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  • 99
    New England Biolabs mse i
    Photorepair of UV-lesions. (A) In vivo photoreactivation test. A. tumefaciens cells of the wild type (WT), the phrA − and the phrB − mutant were spread on LB agar plates, irradiated with UV-B light for 5 min and immediately transferred to darkness (−) or subjected to photoreactivating white light (+). Mean values of CFU ± SE; n = 8 to 14. (B and C) In vitro repair of pyrimidine dimers by PhrA and PhrB. Thymine dimers were created by UV-C illumination of the <t>DNA</t> substrate (first row, +/− UV-C), mixed with enzyme (second row) and incubated for the indicated times in photoreactivating blue light (405 nm, 150 µ mol m −2 s −1 ) or in darkness (*) (third row). Photorepaired DNA can be digested by <t>Mse</t> I (fourth row, +/− Mse I). Shown are representative gels from three independent repair experiments using PhrA or PhrB.
    Mse I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1003 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Thermo Fisher mse i
    Amplified fragment length polymorphic complementary DNA <t>(AFLP-cDNA)</t> display analysis of gene expression. (A) A simple diagram of the AFLP-cDNA display procedures including messenger RNA (mRNA) isolation, cDNA synthesis, restriction digestion, ligation, preselective and selective amplification, and gel electrophoresis. The detailed protocols are described in the text. Only a few hypothetical fragments are shown to illustrate how Eco R I (GAATTC)- and <t>Mse</t> I (TTAA)–digested fragments are ligated and amplified during the analysis. (B) AFLP-cDNA display analysis using leaves of Arabidopsis thaliana diploid (At2), autotetraploid (At4), Arabidopsis arenosa (Aa), and generations 2–5 (S2-5) of new allotetraploids, and a natural Arabidopsis suecica ) are not shown because of space limitations.
    Mse I, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 293 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Fisher Scientific mse i
    Amplified fragment length polymorphic complementary DNA <t>(AFLP-cDNA)</t> display analysis of gene expression. (A) A simple diagram of the AFLP-cDNA display procedures including messenger RNA (mRNA) isolation, cDNA synthesis, restriction digestion, ligation, preselective and selective amplification, and gel electrophoresis. The detailed protocols are described in the text. Only a few hypothetical fragments are shown to illustrate how Eco R I (GAATTC)- and <t>Mse</t> I (TTAA)–digested fragments are ligated and amplified during the analysis. (B) AFLP-cDNA display analysis using leaves of Arabidopsis thaliana diploid (At2), autotetraploid (At4), Arabidopsis arenosa (Aa), and generations 2–5 (S2-5) of new allotetraploids, and a natural Arabidopsis suecica ) are not shown because of space limitations.
    Mse I, supplied by Fisher Scientific, used in various techniques. Bioz Stars score: 92/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    MWG-Biotech mse i
    Amplified fragment length polymorphic complementary DNA <t>(AFLP-cDNA)</t> display analysis of gene expression. (A) A simple diagram of the AFLP-cDNA display procedures including messenger RNA (mRNA) isolation, cDNA synthesis, restriction digestion, ligation, preselective and selective amplification, and gel electrophoresis. The detailed protocols are described in the text. Only a few hypothetical fragments are shown to illustrate how Eco R I (GAATTC)- and <t>Mse</t> I (TTAA)–digested fragments are ligated and amplified during the analysis. (B) AFLP-cDNA display analysis using leaves of Arabidopsis thaliana diploid (At2), autotetraploid (At4), Arabidopsis arenosa (Aa), and generations 2–5 (S2-5) of new allotetraploids, and a natural Arabidopsis suecica ) are not shown because of space limitations.
    Mse I, supplied by MWG-Biotech, used in various techniques. Bioz Stars score: 92/100, based on 17 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Promega mse i
    Amplified fragment length polymorphic complementary DNA <t>(AFLP-cDNA)</t> display analysis of gene expression. (A) A simple diagram of the AFLP-cDNA display procedures including messenger RNA (mRNA) isolation, cDNA synthesis, restriction digestion, ligation, preselective and selective amplification, and gel electrophoresis. The detailed protocols are described in the text. Only a few hypothetical fragments are shown to illustrate how Eco R I (GAATTC)- and <t>Mse</t> I (TTAA)–digested fragments are ligated and amplified during the analysis. (B) AFLP-cDNA display analysis using leaves of Arabidopsis thaliana diploid (At2), autotetraploid (At4), Arabidopsis arenosa (Aa), and generations 2–5 (S2-5) of new allotetraploids, and a natural Arabidopsis suecica ) are not shown because of space limitations.
    Mse I, supplied by Promega, used in various techniques. Bioz Stars score: 92/100, based on 44 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    mse i  (Roche)
    92
    Roche mse i
    Amplified fragment length polymorphic complementary DNA <t>(AFLP-cDNA)</t> display analysis of gene expression. (A) A simple diagram of the AFLP-cDNA display procedures including messenger RNA (mRNA) isolation, cDNA synthesis, restriction digestion, ligation, preselective and selective amplification, and gel electrophoresis. The detailed protocols are described in the text. Only a few hypothetical fragments are shown to illustrate how Eco R I (GAATTC)- and <t>Mse</t> I (TTAA)–digested fragments are ligated and amplified during the analysis. (B) AFLP-cDNA display analysis using leaves of Arabidopsis thaliana diploid (At2), autotetraploid (At4), Arabidopsis arenosa (Aa), and generations 2–5 (S2-5) of new allotetraploids, and a natural Arabidopsis suecica ) are not shown because of space limitations.
    Mse I, supplied by Roche, used in various techniques. Bioz Stars score: 92/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Boehringer Mannheim mse i
    Amplified fragment length polymorphic complementary DNA <t>(AFLP-cDNA)</t> display analysis of gene expression. (A) A simple diagram of the AFLP-cDNA display procedures including messenger RNA (mRNA) isolation, cDNA synthesis, restriction digestion, ligation, preselective and selective amplification, and gel electrophoresis. The detailed protocols are described in the text. Only a few hypothetical fragments are shown to illustrate how Eco R I (GAATTC)- and <t>Mse</t> I (TTAA)–digested fragments are ligated and amplified during the analysis. (B) AFLP-cDNA display analysis using leaves of Arabidopsis thaliana diploid (At2), autotetraploid (At4), Arabidopsis arenosa (Aa), and generations 2–5 (S2-5) of new allotetraploids, and a natural Arabidopsis suecica ) are not shown because of space limitations.
    Mse I, supplied by Boehringer Mannheim, used in various techniques. Bioz Stars score: 92/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    KeyGene mse i
    Amplified fragment length polymorphic complementary DNA <t>(AFLP-cDNA)</t> display analysis of gene expression. (A) A simple diagram of the AFLP-cDNA display procedures including messenger RNA (mRNA) isolation, cDNA synthesis, restriction digestion, ligation, preselective and selective amplification, and gel electrophoresis. The detailed protocols are described in the text. Only a few hypothetical fragments are shown to illustrate how Eco R I (GAATTC)- and <t>Mse</t> I (TTAA)–digested fragments are ligated and amplified during the analysis. (B) AFLP-cDNA display analysis using leaves of Arabidopsis thaliana diploid (At2), autotetraploid (At4), Arabidopsis arenosa (Aa), and generations 2–5 (S2-5) of new allotetraploids, and a natural Arabidopsis suecica ) are not shown because of space limitations.
    Mse I, supplied by KeyGene, used in various techniques. Bioz Stars score: 92/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Thermo Fisher mse i taqi
    Amplified fragment length polymorphic complementary DNA <t>(AFLP-cDNA)</t> display analysis of gene expression. (A) A simple diagram of the AFLP-cDNA display procedures including messenger RNA (mRNA) isolation, cDNA synthesis, restriction digestion, ligation, preselective and selective amplification, and gel electrophoresis. The detailed protocols are described in the text. Only a few hypothetical fragments are shown to illustrate how Eco R I (GAATTC)- and <t>Mse</t> I (TTAA)–digested fragments are ligated and amplified during the analysis. (B) AFLP-cDNA display analysis using leaves of Arabidopsis thaliana diploid (At2), autotetraploid (At4), Arabidopsis arenosa (Aa), and generations 2–5 (S2-5) of new allotetraploids, and a natural Arabidopsis suecica ) are not shown because of space limitations.
    Mse I Taqi, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    TaKaRa mse i
    <t>PCR-RFLP</t> method to identify A. cruentus . a. A single 278-bp fragment was amplified from three cultivated grain species of Amaranthus using primers specific for the SBE locus (see Materials and Methods for details). Markers represent a 100-pb DNA ladder. b. Schematic and result of PCR-RFLP for identifying A. cruentus using intron 11 of the SBE locus. Restriction profiles of PCR amplification of intron 11 of SBE followed by digestion with Mse I. Restriction enzyme cleavage site is shown in bold, and one-base substitution, T-C polymorphism is underlined. Markers represent a100-bp DNA ladder.
    Mse I, supplied by TaKaRa, used in various techniques. Bioz Stars score: 94/100, based on 24 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Thermo Fisher mse i adaptors
    <t>PCR-RFLP</t> method to identify A. cruentus . a. A single 278-bp fragment was amplified from three cultivated grain species of Amaranthus using primers specific for the SBE locus (see Materials and Methods for details). Markers represent a 100-pb DNA ladder. b. Schematic and result of PCR-RFLP for identifying A. cruentus using intron 11 of the SBE locus. Restriction profiles of PCR amplification of intron 11 of SBE followed by digestion with Mse I. Restriction enzyme cleavage site is shown in bold, and one-base substitution, T-C polymorphism is underlined. Markers represent a100-bp DNA ladder.
    Mse I Adaptors, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Boehringer Mannheim endonuclease mse i
    Typing of B. burgdorferi sensu lato isolates by using rrfA-rrlB intergenic spacer PCR-RFLP analysis. The rrfA-rrlB intergenic spacer was amplified by PCR, and this was followed by the analysis of <t>Mse</t> I restriction polymorphism of PCR products. DNA was electrophoresed on a 16% acrylamide gel, stained with ethidium bromide, and UV illuminated. The names of strains in each lane are indicated on the top of each well in the photos. The molecular sizes of DNA fragments (in base pairs) are shown on the right of the gels. Expected fragment sizes for B. burgdorferi sensu stricto strains were 108, 50, 38, and 29 to 28 bp. Expected fragment sizes for B. garinii strains were 108, 95, and 50 bp. Expected fragment sizes for B. afzelii strains were 108, 68, 50, and 20 bp. The 20-bp expected size was not easily visible.
    Endonuclease Mse I, supplied by Boehringer Mannheim, used in various techniques. Bioz Stars score: 85/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Genomed GmbH mse i ca primer
    Typing of B. burgdorferi sensu lato isolates by using rrfA-rrlB intergenic spacer PCR-RFLP analysis. The rrfA-rrlB intergenic spacer was amplified by PCR, and this was followed by the analysis of <t>Mse</t> I restriction polymorphism of PCR products. DNA was electrophoresed on a 16% acrylamide gel, stained with ethidium bromide, and UV illuminated. The names of strains in each lane are indicated on the top of each well in the photos. The molecular sizes of DNA fragments (in base pairs) are shown on the right of the gels. Expected fragment sizes for B. burgdorferi sensu stricto strains were 108, 50, 38, and 29 to 28 bp. Expected fragment sizes for B. garinii strains were 108, 95, and 50 bp. Expected fragment sizes for B. afzelii strains were 108, 68, 50, and 20 bp. The 20-bp expected size was not easily visible.
    Mse I Ca Primer, supplied by Genomed GmbH, used in various techniques. Bioz Stars score: 93/100, based on 18 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Thermo Fisher mse i restriction enzyme
    Typing of B. burgdorferi sensu lato isolates by using rrfA-rrlB intergenic spacer PCR-RFLP analysis. The rrfA-rrlB intergenic spacer was amplified by PCR, and this was followed by the analysis of <t>Mse</t> I restriction polymorphism of PCR products. DNA was electrophoresed on a 16% acrylamide gel, stained with ethidium bromide, and UV illuminated. The names of strains in each lane are indicated on the top of each well in the photos. The molecular sizes of DNA fragments (in base pairs) are shown on the right of the gels. Expected fragment sizes for B. burgdorferi sensu stricto strains were 108, 50, 38, and 29 to 28 bp. Expected fragment sizes for B. garinii strains were 108, 95, and 50 bp. Expected fragment sizes for B. afzelii strains were 108, 68, 50, and 20 bp. The 20-bp expected size was not easily visible.
    Mse I Restriction Enzyme, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Promega restriction enzyme mse i
    Typing of B. burgdorferi sensu lato isolates by using rrfA-rrlB intergenic spacer PCR-RFLP analysis. The rrfA-rrlB intergenic spacer was amplified by PCR, and this was followed by the analysis of <t>Mse</t> I restriction polymorphism of PCR products. DNA was electrophoresed on a 16% acrylamide gel, stained with ethidium bromide, and UV illuminated. The names of strains in each lane are indicated on the top of each well in the photos. The molecular sizes of DNA fragments (in base pairs) are shown on the right of the gels. Expected fragment sizes for B. burgdorferi sensu stricto strains were 108, 50, 38, and 29 to 28 bp. Expected fragment sizes for B. garinii strains were 108, 95, and 50 bp. Expected fragment sizes for B. afzelii strains were 108, 68, 50, and 20 bp. The 20-bp expected size was not easily visible.
    Restriction Enzyme Mse I, supplied by Promega, used in various techniques. Bioz Stars score: 88/100, based on 44 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Thermo Fisher psu i mse i
    Typing of B. burgdorferi sensu lato isolates by using rrfA-rrlB intergenic spacer PCR-RFLP analysis. The rrfA-rrlB intergenic spacer was amplified by PCR, and this was followed by the analysis of <t>Mse</t> I restriction polymorphism of PCR products. DNA was electrophoresed on a 16% acrylamide gel, stained with ethidium bromide, and UV illuminated. The names of strains in each lane are indicated on the top of each well in the photos. The molecular sizes of DNA fragments (in base pairs) are shown on the right of the gels. Expected fragment sizes for B. burgdorferi sensu stricto strains were 108, 50, 38, and 29 to 28 bp. Expected fragment sizes for B. garinii strains were 108, 95, and 50 bp. Expected fragment sizes for B. afzelii strains were 108, 68, 50, and 20 bp. The 20-bp expected size was not easily visible.
    Psu I Mse I, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Thermo Fisher mse i oligonucleotide adapters
    Typing of B. burgdorferi sensu lato isolates by using rrfA-rrlB intergenic spacer PCR-RFLP analysis. The rrfA-rrlB intergenic spacer was amplified by PCR, and this was followed by the analysis of <t>Mse</t> I restriction polymorphism of PCR products. DNA was electrophoresed on a 16% acrylamide gel, stained with ethidium bromide, and UV illuminated. The names of strains in each lane are indicated on the top of each well in the photos. The molecular sizes of DNA fragments (in base pairs) are shown on the right of the gels. Expected fragment sizes for B. burgdorferi sensu stricto strains were 108, 50, 38, and 29 to 28 bp. Expected fragment sizes for B. garinii strains were 108, 95, and 50 bp. Expected fragment sizes for B. afzelii strains were 108, 68, 50, and 20 bp. The 20-bp expected size was not easily visible.
    Mse I Oligonucleotide Adapters, 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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    91
    Thermo Fisher mse i restriction enzymes
    Typing of B. burgdorferi sensu lato isolates by using rrfA-rrlB intergenic spacer PCR-RFLP analysis. The rrfA-rrlB intergenic spacer was amplified by PCR, and this was followed by the analysis of <t>Mse</t> I restriction polymorphism of PCR products. DNA was electrophoresed on a 16% acrylamide gel, stained with ethidium bromide, and UV illuminated. The names of strains in each lane are indicated on the top of each well in the photos. The molecular sizes of DNA fragments (in base pairs) are shown on the right of the gels. Expected fragment sizes for B. burgdorferi sensu stricto strains were 108, 50, 38, and 29 to 28 bp. Expected fragment sizes for B. garinii strains were 108, 95, and 50 bp. Expected fragment sizes for B. afzelii strains were 108, 68, 50, and 20 bp. The 20-bp expected size was not easily visible.
    Mse I Restriction Enzymes, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 20 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Thermo Fisher mse i core primer sequences
    Typing of B. burgdorferi sensu lato isolates by using rrfA-rrlB intergenic spacer PCR-RFLP analysis. The rrfA-rrlB intergenic spacer was amplified by PCR, and this was followed by the analysis of <t>Mse</t> I restriction polymorphism of PCR products. DNA was electrophoresed on a 16% acrylamide gel, stained with ethidium bromide, and UV illuminated. The names of strains in each lane are indicated on the top of each well in the photos. The molecular sizes of DNA fragments (in base pairs) are shown on the right of the gels. Expected fragment sizes for B. burgdorferi sensu stricto strains were 108, 50, 38, and 29 to 28 bp. Expected fragment sizes for B. garinii strains were 108, 95, and 50 bp. Expected fragment sizes for B. afzelii strains were 108, 68, 50, and 20 bp. The 20-bp expected size was not easily visible.
    Mse I Core Primer Sequences, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Thermo Fisher enzyme mse i
    Typing of B. burgdorferi sensu lato isolates by using rrfA-rrlB intergenic spacer PCR-RFLP analysis. The rrfA-rrlB intergenic spacer was amplified by PCR, and this was followed by the analysis of <t>Mse</t> I restriction polymorphism of PCR products. DNA was electrophoresed on a 16% acrylamide gel, stained with ethidium bromide, and UV illuminated. The names of strains in each lane are indicated on the top of each well in the photos. The molecular sizes of DNA fragments (in base pairs) are shown on the right of the gels. Expected fragment sizes for B. burgdorferi sensu stricto strains were 108, 50, 38, and 29 to 28 bp. Expected fragment sizes for B. garinii strains were 108, 95, and 50 bp. Expected fragment sizes for B. afzelii strains were 108, 68, 50, and 20 bp. The 20-bp expected size was not easily visible.
    Enzyme Mse I, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Macrogen mse i adapter
    Image of several patterns amplified after the first enrichment (step 5) using different concentrations of template (ligation reaction) and the primers Eco I-0 and <t>Mse</t> I-0 (preselective modified primers; Vos et al., 1995 ). For each amplification template, 4 μL was loaded. The first lane is a 100-bp DNA ladder (BenchTop 100-bp DNA Ladder, Promega Corporation, Madison, Wisconsin, USA), and the last lane is Marker II (AppliChem GmbH, Darmstadt, Germany). The numbers above the white line indicate the quantity of ligation template used for the PCR enrichment, and numbers below the white line indicate the number of PCR cycles.
    Mse I Adapter, supplied by Macrogen, used in various techniques. Bioz Stars score: 88/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Premier Biosoft mse i fragment
    Amplification of target SSRs present in isolated Pst I– <t>Mse</t> I fragments using primer pairs specific to the conserved DNA sequences flanking the microsatellite repeats. The primer pairs used in each reaction are from left to right: sun24, sun25, sun26, sun27, sun28, sun29, sun30, sun31, sun32, sun33, sun34, sun35 and sun36. A 25 bp DNA ladder (Gibco BRL) was used as a size marker.
    Mse I Fragment, supplied by Premier Biosoft, 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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    85
    Promega endonuclease mse i
    Amplification of target SSRs present in isolated Pst I– <t>Mse</t> I fragments using primer pairs specific to the conserved DNA sequences flanking the microsatellite repeats. The primer pairs used in each reaction are from left to right: sun24, sun25, sun26, sun27, sun28, sun29, sun30, sun31, sun32, sun33, sun34, sun35 and sun36. A 25 bp DNA ladder (Gibco BRL) was used as a size marker.
    Endonuclease Mse I, supplied by Promega, used in various techniques. Bioz Stars score: 85/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Photorepair of UV-lesions. (A) In vivo photoreactivation test. A. tumefaciens cells of the wild type (WT), the phrA − and the phrB − mutant were spread on LB agar plates, irradiated with UV-B light for 5 min and immediately transferred to darkness (−) or subjected to photoreactivating white light (+). Mean values of CFU ± SE; n = 8 to 14. (B and C) In vitro repair of pyrimidine dimers by PhrA and PhrB. Thymine dimers were created by UV-C illumination of the DNA substrate (first row, +/− UV-C), mixed with enzyme (second row) and incubated for the indicated times in photoreactivating blue light (405 nm, 150 µ mol m −2 s −1 ) or in darkness (*) (third row). Photorepaired DNA can be digested by Mse I (fourth row, +/− Mse I). Shown are representative gels from three independent repair experiments using PhrA or PhrB.

    Journal: PLoS ONE

    Article Title: A Photolyase-Like Protein from Agrobacterium tumefaciens with an Iron-Sulfur Cluster

    doi: 10.1371/journal.pone.0026775

    Figure Lengend Snippet: Photorepair of UV-lesions. (A) In vivo photoreactivation test. A. tumefaciens cells of the wild type (WT), the phrA − and the phrB − mutant were spread on LB agar plates, irradiated with UV-B light for 5 min and immediately transferred to darkness (−) or subjected to photoreactivating white light (+). Mean values of CFU ± SE; n = 8 to 14. (B and C) In vitro repair of pyrimidine dimers by PhrA and PhrB. Thymine dimers were created by UV-C illumination of the DNA substrate (first row, +/− UV-C), mixed with enzyme (second row) and incubated for the indicated times in photoreactivating blue light (405 nm, 150 µ mol m −2 s −1 ) or in darkness (*) (third row). Photorepaired DNA can be digested by Mse I (fourth row, +/− Mse I). Shown are representative gels from three independent repair experiments using PhrA or PhrB.

    Article Snippet: Subsequently, proteins were inactivated by heating to 95°C for 10 min and the DNA probe was digested with Mse I (NEB).

    Techniques: In Vivo, Mutagenesis, Irradiation, In Vitro, Incubation

    Amplified fragment length polymorphic complementary DNA (AFLP-cDNA) display analysis of gene expression. (A) A simple diagram of the AFLP-cDNA display procedures including messenger RNA (mRNA) isolation, cDNA synthesis, restriction digestion, ligation, preselective and selective amplification, and gel electrophoresis. The detailed protocols are described in the text. Only a few hypothetical fragments are shown to illustrate how Eco R I (GAATTC)- and Mse I (TTAA)–digested fragments are ligated and amplified during the analysis. (B) AFLP-cDNA display analysis using leaves of Arabidopsis thaliana diploid (At2), autotetraploid (At4), Arabidopsis arenosa (Aa), and generations 2–5 (S2-5) of new allotetraploids, and a natural Arabidopsis suecica ) are not shown because of space limitations.

    Journal: Methods in enzymology

    Article Title: Methods for Genome-Wide Analysis of Gene Expression Changes in Polyploids

    doi: 10.1016/S0076-6879(05)95030-1

    Figure Lengend Snippet: Amplified fragment length polymorphic complementary DNA (AFLP-cDNA) display analysis of gene expression. (A) A simple diagram of the AFLP-cDNA display procedures including messenger RNA (mRNA) isolation, cDNA synthesis, restriction digestion, ligation, preselective and selective amplification, and gel electrophoresis. The detailed protocols are described in the text. Only a few hypothetical fragments are shown to illustrate how Eco R I (GAATTC)- and Mse I (TTAA)–digested fragments are ligated and amplified during the analysis. (B) AFLP-cDNA display analysis using leaves of Arabidopsis thaliana diploid (At2), autotetraploid (At4), Arabidopsis arenosa (Aa), and generations 2–5 (S2-5) of new allotetraploids, and a natural Arabidopsis suecica ) are not shown because of space limitations.

    Article Snippet: To digest cDNA, add 5 μ l of 5× reaction buffer, about 18 μ l of cDNA (~250 ng), 2 μ l of Eco R I/ Mse I (1.25 U/ μ l each) as supplied by the manufacturer (Invitrogen) to a final volume of 25 μ l. Mix gently, centrifuge briefly, and incubate the reaction at 37° for at least 2 h. The reaction is inactivated by heating at 70° for 15 min.

    Techniques: Amplification, Expressing, Isolation, Ligation, Nucleic Acid Electrophoresis

    PCR-RFLP method to identify A. cruentus . a. A single 278-bp fragment was amplified from three cultivated grain species of Amaranthus using primers specific for the SBE locus (see Materials and Methods for details). Markers represent a 100-pb DNA ladder. b. Schematic and result of PCR-RFLP for identifying A. cruentus using intron 11 of the SBE locus. Restriction profiles of PCR amplification of intron 11 of SBE followed by digestion with Mse I. Restriction enzyme cleavage site is shown in bold, and one-base substitution, T-C polymorphism is underlined. Markers represent a100-bp DNA ladder.

    Journal: Breeding Science

    Article Title: A rapid and reliable PCR-restriction fragment length polymorphism (RFLP) marker for the identification of Amaranthus cruentus species

    doi: 10.1270/jsbbs.64.422

    Figure Lengend Snippet: PCR-RFLP method to identify A. cruentus . a. A single 278-bp fragment was amplified from three cultivated grain species of Amaranthus using primers specific for the SBE locus (see Materials and Methods for details). Markers represent a 100-pb DNA ladder. b. Schematic and result of PCR-RFLP for identifying A. cruentus using intron 11 of the SBE locus. Restriction profiles of PCR amplification of intron 11 of SBE followed by digestion with Mse I. Restriction enzyme cleavage site is shown in bold, and one-base substitution, T-C polymorphism is underlined. Markers represent a100-bp DNA ladder.

    Article Snippet: PCR conditions were as follows: 30 cycles of 98°C for 10 s, 55°C for 30 s and 72°C for 30 s. PCR products were digested with the Mse I (Rsp RSII) restriction enzymes (Takara) in a total volume of 20 μl at 60°C for 1 h based on the manufacturer’s instructions, with some modifications.

    Techniques: Polymerase Chain Reaction, Amplification

    Partial sequence alignment of the SBE locus from A. cruentus , A. caudatus and A. hypochondriacus . Solid black box shows the species-specific restriction cleavage site for the enzyme Mse I. Major SNP, T-C polymorphism is underlined. Shaded area is partial exon 12.

    Journal: Breeding Science

    Article Title: A rapid and reliable PCR-restriction fragment length polymorphism (RFLP) marker for the identification of Amaranthus cruentus species

    doi: 10.1270/jsbbs.64.422

    Figure Lengend Snippet: Partial sequence alignment of the SBE locus from A. cruentus , A. caudatus and A. hypochondriacus . Solid black box shows the species-specific restriction cleavage site for the enzyme Mse I. Major SNP, T-C polymorphism is underlined. Shaded area is partial exon 12.

    Article Snippet: PCR conditions were as follows: 30 cycles of 98°C for 10 s, 55°C for 30 s and 72°C for 30 s. PCR products were digested with the Mse I (Rsp RSII) restriction enzymes (Takara) in a total volume of 20 μl at 60°C for 1 h based on the manufacturer’s instructions, with some modifications.

    Techniques: Sequencing

    Typing of B. burgdorferi sensu lato isolates by using rrfA-rrlB intergenic spacer PCR-RFLP analysis. The rrfA-rrlB intergenic spacer was amplified by PCR, and this was followed by the analysis of Mse I restriction polymorphism of PCR products. DNA was electrophoresed on a 16% acrylamide gel, stained with ethidium bromide, and UV illuminated. The names of strains in each lane are indicated on the top of each well in the photos. The molecular sizes of DNA fragments (in base pairs) are shown on the right of the gels. Expected fragment sizes for B. burgdorferi sensu stricto strains were 108, 50, 38, and 29 to 28 bp. Expected fragment sizes for B. garinii strains were 108, 95, and 50 bp. Expected fragment sizes for B. afzelii strains were 108, 68, 50, and 20 bp. The 20-bp expected size was not easily visible.

    Journal: Journal of Clinical Microbiology

    Article Title: Isolation and Characterization of Borrelia burgdorferi Sensu Lato Strains in an Area of Italy Where Lyme Borreliosis Is Endemic

    doi: 10.1128/JCM.39.6.2254-2260.2001

    Figure Lengend Snippet: Typing of B. burgdorferi sensu lato isolates by using rrfA-rrlB intergenic spacer PCR-RFLP analysis. The rrfA-rrlB intergenic spacer was amplified by PCR, and this was followed by the analysis of Mse I restriction polymorphism of PCR products. DNA was electrophoresed on a 16% acrylamide gel, stained with ethidium bromide, and UV illuminated. The names of strains in each lane are indicated on the top of each well in the photos. The molecular sizes of DNA fragments (in base pairs) are shown on the right of the gels. Expected fragment sizes for B. burgdorferi sensu stricto strains were 108, 50, 38, and 29 to 28 bp. Expected fragment sizes for B. garinii strains were 108, 95, and 50 bp. Expected fragment sizes for B. afzelii strains were 108, 68, 50, and 20 bp. The 20-bp expected size was not easily visible.

    Article Snippet: This was followed by endonuclease Mse I (Boehringer Mannheim, Mannheim, Germany) digestion, performed according to the manufacturer's instructions.

    Techniques: Polymerase Chain Reaction, Amplification, Acrylamide Gel Assay, Staining

    Image of several patterns amplified after the first enrichment (step 5) using different concentrations of template (ligation reaction) and the primers Eco I-0 and Mse I-0 (preselective modified primers; Vos et al., 1995 ). For each amplification template, 4 μL was loaded. The first lane is a 100-bp DNA ladder (BenchTop 100-bp DNA Ladder, Promega Corporation, Madison, Wisconsin, USA), and the last lane is Marker II (AppliChem GmbH, Darmstadt, Germany). The numbers above the white line indicate the quantity of ligation template used for the PCR enrichment, and numbers below the white line indicate the number of PCR cycles.

    Journal: Applications in Plant Sciences

    Article Title: SSR-patchwork: An optimized protocol to obtain a rapid and inexpensive SSR library using first-generation sequencing technology 1

    doi: 10.3732/apps.1200158

    Figure Lengend Snippet: Image of several patterns amplified after the first enrichment (step 5) using different concentrations of template (ligation reaction) and the primers Eco I-0 and Mse I-0 (preselective modified primers; Vos et al., 1995 ). For each amplification template, 4 μL was loaded. The first lane is a 100-bp DNA ladder (BenchTop 100-bp DNA Ladder, Promega Corporation, Madison, Wisconsin, USA), and the last lane is Marker II (AppliChem GmbH, Darmstadt, Germany). The numbers above the white line indicate the quantity of ligation template used for the PCR enrichment, and numbers below the white line indicate the number of PCR cycles.

    Article Snippet: Step 4: Adapter preparation and ligation The Eco RI-adapter and Mse I-adapter (Macrogen, Seoul, Korea) were prepared using a touchdown/hold PCR.

    Techniques: Amplification, Ligation, Modification, Marker, Polymerase Chain Reaction

    Image of a gel representing a successful restriction enzyme digestion using both Eco RI and Mse I (Invitrogen, Life Technologies, Paisley, Renfrewshire, United Kingdom) in a Pancratium maritimum template. The first lane is genomic DNA (2 μg), and the second lane is a 100-bp DNA ladder (BenchTop 100-bp DNA Ladder, Promega Corporation, Madison, Wisconsin, USA).

    Journal: Applications in Plant Sciences

    Article Title: SSR-patchwork: An optimized protocol to obtain a rapid and inexpensive SSR library using first-generation sequencing technology 1

    doi: 10.3732/apps.1200158

    Figure Lengend Snippet: Image of a gel representing a successful restriction enzyme digestion using both Eco RI and Mse I (Invitrogen, Life Technologies, Paisley, Renfrewshire, United Kingdom) in a Pancratium maritimum template. The first lane is genomic DNA (2 μg), and the second lane is a 100-bp DNA ladder (BenchTop 100-bp DNA Ladder, Promega Corporation, Madison, Wisconsin, USA).

    Article Snippet: Step 4: Adapter preparation and ligation The Eco RI-adapter and Mse I-adapter (Macrogen, Seoul, Korea) were prepared using a touchdown/hold PCR.

    Techniques:

    Amplification of target SSRs present in isolated Pst I– Mse I fragments using primer pairs specific to the conserved DNA sequences flanking the microsatellite repeats. The primer pairs used in each reaction are from left to right: sun24, sun25, sun26, sun27, sun28, sun29, sun30, sun31, sun32, sun33, sun34, sun35 and sun36. A 25 bp DNA ladder (Gibco BRL) was used as a size marker.

    Journal: Nucleic Acids Research

    Article Title: Sequence tagged microsatellite profiling (STMP): improved isolation of DNA sequence flanking target SSRs

    doi:

    Figure Lengend Snippet: Amplification of target SSRs present in isolated Pst I– Mse I fragments using primer pairs specific to the conserved DNA sequences flanking the microsatellite repeats. The primer pairs used in each reaction are from left to right: sun24, sun25, sun26, sun27, sun28, sun29, sun30, sun31, sun32, sun33, sun34, sun35 and sun36. A 25 bp DNA ladder (Gibco BRL) was used as a size marker.

    Article Snippet: Where more than one putative target fragment was isolated but only one corresponding Pst I– Mse I fragment was expected, additional SSRs were uncovered (e.g. STM 380, Table ).

    Techniques: Amplification, Isolation, Marker

    Amplification of Pst I– Mse I fragments containing SSRs corresponding to sequence tags. Each PCR was performed in replicate using six independently prepared unenriched (UE) and SSR-enriched (E) amplicon pools as template DNA. The sequence tag primers used in each reaction are: ( A ) STM 43, ( B ) STM 409 and ( C ) STM 639. Putative target fragments are indicated by an arrow. A 25 bp DNA ladder (Gibco BRL) was used as a size marker (M).

    Journal: Nucleic Acids Research

    Article Title: Sequence tagged microsatellite profiling (STMP): improved isolation of DNA sequence flanking target SSRs

    doi:

    Figure Lengend Snippet: Amplification of Pst I– Mse I fragments containing SSRs corresponding to sequence tags. Each PCR was performed in replicate using six independently prepared unenriched (UE) and SSR-enriched (E) amplicon pools as template DNA. The sequence tag primers used in each reaction are: ( A ) STM 43, ( B ) STM 409 and ( C ) STM 639. Putative target fragments are indicated by an arrow. A 25 bp DNA ladder (Gibco BRL) was used as a size marker (M).

    Article Snippet: Where more than one putative target fragment was isolated but only one corresponding Pst I– Mse I fragment was expected, additional SSRs were uncovered (e.g. STM 380, Table ).

    Techniques: Amplification, Sequencing, Polymerase Chain Reaction, Marker