rfiii dna Search Results


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  • 92
    New England Biolabs phix174 rf ii dna
    Phix174 Rf Ii Dna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 92/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    New England Biolabs φx174 rfii dna
    φx174 Rfii Dna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    New England Biolabs neb φx174 rfiii
    Neb φx174 Rfiii, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 85/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    New England Biolabs rfii circular double stranded dna dsdna substrates
    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 <t>DNA</t> (filled diamond), <t>dsDNA</t> (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).
    Rfii Circular Double Stranded Dna Dsdna Substrates, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    New England Biolabs φx174 rfii plasmid dna
    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 <t>DNA</t> (filled diamond), <t>dsDNA</t> (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).
    φx174 Rfii Plasmid Dna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 85/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    New England Biolabs rfii
    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 <t>DNA</t> (filled diamond), <t>dsDNA</t> (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).
    Rfii, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 20 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    New England Biolabs φx174 rfii
    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 <t>DNA</t> (filled diamond), <t>dsDNA</t> (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).
    φx174 Rfii, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs virion dna
    ATP hydrolysis stimulation and <t>DNA</t> 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 <t>ATPase</t> 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.
    Virion Dna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 93/100, based on 57 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs low molecular weight lmw dna ladders
    ATP hydrolysis stimulation and <t>DNA</t> 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 <t>ATPase</t> 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.
    Low Molecular Weight Lmw Dna Ladders, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    80
    New England Biolabs bacteriophage φx174 dna
    <t>DNA</t> 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 <t>φX174</t> 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).
    Bacteriophage φx174 Dna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 80/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    96
    New England Biolabs sulfolobus dna polymerase iv
    <t>DNA</t> 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 <t>φX174</t> 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).
    Sulfolobus Dna Polymerase Iv, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Promega single stranded dna binding protein ssb
    <t>DNA</t> 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 <t>φX174</t> 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).
    Single Stranded Dna Binding Protein Ssb, supplied by Promega, used in various techniques. Bioz Stars score: 85/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    New England Biolabs dsdna
    <t>DNA</t> 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 <t>φX174</t> 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).
    Dsdna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 93/100, based on 1594 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Qiagen gel extraction protocol
    <t>DNA</t> 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 <t>φX174</t> 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).
    Gel Extraction Protocol, supplied by Qiagen, used in various techniques. Bioz Stars score: 85/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs quick load purple
    <t>DNA</t> 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 <t>φX174</t> 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).
    Quick Load Purple, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs apali restriction enzyme
    <t>DNA</t> 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 <t>φX174</t> 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).
    Apali Restriction Enzyme, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 20 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    GE Healthcare t4 phosphonucleotide kinase
    <t>DNA</t> 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 <t>φX174</t> 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).
    T4 Phosphonucleotide Kinase, supplied by GE Healthcare, used in various techniques. Bioz Stars score: 85/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen qiaquick gel extraction kit
    <t>DNA</t> 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 <t>φX174</t> 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).
    Qiaquick Gel Extraction Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 113321 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs xhoi endonuclease
    <t>DNA</t> 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 <t>φX174</t> 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).
    Xhoi Endonuclease, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Biotechnology Information pdb protein data bank
    <t>DNA</t> 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 <t>φX174</t> 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).
    Pdb Protein Data Bank, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 85/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    TaKaRa agarose
    <t>DNA</t> 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 <t>φX174</t> 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).
    Agarose, supplied by TaKaRa, used in various techniques. Bioz Stars score: 92/100, based on 159 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs φx174
    <t>DNA</t> 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 <t>φX174</t> 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).
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    Image Search Results


    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).

    Journal: Nucleic Acids Research

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

    doi: 10.1093/nar/gki685

    Figure Lengend 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).

    Article Snippet: ATPase assays Hydrolysis of ATP by Hel308a was measured spectroscopically using malachite green assays ( ). φX174 circular ssDNA and RFII circular double-stranded DNA (dsDNA) substrates were from New England Biolabs.

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

    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.

    Journal: Nucleic Acids Research

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

    doi: 10.1093/nar/gky878

    Figure Lengend 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.

    Article Snippet: DNA substrates For ATPase activation, ΦX174 RFI, RFII or Virion DNA (New England BioLabs®) was used.

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

    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).

    Journal: Journal of Bacteriology

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

    doi:

    Figure Lengend 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).

    Article Snippet: Bacteriophage φX174 DNA (RFI and circular ssDNA) was obtained from New England Biolabs.

    Techniques: