

    3) Product Images from "The bacterial Mre11–Rad50 homolog SbcCD cleaves opposing strands of DNA by two chemically distinct nuclease reactions"

    Article Title: The bacterial Mre11–Rad50 homolog SbcCD cleaves opposing strands of DNA by two chemically distinct nuclease reactions

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gky878

    ATP hydrolysis stimulation and DNA binding of the SbcCD wt complex. ( A ) The ATP hydrolysis rate of SbcCD wt was measured in dependence to increasing plasmid DNA concentrations. Bacteriophage ΦX174 Plasmid DNA (5386 bp in length) was added as single-stranded, supercoiled, nicked or linear DNA. The data were fit to a Michaelis–Menten equation, error bars indicate the deviation from three replicates. ( B ) DNA stimulation of ATP hydrolysis by the nuclease-deficient SbcCD H84Q complex. The steady-state ATPase rates were measured at 37°C in the presence of 1 mM ATP, 5 mM MgCl 2 and 1 mM MnCl 2 . DNA with 20–60 bp in length was added as an activator. The data was fit to a Michaelis-Menten equation, error bars represent the standard deviation of three measurements. ( C ) DNA binding of SbcCD H84Q to 20–50 bp DNA was assayed in the presence of 1 mM ATP, 5 mM MgCl 2 and 1 mM MnCl 2 . DNA concentration was kept at 5 nM; the SbcCD H84Q concentration ranged from 2 to 1000 nM. Data points represent the change in fluorescence anisotropy and the data were fit to a 1 to 1 binding equation. Error bars represent the deviation from three independent experiments.
    Figure Legend Snippet: ATP hydrolysis stimulation and DNA binding of the SbcCD wt complex. ( A ) The ATP hydrolysis rate of SbcCD wt was measured in dependence to increasing plasmid DNA concentrations. Bacteriophage ΦX174 Plasmid DNA (5386 bp in length) was added as single-stranded, supercoiled, nicked or linear DNA. The data were fit to a Michaelis–Menten equation, error bars indicate the deviation from three replicates. ( B ) DNA stimulation of ATP hydrolysis by the nuclease-deficient SbcCD H84Q complex. The steady-state ATPase rates were measured at 37°C in the presence of 1 mM ATP, 5 mM MgCl 2 and 1 mM MnCl 2 . DNA with 20–60 bp in length was added as an activator. The data was fit to a Michaelis-Menten equation, error bars represent the standard deviation of three measurements. ( C ) DNA binding of SbcCD H84Q to 20–50 bp DNA was assayed in the presence of 1 mM ATP, 5 mM MgCl 2 and 1 mM MnCl 2 . DNA concentration was kept at 5 nM; the SbcCD H84Q concentration ranged from 2 to 1000 nM. Data points represent the change in fluorescence anisotropy and the data were fit to a 1 to 1 binding equation. Error bars represent the deviation from three independent experiments.

    Techniques Used: Binding Assay, Plasmid Preparation, Standard Deviation, Concentration Assay, Fluorescence

    4) Product Images from "The bacterial Mre11–Rad50 homolog SbcCD cleaves opposing strands of DNA by two chemically distinct nuclease reactions"

    Article Title: The bacterial Mre11–Rad50 homolog SbcCD cleaves opposing strands of DNA by two chemically distinct nuclease reactions

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gky878

    ATP hydrolysis stimulation and DNA binding of the SbcCD wt complex. ( A ) The ATP hydrolysis rate of SbcCD wt was measured in dependence to increasing plasmid DNA concentrations. Bacteriophage ΦX174 Plasmid DNA (5386 bp in length) was added as single-stranded, supercoiled, nicked or linear DNA. The data were fit to a Michaelis–Menten equation, error bars indicate the deviation from three replicates. ( B ) DNA stimulation of ATP hydrolysis by the nuclease-deficient SbcCD H84Q complex. The steady-state ATPase rates were measured at 37°C in the presence of 1 mM ATP, 5 mM MgCl 2 and 1 mM MnCl 2 . DNA with 20–60 bp in length was added as an activator. The data was fit to a Michaelis-Menten equation, error bars represent the standard deviation of three measurements. ( C ) DNA binding of SbcCD H84Q to 20–50 bp DNA was assayed in the presence of 1 mM ATP, 5 mM MgCl 2 and 1 mM MnCl 2 . DNA concentration was kept at 5 nM; the SbcCD H84Q concentration ranged from 2 to 1000 nM. Data points represent the change in fluorescence anisotropy and the data were fit to a 1 to 1 binding equation. Error bars represent the deviation from three independent experiments.
    Figure Legend Snippet: ATP hydrolysis stimulation and DNA binding of the SbcCD wt complex. ( A ) The ATP hydrolysis rate of SbcCD wt was measured in dependence to increasing plasmid DNA concentrations. Bacteriophage ΦX174 Plasmid DNA (5386 bp in length) was added as single-stranded, supercoiled, nicked or linear DNA. The data were fit to a Michaelis–Menten equation, error bars indicate the deviation from three replicates. ( B ) DNA stimulation of ATP hydrolysis by the nuclease-deficient SbcCD H84Q complex. The steady-state ATPase rates were measured at 37°C in the presence of 1 mM ATP, 5 mM MgCl 2 and 1 mM MnCl 2 . DNA with 20–60 bp in length was added as an activator. The data was fit to a Michaelis-Menten equation, error bars represent the standard deviation of three measurements. ( C ) DNA binding of SbcCD H84Q to 20–50 bp DNA was assayed in the presence of 1 mM ATP, 5 mM MgCl 2 and 1 mM MnCl 2 . DNA concentration was kept at 5 nM; the SbcCD H84Q concentration ranged from 2 to 1000 nM. Data points represent the change in fluorescence anisotropy and the data were fit to a 1 to 1 binding equation. Error bars represent the deviation from three independent experiments.

    Techniques Used: Binding Assay, Plasmid Preparation, Standard Deviation, Concentration Assay, Fluorescence

    5) Product Images from "The bacterial Mre11–Rad50 homolog SbcCD cleaves opposing strands of DNA by two chemically distinct nuclease reactions"

    Article Title: The bacterial Mre11–Rad50 homolog SbcCD cleaves opposing strands of DNA by two chemically distinct nuclease reactions

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gky878

    ATP hydrolysis stimulation and DNA binding of the SbcCD wt complex. ( A ) The ATP hydrolysis rate of SbcCD wt was measured in dependence to increasing plasmid DNA concentrations. Bacteriophage ΦX174 Plasmid DNA (5386 bp in length) was added as single-stranded, supercoiled, nicked or linear DNA. The data were fit to a Michaelis–Menten equation, error bars indicate the deviation from three replicates. ( B ) DNA stimulation of ATP hydrolysis by the nuclease-deficient SbcCD H84Q complex. The steady-state ATPase rates were measured at 37°C in the presence of 1 mM ATP, 5 mM MgCl 2 and 1 mM MnCl 2 . DNA with 20–60 bp in length was added as an activator. The data was fit to a Michaelis-Menten equation, error bars represent the standard deviation of three measurements. ( C ) DNA binding of SbcCD H84Q to 20–50 bp DNA was assayed in the presence of 1 mM ATP, 5 mM MgCl 2 and 1 mM MnCl 2 . DNA concentration was kept at 5 nM; the SbcCD H84Q concentration ranged from 2 to 1000 nM. Data points represent the change in fluorescence anisotropy and the data were fit to a 1 to 1 binding equation. Error bars represent the deviation from three independent experiments.
    Figure Legend Snippet: ATP hydrolysis stimulation and DNA binding of the SbcCD wt complex. ( A ) The ATP hydrolysis rate of SbcCD wt was measured in dependence to increasing plasmid DNA concentrations. Bacteriophage ΦX174 Plasmid DNA (5386 bp in length) was added as single-stranded, supercoiled, nicked or linear DNA. The data were fit to a Michaelis–Menten equation, error bars indicate the deviation from three replicates. ( B ) DNA stimulation of ATP hydrolysis by the nuclease-deficient SbcCD H84Q complex. The steady-state ATPase rates were measured at 37°C in the presence of 1 mM ATP, 5 mM MgCl 2 and 1 mM MnCl 2 . DNA with 20–60 bp in length was added as an activator. The data was fit to a Michaelis-Menten equation, error bars represent the standard deviation of three measurements. ( C ) DNA binding of SbcCD H84Q to 20–50 bp DNA was assayed in the presence of 1 mM ATP, 5 mM MgCl 2 and 1 mM MnCl 2 . DNA concentration was kept at 5 nM; the SbcCD H84Q concentration ranged from 2 to 1000 nM. Data points represent the change in fluorescence anisotropy and the data were fit to a 1 to 1 binding equation. Error bars represent the deviation from three independent experiments.

    Techniques Used: Binding Assay, Plasmid Preparation, Standard Deviation, Concentration Assay, Fluorescence

    6) Product Images from "Archaeal Hel308 helicase targets replication forks in vivo and in vitro and unwinds lagging strands"

    Article Title: Archaeal Hel308 helicase targets replication forks in vivo and in vitro and unwinds lagging strands

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gki685

    Mth810 is the archaeal orthologue of metazoan Hel308 in sequence and minimal helicase function. ( A ) Cartoon showing common features of Hel308 from archaea (Hel308a), human (hHel308) and the N-terminal domain of human PolQ. Helicase motifs, including the Q-motif ( 53 ), are labelled and the Hel308a sequences are given for motif I and IVa with mutagenized residues in bold and underlined. ( B ) Sequence details in helicase motifs V and VI that confirm Hel308a as a Hel308/Mus308 family rather than a RecQ helicase. The corresponding motif of human BLM helicase is shown for comparison (hBLM). In each motif peculiar residues conserved in Hel308/Mus308 helicases are in bold. Motif IVa is highly conserved in RecQ and Hel308 proteins. Invariant residues are in bold and highly conserved residues are underlined. Aligned with Hel308a, human Hel308 and human PolQ are Hel308 from Caenorhabditis elegans (CeHel308), E.coli RecQ (EcRecQ) and a human RecQ, BLM (HsBLM). ( C ) SDS–PAGE gel (10% acrylamide) showing purified recombinant Hel308a (arrowed) from Methanothermobacter . Marker sizes are given on the left of the panel. ( D ) ATPase activity of Hel308a measured as a function of time in reactions containing no DNA (filled diamond), dsDNA (open square) or ssDNA (open circles). Error bars are derived from the means of three independent experiments. ( E ) Unwinding reactions of Hel308a on 3′-ssDNA-tailed duplex (i), 5′-ssDNA-tailed duplex (ii) and untailed duplex (iii). Reactions were for 20 min at 45°C containing 2 nM DNA, with 32 P-labelled strand indicated by filled circle, 5 mM MgCl 2 , 5 mM ATP and zero (lane a); 1, 5, 10, 25 and 50 nM Hel308a (lanes b–f).
    Figure Legend Snippet: Mth810 is the archaeal orthologue of metazoan Hel308 in sequence and minimal helicase function. ( A ) Cartoon showing common features of Hel308 from archaea (Hel308a), human (hHel308) and the N-terminal domain of human PolQ. Helicase motifs, including the Q-motif ( 53 ), are labelled and the Hel308a sequences are given for motif I and IVa with mutagenized residues in bold and underlined. ( B ) Sequence details in helicase motifs V and VI that confirm Hel308a as a Hel308/Mus308 family rather than a RecQ helicase. The corresponding motif of human BLM helicase is shown for comparison (hBLM). In each motif peculiar residues conserved in Hel308/Mus308 helicases are in bold. Motif IVa is highly conserved in RecQ and Hel308 proteins. Invariant residues are in bold and highly conserved residues are underlined. Aligned with Hel308a, human Hel308 and human PolQ are Hel308 from Caenorhabditis elegans (CeHel308), E.coli RecQ (EcRecQ) and a human RecQ, BLM (HsBLM). ( C ) SDS–PAGE gel (10% acrylamide) showing purified recombinant Hel308a (arrowed) from Methanothermobacter . Marker sizes are given on the left of the panel. ( D ) ATPase activity of Hel308a measured as a function of time in reactions containing no DNA (filled diamond), dsDNA (open square) or ssDNA (open circles). Error bars are derived from the means of three independent experiments. ( E ) Unwinding reactions of Hel308a on 3′-ssDNA-tailed duplex (i), 5′-ssDNA-tailed duplex (ii) and untailed duplex (iii). Reactions were for 20 min at 45°C containing 2 nM DNA, with 32 P-labelled strand indicated by filled circle, 5 mM MgCl 2 , 5 mM ATP and zero (lane a); 1, 5, 10, 25 and 50 nM Hel308a (lanes b–f).

    Techniques Used: Sequencing, SDS Page, Purification, Recombinant, Marker, Activity Assay, Derivative Assay

    7) Product Images from "The bacterial Mre11–Rad50 homolog SbcCD cleaves opposing strands of DNA by two chemically distinct nuclease reactions"

    Article Title: The bacterial Mre11–Rad50 homolog SbcCD cleaves opposing strands of DNA by two chemically distinct nuclease reactions

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gky878

    ATP hydrolysis stimulation and DNA binding of the SbcCD wt complex. ( A ) The ATP hydrolysis rate of SbcCD wt was measured in dependence to increasing plasmid DNA concentrations. Bacteriophage ΦX174 Plasmid DNA (5386 bp in length) was added as single-stranded, supercoiled, nicked or linear DNA. The data were fit to a Michaelis–Menten equation, error bars indicate the deviation from three replicates. ( B ) DNA stimulation of ATP hydrolysis by the nuclease-deficient SbcCD H84Q complex. The steady-state ATPase rates were measured at 37°C in the presence of 1 mM ATP, 5 mM MgCl 2 and 1 mM MnCl 2 . DNA with 20–60 bp in length was added as an activator. The data was fit to a Michaelis-Menten equation, error bars represent the standard deviation of three measurements. ( C ) DNA binding of SbcCD H84Q to 20–50 bp DNA was assayed in the presence of 1 mM ATP, 5 mM MgCl 2 and 1 mM MnCl 2 . DNA concentration was kept at 5 nM; the SbcCD H84Q concentration ranged from 2 to 1000 nM. Data points represent the change in fluorescence anisotropy and the data were fit to a 1 to 1 binding equation. Error bars represent the deviation from three independent experiments.
    Figure Legend Snippet: ATP hydrolysis stimulation and DNA binding of the SbcCD wt complex. ( A ) The ATP hydrolysis rate of SbcCD wt was measured in dependence to increasing plasmid DNA concentrations. Bacteriophage ΦX174 Plasmid DNA (5386 bp in length) was added as single-stranded, supercoiled, nicked or linear DNA. The data were fit to a Michaelis–Menten equation, error bars indicate the deviation from three replicates. ( B ) DNA stimulation of ATP hydrolysis by the nuclease-deficient SbcCD H84Q complex. The steady-state ATPase rates were measured at 37°C in the presence of 1 mM ATP, 5 mM MgCl 2 and 1 mM MnCl 2 . DNA with 20–60 bp in length was added as an activator. The data was fit to a Michaelis-Menten equation, error bars represent the standard deviation of three measurements. ( C ) DNA binding of SbcCD H84Q to 20–50 bp DNA was assayed in the presence of 1 mM ATP, 5 mM MgCl 2 and 1 mM MnCl 2 . DNA concentration was kept at 5 nM; the SbcCD H84Q concentration ranged from 2 to 1000 nM. Data points represent the change in fluorescence anisotropy and the data were fit to a 1 to 1 binding equation. Error bars represent the deviation from three independent experiments.

    Techniques Used: Binding Assay, Plasmid Preparation, Standard Deviation, Concentration Assay, Fluorescence

    8) Product Images from "Archaeal Hel308 helicase targets replication forks in vivo and in vitro and unwinds lagging strands"

    Article Title: Archaeal Hel308 helicase targets replication forks in vivo and in vitro and unwinds lagging strands

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gki685

    Hel308a targets DNA forks for unwinding and binds to duplex substrates with branchpoints. ( A ) Time-course unwinding of four substrates acted on by Hel308a: fork-2 (filled circles), fork-1 (filled squares), 3′-ssDNA-tailed duplex (open circles) and Holliday junction (open squares). Substrates used are annotated to the right of the graph. Reactions were at 45°C for the times shown and contained 2 nM DNA, 5 mM MgCl 2 , 5 mM ATP and 20 nM Hel308a. Error bars are mostly hidden by data points and were derived from means of three independent assays. ( B ) Gel-retardation binding assays of Hel308a on fully base-paired, static Holliday junction (lanes a–f), static Holliday junction containing a backbone nick indicated by an arrowhead (lanes g–l), fully base-paired fork-3 (lanes m–r), fork-3 lacking a leading strand (lanes s–x) and fork-3 lacking a lagging strand (lanes y–4). Reactions were at 45°C for 10 min in 1 mM magnesium and contained 2 nM DNA and Hel308a at 0, 1, 2, 10, 50 and100 nM. ( C ) Hel308a K51L protein is unable to unwind fork-2 (lanes g–l), compared with wild-type protein (lanes a–f). Reactions were for 20 min at 45°C containing 2 nM DNA, 5 mM MgCl 2 , 5 mM ATP and 0, 1, 5, 10, 25 or 50 nM Hel308a. Binding of wild-type Hel308a (lanes m–o) and K51L Hel308a (lanes p–r) to fork 2 were in reactions for 10 min at 45°C containing 5 mM MgCl 2 , 2 nM fork-2 (labelled on strand 1) and 0, 10 or 100 nM Hel308a protein.
    Figure Legend Snippet: Hel308a targets DNA forks for unwinding and binds to duplex substrates with branchpoints. ( A ) Time-course unwinding of four substrates acted on by Hel308a: fork-2 (filled circles), fork-1 (filled squares), 3′-ssDNA-tailed duplex (open circles) and Holliday junction (open squares). Substrates used are annotated to the right of the graph. Reactions were at 45°C for the times shown and contained 2 nM DNA, 5 mM MgCl 2 , 5 mM ATP and 20 nM Hel308a. Error bars are mostly hidden by data points and were derived from means of three independent assays. ( B ) Gel-retardation binding assays of Hel308a on fully base-paired, static Holliday junction (lanes a–f), static Holliday junction containing a backbone nick indicated by an arrowhead (lanes g–l), fully base-paired fork-3 (lanes m–r), fork-3 lacking a leading strand (lanes s–x) and fork-3 lacking a lagging strand (lanes y–4). Reactions were at 45°C for 10 min in 1 mM magnesium and contained 2 nM DNA and Hel308a at 0, 1, 2, 10, 50 and100 nM. ( C ) Hel308a K51L protein is unable to unwind fork-2 (lanes g–l), compared with wild-type protein (lanes a–f). Reactions were for 20 min at 45°C containing 2 nM DNA, 5 mM MgCl 2 , 5 mM ATP and 0, 1, 5, 10, 25 or 50 nM Hel308a. Binding of wild-type Hel308a (lanes m–o) and K51L Hel308a (lanes p–r) to fork 2 were in reactions for 10 min at 45°C containing 5 mM MgCl 2 , 2 nM fork-2 (labelled on strand 1) and 0, 10 or 100 nM Hel308a protein.

    Techniques Used: Derivative Assay, Electrophoretic Mobility Shift Assay, Binding Assay

    Mth810 is the archaeal orthologue of metazoan Hel308 in sequence and minimal helicase function. ( A ) Cartoon showing common features of Hel308 from archaea (Hel308a), human (hHel308) and the N-terminal domain of human PolQ. Helicase motifs, including the Q-motif ( 53 ), are labelled and the Hel308a sequences are given for motif I and IVa with mutagenized residues in bold and underlined. ( B ) Sequence details in helicase motifs V and VI that confirm Hel308a as a Hel308/Mus308 family rather than a RecQ helicase. The corresponding motif of human BLM helicase is shown for comparison (hBLM). In each motif peculiar residues conserved in Hel308/Mus308 helicases are in bold. Motif IVa is highly conserved in RecQ and Hel308 proteins. Invariant residues are in bold and highly conserved residues are underlined. Aligned with Hel308a, human Hel308 and human PolQ are Hel308 from Caenorhabditis elegans (CeHel308), E.coli RecQ (EcRecQ) and a human RecQ, BLM (HsBLM). ( C ) SDS–PAGE gel (10% acrylamide) showing purified recombinant Hel308a (arrowed) from Methanothermobacter . Marker sizes are given on the left of the panel. ( D ) ATPase activity of Hel308a measured as a function of time in reactions containing no DNA (filled diamond), dsDNA (open square) or ssDNA (open circles). Error bars are derived from the means of three independent experiments. ( E ) Unwinding reactions of Hel308a on 3′-ssDNA-tailed duplex (i), 5′-ssDNA-tailed duplex (ii) and untailed duplex (iii). Reactions were for 20 min at 45°C containing 2 nM DNA, with 32 P-labelled strand indicated by filled circle, 5 mM MgCl 2 , 5 mM ATP and zero (lane a); 1, 5, 10, 25 and 50 nM Hel308a (lanes b–f).
    Figure Legend Snippet: Mth810 is the archaeal orthologue of metazoan Hel308 in sequence and minimal helicase function. ( A ) Cartoon showing common features of Hel308 from archaea (Hel308a), human (hHel308) and the N-terminal domain of human PolQ. Helicase motifs, including the Q-motif ( 53 ), are labelled and the Hel308a sequences are given for motif I and IVa with mutagenized residues in bold and underlined. ( B ) Sequence details in helicase motifs V and VI that confirm Hel308a as a Hel308/Mus308 family rather than a RecQ helicase. The corresponding motif of human BLM helicase is shown for comparison (hBLM). In each motif peculiar residues conserved in Hel308/Mus308 helicases are in bold. Motif IVa is highly conserved in RecQ and Hel308 proteins. Invariant residues are in bold and highly conserved residues are underlined. Aligned with Hel308a, human Hel308 and human PolQ are Hel308 from Caenorhabditis elegans (CeHel308), E.coli RecQ (EcRecQ) and a human RecQ, BLM (HsBLM). ( C ) SDS–PAGE gel (10% acrylamide) showing purified recombinant Hel308a (arrowed) from Methanothermobacter . Marker sizes are given on the left of the panel. ( D ) ATPase activity of Hel308a measured as a function of time in reactions containing no DNA (filled diamond), dsDNA (open square) or ssDNA (open circles). Error bars are derived from the means of three independent experiments. ( E ) Unwinding reactions of Hel308a on 3′-ssDNA-tailed duplex (i), 5′-ssDNA-tailed duplex (ii) and untailed duplex (iii). Reactions were for 20 min at 45°C containing 2 nM DNA, with 32 P-labelled strand indicated by filled circle, 5 mM MgCl 2 , 5 mM ATP and zero (lane a); 1, 5, 10, 25 and 50 nM Hel308a (lanes b–f).

    Techniques Used: Sequencing, SDS Page, Purification, Recombinant, Marker, Activity Assay, Derivative Assay

    Models proposing how Hel308 helicases may function in archaea and metazoans. ( A ) Displacement of the lagging strand by the Hel308 helicase (Hel) domain of PolQ may provide access for the translesion polymerase domain to DNA damage (grey square, e.g. AP-sites) located on the lagging strand template. ( B ) Hel308a/Hel308 (Hel) unwinding of the lagging strand at fork with a compromised leading or lagging strand provides a template for loading of replication restart apparatus, possibly Pol-α-primase (αPri). In each model, translocation of the helicase is indicted by a dotted arrow, away from the fork branchpoint in a 3′–5′ direction with respect to the lagging strand template.
    Figure Legend Snippet: Models proposing how Hel308 helicases may function in archaea and metazoans. ( A ) Displacement of the lagging strand by the Hel308 helicase (Hel) domain of PolQ may provide access for the translesion polymerase domain to DNA damage (grey square, e.g. AP-sites) located on the lagging strand template. ( B ) Hel308a/Hel308 (Hel) unwinding of the lagging strand at fork with a compromised leading or lagging strand provides a template for loading of replication restart apparatus, possibly Pol-α-primase (αPri). In each model, translocation of the helicase is indicted by a dotted arrow, away from the fork branchpoint in a 3′–5′ direction with respect to the lagging strand template.

    Techniques Used: Translocation Assay

    Hel308 from archaea preferentially targets fork DNA for unwinding. ( A ) Gel-retardation binding assays of Hel308a on the substrates in Figure 2E in 1 mM magnesium. Reactions were at 45°C for 10 min and contained 2 nM DNA substrate mixed with 0, 1, 2, 10, 50 and 100 nM Hel308a. ( B ) The same reactions as in (A), but containing an additional 1 mM ATP in the gel, and all buffers. ( C ). Unwinding reactions of Hel308a on flayed duplex (lanes a–f), fork with leading strand only (lanes g–l), fork with lagging strand only (fork-2, lanes m–r), fork with both leading and lagging strands (fork-1, lanes s–x) and Holliday junction (lanes y–dd). Reactions were for 20 min at 45°C containing 2 nM DNA, 5 mM MgCl 2 , 5 mM ATP and zero (lanes a, g, m, s and y) or 1, 5, 10, 25 and 50 nM Hel308a.
    Figure Legend Snippet: Hel308 from archaea preferentially targets fork DNA for unwinding. ( A ) Gel-retardation binding assays of Hel308a on the substrates in Figure 2E in 1 mM magnesium. Reactions were at 45°C for 10 min and contained 2 nM DNA substrate mixed with 0, 1, 2, 10, 50 and 100 nM Hel308a. ( B ) The same reactions as in (A), but containing an additional 1 mM ATP in the gel, and all buffers. ( C ). Unwinding reactions of Hel308a on flayed duplex (lanes a–f), fork with leading strand only (lanes g–l), fork with lagging strand only (fork-2, lanes m–r), fork with both leading and lagging strands (fork-1, lanes s–x) and Holliday junction (lanes y–dd). Reactions were for 20 min at 45°C containing 2 nM DNA, 5 mM MgCl 2 , 5 mM ATP and zero (lanes a, g, m, s and y) or 1, 5, 10, 25 and 50 nM Hel308a.

    Techniques Used: Electrophoretic Mobility Shift Assay, Binding Assay

    Hel308a unwinds lagging strands from nicks and the fork branchpoint. ( A ) Products from unwinding fork-2 by hel308a as a function of time. Reactions contained 2 nM DNA and 20 nM Hel308a in 5 mM MgCl 2 , 5 mM ATP at 45°C. ( B ) Reactions showing unwinding of strands in fork-1 by Hel308a. Cartoons of the substrate are shown above the panel in each case with the labelled strand denoted by a filled circle. Strands are numbered on one of these cartoons. Reactions were at 45°C for 20 min containing 5 mM MgCl 2 , 5 mM ATP, 2 nM DNA and zero (0) or 50 nM Hel308a (H). Lanes marked B contained no Hel308a and the reactions were heated to 95°C for 20 min. Letters X, Y and Z highlight the major product of unwinding in each reaction containing Hel308a. Substrate markers corresponding to fork lacking a lagging strand (M1), flayed duplex (M2) and partial duplex (M3) are annotated beside the panel. ( C ) Time-course unwinding of fork-3 and its corresponding nicked duplex DNA substrate. Substrates used are annotated to the right of the graph. Reactions were at 45°C for the times shown and contained 2 nM DNA, 5 mM MgCl 2 , 5 mM ATP and 20 nM Hel308a. Error bars derive from means of two independent assays. ( D ) Unwinding of the invading strand of D-loop substrates by Hel308a. The D-loop substrates used are annotated above the panel and reactions products are displayed to the right of the panel. Reactions were for 20 min at 45°C containing 2 nM DNA, 5 mM MgCl 2 , 5 mM ATP and zero or 1, 5, 10, 25 and 50 nM Hel308a.
    Figure Legend Snippet: Hel308a unwinds lagging strands from nicks and the fork branchpoint. ( A ) Products from unwinding fork-2 by hel308a as a function of time. Reactions contained 2 nM DNA and 20 nM Hel308a in 5 mM MgCl 2 , 5 mM ATP at 45°C. ( B ) Reactions showing unwinding of strands in fork-1 by Hel308a. Cartoons of the substrate are shown above the panel in each case with the labelled strand denoted by a filled circle. Strands are numbered on one of these cartoons. Reactions were at 45°C for 20 min containing 5 mM MgCl 2 , 5 mM ATP, 2 nM DNA and zero (0) or 50 nM Hel308a (H). Lanes marked B contained no Hel308a and the reactions were heated to 95°C for 20 min. Letters X, Y and Z highlight the major product of unwinding in each reaction containing Hel308a. Substrate markers corresponding to fork lacking a lagging strand (M1), flayed duplex (M2) and partial duplex (M3) are annotated beside the panel. ( C ) Time-course unwinding of fork-3 and its corresponding nicked duplex DNA substrate. Substrates used are annotated to the right of the graph. Reactions were at 45°C for the times shown and contained 2 nM DNA, 5 mM MgCl 2 , 5 mM ATP and 20 nM Hel308a. Error bars derive from means of two independent assays. ( D ) Unwinding of the invading strand of D-loop substrates by Hel308a. The D-loop substrates used are annotated above the panel and reactions products are displayed to the right of the panel. Reactions were for 20 min at 45°C containing 2 nM DNA, 5 mM MgCl 2 , 5 mM ATP and zero or 1, 5, 10, 25 and 50 nM Hel308a.

    Techniques Used:

    9) Product Images from "The bacterial Mre11–Rad50 homolog SbcCD cleaves opposing strands of DNA by two chemically distinct nuclease reactions"

    Article Title: The bacterial Mre11–Rad50 homolog SbcCD cleaves opposing strands of DNA by two chemically distinct nuclease reactions

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gky878

    ATP hydrolysis stimulation and DNA binding of the SbcCD wt complex. ( A ) The ATP hydrolysis rate of SbcCD wt was measured in dependence to increasing plasmid DNA concentrations. Bacteriophage ΦX174 Plasmid DNA (5386 bp in length) was added as single-stranded, supercoiled, nicked or linear DNA. The data were fit to a Michaelis–Menten equation, error bars indicate the deviation from three replicates. ( B ) DNA stimulation of ATP hydrolysis by the nuclease-deficient SbcCD H84Q complex. The steady-state ATPase rates were measured at 37°C in the presence of 1 mM ATP, 5 mM MgCl 2 and 1 mM MnCl 2 . DNA with 20–60 bp in length was added as an activator. The data was fit to a Michaelis-Menten equation, error bars represent the standard deviation of three measurements. ( C ) DNA binding of SbcCD H84Q to 20–50 bp DNA was assayed in the presence of 1 mM ATP, 5 mM MgCl 2 and 1 mM MnCl 2 . DNA concentration was kept at 5 nM; the SbcCD H84Q concentration ranged from 2 to 1000 nM. Data points represent the change in fluorescence anisotropy and the data were fit to a 1 to 1 binding equation. Error bars represent the deviation from three independent experiments.
    Figure Legend Snippet: ATP hydrolysis stimulation and DNA binding of the SbcCD wt complex. ( A ) The ATP hydrolysis rate of SbcCD wt was measured in dependence to increasing plasmid DNA concentrations. Bacteriophage ΦX174 Plasmid DNA (5386 bp in length) was added as single-stranded, supercoiled, nicked or linear DNA. The data were fit to a Michaelis–Menten equation, error bars indicate the deviation from three replicates. ( B ) DNA stimulation of ATP hydrolysis by the nuclease-deficient SbcCD H84Q complex. The steady-state ATPase rates were measured at 37°C in the presence of 1 mM ATP, 5 mM MgCl 2 and 1 mM MnCl 2 . DNA with 20–60 bp in length was added as an activator. The data was fit to a Michaelis-Menten equation, error bars represent the standard deviation of three measurements. ( C ) DNA binding of SbcCD H84Q to 20–50 bp DNA was assayed in the presence of 1 mM ATP, 5 mM MgCl 2 and 1 mM MnCl 2 . DNA concentration was kept at 5 nM; the SbcCD H84Q concentration ranged from 2 to 1000 nM. Data points represent the change in fluorescence anisotropy and the data were fit to a 1 to 1 binding equation. Error bars represent the deviation from three independent experiments.

    Techniques Used: Binding Assay, Plasmid Preparation, Standard Deviation, Concentration Assay, Fluorescence

    10) Product Images from "Archaeal Hel308 helicase targets replication forks in vivo and in vitro and unwinds lagging strands"

    Article Title: Archaeal Hel308 helicase targets replication forks in vivo and in vitro and unwinds lagging strands

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gki685

    Mth810 is the archaeal orthologue of metazoan Hel308 in sequence and minimal helicase function. ( A ) Cartoon showing common features of Hel308 from archaea (Hel308a), human (hHel308) and the N-terminal domain of human PolQ. Helicase motifs, including the Q-motif ( 53 ), are labelled and the Hel308a sequences are given for motif I and IVa with mutagenized residues in bold and underlined. ( B ) Sequence details in helicase motifs V and VI that confirm Hel308a as a Hel308/Mus308 family rather than a RecQ helicase. The corresponding motif of human BLM helicase is shown for comparison (hBLM). In each motif peculiar residues conserved in Hel308/Mus308 helicases are in bold. Motif IVa is highly conserved in RecQ and Hel308 proteins. Invariant residues are in bold and highly conserved residues are underlined. Aligned with Hel308a, human Hel308 and human PolQ are Hel308 from Caenorhabditis elegans (CeHel308), E.coli RecQ (EcRecQ) and a human RecQ, BLM (HsBLM). ( C ) SDS–PAGE gel (10% acrylamide) showing purified recombinant Hel308a (arrowed) from Methanothermobacter . Marker sizes are given on the left of the panel. ( D ) ATPase activity of Hel308a measured as a function of time in reactions containing no DNA (filled diamond), dsDNA (open square) or ssDNA (open circles). Error bars are derived from the means of three independent experiments. ( E ) Unwinding reactions of Hel308a on 3′-ssDNA-tailed duplex (i), 5′-ssDNA-tailed duplex (ii) and untailed duplex (iii). Reactions were for 20 min at 45°C containing 2 nM DNA, with 32 P-labelled strand indicated by filled circle, 5 mM MgCl 2 , 5 mM ATP and zero (lane a); 1, 5, 10, 25 and 50 nM Hel308a (lanes b–f).
    Figure Legend Snippet: Mth810 is the archaeal orthologue of metazoan Hel308 in sequence and minimal helicase function. ( A ) Cartoon showing common features of Hel308 from archaea (Hel308a), human (hHel308) and the N-terminal domain of human PolQ. Helicase motifs, including the Q-motif ( 53 ), are labelled and the Hel308a sequences are given for motif I and IVa with mutagenized residues in bold and underlined. ( B ) Sequence details in helicase motifs V and VI that confirm Hel308a as a Hel308/Mus308 family rather than a RecQ helicase. The corresponding motif of human BLM helicase is shown for comparison (hBLM). In each motif peculiar residues conserved in Hel308/Mus308 helicases are in bold. Motif IVa is highly conserved in RecQ and Hel308 proteins. Invariant residues are in bold and highly conserved residues are underlined. Aligned with Hel308a, human Hel308 and human PolQ are Hel308 from Caenorhabditis elegans (CeHel308), E.coli RecQ (EcRecQ) and a human RecQ, BLM (HsBLM). ( C ) SDS–PAGE gel (10% acrylamide) showing purified recombinant Hel308a (arrowed) from Methanothermobacter . Marker sizes are given on the left of the panel. ( D ) ATPase activity of Hel308a measured as a function of time in reactions containing no DNA (filled diamond), dsDNA (open square) or ssDNA (open circles). Error bars are derived from the means of three independent experiments. ( E ) Unwinding reactions of Hel308a on 3′-ssDNA-tailed duplex (i), 5′-ssDNA-tailed duplex (ii) and untailed duplex (iii). Reactions were for 20 min at 45°C containing 2 nM DNA, with 32 P-labelled strand indicated by filled circle, 5 mM MgCl 2 , 5 mM ATP and zero (lane a); 1, 5, 10, 25 and 50 nM Hel308a (lanes b–f).

    Techniques Used: Sequencing, SDS Page, Purification, Recombinant, Marker, Activity Assay, Derivative Assay

    11) Product Images from "Efficient Strand Transfer by the RadA Recombinase from the Hyperthermophilic Archaeon Desulfurococcus amylolyticus"

    Article Title: Efficient Strand Transfer by the RadA Recombinase from the Hyperthermophilic Archaeon Desulfurococcus amylolyticus

    Journal: Journal of Bacteriology

    doi:

    DNA strand exchange reaction. A scheme of the reaction (a), the temperature (b) and kinetic (c) characteristics, and control reactions (d) are shown. In panels b and c, the reaction mixture (20 μl) contained TAcMD buffer (pH 7.9), 2.5 mM ATP, 8 μM RadA Da , 8 μM M13mp18 ssDNA, and 16 μM linearized M13mp18 dsDNA. The latter was added to initiate the reaction after 5 min of preincubation at the temperature indicated. In panel d (homologous controls, lanes 1 to 5), the reaction mixture (20 μl) was the same as described above, but either without RadA Da (lane 1) or with RadA Da degraded by proteinase K (PrK) (lane 2); a complete mixture (lane 3); the same mixture as in lane 3, but without ATP (lane 4); or the same mixture as in lane 3, but without Mg +2 (lane 5). In panel d (heterologous controls, lanes 6 to 8), the reaction mixture (20 μl) contained TAcMD buffer (pH 7.9), 2.5 mM ATP, 8 μM RadA Da , 8 μM M13mp18 ssDNA, and 16 μM linearized φX174 dsDNA (lane 6) or 8 μM φX174 ssDNA and 16 μM linearized M13mp18 dsDNA (lane 7), or 8 μM φX174 ssDNA and 16 μM linearized φX174 dsDNA (lane 8, showing the strand exchange reaction with φX174 DNA substrates).
    Figure Legend Snippet: DNA strand exchange reaction. A scheme of the reaction (a), the temperature (b) and kinetic (c) characteristics, and control reactions (d) are shown. In panels b and c, the reaction mixture (20 μl) contained TAcMD buffer (pH 7.9), 2.5 mM ATP, 8 μM RadA Da , 8 μM M13mp18 ssDNA, and 16 μM linearized M13mp18 dsDNA. The latter was added to initiate the reaction after 5 min of preincubation at the temperature indicated. In panel d (homologous controls, lanes 1 to 5), the reaction mixture (20 μl) was the same as described above, but either without RadA Da (lane 1) or with RadA Da degraded by proteinase K (PrK) (lane 2); a complete mixture (lane 3); the same mixture as in lane 3, but without ATP (lane 4); or the same mixture as in lane 3, but without Mg +2 (lane 5). In panel d (heterologous controls, lanes 6 to 8), the reaction mixture (20 μl) contained TAcMD buffer (pH 7.9), 2.5 mM ATP, 8 μM RadA Da , 8 μM M13mp18 ssDNA, and 16 μM linearized φX174 dsDNA (lane 6) or 8 μM φX174 ssDNA and 16 μM linearized M13mp18 dsDNA (lane 7), or 8 μM φX174 ssDNA and 16 μM linearized φX174 dsDNA (lane 8, showing the strand exchange reaction with φX174 DNA substrates).

    Techniques Used:

    Related Articles

    Labeling:

    Article Title: Proteolysis of Xenopus Cip-type CDK inhibitor, p16Xic2, is regulated by PCNA binding and CDK2 phosphorylation
    Article Snippet: .. Proteins labeled with 35 S-methionine were added to extracts at a final dilution of 1:15 in the presence or absence of 10 ng/ul demembranated XSC or ΦX174 single-stranded DNA (New England Biolab, N3023S). .. The reactions were analyzed by PhosphorImager and quantitation was performed using ImageQuant™ software (Molecular Dynamics).

    Purification:

    Article Title: Metagenomic Assay for Identification of Microbial Pathogens in Tumor Tissues
    Article Snippet: .. Purified phiX174 virion DNA was purchased from New England Biolabs (N3023S; Ipswich, MA, USA), total DNA from human MRC-5 cells infected with cytomegalovirus (human herpesvirus 5 strain AD169) was ATCC VR-538D, total DNA from human A549 cells infected with adenovirus type 5 (HAdV-5 strain Adenoid 75) was ATCC VR-5D, and total RNA from human HEp-2 cells infected with respiratory syncytial virus (HRSV strain Long) was ATCC VR-26D, all purchased from ATCC (Manassas, VA, USA). .. Plasmid minipreps were prepared from pBR322 subclones carrying JC or BK polyomavirus genomes (J. C. Alwine, University of Pennsylvania, Philadelphia, PA) and from pUC19 carrying the human papillomavirus 16 (HPV16) genome (obtained from Peter Howley, Harvard Medical School, Boston, MA).

    Polymerase Chain Reaction:

    Article Title: Ctp1 protein–DNA filaments promote DNA bridging and DNA double-strand break repair
    Article Snippet: .. 500-bp dsDNA was generated by PCR using a phiX174 Virion DNA template (New England BioLabs Inc., Ipswich, MA) and primers 5′-FAM-AGTTTTATCGCTTCCATGAC-3′ (where FAM represents fluorescein amidite) and 5′-TCAGAAAATCGAAATCATCTTC-3′ (Integrated DNA Technologies, Coralville, IA). .. The 500-bp dsDNA was gel-purified using a QiaQuick gel extraction kit (Qiagen, Hilden, Germany).

    Generated:

    Article Title: Ctp1 protein–DNA filaments promote DNA bridging and DNA double-strand break repair
    Article Snippet: .. 500-bp dsDNA was generated by PCR using a phiX174 Virion DNA template (New England BioLabs Inc., Ipswich, MA) and primers 5′-FAM-AGTTTTATCGCTTCCATGAC-3′ (where FAM represents fluorescein amidite) and 5′-TCAGAAAATCGAAATCATCTTC-3′ (Integrated DNA Technologies, Coralville, IA). .. The 500-bp dsDNA was gel-purified using a QiaQuick gel extraction kit (Qiagen, Hilden, Germany).

    Infection:

    Article Title: Metagenomic Assay for Identification of Microbial Pathogens in Tumor Tissues
    Article Snippet: .. Purified phiX174 virion DNA was purchased from New England Biolabs (N3023S; Ipswich, MA, USA), total DNA from human MRC-5 cells infected with cytomegalovirus (human herpesvirus 5 strain AD169) was ATCC VR-538D, total DNA from human A549 cells infected with adenovirus type 5 (HAdV-5 strain Adenoid 75) was ATCC VR-5D, and total RNA from human HEp-2 cells infected with respiratory syncytial virus (HRSV strain Long) was ATCC VR-26D, all purchased from ATCC (Manassas, VA, USA). .. Plasmid minipreps were prepared from pBR322 subclones carrying JC or BK polyomavirus genomes (J. C. Alwine, University of Pennsylvania, Philadelphia, PA) and from pUC19 carrying the human papillomavirus 16 (HPV16) genome (obtained from Peter Howley, Harvard Medical School, Boston, MA).

    IA:

    Article Title: Ctp1 protein–DNA filaments promote DNA bridging and DNA double-strand break repair
    Article Snippet: .. 500-bp dsDNA was generated by PCR using a phiX174 Virion DNA template (New England BioLabs Inc., Ipswich, MA) and primers 5′-FAM-AGTTTTATCGCTTCCATGAC-3′ (where FAM represents fluorescein amidite) and 5′-TCAGAAAATCGAAATCATCTTC-3′ (Integrated DNA Technologies, Coralville, IA). .. The 500-bp dsDNA was gel-purified using a QiaQuick gel extraction kit (Qiagen, Hilden, Germany).

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