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  • 95
    New England Biolabs dde
    Tev-mTALEN activity in HEK293T cells on an episomal target. (A) Schematic of the vectors used for co-transfection experiments. For the expression vector, the Tev-mTALEN gene is separated from the mCherry translation reporter by a T2A peptide. (B) Example of Tev-mTALEN expression vector transfection efficiency and expression in HEK293T cells, with bright field image on the left and the epifluorescent image (1-sec exposure) of the same field of view on the right. (C) Schematic of the TP15 target, with a <t>Dde</t> I restriction site and sizes of Dde I digestion products indicated. (D) Agarose gel of a representative assay in which the target region was amplified by <t>PCR</t> from total DNA isolated 48 hr after transfection, and products were digested with Dde I (+) or incubated in buffer without Dde I (−); product resistant to cleavage by Dde I, which would result from mutagenic repair after cleavage by the mTALEN, is labeled with an asterisk (*). (E) Examples of mutations in the target resulting from co-transfection with N169-T120 or D184-V152 Tev-mTALENs. The Dde I-resistant product from (C) was cloned and several clones were sequenced. Dashes indicate the length of deletions observed in individual clones relative to the wild-type sequence.
    Dde, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 129 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Thermo Fisher dde i
    Tev-mTALEN activity in HEK293T cells on an episomal target. (A) Schematic of the vectors used for co-transfection experiments. For the expression vector, the Tev-mTALEN gene is separated from the mCherry translation reporter by a T2A peptide. (B) Example of Tev-mTALEN expression vector transfection efficiency and expression in HEK293T cells, with bright field image on the left and the epifluorescent image (1-sec exposure) of the same field of view on the right. (C) Schematic of the TP15 target, with a <t>Dde</t> I restriction site and sizes of Dde I digestion products indicated. (D) Agarose gel of a representative assay in which the target region was amplified by <t>PCR</t> from total DNA isolated 48 hr after transfection, and products were digested with Dde I (+) or incubated in buffer without Dde I (−); product resistant to cleavage by Dde I, which would result from mutagenic repair after cleavage by the mTALEN, is labeled with an asterisk (*). (E) Examples of mutations in the target resulting from co-transfection with N169-T120 or D184-V152 Tev-mTALENs. The Dde I-resistant product from (C) was cloned and several clones were sequenced. Dashes indicate the length of deletions observed in individual clones relative to the wild-type sequence.
    Dde I, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 101 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs endonucleases dde
    Tev-mTALEN activity in HEK293T cells on an episomal target. (A) Schematic of the vectors used for co-transfection experiments. For the expression vector, the Tev-mTALEN gene is separated from the mCherry translation reporter by a T2A peptide. (B) Example of Tev-mTALEN expression vector transfection efficiency and expression in HEK293T cells, with bright field image on the left and the epifluorescent image (1-sec exposure) of the same field of view on the right. (C) Schematic of the TP15 target, with a <t>Dde</t> I restriction site and sizes of Dde I digestion products indicated. (D) Agarose gel of a representative assay in which the target region was amplified by <t>PCR</t> from total DNA isolated 48 hr after transfection, and products were digested with Dde I (+) or incubated in buffer without Dde I (−); product resistant to cleavage by Dde I, which would result from mutagenic repair after cleavage by the mTALEN, is labeled with an asterisk (*). (E) Examples of mutations in the target resulting from co-transfection with N169-T120 or D184-V152 Tev-mTALENs. The Dde I-resistant product from (C) was cloned and several clones were sequenced. Dashes indicate the length of deletions observed in individual clones relative to the wild-type sequence.
    Endonucleases Dde, supplied by New England Biolabs, 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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    80
    Boehringer Mannheim restriction endonuclease dde i
    (A) 16S <t>PCR-RFLP</t> patterns observed with Dde I. (B) 16S PCR-RFLP patterns observed with Taq I and Bsr I. Letter above each lane denotes pattern obtained. Lane M, 100-bp ladder (New England Biolabs). The numbers are molecular sizes in kilobases.
    Restriction Endonuclease Dde I, supplied by Boehringer Mannheim, used in various techniques. Bioz Stars score: 80/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    GE Healthcare dde i
    (A) 16S <t>PCR-RFLP</t> patterns observed with Dde I. (B) 16S PCR-RFLP patterns observed with Taq I and Bsr I. Letter above each lane denotes pattern obtained. Lane M, 100-bp ladder (New England Biolabs). The numbers are molecular sizes in kilobases.
    Dde I, supplied by GE Healthcare, 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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    New England Biolabs restriction enzyme dde i
    Genetic and structural analysis of the m.15533A > G mutation. (A) Electropherogram showing the nucleotide change in patient's muscle DNA, indicated by arrowheads. (B) PCR-RFLP analysis of the MT-CYB mutation. Uncut (wild-type) DNA consists of a 150 bp PCR product. The mutated sequence contains one <t>Dde</t> I restriction site that results in two products of 90 and 60 bp after digestion. The control sequence contains one Mse I restriction site that results in the same two products after digestion. C, wild-type control; F, proband's fibroblasts DNA; M, proband's muscle DNA; Cy, control cybrid; 1, 2 and 3 refer to three independent mutant cybrid clones. (C) Alignment of cytochrome b amino acid sequences from selected species. Asparagine at amino acid position 263 is indicated with an arrow. (D) Partial 3D-images of the cytochrome b protein. The left panel shows the interaction site between the asparagine 263 (indicated in red) of cytochrome b and the aspartate 2 of the cytochrome c1 subunit (coloured in green). This is the closest negatively charged side-chain of cytochrome c1, which is facing the same aqueous pocket at a distance of 11.25 Armstrongs. Asparagine at position 260 of cytochrome b is indicated in blue. The central panel shows the 3D-structure of the asparagine 263 (in blue) in controls. The right panel shows the predicted structural effect of the N263D substitution (in red) in the patient. The images were obtained using the Chimera software [20] .
    Restriction Enzyme Dde I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 85/100, based on 27 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    New England Biolabs dde i restriction endonuclease
    Genetic and structural analysis of the m.15533A > G mutation. (A) Electropherogram showing the nucleotide change in patient's muscle DNA, indicated by arrowheads. (B) PCR-RFLP analysis of the MT-CYB mutation. Uncut (wild-type) DNA consists of a 150 bp PCR product. The mutated sequence contains one <t>Dde</t> I restriction site that results in two products of 90 and 60 bp after digestion. The control sequence contains one Mse I restriction site that results in the same two products after digestion. C, wild-type control; F, proband's fibroblasts DNA; M, proband's muscle DNA; Cy, control cybrid; 1, 2 and 3 refer to three independent mutant cybrid clones. (C) Alignment of cytochrome b amino acid sequences from selected species. Asparagine at amino acid position 263 is indicated with an arrow. (D) Partial 3D-images of the cytochrome b protein. The left panel shows the interaction site between the asparagine 263 (indicated in red) of cytochrome b and the aspartate 2 of the cytochrome c1 subunit (coloured in green). This is the closest negatively charged side-chain of cytochrome c1, which is facing the same aqueous pocket at a distance of 11.25 Armstrongs. Asparagine at position 260 of cytochrome b is indicated in blue. The central panel shows the 3D-structure of the asparagine 263 (in blue) in controls. The right panel shows the predicted structural effect of the N263D substitution (in red) in the patient. The images were obtained using the Chimera software [20] .
    Dde I Restriction Endonuclease, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 21 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Anatrace n dodecyl β d maltoside ddm
    Genetic and structural analysis of the m.15533A > G mutation. (A) Electropherogram showing the nucleotide change in patient's muscle DNA, indicated by arrowheads. (B) PCR-RFLP analysis of the MT-CYB mutation. Uncut (wild-type) DNA consists of a 150 bp PCR product. The mutated sequence contains one <t>Dde</t> I restriction site that results in two products of 90 and 60 bp after digestion. The control sequence contains one Mse I restriction site that results in the same two products after digestion. C, wild-type control; F, proband's fibroblasts DNA; M, proband's muscle DNA; Cy, control cybrid; 1, 2 and 3 refer to three independent mutant cybrid clones. (C) Alignment of cytochrome b amino acid sequences from selected species. Asparagine at amino acid position 263 is indicated with an arrow. (D) Partial 3D-images of the cytochrome b protein. The left panel shows the interaction site between the asparagine 263 (indicated in red) of cytochrome b and the aspartate 2 of the cytochrome c1 subunit (coloured in green). This is the closest negatively charged side-chain of cytochrome c1, which is facing the same aqueous pocket at a distance of 11.25 Armstrongs. Asparagine at position 260 of cytochrome b is indicated in blue. The central panel shows the 3D-structure of the asparagine 263 (in blue) in controls. The right panel shows the predicted structural effect of the N263D substitution (in red) in the patient. The images were obtained using the Chimera software [20] .
    N Dodecyl β D Maltoside Ddm, supplied by Anatrace, used in various techniques. Bioz Stars score: 91/100, based on 346 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    New England Biolabs hpy31
    Genetic and structural analysis of the m.15533A > G mutation. (A) Electropherogram showing the nucleotide change in patient's muscle DNA, indicated by arrowheads. (B) PCR-RFLP analysis of the MT-CYB mutation. Uncut (wild-type) DNA consists of a 150 bp PCR product. The mutated sequence contains one <t>Dde</t> I restriction site that results in two products of 90 and 60 bp after digestion. The control sequence contains one Mse I restriction site that results in the same two products after digestion. C, wild-type control; F, proband's fibroblasts DNA; M, proband's muscle DNA; Cy, control cybrid; 1, 2 and 3 refer to three independent mutant cybrid clones. (C) Alignment of cytochrome b amino acid sequences from selected species. Asparagine at amino acid position 263 is indicated with an arrow. (D) Partial 3D-images of the cytochrome b protein. The left panel shows the interaction site between the asparagine 263 (indicated in red) of cytochrome b and the aspartate 2 of the cytochrome c1 subunit (coloured in green). This is the closest negatively charged side-chain of cytochrome c1, which is facing the same aqueous pocket at a distance of 11.25 Armstrongs. Asparagine at position 260 of cytochrome b is indicated in blue. The central panel shows the 3D-structure of the asparagine 263 (in blue) in controls. The right panel shows the predicted structural effect of the N263D substitution (in red) in the patient. The images were obtained using the Chimera software [20] .
    Hpy31, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    New England Biolabs apo i
    Genetic and structural analysis of the m.15533A > G mutation. (A) Electropherogram showing the nucleotide change in patient's muscle DNA, indicated by arrowheads. (B) PCR-RFLP analysis of the MT-CYB mutation. Uncut (wild-type) DNA consists of a 150 bp PCR product. The mutated sequence contains one <t>Dde</t> I restriction site that results in two products of 90 and 60 bp after digestion. The control sequence contains one Mse I restriction site that results in the same two products after digestion. C, wild-type control; F, proband's fibroblasts DNA; M, proband's muscle DNA; Cy, control cybrid; 1, 2 and 3 refer to three independent mutant cybrid clones. (C) Alignment of cytochrome b amino acid sequences from selected species. Asparagine at amino acid position 263 is indicated with an arrow. (D) Partial 3D-images of the cytochrome b protein. The left panel shows the interaction site between the asparagine 263 (indicated in red) of cytochrome b and the aspartate 2 of the cytochrome c1 subunit (coloured in green). This is the closest negatively charged side-chain of cytochrome c1, which is facing the same aqueous pocket at a distance of 11.25 Armstrongs. Asparagine at position 260 of cytochrome b is indicated in blue. The central panel shows the 3D-structure of the asparagine 263 (in blue) in controls. The right panel shows the predicted structural effect of the N263D substitution (in red) in the patient. The images were obtained using the Chimera software [20] .
    Apo I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 129 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs hha i
    URA5–restriction fragment length polymorphism (RFLP) profiles for selected human, animal, and environmental Cryptococcus gattii isolates. A) URA5-RFLP to determine the molecular type using <t>Hha</t> I and Sau96 I endonucleases ( 14 ). B) URA5-RFLP to confirm molecular type and determine VGII subtype, using Hha I, Dde I, and BsrG I endonucleases.
    Hha I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 800 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs dra i
    URA5–restriction fragment length polymorphism (RFLP) profiles for selected human, animal, and environmental Cryptococcus gattii isolates. A) URA5-RFLP to determine the molecular type using <t>Hha</t> I and Sau96 I endonucleases ( 14 ). B) URA5-RFLP to confirm molecular type and determine VGII subtype, using Hha I, Dde I, and BsrG I endonucleases.
    Dra I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 97/100, based on 316 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs mse i
    PCR-RFLP analysis (lanes 2 to 11, <t>Taq</t> I digestion; lanes 12 to 21, <t>Mse</t> I digestion) of the gltA ). Lanes 1 and 22, standard 100-bp molecular ladder; lanes 2 to 9 and 12 to 19, coyote isolates; lanes 10 and 20, B. vinsonii subsp. berkhoffii ATCC 51672; lanes 11 and 21, B. henselae (strain U-4; University of California, Davis).
    Mse I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1428 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs hpa ii
    PCR-RFLP analysis (lanes 2 to 11, <t>Taq</t> I digestion; lanes 12 to 21, <t>Mse</t> I digestion) of the gltA ). Lanes 1 and 22, standard 100-bp molecular ladder; lanes 2 to 9 and 12 to 19, coyote isolates; lanes 10 and 20, B. vinsonii subsp. berkhoffii ATCC 51672; lanes 11 and 21, B. henselae (strain U-4; University of California, Davis).
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    New England Biolabs alu i
    PCR-RFLP analysis (lanes 2 to 11, <t>Taq</t> I digestion; lanes 12 to 21, <t>Mse</t> I digestion) of the gltA ). Lanes 1 and 22, standard 100-bp molecular ladder; lanes 2 to 9 and 12 to 19, coyote isolates; lanes 10 and 20, B. vinsonii subsp. berkhoffii ATCC 51672; lanes 11 and 21, B. henselae (strain U-4; University of California, Davis).
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    New England Biolabs fok i
    PCR-RFLP analysis (lanes 2 to 11, <t>Taq</t> I digestion; lanes 12 to 21, <t>Mse</t> I digestion) of the gltA ). Lanes 1 and 22, standard 100-bp molecular ladder; lanes 2 to 9 and 12 to 19, coyote isolates; lanes 10 and 20, B. vinsonii subsp. berkhoffii ATCC 51672; lanes 11 and 21, B. henselae (strain U-4; University of California, Davis).
    Fok I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 138 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs mnl i
    PCR-RFLP analysis of the 16S <t>rRNA</t> gene of coyote isolates with Dde I (A) or <t>Mnl</t> I (B) restriction endonuclease. Lanes 1 to 12, coyote isolates; lane 13, B. vinsonii subsp. berkhoffii ATCC 51672; lane 14, 100-bp molecular ladder.
    Mnl I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 148 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs taq i
    PCR-RFLP analysis of the 16S <t>rRNA</t> gene of coyote isolates with Dde I (A) or <t>Mnl</t> I (B) restriction endonuclease. Lanes 1 to 12, coyote isolates; lane 13, B. vinsonii subsp. berkhoffii ATCC 51672; lane 14, 100-bp molecular ladder.
    Taq I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 508 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs rsa i
    PCR-RFLP analysis of the 16S <t>rRNA</t> gene of coyote isolates with Dde I (A) or <t>Mnl</t> I (B) restriction endonuclease. Lanes 1 to 12, coyote isolates; lane 13, B. vinsonii subsp. berkhoffii ATCC 51672; lane 14, 100-bp molecular ladder.
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    New England Biolabs bsrg i
    URA5–restriction fragment length polymorphism (RFLP) profiles for selected human, animal, and environmental Cryptococcus gattii isolates. A) URA5-RFLP to determine the molecular type using <t>Hha</t> I and Sau96 I endonucleases ( 14 ). B) URA5-RFLP to confirm molecular type and determine VGII subtype, using Hha I, Dde I, and <t>BsrG</t> I endonucleases.
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    New England Biolabs sfc i
    URA5–restriction fragment length polymorphism (RFLP) profiles for selected human, animal, and environmental Cryptococcus gattii isolates. A) URA5-RFLP to determine the molecular type using <t>Hha</t> I and Sau96 I endonucleases ( 14 ). B) URA5-RFLP to confirm molecular type and determine VGII subtype, using Hha I, Dde I, and <t>BsrG</t> I endonucleases.
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    New England Biolabs aci i
    PCR-RFLP of a gltA gene fragment using the restriction endonuclease <t>Aci</t> I. Lanes 1, 4 and 19 show 100 BP Ladder; Lane 2, Mt Lion L27-96; Lane 3, Mt Lion L42-94; Lane 5, Mt Lion L-39-97; Lane 6, Mt Lion FM98061; Lane 7, Bobcat L08-96; Lane 8, Bobcat L17-96; Lane 9, Bobcat DS08; Lane 10, Bobcat L10-97; Lane 11, Bobcat L11-97; Lane 12, Bobcat SC443; lane 13, Bobcat DS507; Lane 14, B . henselae Type I; Lane 15, B . henselae Type II; Lane 16, B . clarridgeiae ; Lane 17, B . koehlerae ; Lane18, B . bovis (“weissii” isolate).
    Aci I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 98/100, based on 243 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Tev-mTALEN activity in HEK293T cells on an episomal target. (A) Schematic of the vectors used for co-transfection experiments. For the expression vector, the Tev-mTALEN gene is separated from the mCherry translation reporter by a T2A peptide. (B) Example of Tev-mTALEN expression vector transfection efficiency and expression in HEK293T cells, with bright field image on the left and the epifluorescent image (1-sec exposure) of the same field of view on the right. (C) Schematic of the TP15 target, with a Dde I restriction site and sizes of Dde I digestion products indicated. (D) Agarose gel of a representative assay in which the target region was amplified by PCR from total DNA isolated 48 hr after transfection, and products were digested with Dde I (+) or incubated in buffer without Dde I (−); product resistant to cleavage by Dde I, which would result from mutagenic repair after cleavage by the mTALEN, is labeled with an asterisk (*). (E) Examples of mutations in the target resulting from co-transfection with N169-T120 or D184-V152 Tev-mTALENs. The Dde I-resistant product from (C) was cloned and several clones were sequenced. Dashes indicate the length of deletions observed in individual clones relative to the wild-type sequence.

    Journal: G3: Genes|Genomes|Genetics

    Article Title: The I-TevI Nuclease and Linker Domains Contribute to the Specificity of Monomeric TALENs

    doi: 10.1534/g3.114.011445

    Figure Lengend Snippet: Tev-mTALEN activity in HEK293T cells on an episomal target. (A) Schematic of the vectors used for co-transfection experiments. For the expression vector, the Tev-mTALEN gene is separated from the mCherry translation reporter by a T2A peptide. (B) Example of Tev-mTALEN expression vector transfection efficiency and expression in HEK293T cells, with bright field image on the left and the epifluorescent image (1-sec exposure) of the same field of view on the right. (C) Schematic of the TP15 target, with a Dde I restriction site and sizes of Dde I digestion products indicated. (D) Agarose gel of a representative assay in which the target region was amplified by PCR from total DNA isolated 48 hr after transfection, and products were digested with Dde I (+) or incubated in buffer without Dde I (−); product resistant to cleavage by Dde I, which would result from mutagenic repair after cleavage by the mTALEN, is labeled with an asterisk (*). (E) Examples of mutations in the target resulting from co-transfection with N169-T120 or D184-V152 Tev-mTALENs. The Dde I-resistant product from (C) was cloned and several clones were sequenced. Dashes indicate the length of deletions observed in individual clones relative to the wild-type sequence.

    Article Snippet: After gel purification, 250 ng of each PCR product was incubated with 2 U of Dde I (N.E.B.) in 1× NEBuffer 2 for 1 hr at 37°.

    Techniques: Activity Assay, Cotransfection, Expressing, Plasmid Preparation, Transfection, Size-exclusion Chromatography, Agarose Gel Electrophoresis, Amplification, Polymerase Chain Reaction, Isolation, Incubation, Labeling, Clone Assay, Sequencing

    (A) 16S PCR-RFLP patterns observed with Dde I. (B) 16S PCR-RFLP patterns observed with Taq I and Bsr I. Letter above each lane denotes pattern obtained. Lane M, 100-bp ladder (New England Biolabs). The numbers are molecular sizes in kilobases.

    Journal: Journal of Clinical Microbiology

    Article Title: Rapid Identification of Campylobacter, Arcobacter, and Helicobacter Isolates by PCR-Restriction Fragment Length Polymorphism Analysis of the 16S rRNA Gene

    doi:

    Figure Lengend Snippet: (A) 16S PCR-RFLP patterns observed with Dde I. (B) 16S PCR-RFLP patterns observed with Taq I and Bsr I. Letter above each lane denotes pattern obtained. Lane M, 100-bp ladder (New England Biolabs). The numbers are molecular sizes in kilobases.

    Article Snippet: For restriction endonuclease digestion a 20-μl reaction mixture which included 10 μl of the PCR amplicon with 10 U of the restriction endonuclease Dde I (Boehringer-Mannheim, Indianapolis, Ind.), Taq I (Boehringer-Mannheim), or Bsr I (New England Biolabs, Inc., Beverly, Mass.) was employed, following conditions recommended by the respective manufacturers.

    Techniques: Polymerase Chain Reaction

    Genetic and structural analysis of the m.15533A > G mutation. (A) Electropherogram showing the nucleotide change in patient's muscle DNA, indicated by arrowheads. (B) PCR-RFLP analysis of the MT-CYB mutation. Uncut (wild-type) DNA consists of a 150 bp PCR product. The mutated sequence contains one Dde I restriction site that results in two products of 90 and 60 bp after digestion. The control sequence contains one Mse I restriction site that results in the same two products after digestion. C, wild-type control; F, proband's fibroblasts DNA; M, proband's muscle DNA; Cy, control cybrid; 1, 2 and 3 refer to three independent mutant cybrid clones. (C) Alignment of cytochrome b amino acid sequences from selected species. Asparagine at amino acid position 263 is indicated with an arrow. (D) Partial 3D-images of the cytochrome b protein. The left panel shows the interaction site between the asparagine 263 (indicated in red) of cytochrome b and the aspartate 2 of the cytochrome c1 subunit (coloured in green). This is the closest negatively charged side-chain of cytochrome c1, which is facing the same aqueous pocket at a distance of 11.25 Armstrongs. Asparagine at position 260 of cytochrome b is indicated in blue. The central panel shows the 3D-structure of the asparagine 263 (in blue) in controls. The right panel shows the predicted structural effect of the N263D substitution (in red) in the patient. The images were obtained using the Chimera software [20] .

    Journal: PLoS ONE

    Article Title: Impact of the Mitochondrial Genetic Background in Complex III Deficiency

    doi: 10.1371/journal.pone.0012801

    Figure Lengend Snippet: Genetic and structural analysis of the m.15533A > G mutation. (A) Electropherogram showing the nucleotide change in patient's muscle DNA, indicated by arrowheads. (B) PCR-RFLP analysis of the MT-CYB mutation. Uncut (wild-type) DNA consists of a 150 bp PCR product. The mutated sequence contains one Dde I restriction site that results in two products of 90 and 60 bp after digestion. The control sequence contains one Mse I restriction site that results in the same two products after digestion. C, wild-type control; F, proband's fibroblasts DNA; M, proband's muscle DNA; Cy, control cybrid; 1, 2 and 3 refer to three independent mutant cybrid clones. (C) Alignment of cytochrome b amino acid sequences from selected species. Asparagine at amino acid position 263 is indicated with an arrow. (D) Partial 3D-images of the cytochrome b protein. The left panel shows the interaction site between the asparagine 263 (indicated in red) of cytochrome b and the aspartate 2 of the cytochrome c1 subunit (coloured in green). This is the closest negatively charged side-chain of cytochrome c1, which is facing the same aqueous pocket at a distance of 11.25 Armstrongs. Asparagine at position 260 of cytochrome b is indicated in blue. The central panel shows the 3D-structure of the asparagine 263 (in blue) in controls. The right panel shows the predicted structural effect of the N263D substitution (in red) in the patient. The images were obtained using the Chimera software [20] .

    Article Snippet: To quantify the heteroplasmy levels of the m.15533 A > G mutation, PCR-restriction fragment length polymorphism (RFLP) analysis was performed in the proband's family using the following primers: 5′-CACTATTCTCACCAGACCTC-3′ , (forward) and 5′-ACGCCTCCTAGTTTGTTAGG-3′ (reverse), and digestion with the restriction enzyme Dde I (New England Biolabs).

    Techniques: Mutagenesis, Polymerase Chain Reaction, Sequencing, Software

    URA5–restriction fragment length polymorphism (RFLP) profiles for selected human, animal, and environmental Cryptococcus gattii isolates. A) URA5-RFLP to determine the molecular type using Hha I and Sau96 I endonucleases ( 14 ). B) URA5-RFLP to confirm molecular type and determine VGII subtype, using Hha I, Dde I, and BsrG I endonucleases.

    Journal: Emerging Infectious Diseases

    Article Title: Spread of Cryptococcus gattii in British Columbia, Canada, and Detection in the Pacific Northwest, USA

    doi: 10.3201/eid1301.060827

    Figure Lengend Snippet: URA5–restriction fragment length polymorphism (RFLP) profiles for selected human, animal, and environmental Cryptococcus gattii isolates. A) URA5-RFLP to determine the molecular type using Hha I and Sau96 I endonucleases ( 14 ). B) URA5-RFLP to confirm molecular type and determine VGII subtype, using Hha I, Dde I, and BsrG I endonucleases.

    Article Snippet: The URA5 gene was amplified as previously described ( ) and then completely digested at 37°C in a 20-μL reaction containing 1× NEB2 buffer, 1× bovine serum albumin, and 4 U each of Hha I, Dde I, and BsrG I (New England Biolabs, Inc., Ipswich, MA, USA).

    Techniques:

    PCR-RFLP analysis (lanes 2 to 11, Taq I digestion; lanes 12 to 21, Mse I digestion) of the gltA ). Lanes 1 and 22, standard 100-bp molecular ladder; lanes 2 to 9 and 12 to 19, coyote isolates; lanes 10 and 20, B. vinsonii subsp. berkhoffii ATCC 51672; lanes 11 and 21, B. henselae (strain U-4; University of California, Davis).

    Journal: Journal of Clinical Microbiology

    Article Title: Coyotes (Canis latrans) as the Reservoir for a Human Pathogenic Bartonella sp.: Molecular Epidemiology of Bartonella vinsonii subsp. berkhoffii Infection in Coyotes from Central Coastal California

    doi:

    Figure Lengend Snippet: PCR-RFLP analysis (lanes 2 to 11, Taq I digestion; lanes 12 to 21, Mse I digestion) of the gltA ). Lanes 1 and 22, standard 100-bp molecular ladder; lanes 2 to 9 and 12 to 19, coyote isolates; lanes 10 and 20, B. vinsonii subsp. berkhoffii ATCC 51672; lanes 11 and 21, B. henselae (strain U-4; University of California, Davis).

    Article Snippet: Taq I and Mse I (New England BioLabs) restriction endonucleases were utilized when using the set of primers suggested by Norman et al. ( ).

    Techniques: Polymerase Chain Reaction

    PCR-RFLP analysis of the 16S rRNA gene of coyote isolates with Dde I (A) or Mnl I (B) restriction endonuclease. Lanes 1 to 12, coyote isolates; lane 13, B. vinsonii subsp. berkhoffii ATCC 51672; lane 14, 100-bp molecular ladder.

    Journal: Journal of Clinical Microbiology

    Article Title: Coyotes (Canis latrans) as the Reservoir for a Human Pathogenic Bartonella sp.: Molecular Epidemiology of Bartonella vinsonii subsp. berkhoffii Infection in Coyotes from Central Coastal California

    doi:

    Figure Lengend Snippet: PCR-RFLP analysis of the 16S rRNA gene of coyote isolates with Dde I (A) or Mnl I (B) restriction endonuclease. Lanes 1 to 12, coyote isolates; lane 13, B. vinsonii subsp. berkhoffii ATCC 51672; lane 14, 100-bp molecular ladder.

    Article Snippet: The amplified product of the 16S rRNA gene was digested with Dde I (Boehringer GmbH, Mannheim, Germany) and Mnl I (New England BioLabs) restriction endonucleases.

    Techniques: Polymerase Chain Reaction

    URA5–restriction fragment length polymorphism (RFLP) profiles for selected human, animal, and environmental Cryptococcus gattii isolates. A) URA5-RFLP to determine the molecular type using Hha I and Sau96 I endonucleases ( 14 ). B) URA5-RFLP to confirm molecular type and determine VGII subtype, using Hha I, Dde I, and BsrG I endonucleases.

    Journal: Emerging Infectious Diseases

    Article Title: Spread of Cryptococcus gattii in British Columbia, Canada, and Detection in the Pacific Northwest, USA

    doi: 10.3201/eid1301.060827

    Figure Lengend Snippet: URA5–restriction fragment length polymorphism (RFLP) profiles for selected human, animal, and environmental Cryptococcus gattii isolates. A) URA5-RFLP to determine the molecular type using Hha I and Sau96 I endonucleases ( 14 ). B) URA5-RFLP to confirm molecular type and determine VGII subtype, using Hha I, Dde I, and BsrG I endonucleases.

    Article Snippet: The URA5 gene was amplified as previously described ( ) and then completely digested at 37°C in a 20-μL reaction containing 1× NEB2 buffer, 1× bovine serum albumin, and 4 U each of Hha I, Dde I, and BsrG I (New England Biolabs, Inc., Ipswich, MA, USA).

    Techniques:

    PCR-RFLP of a gltA gene fragment using the restriction endonuclease Aci I. Lanes 1, 4 and 19 show 100 BP Ladder; Lane 2, Mt Lion L27-96; Lane 3, Mt Lion L42-94; Lane 5, Mt Lion L-39-97; Lane 6, Mt Lion FM98061; Lane 7, Bobcat L08-96; Lane 8, Bobcat L17-96; Lane 9, Bobcat DS08; Lane 10, Bobcat L10-97; Lane 11, Bobcat L11-97; Lane 12, Bobcat SC443; lane 13, Bobcat DS507; Lane 14, B . henselae Type I; Lane 15, B . henselae Type II; Lane 16, B . clarridgeiae ; Lane 17, B . koehlerae ; Lane18, B . bovis (“weissii” isolate).

    Journal: PLoS ONE

    Article Title: Isolation of Bartonella henselae and Two New Bartonella Subspecies, Bartonellakoehlerae Subspecies boulouisii subsp. nov. and Bartonella koehlerae Subspecies bothieri subsp. nov. from Free-Ranging Californian Mountain Lions and Bobcats

    doi: 10.1371/journal.pone.0148299

    Figure Lengend Snippet: PCR-RFLP of a gltA gene fragment using the restriction endonuclease Aci I. Lanes 1, 4 and 19 show 100 BP Ladder; Lane 2, Mt Lion L27-96; Lane 3, Mt Lion L42-94; Lane 5, Mt Lion L-39-97; Lane 6, Mt Lion FM98061; Lane 7, Bobcat L08-96; Lane 8, Bobcat L17-96; Lane 9, Bobcat DS08; Lane 10, Bobcat L10-97; Lane 11, Bobcat L11-97; Lane 12, Bobcat SC443; lane 13, Bobcat DS507; Lane 14, B . henselae Type I; Lane 15, B . henselae Type II; Lane 16, B . clarridgeiae ; Lane 17, B . koehlerae ; Lane18, B . bovis (“weissii” isolate).

    Article Snippet: The amplified product of the gltA gene was digested with Taq I (Promega, Madison, WI), Hha I (New England Biolabs, Beverly, M.A.), Mse I (New England Biolabs) and Aci I (New England Biolabs); the amplified product of the 16S rRNA gene was digested with Dde I (New England Biolabs); the amplified product of the ribC gene was digested with Taq I; and the amplified product of the 16S-23S ITS region was digested with Taq I and Hae III.

    Techniques: Polymerase Chain Reaction