φx174 dna Search Results


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  • 87
    New England Biolabs phix174 rf i dna
    Phix174 Rf I Dna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 87/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    Thermo Fisher φx174 dna hinfi marker
    φx174 Dna Hinfi Marker, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 95/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    New England Biolabs phix174 virion dna
    Phix174 Virion Dna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 30 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Promega hae iii digested φx174 dna molecular size markers
    Hae Iii Digested φx174 Dna Molecular Size Markers, supplied by Promega, used in various techniques. Bioz Stars score: 85/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Thermo Fisher supercoiled φx174 dna
    Comparative experiments of the oxidative cleavage of <t>ΦX174</t> plasmid <t>DNA</t> performed by 2 and 3 . Lane 1 control DNA. Lane 2 250 nM solution of 2 . Lane 3 50 nM 2 , in the presence of 5 mM mercaptopropionic acid (MPA). Lane 4 100 nM 2 , in the presence of 5 mM MPA. Lane 5 250 nM 2 , in the presence of 5 mM MPA. Lane 6 250 nM 3 . Lane 7 50 nM 3 , in the presence of 5 mM MPA. Lane 8 100 nM 3 , in the presence of 5 mM MPA. Lane 9 250 nM 3 , in the presence of 5 mM MPA
    Supercoiled φx174 Dna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Promega φx174 dna hinfi dephosphorylated dna fragments
    In vitro reconstitution of TC-BER. For radioactive incorporation into pUC-TS-5-OHU (with [α- 32 P]dTMP ( lanes 1–7 ) or [α- 32 P]dAMP ( lane 8 )), 10 pmol of substrate was incubated with 0.5 pmol of NEIL2 ( lanes 1 and 3–8 ), 25 fmol of PNK, 0.25 pmol each of Pol β and Lig IIIα, and an RNAP II fraction containing TBP, TFIIB, and E/F/H (Protein One, except in lane 5 without the transcription factors) in the presence (+) or absence (−) of NTPs, as described under “Experimental Procedures.” Lane 1 , undamaged <t>DNA;</t> lane 9 , end-labeled ϕX174 <t>HinfI</t> DNA marker (Promega). Complete repair is indicated by the [ 32 P]dTMP incorporation. The repaired plasmid was linearized with EcoRI/HindIII and analyzed in a 6% TBE-urea gel; the gel was dried and the reaction products were analyzed and quantitated with a PhosphorImager. Bottom , histograms indicating the -fold increase in repair activity; activity without NTPs ( lane 3 ) was set to 1. Error bars , S.E.
    φx174 Dna Hinfi Dephosphorylated Dna Fragments, supplied by Promega, used in various techniques. Bioz Stars score: 86/100, based on 28 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Illumina Inc φx174 dna
    In vitro reconstitution of TC-BER. For radioactive incorporation into pUC-TS-5-OHU (with [α- 32 P]dTMP ( lanes 1–7 ) or [α- 32 P]dAMP ( lane 8 )), 10 pmol of substrate was incubated with 0.5 pmol of NEIL2 ( lanes 1 and 3–8 ), 25 fmol of PNK, 0.25 pmol each of Pol β and Lig IIIα, and an RNAP II fraction containing TBP, TFIIB, and E/F/H (Protein One, except in lane 5 without the transcription factors) in the presence (+) or absence (−) of NTPs, as described under “Experimental Procedures.” Lane 1 , undamaged <t>DNA;</t> lane 9 , end-labeled ϕX174 <t>HinfI</t> DNA marker (Promega). Complete repair is indicated by the [ 32 P]dTMP incorporation. The repaired plasmid was linearized with EcoRI/HindIII and analyzed in a 6% TBE-urea gel; the gel was dried and the reaction products were analyzed and quantitated with a PhosphorImager. Bottom , histograms indicating the -fold increase in repair activity; activity without NTPs ( lane 3 ) was set to 1. Error bars , S.E.
    φx174 Dna, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 93/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Thermo Fisher φx174 dna
    In vitro reconstitution of TC-BER. For radioactive incorporation into pUC-TS-5-OHU (with [α- 32 P]dTMP ( lanes 1–7 ) or [α- 32 P]dAMP ( lane 8 )), 10 pmol of substrate was incubated with 0.5 pmol of NEIL2 ( lanes 1 and 3–8 ), 25 fmol of PNK, 0.25 pmol each of Pol β and Lig IIIα, and an RNAP II fraction containing TBP, TFIIB, and E/F/H (Protein One, except in lane 5 without the transcription factors) in the presence (+) or absence (−) of NTPs, as described under “Experimental Procedures.” Lane 1 , undamaged <t>DNA;</t> lane 9 , end-labeled ϕX174 <t>HinfI</t> DNA marker (Promega). Complete repair is indicated by the [ 32 P]dTMP incorporation. The repaired plasmid was linearized with EcoRI/HindIII and analyzed in a 6% TBE-urea gel; the gel was dried and the reaction products were analyzed and quantitated with a PhosphorImager. Bottom , histograms indicating the -fold increase in repair activity; activity without NTPs ( lane 3 ) was set to 1. Error bars , S.E.
    φx174 Dna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 88/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Promega φx174 double stranded plasmid dna
    In vitro reconstitution of TC-BER. For radioactive incorporation into pUC-TS-5-OHU (with [α- 32 P]dTMP ( lanes 1–7 ) or [α- 32 P]dAMP ( lane 8 )), 10 pmol of substrate was incubated with 0.5 pmol of NEIL2 ( lanes 1 and 3–8 ), 25 fmol of PNK, 0.25 pmol each of Pol β and Lig IIIα, and an RNAP II fraction containing TBP, TFIIB, and E/F/H (Protein One, except in lane 5 without the transcription factors) in the presence (+) or absence (−) of NTPs, as described under “Experimental Procedures.” Lane 1 , undamaged <t>DNA;</t> lane 9 , end-labeled ϕX174 <t>HinfI</t> DNA marker (Promega). Complete repair is indicated by the [ 32 P]dTMP incorporation. The repaired plasmid was linearized with EcoRI/HindIII and analyzed in a 6% TBE-urea gel; the gel was dried and the reaction products were analyzed and quantitated with a PhosphorImager. Bottom , histograms indicating the -fold increase in repair activity; activity without NTPs ( lane 3 ) was set to 1. Error bars , S.E.
    φx174 Double Stranded Plasmid Dna, supplied by Promega, used in various techniques. Bioz Stars score: 85/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher φx174 replicative form dna hae iii fragments
    In vitro reconstitution of TC-BER. For radioactive incorporation into pUC-TS-5-OHU (with [α- 32 P]dTMP ( lanes 1–7 ) or [α- 32 P]dAMP ( lane 8 )), 10 pmol of substrate was incubated with 0.5 pmol of NEIL2 ( lanes 1 and 3–8 ), 25 fmol of PNK, 0.25 pmol each of Pol β and Lig IIIα, and an RNAP II fraction containing TBP, TFIIB, and E/F/H (Protein One, except in lane 5 without the transcription factors) in the presence (+) or absence (−) of NTPs, as described under “Experimental Procedures.” Lane 1 , undamaged <t>DNA;</t> lane 9 , end-labeled ϕX174 <t>HinfI</t> DNA marker (Promega). Complete repair is indicated by the [ 32 P]dTMP incorporation. The repaired plasmid was linearized with EcoRI/HindIII and analyzed in a 6% TBE-urea gel; the gel was dried and the reaction products were analyzed and quantitated with a PhosphorImager. Bottom , histograms indicating the -fold increase in repair activity; activity without NTPs ( lane 3 ) was set to 1. Error bars , S.E.
    φx174 Replicative Form Dna Hae Iii Fragments, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Thermo Fisher φx174 rf1 dna
    In vitro reconstitution of TC-BER. For radioactive incorporation into pUC-TS-5-OHU (with [α- 32 P]dTMP ( lanes 1–7 ) or [α- 32 P]dAMP ( lane 8 )), 10 pmol of substrate was incubated with 0.5 pmol of NEIL2 ( lanes 1 and 3–8 ), 25 fmol of PNK, 0.25 pmol each of Pol β and Lig IIIα, and an RNAP II fraction containing TBP, TFIIB, and E/F/H (Protein One, except in lane 5 without the transcription factors) in the presence (+) or absence (−) of NTPs, as described under “Experimental Procedures.” Lane 1 , undamaged <t>DNA;</t> lane 9 , end-labeled ϕX174 <t>HinfI</t> DNA marker (Promega). Complete repair is indicated by the [ 32 P]dTMP incorporation. The repaired plasmid was linearized with EcoRI/HindIII and analyzed in a 6% TBE-urea gel; the gel was dried and the reaction products were analyzed and quantitated with a PhosphorImager. Bottom , histograms indicating the -fold increase in repair activity; activity without NTPs ( lane 3 ) was set to 1. Error bars , S.E.
    φx174 Rf1 Dna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 88/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Thermo Fisher 5 end labeled hin fi digested φx174 single stranded dna
    In vitro reconstitution of TC-BER. For radioactive incorporation into pUC-TS-5-OHU (with [α- 32 P]dTMP ( lanes 1–7 ) or [α- 32 P]dAMP ( lane 8 )), 10 pmol of substrate was incubated with 0.5 pmol of NEIL2 ( lanes 1 and 3–8 ), 25 fmol of PNK, 0.25 pmol each of Pol β and Lig IIIα, and an RNAP II fraction containing TBP, TFIIB, and E/F/H (Protein One, except in lane 5 without the transcription factors) in the presence (+) or absence (−) of NTPs, as described under “Experimental Procedures.” Lane 1 , undamaged <t>DNA;</t> lane 9 , end-labeled ϕX174 <t>HinfI</t> DNA marker (Promega). Complete repair is indicated by the [ 32 P]dTMP incorporation. The repaired plasmid was linearized with EcoRI/HindIII and analyzed in a 6% TBE-urea gel; the gel was dried and the reaction products were analyzed and quantitated with a PhosphorImager. Bottom , histograms indicating the -fold increase in repair activity; activity without NTPs ( lane 3 ) was set to 1. Error bars , S.E.
    5 End Labeled Hin Fi Digested φx174 Single Stranded Dna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Thermo Fisher bsu ri hydrolyzed φx174 dna
    In vitro reconstitution of TC-BER. For radioactive incorporation into pUC-TS-5-OHU (with [α- 32 P]dTMP ( lanes 1–7 ) or [α- 32 P]dAMP ( lane 8 )), 10 pmol of substrate was incubated with 0.5 pmol of NEIL2 ( lanes 1 and 3–8 ), 25 fmol of PNK, 0.25 pmol each of Pol β and Lig IIIα, and an RNAP II fraction containing TBP, TFIIB, and E/F/H (Protein One, except in lane 5 without the transcription factors) in the presence (+) or absence (−) of NTPs, as described under “Experimental Procedures.” Lane 1 , undamaged <t>DNA;</t> lane 9 , end-labeled ϕX174 <t>HinfI</t> DNA marker (Promega). Complete repair is indicated by the [ 32 P]dTMP incorporation. The repaired plasmid was linearized with EcoRI/HindIII and analyzed in a 6% TBE-urea gel; the gel was dried and the reaction products were analyzed and quantitated with a PhosphorImager. Bottom , histograms indicating the -fold increase in repair activity; activity without NTPs ( lane 3 ) was set to 1. Error bars , S.E.
    Bsu Ri Hydrolyzed φx174 Dna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 86/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    80
    Boehringer Mannheim phage φx174 dna
    PCR amplification and Hae III RFLP patterns of pure cultures. PCR amplification (30 cycles) of 16S <t>DNA</t> coding for rRNA of pure cultures was performed either with a universal SSU primer set (a) or with the Ps-PCR primer set (b). (a1 and b1) Amplification products from cultures (lanes 1 to 18) and a negative control (neg) on 1% agarose gels. The molecular weight marker (MW) was λ Hin dIII. (a2 and b2) Hae III RFLP patterns on 2% agarose gels. The molecular weight marker (MW) was <t>ΦX174</t> Hae III. The 18 cultures were “ Pseudomonas ” boreopolis (ATCC 3242) (lane 1), Burkholderia andropogonis (ATCC 23061) (lane 2), P. cichorii (ATCC 10857) (lane 3), P. syringae pv. syringae (Biolog 7350) (lane 4), “ P .” floridana (ATCC 25616) (lane 5), “ Pseudomonas ” sp.-like group II (Biolog 1574) (lane 6), P. taetrolens (Biolog 8570) (lane 7), P. putida biotype B (ATCC 17527) (lane 8), P. synxantha (ATCC 9890) (lane 9), P. fragi (ATCC 4973) (lane 10), P. recinovorans (ATCC 14235) (lane 11), P. mendocina (ATCC 25411) (lane 12), P. agarici (ATCC 25941) (lane 13), P. fulva (ATCC 31418) (lane 14), P. stutzeri (ATCC 17588) (lane 15), P. alcaligenes (ATCC 14909) (lane 16), P. fluorescens biotype G (isolate 27cm) (lane 17), and P. marginalis (isolate A5P4C3) (lane 18). The Pseudomonas genus names that are in quotation marks are not Pseudomonas (sensu stricto) cultures.)
    Phage φx174 Dna, supplied by Boehringer Mannheim, used in various techniques. Bioz Stars score: 80/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Thermo Fisher phage φx174 dna
    BcnI reactions on the supercoiled <t>ΦX174</t> <t>DNA.</t> The scheme above panel (A) illustrates the various DNA forms that can exist during BcnI reactions on supercoiled phage ΦX174 DNA bearing a single BcnI recognition site. ( A ) Single turnover reaction with 2 nM of DNA substrate and 200 nM of BcnI. The flow diagram above the graph schematically depicts the experiment performed in a quench-flow device (see ‘Materials and Methods’ section for details). Three DNA forms are shown: supercoiled DNA (SC, filled circles), open circular intermediate (OC, down triangles) and full length linear product (FLL, filled squares). All data points are presented as mean values from three independent experiments ±1 SD. Continuous lines are the best fit to the reaction equation SC − k 1 →OC − k 2 →FLL that gave k 1 = 8.3 ± 0.2 s −1 (the rate constant for nicking of the first DNA strand) and k 2 = 0.27 ± 0.1 s −1 (the rate constant for cleavage of the second DNA strand). ( B ) Steady-state experiment. All data points are mean values from seven independent experiments ±1 SD. The reaction contained 2 nM DNA and 0.1 nM BcnI. The initial SC cleavage and FLL formation rates (0.0036 ± 0.0003 nM s −1 and 0.0028 ± 0.0003 nM s −1 , respectively), determined from linear fits (solid lines), indicate that BcnI converts 77% (ratio 0.0028/0.00365) of the initial substrate SC into the final reaction product FLL during a single binding event. The reaction k cat equals 0.036 ± 0.003 s −1 (0.0036 nM s −1 /0.1 nM BcnI).
    Phage φx174 Dna, supplied by Thermo Fisher, 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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    85
    Thermo Fisher bacteriophage φx174 rf1 dna
    BcnI reactions on the supercoiled <t>ΦX174</t> <t>DNA.</t> The scheme above panel (A) illustrates the various DNA forms that can exist during BcnI reactions on supercoiled phage ΦX174 DNA bearing a single BcnI recognition site. ( A ) Single turnover reaction with 2 nM of DNA substrate and 200 nM of BcnI. The flow diagram above the graph schematically depicts the experiment performed in a quench-flow device (see ‘Materials and Methods’ section for details). Three DNA forms are shown: supercoiled DNA (SC, filled circles), open circular intermediate (OC, down triangles) and full length linear product (FLL, filled squares). All data points are presented as mean values from three independent experiments ±1 SD. Continuous lines are the best fit to the reaction equation SC − k 1 →OC − k 2 →FLL that gave k 1 = 8.3 ± 0.2 s −1 (the rate constant for nicking of the first DNA strand) and k 2 = 0.27 ± 0.1 s −1 (the rate constant for cleavage of the second DNA strand). ( B ) Steady-state experiment. All data points are mean values from seven independent experiments ±1 SD. The reaction contained 2 nM DNA and 0.1 nM BcnI. The initial SC cleavage and FLL formation rates (0.0036 ± 0.0003 nM s −1 and 0.0028 ± 0.0003 nM s −1 , respectively), determined from linear fits (solid lines), indicate that BcnI converts 77% (ratio 0.0028/0.00365) of the initial substrate SC into the final reaction product FLL during a single binding event. The reaction k cat equals 0.036 ± 0.003 s −1 (0.0036 nM s −1 /0.1 nM BcnI).
    Bacteriophage φx174 Rf1 Dna, supplied by Thermo Fisher, 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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    95
    New England Biolabs topoisomerase i relaxation assay φx174 rf i dna
    BcnI reactions on the supercoiled <t>ΦX174</t> <t>DNA.</t> The scheme above panel (A) illustrates the various DNA forms that can exist during BcnI reactions on supercoiled phage ΦX174 DNA bearing a single BcnI recognition site. ( A ) Single turnover reaction with 2 nM of DNA substrate and 200 nM of BcnI. The flow diagram above the graph schematically depicts the experiment performed in a quench-flow device (see ‘Materials and Methods’ section for details). Three DNA forms are shown: supercoiled DNA (SC, filled circles), open circular intermediate (OC, down triangles) and full length linear product (FLL, filled squares). All data points are presented as mean values from three independent experiments ±1 SD. Continuous lines are the best fit to the reaction equation SC − k 1 →OC − k 2 →FLL that gave k 1 = 8.3 ± 0.2 s −1 (the rate constant for nicking of the first DNA strand) and k 2 = 0.27 ± 0.1 s −1 (the rate constant for cleavage of the second DNA strand). ( B ) Steady-state experiment. All data points are mean values from seven independent experiments ±1 SD. The reaction contained 2 nM DNA and 0.1 nM BcnI. The initial SC cleavage and FLL formation rates (0.0036 ± 0.0003 nM s −1 and 0.0028 ± 0.0003 nM s −1 , respectively), determined from linear fits (solid lines), indicate that BcnI converts 77% (ratio 0.0028/0.00365) of the initial substrate SC into the final reaction product FLL during a single binding event. The reaction k cat equals 0.036 ± 0.003 s −1 (0.0036 nM s −1 /0.1 nM BcnI).
    Topoisomerase I Relaxation Assay φx174 Rf I Dna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    TaKaRa dna marker φx174 hinc ii
    BcnI reactions on the supercoiled <t>ΦX174</t> <t>DNA.</t> The scheme above panel (A) illustrates the various DNA forms that can exist during BcnI reactions on supercoiled phage ΦX174 DNA bearing a single BcnI recognition site. ( A ) Single turnover reaction with 2 nM of DNA substrate and 200 nM of BcnI. The flow diagram above the graph schematically depicts the experiment performed in a quench-flow device (see ‘Materials and Methods’ section for details). Three DNA forms are shown: supercoiled DNA (SC, filled circles), open circular intermediate (OC, down triangles) and full length linear product (FLL, filled squares). All data points are presented as mean values from three independent experiments ±1 SD. Continuous lines are the best fit to the reaction equation SC − k 1 →OC − k 2 →FLL that gave k 1 = 8.3 ± 0.2 s −1 (the rate constant for nicking of the first DNA strand) and k 2 = 0.27 ± 0.1 s −1 (the rate constant for cleavage of the second DNA strand). ( B ) Steady-state experiment. All data points are mean values from seven independent experiments ±1 SD. The reaction contained 2 nM DNA and 0.1 nM BcnI. The initial SC cleavage and FLL formation rates (0.0036 ± 0.0003 nM s −1 and 0.0028 ± 0.0003 nM s −1 , respectively), determined from linear fits (solid lines), indicate that BcnI converts 77% (ratio 0.0028/0.00365) of the initial substrate SC into the final reaction product FLL during a single binding event. The reaction k cat equals 0.036 ± 0.003 s −1 (0.0036 nM s −1 /0.1 nM BcnI).
    Dna Marker φx174 Hinc Ii, supplied by TaKaRa, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    80
    Boehringer Mannheim hae iii digested φx174 dna
    BcnI reactions on the supercoiled <t>ΦX174</t> <t>DNA.</t> The scheme above panel (A) illustrates the various DNA forms that can exist during BcnI reactions on supercoiled phage ΦX174 DNA bearing a single BcnI recognition site. ( A ) Single turnover reaction with 2 nM of DNA substrate and 200 nM of BcnI. The flow diagram above the graph schematically depicts the experiment performed in a quench-flow device (see ‘Materials and Methods’ section for details). Three DNA forms are shown: supercoiled DNA (SC, filled circles), open circular intermediate (OC, down triangles) and full length linear product (FLL, filled squares). All data points are presented as mean values from three independent experiments ±1 SD. Continuous lines are the best fit to the reaction equation SC − k 1 →OC − k 2 →FLL that gave k 1 = 8.3 ± 0.2 s −1 (the rate constant for nicking of the first DNA strand) and k 2 = 0.27 ± 0.1 s −1 (the rate constant for cleavage of the second DNA strand). ( B ) Steady-state experiment. All data points are mean values from seven independent experiments ±1 SD. The reaction contained 2 nM DNA and 0.1 nM BcnI. The initial SC cleavage and FLL formation rates (0.0036 ± 0.0003 nM s −1 and 0.0028 ± 0.0003 nM s −1 , respectively), determined from linear fits (solid lines), indicate that BcnI converts 77% (ratio 0.0028/0.00365) of the initial substrate SC into the final reaction product FLL during a single binding event. The reaction k cat equals 0.036 ± 0.003 s −1 (0.0036 nM s −1 /0.1 nM BcnI).
    Hae Iii Digested φx174 Dna, supplied by Boehringer Mannheim, used in various techniques. Bioz Stars score: 80/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    GE Healthcare hae iii digested φx174 dna markers
    BcnI reactions on the supercoiled <t>ΦX174</t> <t>DNA.</t> The scheme above panel (A) illustrates the various DNA forms that can exist during BcnI reactions on supercoiled phage ΦX174 DNA bearing a single BcnI recognition site. ( A ) Single turnover reaction with 2 nM of DNA substrate and 200 nM of BcnI. The flow diagram above the graph schematically depicts the experiment performed in a quench-flow device (see ‘Materials and Methods’ section for details). Three DNA forms are shown: supercoiled DNA (SC, filled circles), open circular intermediate (OC, down triangles) and full length linear product (FLL, filled squares). All data points are presented as mean values from three independent experiments ±1 SD. Continuous lines are the best fit to the reaction equation SC − k 1 →OC − k 2 →FLL that gave k 1 = 8.3 ± 0.2 s −1 (the rate constant for nicking of the first DNA strand) and k 2 = 0.27 ± 0.1 s −1 (the rate constant for cleavage of the second DNA strand). ( B ) Steady-state experiment. All data points are mean values from seven independent experiments ±1 SD. The reaction contained 2 nM DNA and 0.1 nM BcnI. The initial SC cleavage and FLL formation rates (0.0036 ± 0.0003 nM s −1 and 0.0028 ± 0.0003 nM s −1 , respectively), determined from linear fits (solid lines), indicate that BcnI converts 77% (ratio 0.0028/0.00365) of the initial substrate SC into the final reaction product FLL during a single binding event. The reaction k cat equals 0.036 ± 0.003 s −1 (0.0036 nM s −1 /0.1 nM BcnI).
    Hae Iii Digested φx174 Dna Markers, supplied by GE Healthcare, used in various techniques. Bioz Stars score: 94/100, based on 18 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Comparative experiments of the oxidative cleavage of ΦX174 plasmid DNA performed by 2 and 3 . Lane 1 control DNA. Lane 2 250 nM solution of 2 . Lane 3 50 nM 2 , in the presence of 5 mM mercaptopropionic acid (MPA). Lane 4 100 nM 2 , in the presence of 5 mM MPA. Lane 5 250 nM 2 , in the presence of 5 mM MPA. Lane 6 250 nM 3 . Lane 7 50 nM 3 , in the presence of 5 mM MPA. Lane 8 100 nM 3 , in the presence of 5 mM MPA. Lane 9 250 nM 3 , in the presence of 5 mM MPA

    Journal: Journal of Biological Inorganic Chemistry

    Article Title: DNA cleavage and binding selectivity of a heterodinuclear Pt-Cu(3-Clip-Phen) complex

    doi: 10.1007/s00775-008-0346-y

    Figure Lengend Snippet: Comparative experiments of the oxidative cleavage of ΦX174 plasmid DNA performed by 2 and 3 . Lane 1 control DNA. Lane 2 250 nM solution of 2 . Lane 3 50 nM 2 , in the presence of 5 mM mercaptopropionic acid (MPA). Lane 4 100 nM 2 , in the presence of 5 mM MPA. Lane 5 250 nM 2 , in the presence of 5 mM MPA. Lane 6 250 nM 3 . Lane 7 50 nM 3 , in the presence of 5 mM MPA. Lane 8 100 nM 3 , in the presence of 5 mM MPA. Lane 9 250 nM 3 , in the presence of 5 mM MPA

    Article Snippet: Five microliters of the complex solution was added to 10 μL of supercoiled ΦX174 DNA (Invitrogen, 7 nM, 40 μM base pairs) in 6 mM NaCl, 20 mM sodium phosphate buffer (pH 7.2), and incubated for 20 h at 37 °C.

    Techniques: Plasmid Preparation

    In vitro reconstitution of TC-BER. For radioactive incorporation into pUC-TS-5-OHU (with [α- 32 P]dTMP ( lanes 1–7 ) or [α- 32 P]dAMP ( lane 8 )), 10 pmol of substrate was incubated with 0.5 pmol of NEIL2 ( lanes 1 and 3–8 ), 25 fmol of PNK, 0.25 pmol each of Pol β and Lig IIIα, and an RNAP II fraction containing TBP, TFIIB, and E/F/H (Protein One, except in lane 5 without the transcription factors) in the presence (+) or absence (−) of NTPs, as described under “Experimental Procedures.” Lane 1 , undamaged DNA; lane 9 , end-labeled ϕX174 HinfI DNA marker (Promega). Complete repair is indicated by the [ 32 P]dTMP incorporation. The repaired plasmid was linearized with EcoRI/HindIII and analyzed in a 6% TBE-urea gel; the gel was dried and the reaction products were analyzed and quantitated with a PhosphorImager. Bottom , histograms indicating the -fold increase in repair activity; activity without NTPs ( lane 3 ) was set to 1. Error bars , S.E.

    Journal: The Journal of Biological Chemistry

    Article Title: Preferential Repair of Oxidized Base Damage in the Transcribed Genes of Mammalian Cells *

    doi: 10.1074/jbc.M110.198796

    Figure Lengend Snippet: In vitro reconstitution of TC-BER. For radioactive incorporation into pUC-TS-5-OHU (with [α- 32 P]dTMP ( lanes 1–7 ) or [α- 32 P]dAMP ( lane 8 )), 10 pmol of substrate was incubated with 0.5 pmol of NEIL2 ( lanes 1 and 3–8 ), 25 fmol of PNK, 0.25 pmol each of Pol β and Lig IIIα, and an RNAP II fraction containing TBP, TFIIB, and E/F/H (Protein One, except in lane 5 without the transcription factors) in the presence (+) or absence (−) of NTPs, as described under “Experimental Procedures.” Lane 1 , undamaged DNA; lane 9 , end-labeled ϕX174 HinfI DNA marker (Promega). Complete repair is indicated by the [ 32 P]dTMP incorporation. The repaired plasmid was linearized with EcoRI/HindIII and analyzed in a 6% TBE-urea gel; the gel was dried and the reaction products were analyzed and quantitated with a PhosphorImager. Bottom , histograms indicating the -fold increase in repair activity; activity without NTPs ( lane 3 ) was set to 1. Error bars , S.E.

    Article Snippet: The reactions were carried out at 30 °C for 90 min in a 50-μl reaction mixture and then stopped with 2% SDS in 0.2 m Tris-HCl (pH 7.5) and 10 μg/ml proteinase K. The nucleic acids were precipitated with ethanol, digested with EcoRI/HindIII, and once again ethanol-precipitated before final resuspension in formamide dye and denaturation at 90 °C for 3 min. Products were resolved alongside a φX174 HinfI DNA marker (Promega) on a 6% denaturing polyacrylamide gel in Tris borate-EDTA containing 8 m urea.

    Techniques: In Vitro, Incubation, Labeling, Marker, Plasmid Preparation, Activity Assay

    PCR amplification and Hae III RFLP patterns of pure cultures. PCR amplification (30 cycles) of 16S DNA coding for rRNA of pure cultures was performed either with a universal SSU primer set (a) or with the Ps-PCR primer set (b). (a1 and b1) Amplification products from cultures (lanes 1 to 18) and a negative control (neg) on 1% agarose gels. The molecular weight marker (MW) was λ Hin dIII. (a2 and b2) Hae III RFLP patterns on 2% agarose gels. The molecular weight marker (MW) was ΦX174 Hae III. The 18 cultures were “ Pseudomonas ” boreopolis (ATCC 3242) (lane 1), Burkholderia andropogonis (ATCC 23061) (lane 2), P. cichorii (ATCC 10857) (lane 3), P. syringae pv. syringae (Biolog 7350) (lane 4), “ P .” floridana (ATCC 25616) (lane 5), “ Pseudomonas ” sp.-like group II (Biolog 1574) (lane 6), P. taetrolens (Biolog 8570) (lane 7), P. putida biotype B (ATCC 17527) (lane 8), P. synxantha (ATCC 9890) (lane 9), P. fragi (ATCC 4973) (lane 10), P. recinovorans (ATCC 14235) (lane 11), P. mendocina (ATCC 25411) (lane 12), P. agarici (ATCC 25941) (lane 13), P. fulva (ATCC 31418) (lane 14), P. stutzeri (ATCC 17588) (lane 15), P. alcaligenes (ATCC 14909) (lane 16), P. fluorescens biotype G (isolate 27cm) (lane 17), and P. marginalis (isolate A5P4C3) (lane 18). The Pseudomonas genus names that are in quotation marks are not Pseudomonas (sensu stricto) cultures.)

    Journal: Applied and Environmental Microbiology

    Article Title: A Highly Selective PCR Protocol for Detecting 16S rRNA Genes of the Genus Pseudomonas (Sensu Stricto) in Environmental Samples

    doi:

    Figure Lengend Snippet: PCR amplification and Hae III RFLP patterns of pure cultures. PCR amplification (30 cycles) of 16S DNA coding for rRNA of pure cultures was performed either with a universal SSU primer set (a) or with the Ps-PCR primer set (b). (a1 and b1) Amplification products from cultures (lanes 1 to 18) and a negative control (neg) on 1% agarose gels. The molecular weight marker (MW) was λ Hin dIII. (a2 and b2) Hae III RFLP patterns on 2% agarose gels. The molecular weight marker (MW) was ΦX174 Hae III. The 18 cultures were “ Pseudomonas ” boreopolis (ATCC 3242) (lane 1), Burkholderia andropogonis (ATCC 23061) (lane 2), P. cichorii (ATCC 10857) (lane 3), P. syringae pv. syringae (Biolog 7350) (lane 4), “ P .” floridana (ATCC 25616) (lane 5), “ Pseudomonas ” sp.-like group II (Biolog 1574) (lane 6), P. taetrolens (Biolog 8570) (lane 7), P. putida biotype B (ATCC 17527) (lane 8), P. synxantha (ATCC 9890) (lane 9), P. fragi (ATCC 4973) (lane 10), P. recinovorans (ATCC 14235) (lane 11), P. mendocina (ATCC 25411) (lane 12), P. agarici (ATCC 25941) (lane 13), P. fulva (ATCC 31418) (lane 14), P. stutzeri (ATCC 17588) (lane 15), P. alcaligenes (ATCC 14909) (lane 16), P. fluorescens biotype G (isolate 27cm) (lane 17), and P. marginalis (isolate A5P4C3) (lane 18). The Pseudomonas genus names that are in quotation marks are not Pseudomonas (sensu stricto) cultures.)

    Article Snippet: Molecular weight markers were either phage λ DNA digested with Hin dIII (Gibco/BRL, Life Technologies, Inc.) or phage ΦX174 DNA digested with Hae III (Boehringer Mannheim).

    Techniques: Polymerase Chain Reaction, Amplification, Negative Control, Molecular Weight, Marker

    Ps-PCR products and Hae III RFLP patterns obtained from bulk DNA purified from an agricultural soil sample. PCR amplification (40 cycles) was performed with DNA from two soil subsamples (1 and 2) with annealing temperatures of either 62 or 65°C (62 or 65, respectively). (a) PCR products in a 1% agarose gel (only products of the 62°C annealing are shown). The molecular weight marker was λ Hin dIII. (b) Hae III RFLP patterns in a 2% agarose gel. The molecular weight marker (MW) was ΦX174 Hae III. Arrows, positions of RFLP pattern A shown in Fig. 1b2 (lanes 3, 4, 7 to 12, and 14 to 17).

    Journal: Applied and Environmental Microbiology

    Article Title: A Highly Selective PCR Protocol for Detecting 16S rRNA Genes of the Genus Pseudomonas (Sensu Stricto) in Environmental Samples

    doi:

    Figure Lengend Snippet: Ps-PCR products and Hae III RFLP patterns obtained from bulk DNA purified from an agricultural soil sample. PCR amplification (40 cycles) was performed with DNA from two soil subsamples (1 and 2) with annealing temperatures of either 62 or 65°C (62 or 65, respectively). (a) PCR products in a 1% agarose gel (only products of the 62°C annealing are shown). The molecular weight marker was λ Hin dIII. (b) Hae III RFLP patterns in a 2% agarose gel. The molecular weight marker (MW) was ΦX174 Hae III. Arrows, positions of RFLP pattern A shown in Fig. 1b2 (lanes 3, 4, 7 to 12, and 14 to 17).

    Article Snippet: Molecular weight markers were either phage λ DNA digested with Hin dIII (Gibco/BRL, Life Technologies, Inc.) or phage ΦX174 DNA digested with Hae III (Boehringer Mannheim).

    Techniques: Polymerase Chain Reaction, Purification, Amplification, Agarose Gel Electrophoresis, Molecular Weight, Marker

    BcnI reactions on the supercoiled ΦX174 DNA. The scheme above panel (A) illustrates the various DNA forms that can exist during BcnI reactions on supercoiled phage ΦX174 DNA bearing a single BcnI recognition site. ( A ) Single turnover reaction with 2 nM of DNA substrate and 200 nM of BcnI. The flow diagram above the graph schematically depicts the experiment performed in a quench-flow device (see ‘Materials and Methods’ section for details). Three DNA forms are shown: supercoiled DNA (SC, filled circles), open circular intermediate (OC, down triangles) and full length linear product (FLL, filled squares). All data points are presented as mean values from three independent experiments ±1 SD. Continuous lines are the best fit to the reaction equation SC − k 1 →OC − k 2 →FLL that gave k 1 = 8.3 ± 0.2 s −1 (the rate constant for nicking of the first DNA strand) and k 2 = 0.27 ± 0.1 s −1 (the rate constant for cleavage of the second DNA strand). ( B ) Steady-state experiment. All data points are mean values from seven independent experiments ±1 SD. The reaction contained 2 nM DNA and 0.1 nM BcnI. The initial SC cleavage and FLL formation rates (0.0036 ± 0.0003 nM s −1 and 0.0028 ± 0.0003 nM s −1 , respectively), determined from linear fits (solid lines), indicate that BcnI converts 77% (ratio 0.0028/0.00365) of the initial substrate SC into the final reaction product FLL during a single binding event. The reaction k cat equals 0.036 ± 0.003 s −1 (0.0036 nM s −1 /0.1 nM BcnI).

    Journal: Nucleic Acids Research

    Article Title: Target site cleavage by the monomeric restriction enzyme BcnI requires translocation to a random DNA sequence and a switch in enzyme orientation

    doi: 10.1093/nar/gkr588

    Figure Lengend Snippet: BcnI reactions on the supercoiled ΦX174 DNA. The scheme above panel (A) illustrates the various DNA forms that can exist during BcnI reactions on supercoiled phage ΦX174 DNA bearing a single BcnI recognition site. ( A ) Single turnover reaction with 2 nM of DNA substrate and 200 nM of BcnI. The flow diagram above the graph schematically depicts the experiment performed in a quench-flow device (see ‘Materials and Methods’ section for details). Three DNA forms are shown: supercoiled DNA (SC, filled circles), open circular intermediate (OC, down triangles) and full length linear product (FLL, filled squares). All data points are presented as mean values from three independent experiments ±1 SD. Continuous lines are the best fit to the reaction equation SC − k 1 →OC − k 2 →FLL that gave k 1 = 8.3 ± 0.2 s −1 (the rate constant for nicking of the first DNA strand) and k 2 = 0.27 ± 0.1 s −1 (the rate constant for cleavage of the second DNA strand). ( B ) Steady-state experiment. All data points are mean values from seven independent experiments ±1 SD. The reaction contained 2 nM DNA and 0.1 nM BcnI. The initial SC cleavage and FLL formation rates (0.0036 ± 0.0003 nM s −1 and 0.0028 ± 0.0003 nM s −1 , respectively), determined from linear fits (solid lines), indicate that BcnI converts 77% (ratio 0.0028/0.00365) of the initial substrate SC into the final reaction product FLL during a single binding event. The reaction k cat equals 0.036 ± 0.003 s −1 (0.0036 nM s −1 /0.1 nM BcnI).

    Article Snippet: Double-stranded phage ΦX174 DNA was obtained from Fermentas (Vilnius, Lithuania).

    Techniques: Flow Cytometry, Binding Assay