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    MboII
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    MboII 1 500 units
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    r0148l
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    Category:
    Restriction Enzymes
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    Structured Review

    New England Biolabs mboii
    MboII
    MboII 1 500 units
    https://www.bioz.com/result/mboii/product/New England Biolabs
    Average 94 stars, based on 71 article reviews
    Price from $9.99 to $1999.99
    mboii - by Bioz Stars, 2020-09
    94/100 stars

    Images

    1) Product Images from "Inactivation of Individual SeqA Binding Sites of the E. coli Origin Reveals Robustness of Replication Initiation Synchrony"

    Article Title: Inactivation of Individual SeqA Binding Sites of the E. coli Origin Reveals Robustness of Replication Initiation Synchrony

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0166722

    Sequence of oriC showing its major protein binding sites. (A) Sequence of oriC that includes the minimal region (coordinates 1–246) required for origin function. The coordinate 1 correspondence to 3923744 of gb|U00096.3|. The region includes several GATC sites (shown in red) which are methylated by the Dam methylase enzyme. There are three 13-mer repeats of AT rich sequences where the origin initially unwinds. The remainder of the origin has mainly 9-mer DnaA binding sites as well as sites for binding IHF and FIS proteins. DnaA sites have either high (R1, R2 and R4) or low (τ1, R5, τ2, I1, I2, C3, C2, I3 and C1) affinity for DnaA. The numbers #1–9 mark the GATC sites studied here. A TaqI site (TCGA) overlapping each of the nine GATC sites was created by converting their two upstream bases to TC ( NNGA TC to TCGA TC). (B) A linear map of oriC features described above. The map also shows location of sites for restriction enzymes MboII and HphI that naturally occurs in oriC .
    Figure Legend Snippet: Sequence of oriC showing its major protein binding sites. (A) Sequence of oriC that includes the minimal region (coordinates 1–246) required for origin function. The coordinate 1 correspondence to 3923744 of gb|U00096.3|. The region includes several GATC sites (shown in red) which are methylated by the Dam methylase enzyme. There are three 13-mer repeats of AT rich sequences where the origin initially unwinds. The remainder of the origin has mainly 9-mer DnaA binding sites as well as sites for binding IHF and FIS proteins. DnaA sites have either high (R1, R2 and R4) or low (τ1, R5, τ2, I1, I2, C3, C2, I3 and C1) affinity for DnaA. The numbers #1–9 mark the GATC sites studied here. A TaqI site (TCGA) overlapping each of the nine GATC sites was created by converting their two upstream bases to TC ( NNGA TC to TCGA TC). (B) A linear map of oriC features described above. The map also shows location of sites for restriction enzymes MboII and HphI that naturally occurs in oriC .

    Techniques Used: Sequencing, Protein Binding, Methylation, Binding Assay, Immunohistofluorescence

    Effect of GATC mutations in oriC on initiation synchrony and the level of HM DNA at the MboII site of oriC . (A) The top line shows a schematic map of oriC as in Fig 1B except for an additional GATC site (#3*) included in this study. In these experiments oriC was marked with a zeo drug R cassette. GATC sites at positions #1–9 and #3* were individually mutated to GTTC and the mutant cells were analyzed by flow cytometry as in Fig 3A before and after replication run-out. Cells were also studied after combining some of the mutations (#5–6 etc.). (B) HM DNA levels as in Fig 2A except that the levels were measured at the MboII site for all. The black bar represents the HM DNA level in the WT strain ( zeo marked but without any GATC mutation within oriC ) and the grey bars the same strain with individual or multiple GATC mutations. The error bars were determined as in Fig 2B . Mutants whose HM DNA levels were significantly different from the WT ( p- value
    Figure Legend Snippet: Effect of GATC mutations in oriC on initiation synchrony and the level of HM DNA at the MboII site of oriC . (A) The top line shows a schematic map of oriC as in Fig 1B except for an additional GATC site (#3*) included in this study. In these experiments oriC was marked with a zeo drug R cassette. GATC sites at positions #1–9 and #3* were individually mutated to GTTC and the mutant cells were analyzed by flow cytometry as in Fig 3A before and after replication run-out. Cells were also studied after combining some of the mutations (#5–6 etc.). (B) HM DNA levels as in Fig 2A except that the levels were measured at the MboII site for all. The black bar represents the HM DNA level in the WT strain ( zeo marked but without any GATC mutation within oriC ) and the grey bars the same strain with individual or multiple GATC mutations. The error bars were determined as in Fig 2B . Mutants whose HM DNA levels were significantly different from the WT ( p- value

    Techniques Used: Mutagenesis, Flow Cytometry, Cytometry

    2) Product Images from "Multipronged regulatory functions of a novel endonuclease (TieA) from Helicobacter pylori"

    Article Title: Multipronged regulatory functions of a novel endonuclease (TieA) from Helicobacter pylori

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkw730

    ( A ) Binding of TieA to dsDNA: electrophoretic mobility shift assays were carried out by incubating different concentrations of TieA (0.1, 0.5, 1 and 2 μg) with 0.5 nM 32 P-labeled DNA substrates. Samples were subjected to electrophoresis on native PAGE and visualized by autoradiography as mentioned in materials and methods section. ( B ) TieA binds to DNA non-specifically: electrophoretic mobility shift assays were carried out by incubating 1 μg of TieA with mutated oligos 1–5 (see Supplementary Table S1). ( C ) Nuclease activity of TieA: different concentrations of TieA (0.01, 0.1, 0.2, 0.5, 1 and 2 μg corresponding to lanes 7-12, respectively) were incubated with 1 μg of pUC19 DNA for 1 h at 37 °C. The reaction was stopped by addition of 10 mM EDTA and samples were deprotonized by adding proteinase K (10 μg/sample) in presence of 0.05% SDS for 15 min at 65°C. The digested products were separated on 1.2% agarose gel. Rv3131 (0.5 μg) was used as a negative control in lane 6. MboII (1 unit/reaction) and DNase I (1 unit/reaction) served as positive controls in lanes 3 and 5, respectively. Lane 4 represents heat inactivated TieA. ( D ) TieA cleaves both pUC19 (circular) and Lambda DNA (linear): pUC19 and Lambda DNA were incubated with TieA (lanes 5, 6, 14 and 15) for 1 h at 37°C and processed as described above. MboII (lanes 3 and 12) and DNase I (lanes 4 and 13) were used as positive controls. Rv3131 protein was used as a negative control (lanes 7 and 16). Ca 2+ –Mg 2+ dependent nuclease activity of TieA was confirmed by pre-incubating pUC19/Lambda DNA with either SDS (0.05%) or EDTA (10 mM) for 10 min (lanes 8, 9, 17 and 18) and later 1 μg of TieA was added and further processed as described above. Data are representative of three independent experiments. HI: heat inactivated.
    Figure Legend Snippet: ( A ) Binding of TieA to dsDNA: electrophoretic mobility shift assays were carried out by incubating different concentrations of TieA (0.1, 0.5, 1 and 2 μg) with 0.5 nM 32 P-labeled DNA substrates. Samples were subjected to electrophoresis on native PAGE and visualized by autoradiography as mentioned in materials and methods section. ( B ) TieA binds to DNA non-specifically: electrophoretic mobility shift assays were carried out by incubating 1 μg of TieA with mutated oligos 1–5 (see Supplementary Table S1). ( C ) Nuclease activity of TieA: different concentrations of TieA (0.01, 0.1, 0.2, 0.5, 1 and 2 μg corresponding to lanes 7-12, respectively) were incubated with 1 μg of pUC19 DNA for 1 h at 37 °C. The reaction was stopped by addition of 10 mM EDTA and samples were deprotonized by adding proteinase K (10 μg/sample) in presence of 0.05% SDS for 15 min at 65°C. The digested products were separated on 1.2% agarose gel. Rv3131 (0.5 μg) was used as a negative control in lane 6. MboII (1 unit/reaction) and DNase I (1 unit/reaction) served as positive controls in lanes 3 and 5, respectively. Lane 4 represents heat inactivated TieA. ( D ) TieA cleaves both pUC19 (circular) and Lambda DNA (linear): pUC19 and Lambda DNA were incubated with TieA (lanes 5, 6, 14 and 15) for 1 h at 37°C and processed as described above. MboII (lanes 3 and 12) and DNase I (lanes 4 and 13) were used as positive controls. Rv3131 protein was used as a negative control (lanes 7 and 16). Ca 2+ –Mg 2+ dependent nuclease activity of TieA was confirmed by pre-incubating pUC19/Lambda DNA with either SDS (0.05%) or EDTA (10 mM) for 10 min (lanes 8, 9, 17 and 18) and later 1 μg of TieA was added and further processed as described above. Data are representative of three independent experiments. HI: heat inactivated.

    Techniques Used: Binding Assay, Electrophoretic Mobility Shift Assay, Labeling, Electrophoresis, Clear Native PAGE, Autoradiography, Activity Assay, Incubation, Agarose Gel Electrophoresis, Negative Control, Lambda DNA Preparation

    3) Product Images from "Selection of Rodent Species Appropriate for mtDNA Transfer to Generate Transmitochondrial Mito-Mice Expressing Mitochondrial Respiration Defects"

    Article Title: Selection of Rodent Species Appropriate for mtDNA Transfer to Generate Transmitochondrial Mito-Mice Expressing Mitochondrial Respiration Defects

    Journal: Experimental Animals

    doi: 10.1538/expanim..21

    Characterization of transmitochondrial cybrids with mtDNA from various rodent species. Transmitochondrial cybrids B82mtB6, B82mtSpr, B82mtCar, B82mtAsp, and B82mtRat possessed nuclear DNA from M. musculus and mtDNA from M. musculus , M. spretus , M. caroli , A. speciosus and R. norvegicus , respectively. B82mtCOI M cybrids possessed M. musculus mtDNA with a pathogenic T6589C mutation in the mt-Co1 gene that induces respiration defects [ 11 ]. (A) Phylogenetic trees constructed by comparison of the sequence of the mt-Cytb gene encoded by mtDNA. On the basis of Kimura’s two-parameter model [ 24 ], we used mt-Cytb gene sequence data (positions 14139 to 15266) to create phylogenetic trees with PHYLIP software (http://www.phylip.com/). Branch lengths show evolutionary distance from M. musculus . The tree is rooted using Cricetulus griseus (Chinese hamster) sequence data. Values on each branch indicate base substitution in the mt-Cytb gene. (B) Genotyping of mtDNA. On Dra I digestion of the PCR products, B82mtB6 cells with M. musculus mtDNA gave a 327-bp fragment, whereas B82mtCar cells with M. caroli mtDNA gave a 267-bp fragment and a 39-bp fragment (not detectable) by a gain of a Dra I site and a 21-bp deletion in the mt-Dcr region. On Mbo II digestion of the PCR products, B82mtB6 cybrids with M. musculus mtDNA gave a 250-bp fragment, whereas B82mtAsp cybrids with A. speciosus mtDNA gave a 219-bp fragment and a 31-bp fragment (not detectable) by the gain of an Mbo II site in the mt-Cytb gene. (C) Estimation of O 2 consumption rates. B82mtB6 cells carrying nuclear and mitochondrial genomes from M. musculus were used as standards expressing normal respiratory function. Asterisks indicate a P -value less than 0.05 and double asterisks indicate a P -value less than 0.01.
    Figure Legend Snippet: Characterization of transmitochondrial cybrids with mtDNA from various rodent species. Transmitochondrial cybrids B82mtB6, B82mtSpr, B82mtCar, B82mtAsp, and B82mtRat possessed nuclear DNA from M. musculus and mtDNA from M. musculus , M. spretus , M. caroli , A. speciosus and R. norvegicus , respectively. B82mtCOI M cybrids possessed M. musculus mtDNA with a pathogenic T6589C mutation in the mt-Co1 gene that induces respiration defects [ 11 ]. (A) Phylogenetic trees constructed by comparison of the sequence of the mt-Cytb gene encoded by mtDNA. On the basis of Kimura’s two-parameter model [ 24 ], we used mt-Cytb gene sequence data (positions 14139 to 15266) to create phylogenetic trees with PHYLIP software (http://www.phylip.com/). Branch lengths show evolutionary distance from M. musculus . The tree is rooted using Cricetulus griseus (Chinese hamster) sequence data. Values on each branch indicate base substitution in the mt-Cytb gene. (B) Genotyping of mtDNA. On Dra I digestion of the PCR products, B82mtB6 cells with M. musculus mtDNA gave a 327-bp fragment, whereas B82mtCar cells with M. caroli mtDNA gave a 267-bp fragment and a 39-bp fragment (not detectable) by a gain of a Dra I site and a 21-bp deletion in the mt-Dcr region. On Mbo II digestion of the PCR products, B82mtB6 cybrids with M. musculus mtDNA gave a 250-bp fragment, whereas B82mtAsp cybrids with A. speciosus mtDNA gave a 219-bp fragment and a 31-bp fragment (not detectable) by the gain of an Mbo II site in the mt-Cytb gene. (C) Estimation of O 2 consumption rates. B82mtB6 cells carrying nuclear and mitochondrial genomes from M. musculus were used as standards expressing normal respiratory function. Asterisks indicate a P -value less than 0.05 and double asterisks indicate a P -value less than 0.01.

    Techniques Used: Mutagenesis, Construct, Sequencing, Software, Polymerase Chain Reaction, Expressing

    4) Product Images from "Prevalence of A2143G mutation of H. pylori-23S rRNA in Chinese subjects with and without clarithromycin use history"

    Article Title: Prevalence of A2143G mutation of H. pylori-23S rRNA in Chinese subjects with and without clarithromycin use history

    Journal: BMC Microbiology

    doi: 10.1186/1471-2180-8-81

    Chromatograms of PCR-RFLP assays and sequencing for detection of nucleotide alterations of 23S rRNA . H. Pylori 26695 and CLR r -1 were used as negative and positive control of A2143G mutation. BsaI digestion of the PCR products of representative samples was displayed on 8% PAGE gel. The 289 bp A2143G-positive PCR products were cleaved into a 199 bp and a 90 bp fragments ( A ). The A2143G mutation was also confirmed by sequencing of the PCR products of 23S rRNA ( B , displayed 2140–2154 fragment). H. Pylori 26695 and a 2142G clone were used as negative and positive control of A2142G mutation. MboII digestion of the PCR products of representative samples was displayed on 2% agarose gel. The 289 bp A2142G-positive PCR products of 2142G were cleaved into an 182 bp and a 107 bp fragments. The PCR product of GJ2040 was cleaved into a 164 bp and a 125 bp fragments; and the product of GJ2111 was cleaved into 245 bp and 44 bp fragment(s) ( C ). The A2142G and other mutations were confirmed by sequencing ( D ). Two new MboII -sensitive sequences were characterized as CTTCA (2222–2226) for GJ2040 and GAAG (2081–2084) for GJ2111.
    Figure Legend Snippet: Chromatograms of PCR-RFLP assays and sequencing for detection of nucleotide alterations of 23S rRNA . H. Pylori 26695 and CLR r -1 were used as negative and positive control of A2143G mutation. BsaI digestion of the PCR products of representative samples was displayed on 8% PAGE gel. The 289 bp A2143G-positive PCR products were cleaved into a 199 bp and a 90 bp fragments ( A ). The A2143G mutation was also confirmed by sequencing of the PCR products of 23S rRNA ( B , displayed 2140–2154 fragment). H. Pylori 26695 and a 2142G clone were used as negative and positive control of A2142G mutation. MboII digestion of the PCR products of representative samples was displayed on 2% agarose gel. The 289 bp A2142G-positive PCR products of 2142G were cleaved into an 182 bp and a 107 bp fragments. The PCR product of GJ2040 was cleaved into a 164 bp and a 125 bp fragments; and the product of GJ2111 was cleaved into 245 bp and 44 bp fragment(s) ( C ). The A2142G and other mutations were confirmed by sequencing ( D ). Two new MboII -sensitive sequences were characterized as CTTCA (2222–2226) for GJ2040 and GAAG (2081–2084) for GJ2111.

    Techniques Used: Polymerase Chain Reaction, Sequencing, Positive Control, Mutagenesis, Polyacrylamide Gel Electrophoresis, Agarose Gel Electrophoresis

    5) Product Images from "Molecular Characterization of Cronobacter Lipopolysaccharide O-Antigen Gene Clusters and Development of Serotype-Specific PCR Assays ▿"

    Article Title: Molecular Characterization of Cronobacter Lipopolysaccharide O-Antigen Gene Clusters and Development of Serotype-Specific PCR Assays ▿

    Journal: Applied and Environmental Microbiology

    doi: 10.1128/AEM.00162-11

    RFLP analysis of Cronobacter O-antigen amplicons with MboII restriction digestion.
    Figure Legend Snippet: RFLP analysis of Cronobacter O-antigen amplicons with MboII restriction digestion.

    Techniques Used:

    6) Product Images from "Molecular Analysis of the Enterobacter sakazakii O-Antigen Gene Locus "

    Article Title: Molecular Analysis of the Enterobacter sakazakii O-Antigen Gene Locus

    Journal: Applied and Environmental Microbiology

    doi: 10.1128/AEM.02302-07

    Restriction length profiles of rfb -encoding locus of E. sakazakii following MboII digestion. Lane 1, ATCC BAA-894; lane 2, E824; lane 3, E825; lane 4, NCTC 11467; lane 5, NCTC 8155; lane 6, 336; lane 7, 344; lane 8, 109; lane 9, CFS06; lane 10, E787; lane 11, 82; lane 12, 102; lane M1, 100-bp DNA ladder (New England Biolabs, Hertfordshire, England); lane M2, DNA molecular weight marker XVI (Roche, Mannheim, Germany). Black and gray boxes indicate profiles of strains corresponding to O:1 and O:2 serotypes, respectively.
    Figure Legend Snippet: Restriction length profiles of rfb -encoding locus of E. sakazakii following MboII digestion. Lane 1, ATCC BAA-894; lane 2, E824; lane 3, E825; lane 4, NCTC 11467; lane 5, NCTC 8155; lane 6, 336; lane 7, 344; lane 8, 109; lane 9, CFS06; lane 10, E787; lane 11, 82; lane 12, 102; lane M1, 100-bp DNA ladder (New England Biolabs, Hertfordshire, England); lane M2, DNA molecular weight marker XVI (Roche, Mannheim, Germany). Black and gray boxes indicate profiles of strains corresponding to O:1 and O:2 serotypes, respectively.

    Techniques Used: Molecular Weight, Marker

    7) Product Images from "Biomolecular computers with multiple restriction enzymes"

    Article Title: Biomolecular computers with multiple restriction enzymes

    Journal: Genetics and Molecular Biology

    doi: 10.1590/1678-4685-GMB-2016-0132

    The action of restriction enzymes (A) Bae I, (B) Bbv I, (C) Acu I and (D) Mbo II. Y indicates a pyrimidine whereas R indicates a purine.
    Figure Legend Snippet: The action of restriction enzymes (A) Bae I, (B) Bbv I, (C) Acu I and (D) Mbo II. Y indicates a pyrimidine whereas R indicates a purine.

    Techniques Used:

    Schematic diagram of the laboratory implementation of automaton M 1 using four endonucleases ( Bae I, Mbo II, Acu I and Bbv I) on the word abba . The transition molecules allow alternating and autonomous cleavage of DNA molecules that represent the input molecule. A detector is required for recognition of the final product of computation.
    Figure Legend Snippet: Schematic diagram of the laboratory implementation of automaton M 1 using four endonucleases ( Bae I, Mbo II, Acu I and Bbv I) on the word abba . The transition molecules allow alternating and autonomous cleavage of DNA molecules that represent the input molecule. A detector is required for recognition of the final product of computation.

    Techniques Used:

    Finite automata with nine states. (A) All possible 162 transition rules for a nine-state, two-symbol nondeterministic finite automaton. On each arrow the symbols a and b should be placed. These 162 transition rules are coded by DNA molecules – see all 162 transition molecules in Tables S1 - S8 . (B) Graph showing an example of a four-state, two-symbol finite automaton M 1 . State s 2 corresponds simultaneously to the initial and final states. This four-state automaton requires the autonomous action of four restriction enzymes and alternative splicing by the restriction enzymes Bae I, Bbv I, Acu I and Mbo I. (C) An example of a nine-state automaton ( s 2 – initial state, s 1 – final state).
    Figure Legend Snippet: Finite automata with nine states. (A) All possible 162 transition rules for a nine-state, two-symbol nondeterministic finite automaton. On each arrow the symbols a and b should be placed. These 162 transition rules are coded by DNA molecules – see all 162 transition molecules in Tables S1 - S8 . (B) Graph showing an example of a four-state, two-symbol finite automaton M 1 . State s 2 corresponds simultaneously to the initial and final states. This four-state automaton requires the autonomous action of four restriction enzymes and alternative splicing by the restriction enzymes Bae I, Bbv I, Acu I and Mbo I. (C) An example of a nine-state automaton ( s 2 – initial state, s 1 – final state).

    Techniques Used:

    Related Articles

    Polymerase Chain Reaction:

    Article Title: Selection of Rodent Species Appropriate for mtDNA Transfer to Generate Transmitochondrial Mito-Mice Expressing Mitochondrial Respiration Defects
    Article Snippet: .. The PCR amplicon contains a region of the mt-Cytb gene with an Mbo II (NEB) restriction site (control mouse mtDNA was not cleaved), and generates 219-bp and 31-bp fragments onMbo II digestion. ..

    Article Title: Molecular Analysis of the Enterobacter sakazakii O-Antigen Gene Locus
    Article Snippet: .. Ten microliters of O-antigen PCR product was digested with 12.5 U MboII (New England Biolabs, Herts, United Kingdom) in the supplied buffer. .. The mixture was incubated at 37°C for 2 h, followed by a final denaturation step of 70°C for 10 min to denature the endonuclease as it remains attached to DNA after cleavage ( ).

    Article Title: Molecular Characterization of Cronobacter Lipopolysaccharide O-Antigen Gene Clusters and Development of Serotype-Specific PCR Assays ▿
    Article Snippet: .. O-antigen PCR amplicons (1.5 μg) were digested with MboII (New England BioLabs, Ipswich, MA) according to the manufacturer's instructions. .. Restriction digests were subjected to gel electrophoresis using 1.5% agarose gels and were visualized with ethidium bromide.

    Amplification:

    Article Title: Selection of Rodent Species Appropriate for mtDNA Transfer to Generate Transmitochondrial Mito-Mice Expressing Mitochondrial Respiration Defects
    Article Snippet: .. The PCR amplicon contains a region of the mt-Cytb gene with an Mbo II (NEB) restriction site (control mouse mtDNA was not cleaved), and generates 219-bp and 31-bp fragments onMbo II digestion. ..

    Article Title: Prevalence of A2143G mutation of H. pylori-23S rRNA in Chinese subjects with and without clarithromycin use history
    Article Snippet: .. RFLP assays The 289 bp amplicon of 23S rRNA was digested with the restriction enzymes BsaI and MboII (New England Biolabs, USA) in order to detect A2143G and A2142G point mutations, respectively (Fig ) [ , ]. ..

    Article Title: Submicroscopic carriage of Plasmodium falciparum and Plasmodium vivax in a low endemic area in Ethiopia where no parasitaemia was detected by microscopy or rapid diagnostic test
    Article Snippet: .. The fragments amplified with the 563CT primers were digested overnight at 37°C with the restriction enzyme MboII (NEBioLabs, USA). .. The digested DNA was analysed with 2.5% MetaPhor Agarose (Lonza, USA) gel electrophoresis.

    other:

    Article Title: Biomolecular computers with multiple restriction enzymes
    Article Snippet: Enzymes The restriction enzymes Acu I, Bae I,Bbv I, Mbo II, Btgz I and T4 DNA ligase were obtained from New England Biolabs (Ipswich, MA, USA).

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    New England Biolabs mboii
    Sequence of oriC showing its major protein binding sites. (A) Sequence of oriC that includes the minimal region (coordinates 1–246) required for origin function. The coordinate 1 correspondence to 3923744 of gb|U00096.3|. The region includes several GATC sites (shown in red) which are methylated by the Dam methylase enzyme. There are three 13-mer repeats of AT rich sequences where the origin initially unwinds. The remainder of the origin has mainly 9-mer DnaA binding sites as well as sites for binding IHF and FIS proteins. DnaA sites have either high (R1, R2 and R4) or low (τ1, R5, τ2, I1, I2, C3, C2, I3 and C1) affinity for DnaA. The numbers #1–9 mark the GATC sites studied here. A TaqI site (TCGA) overlapping each of the nine GATC sites was created by converting their two upstream bases to TC ( NNGA TC to TCGA TC). (B) A linear map of oriC features described above. The map also shows location of sites for restriction enzymes <t>MboII</t> and <t>HphI</t> that naturally occurs in oriC .
    Mboii, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 58 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mboii/product/New England Biolabs
    Average 94 stars, based on 58 article reviews
    Price from $9.99 to $1999.99
    mboii - by Bioz Stars, 2020-09
    94/100 stars
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    Sequence of oriC showing its major protein binding sites. (A) Sequence of oriC that includes the minimal region (coordinates 1–246) required for origin function. The coordinate 1 correspondence to 3923744 of gb|U00096.3|. The region includes several GATC sites (shown in red) which are methylated by the Dam methylase enzyme. There are three 13-mer repeats of AT rich sequences where the origin initially unwinds. The remainder of the origin has mainly 9-mer DnaA binding sites as well as sites for binding IHF and FIS proteins. DnaA sites have either high (R1, R2 and R4) or low (τ1, R5, τ2, I1, I2, C3, C2, I3 and C1) affinity for DnaA. The numbers #1–9 mark the GATC sites studied here. A TaqI site (TCGA) overlapping each of the nine GATC sites was created by converting their two upstream bases to TC ( NNGA TC to TCGA TC). (B) A linear map of oriC features described above. The map also shows location of sites for restriction enzymes MboII and HphI that naturally occurs in oriC .

    Journal: PLoS ONE

    Article Title: Inactivation of Individual SeqA Binding Sites of the E. coli Origin Reveals Robustness of Replication Initiation Synchrony

    doi: 10.1371/journal.pone.0166722

    Figure Lengend Snippet: Sequence of oriC showing its major protein binding sites. (A) Sequence of oriC that includes the minimal region (coordinates 1–246) required for origin function. The coordinate 1 correspondence to 3923744 of gb|U00096.3|. The region includes several GATC sites (shown in red) which are methylated by the Dam methylase enzyme. There are three 13-mer repeats of AT rich sequences where the origin initially unwinds. The remainder of the origin has mainly 9-mer DnaA binding sites as well as sites for binding IHF and FIS proteins. DnaA sites have either high (R1, R2 and R4) or low (τ1, R5, τ2, I1, I2, C3, C2, I3 and C1) affinity for DnaA. The numbers #1–9 mark the GATC sites studied here. A TaqI site (TCGA) overlapping each of the nine GATC sites was created by converting their two upstream bases to TC ( NNGA TC to TCGA TC). (B) A linear map of oriC features described above. The map also shows location of sites for restriction enzymes MboII and HphI that naturally occurs in oriC .

    Article Snippet: The DNA was digested for an hour with 3 units of MboII or HphI at 37°C, or TaqI at 65°C (New England Biolabs).

    Techniques: Sequencing, Protein Binding, Methylation, Binding Assay, Immunohistofluorescence

    Effect of GATC mutations in oriC on initiation synchrony and the level of HM DNA at the MboII site of oriC . (A) The top line shows a schematic map of oriC as in Fig 1B except for an additional GATC site (#3*) included in this study. In these experiments oriC was marked with a zeo drug R cassette. GATC sites at positions #1–9 and #3* were individually mutated to GTTC and the mutant cells were analyzed by flow cytometry as in Fig 3A before and after replication run-out. Cells were also studied after combining some of the mutations (#5–6 etc.). (B) HM DNA levels as in Fig 2A except that the levels were measured at the MboII site for all. The black bar represents the HM DNA level in the WT strain ( zeo marked but without any GATC mutation within oriC ) and the grey bars the same strain with individual or multiple GATC mutations. The error bars were determined as in Fig 2B . Mutants whose HM DNA levels were significantly different from the WT ( p- value

    Journal: PLoS ONE

    Article Title: Inactivation of Individual SeqA Binding Sites of the E. coli Origin Reveals Robustness of Replication Initiation Synchrony

    doi: 10.1371/journal.pone.0166722

    Figure Lengend Snippet: Effect of GATC mutations in oriC on initiation synchrony and the level of HM DNA at the MboII site of oriC . (A) The top line shows a schematic map of oriC as in Fig 1B except for an additional GATC site (#3*) included in this study. In these experiments oriC was marked with a zeo drug R cassette. GATC sites at positions #1–9 and #3* were individually mutated to GTTC and the mutant cells were analyzed by flow cytometry as in Fig 3A before and after replication run-out. Cells were also studied after combining some of the mutations (#5–6 etc.). (B) HM DNA levels as in Fig 2A except that the levels were measured at the MboII site for all. The black bar represents the HM DNA level in the WT strain ( zeo marked but without any GATC mutation within oriC ) and the grey bars the same strain with individual or multiple GATC mutations. The error bars were determined as in Fig 2B . Mutants whose HM DNA levels were significantly different from the WT ( p- value

    Article Snippet: The DNA was digested for an hour with 3 units of MboII or HphI at 37°C, or TaqI at 65°C (New England Biolabs).

    Techniques: Mutagenesis, Flow Cytometry, Cytometry

    ( A ) Binding of TieA to dsDNA: electrophoretic mobility shift assays were carried out by incubating different concentrations of TieA (0.1, 0.5, 1 and 2 μg) with 0.5 nM 32 P-labeled DNA substrates. Samples were subjected to electrophoresis on native PAGE and visualized by autoradiography as mentioned in materials and methods section. ( B ) TieA binds to DNA non-specifically: electrophoretic mobility shift assays were carried out by incubating 1 μg of TieA with mutated oligos 1–5 (see Supplementary Table S1). ( C ) Nuclease activity of TieA: different concentrations of TieA (0.01, 0.1, 0.2, 0.5, 1 and 2 μg corresponding to lanes 7-12, respectively) were incubated with 1 μg of pUC19 DNA for 1 h at 37 °C. The reaction was stopped by addition of 10 mM EDTA and samples were deprotonized by adding proteinase K (10 μg/sample) in presence of 0.05% SDS for 15 min at 65°C. The digested products were separated on 1.2% agarose gel. Rv3131 (0.5 μg) was used as a negative control in lane 6. MboII (1 unit/reaction) and DNase I (1 unit/reaction) served as positive controls in lanes 3 and 5, respectively. Lane 4 represents heat inactivated TieA. ( D ) TieA cleaves both pUC19 (circular) and Lambda DNA (linear): pUC19 and Lambda DNA were incubated with TieA (lanes 5, 6, 14 and 15) for 1 h at 37°C and processed as described above. MboII (lanes 3 and 12) and DNase I (lanes 4 and 13) were used as positive controls. Rv3131 protein was used as a negative control (lanes 7 and 16). Ca 2+ –Mg 2+ dependent nuclease activity of TieA was confirmed by pre-incubating pUC19/Lambda DNA with either SDS (0.05%) or EDTA (10 mM) for 10 min (lanes 8, 9, 17 and 18) and later 1 μg of TieA was added and further processed as described above. Data are representative of three independent experiments. HI: heat inactivated.

    Journal: Nucleic Acids Research

    Article Title: Multipronged regulatory functions of a novel endonuclease (TieA) from Helicobacter pylori

    doi: 10.1093/nar/gkw730

    Figure Lengend Snippet: ( A ) Binding of TieA to dsDNA: electrophoretic mobility shift assays were carried out by incubating different concentrations of TieA (0.1, 0.5, 1 and 2 μg) with 0.5 nM 32 P-labeled DNA substrates. Samples were subjected to electrophoresis on native PAGE and visualized by autoradiography as mentioned in materials and methods section. ( B ) TieA binds to DNA non-specifically: electrophoretic mobility shift assays were carried out by incubating 1 μg of TieA with mutated oligos 1–5 (see Supplementary Table S1). ( C ) Nuclease activity of TieA: different concentrations of TieA (0.01, 0.1, 0.2, 0.5, 1 and 2 μg corresponding to lanes 7-12, respectively) were incubated with 1 μg of pUC19 DNA for 1 h at 37 °C. The reaction was stopped by addition of 10 mM EDTA and samples were deprotonized by adding proteinase K (10 μg/sample) in presence of 0.05% SDS for 15 min at 65°C. The digested products were separated on 1.2% agarose gel. Rv3131 (0.5 μg) was used as a negative control in lane 6. MboII (1 unit/reaction) and DNase I (1 unit/reaction) served as positive controls in lanes 3 and 5, respectively. Lane 4 represents heat inactivated TieA. ( D ) TieA cleaves both pUC19 (circular) and Lambda DNA (linear): pUC19 and Lambda DNA were incubated with TieA (lanes 5, 6, 14 and 15) for 1 h at 37°C and processed as described above. MboII (lanes 3 and 12) and DNase I (lanes 4 and 13) were used as positive controls. Rv3131 protein was used as a negative control (lanes 7 and 16). Ca 2+ –Mg 2+ dependent nuclease activity of TieA was confirmed by pre-incubating pUC19/Lambda DNA with either SDS (0.05%) or EDTA (10 mM) for 10 min (lanes 8, 9, 17 and 18) and later 1 μg of TieA was added and further processed as described above. Data are representative of three independent experiments. HI: heat inactivated.

    Article Snippet: The cleavage reaction was initiated with the addition of MboII or DNase I (1 U/reaction, New England Biolabs) enzyme.

    Techniques: Binding Assay, Electrophoretic Mobility Shift Assay, Labeling, Electrophoresis, Clear Native PAGE, Autoradiography, Activity Assay, Incubation, Agarose Gel Electrophoresis, Negative Control, Lambda DNA Preparation

    Characterization of transmitochondrial cybrids with mtDNA from various rodent species. Transmitochondrial cybrids B82mtB6, B82mtSpr, B82mtCar, B82mtAsp, and B82mtRat possessed nuclear DNA from M. musculus and mtDNA from M. musculus , M. spretus , M. caroli , A. speciosus and R. norvegicus , respectively. B82mtCOI M cybrids possessed M. musculus mtDNA with a pathogenic T6589C mutation in the mt-Co1 gene that induces respiration defects [ 11 ]. (A) Phylogenetic trees constructed by comparison of the sequence of the mt-Cytb gene encoded by mtDNA. On the basis of Kimura’s two-parameter model [ 24 ], we used mt-Cytb gene sequence data (positions 14139 to 15266) to create phylogenetic trees with PHYLIP software (http://www.phylip.com/). Branch lengths show evolutionary distance from M. musculus . The tree is rooted using Cricetulus griseus (Chinese hamster) sequence data. Values on each branch indicate base substitution in the mt-Cytb gene. (B) Genotyping of mtDNA. On Dra I digestion of the PCR products, B82mtB6 cells with M. musculus mtDNA gave a 327-bp fragment, whereas B82mtCar cells with M. caroli mtDNA gave a 267-bp fragment and a 39-bp fragment (not detectable) by a gain of a Dra I site and a 21-bp deletion in the mt-Dcr region. On Mbo II digestion of the PCR products, B82mtB6 cybrids with M. musculus mtDNA gave a 250-bp fragment, whereas B82mtAsp cybrids with A. speciosus mtDNA gave a 219-bp fragment and a 31-bp fragment (not detectable) by the gain of an Mbo II site in the mt-Cytb gene. (C) Estimation of O 2 consumption rates. B82mtB6 cells carrying nuclear and mitochondrial genomes from M. musculus were used as standards expressing normal respiratory function. Asterisks indicate a P -value less than 0.05 and double asterisks indicate a P -value less than 0.01.

    Journal: Experimental Animals

    Article Title: Selection of Rodent Species Appropriate for mtDNA Transfer to Generate Transmitochondrial Mito-Mice Expressing Mitochondrial Respiration Defects

    doi: 10.1538/expanim..21

    Figure Lengend Snippet: Characterization of transmitochondrial cybrids with mtDNA from various rodent species. Transmitochondrial cybrids B82mtB6, B82mtSpr, B82mtCar, B82mtAsp, and B82mtRat possessed nuclear DNA from M. musculus and mtDNA from M. musculus , M. spretus , M. caroli , A. speciosus and R. norvegicus , respectively. B82mtCOI M cybrids possessed M. musculus mtDNA with a pathogenic T6589C mutation in the mt-Co1 gene that induces respiration defects [ 11 ]. (A) Phylogenetic trees constructed by comparison of the sequence of the mt-Cytb gene encoded by mtDNA. On the basis of Kimura’s two-parameter model [ 24 ], we used mt-Cytb gene sequence data (positions 14139 to 15266) to create phylogenetic trees with PHYLIP software (http://www.phylip.com/). Branch lengths show evolutionary distance from M. musculus . The tree is rooted using Cricetulus griseus (Chinese hamster) sequence data. Values on each branch indicate base substitution in the mt-Cytb gene. (B) Genotyping of mtDNA. On Dra I digestion of the PCR products, B82mtB6 cells with M. musculus mtDNA gave a 327-bp fragment, whereas B82mtCar cells with M. caroli mtDNA gave a 267-bp fragment and a 39-bp fragment (not detectable) by a gain of a Dra I site and a 21-bp deletion in the mt-Dcr region. On Mbo II digestion of the PCR products, B82mtB6 cybrids with M. musculus mtDNA gave a 250-bp fragment, whereas B82mtAsp cybrids with A. speciosus mtDNA gave a 219-bp fragment and a 31-bp fragment (not detectable) by the gain of an Mbo II site in the mt-Cytb gene. (C) Estimation of O 2 consumption rates. B82mtB6 cells carrying nuclear and mitochondrial genomes from M. musculus were used as standards expressing normal respiratory function. Asterisks indicate a P -value less than 0.05 and double asterisks indicate a P -value less than 0.01.

    Article Snippet: The PCR amplicon contains a region of the mt-Cytb gene with an Mbo II (NEB) restriction site (control mouse mtDNA was not cleaved), and generates 219-bp and 31-bp fragments onMbo II digestion.

    Techniques: Mutagenesis, Construct, Sequencing, Software, Polymerase Chain Reaction, Expressing

    Chromatograms of PCR-RFLP assays and sequencing for detection of nucleotide alterations of 23S rRNA . H. Pylori 26695 and CLR r -1 were used as negative and positive control of A2143G mutation. BsaI digestion of the PCR products of representative samples was displayed on 8% PAGE gel. The 289 bp A2143G-positive PCR products were cleaved into a 199 bp and a 90 bp fragments ( A ). The A2143G mutation was also confirmed by sequencing of the PCR products of 23S rRNA ( B , displayed 2140–2154 fragment). H. Pylori 26695 and a 2142G clone were used as negative and positive control of A2142G mutation. MboII digestion of the PCR products of representative samples was displayed on 2% agarose gel. The 289 bp A2142G-positive PCR products of 2142G were cleaved into an 182 bp and a 107 bp fragments. The PCR product of GJ2040 was cleaved into a 164 bp and a 125 bp fragments; and the product of GJ2111 was cleaved into 245 bp and 44 bp fragment(s) ( C ). The A2142G and other mutations were confirmed by sequencing ( D ). Two new MboII -sensitive sequences were characterized as CTTCA (2222–2226) for GJ2040 and GAAG (2081–2084) for GJ2111.

    Journal: BMC Microbiology

    Article Title: Prevalence of A2143G mutation of H. pylori-23S rRNA in Chinese subjects with and without clarithromycin use history

    doi: 10.1186/1471-2180-8-81

    Figure Lengend Snippet: Chromatograms of PCR-RFLP assays and sequencing for detection of nucleotide alterations of 23S rRNA . H. Pylori 26695 and CLR r -1 were used as negative and positive control of A2143G mutation. BsaI digestion of the PCR products of representative samples was displayed on 8% PAGE gel. The 289 bp A2143G-positive PCR products were cleaved into a 199 bp and a 90 bp fragments ( A ). The A2143G mutation was also confirmed by sequencing of the PCR products of 23S rRNA ( B , displayed 2140–2154 fragment). H. Pylori 26695 and a 2142G clone were used as negative and positive control of A2142G mutation. MboII digestion of the PCR products of representative samples was displayed on 2% agarose gel. The 289 bp A2142G-positive PCR products of 2142G were cleaved into an 182 bp and a 107 bp fragments. The PCR product of GJ2040 was cleaved into a 164 bp and a 125 bp fragments; and the product of GJ2111 was cleaved into 245 bp and 44 bp fragment(s) ( C ). The A2142G and other mutations were confirmed by sequencing ( D ). Two new MboII -sensitive sequences were characterized as CTTCA (2222–2226) for GJ2040 and GAAG (2081–2084) for GJ2111.

    Article Snippet: RFLP assays The 289 bp amplicon of 23S rRNA was digested with the restriction enzymes BsaI and MboII (New England Biolabs, USA) in order to detect A2143G and A2142G point mutations, respectively (Fig ) [ , ].

    Techniques: Polymerase Chain Reaction, Sequencing, Positive Control, Mutagenesis, Polyacrylamide Gel Electrophoresis, Agarose Gel Electrophoresis