dde 1 enzyme  (New England Biolabs)


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    Structured Review

    New England Biolabs dde 1 enzyme
    Dde 1 Enzyme, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 85/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dde 1 enzyme/product/New England Biolabs
    Average 85 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
    dde 1 enzyme - by Bioz Stars, 2020-08
    85/100 stars

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    Article Snippet: The PCR cycling conditions include initial denaturation at 95° C for 12 min followed by 35 cycles of denaturation at 95° C for 30 s, annealing at 59° C for 20 s, extension at 72° C for 40 s and final extension at 72° C for 6 min. After amplification, PCR products were subjected for restriction digestion using Dde 1 enzyme (New England Biolabs, USA).

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    New England Biolabs 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 New England Biolabs, used in various techniques. Bioz Stars score: 97/100, based on 59 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 97 stars, based on 59 article reviews
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    New England Biolabs restriction endonucleases dde
    Chromatin remodeling at the Oct-Sox binding motif in Oct4 and Nanog. (A) Schematic showing the location of the Oct-Sox binding motif and adjacent restriction enzyme cut site within the forward and reverse primers for Oct4 and Nanog . Shown are the effects of open and condensed chromatin on the accessibility of <t>Dde</t> I and <t>Mse</t> I at Oct4 and Nanog , respectively. (B) qPCR analysis of restriction enzyme accessibility at the Oct-Sox binding motif in Oct4 and Nanog at 0, 48, and 96 h after induction of Cdx2. As a negative control, the accessibility of Mse I at an intergenic region was assessed. Data are presented as the percentage of DNA cut by the respective restriction enzyme. An assay was performed on a total of three biological replicates. For each biological replicate, two PCR reactions were performed in duplicate. (C) Histone H3 ChIP analysis at the Oct-Sox binding motif in Oct4 and Nanog at 0, 48, and 96 h after induction of Cdx2. The enrichment of histone H3 on Gapdh was utilized as a control. As a negative control, a rabbit nonspecific IgG was used. A total of two ChIP replicates were performed for each biological replicate. * P
    Restriction Endonucleases Dde, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    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

    PCR-RFLP of B. quintana and B. henselae from clinical specimens. Lane 1, 50-bp ladder, lanes 2 to 4, B. quintana H93-176; lanes 5 to 7, B. henselae B92-007003; lane 8, blank; lanes 9 to 11, B. quintana B93-007356; lane 12, 50-bp ladder. PCR products were left uncut (lanes 2, 5, and 9) or were cut with Dde I (lanes 3, 6, and 10) or Mse I (lanes 4, 7, and 11).

    Journal: Journal of Clinical Microbiology

    Article Title: Identification of Bartonella Species Directly in Clinical Specimens by PCR-Restriction Fragment Length Polymorphism Analysis of a 16S rRNA Gene Fragment

    doi:

    Figure Lengend Snippet: PCR-RFLP of B. quintana and B. henselae from clinical specimens. Lane 1, 50-bp ladder, lanes 2 to 4, B. quintana H93-176; lanes 5 to 7, B. henselae B92-007003; lane 8, blank; lanes 9 to 11, B. quintana B93-007356; lane 12, 50-bp ladder. PCR products were left uncut (lanes 2, 5, and 9) or were cut with Dde I (lanes 3, 6, and 10) or Mse I (lanes 4, 7, and 11).

    Article Snippet: For digestion of PCR-amplified DNA from cultures and clinical specimens, 10 to 15 μl of PCR-amplified DNA was restricted with 10 U of Dde I and Mse I in a total volume of 15 to 20 μl, respectively, according to the manufacturer's specifications (New England Biolabs, Inc., Beverly, Mass.).

    Techniques: Polymerase Chain Reaction

    PCR-RFLP of pal and detection of its gene product, PAL, from clonally diverse A. actinomycetemcomitans strains. Panel A: Agarose gel electrophoresis of the PCR products shows amplicons with the expected size of pal (425 bp) for each strain. Panels B and C: Agarose gel electrophoresis of the purified PCR amplicons digested with Dde I and Bsp MI, separately. Panel D: immunoblot analysis of the A. actinomycetemcomitans whole cell protein preparations using anti-AaPAL peptide antiserum shows the expected 17-kDa signal for each strain. Lanes 1 through 12 strain identification (serotype; genotype): ATCC 29523 (a; 1), SA5002 (a; 1), ATCC 43718 (b; 2), SA5003 (b; 8), ATCC 33384 (c; 3), SA5005 (c; 3), SA5001 (d; 5), SA5007 (d; 22), SA5008 (e; 6), SA5011 (e; 20), CU1000R (f; nd*), SA5022 (f; 19) and standards (S). *nd: not determined.

    Journal: BMC Microbiology

    Article Title: Vesicle-independent extracellular release of a proinflammatory outer membrane lipoprotein in free-soluble form

    doi: 10.1186/1471-2180-8-18

    Figure Lengend Snippet: PCR-RFLP of pal and detection of its gene product, PAL, from clonally diverse A. actinomycetemcomitans strains. Panel A: Agarose gel electrophoresis of the PCR products shows amplicons with the expected size of pal (425 bp) for each strain. Panels B and C: Agarose gel electrophoresis of the purified PCR amplicons digested with Dde I and Bsp MI, separately. Panel D: immunoblot analysis of the A. actinomycetemcomitans whole cell protein preparations using anti-AaPAL peptide antiserum shows the expected 17-kDa signal for each strain. Lanes 1 through 12 strain identification (serotype; genotype): ATCC 29523 (a; 1), SA5002 (a; 1), ATCC 43718 (b; 2), SA5003 (b; 8), ATCC 33384 (c; 3), SA5005 (c; 3), SA5001 (d; 5), SA5007 (d; 22), SA5008 (e; 6), SA5011 (e; 20), CU1000R (f; nd*), SA5022 (f; 19) and standards (S). *nd: not determined.

    Article Snippet: PCR-restriction fragment length polymorphism (PCR-RFLP) of the A. actinomycetemcomitans pal sequence For RFLP, PCR amplicons generated by the primers PAL-SA 5'-GCTGGTTCTGTGGCTGTGT and PAL-MK 5'-ACTGCACGACGGTTTTTAGC were purified (QIAquick® Gel Extraction Kit, Qiagen GmbH, Helden, Germany) and digested with Bsp MI and Dde I (New England BioLabs, Beverly, MA, USA), respectively, prior to analysis on agarose (1.8%) gel electrophoresis.

    Techniques: Polymerase Chain Reaction, Agarose Gel Electrophoresis, Purification

    Chromatin remodeling at the Oct-Sox binding motif in Oct4 and Nanog. (A) Schematic showing the location of the Oct-Sox binding motif and adjacent restriction enzyme cut site within the forward and reverse primers for Oct4 and Nanog . Shown are the effects of open and condensed chromatin on the accessibility of Dde I and Mse I at Oct4 and Nanog , respectively. (B) qPCR analysis of restriction enzyme accessibility at the Oct-Sox binding motif in Oct4 and Nanog at 0, 48, and 96 h after induction of Cdx2. As a negative control, the accessibility of Mse I at an intergenic region was assessed. Data are presented as the percentage of DNA cut by the respective restriction enzyme. An assay was performed on a total of three biological replicates. For each biological replicate, two PCR reactions were performed in duplicate. (C) Histone H3 ChIP analysis at the Oct-Sox binding motif in Oct4 and Nanog at 0, 48, and 96 h after induction of Cdx2. The enrichment of histone H3 on Gapdh was utilized as a control. As a negative control, a rabbit nonspecific IgG was used. A total of two ChIP replicates were performed for each biological replicate. * P

    Journal: Stem Cells and Development

    Article Title: Transcriptional Reprogramming and Chromatin Remodeling Accompanies Oct4 and Nanog Silencing in Mouse Trophoblast Lineage

    doi: 10.1089/scd.2013.0328

    Figure Lengend Snippet: Chromatin remodeling at the Oct-Sox binding motif in Oct4 and Nanog. (A) Schematic showing the location of the Oct-Sox binding motif and adjacent restriction enzyme cut site within the forward and reverse primers for Oct4 and Nanog . Shown are the effects of open and condensed chromatin on the accessibility of Dde I and Mse I at Oct4 and Nanog , respectively. (B) qPCR analysis of restriction enzyme accessibility at the Oct-Sox binding motif in Oct4 and Nanog at 0, 48, and 96 h after induction of Cdx2. As a negative control, the accessibility of Mse I at an intergenic region was assessed. Data are presented as the percentage of DNA cut by the respective restriction enzyme. An assay was performed on a total of three biological replicates. For each biological replicate, two PCR reactions were performed in duplicate. (C) Histone H3 ChIP analysis at the Oct-Sox binding motif in Oct4 and Nanog at 0, 48, and 96 h after induction of Cdx2. The enrichment of histone H3 on Gapdh was utilized as a control. As a negative control, a rabbit nonspecific IgG was used. A total of two ChIP replicates were performed for each biological replicate. * P

    Article Snippet: Isolated nuclei were then treated with restriction endonucleases Dde I or Mse I (New England Biolabs) that were specific for single-cut sites located within the amplicons for Oct4 and Nanog , respectively.

    Techniques: Binding Assay, Real-time Polymerase Chain Reaction, Negative Control, Polymerase Chain Reaction, Chromatin Immunoprecipitation