Structured Review

Roche ecorv
Measured cleavage rate versus DNA tension. ( a ) The effect of tension on cleavage of linearized pCco5 by <t>EcoRV</t> (number of recognition sites n = 1). EcoRV concentration was 25 nM in terms of dimers. The total amount of cutting events was 68. ( b ) EcoRV on Lambda phage DNA ( n = 21), 32 cutting events. ( c ) Tension dependence on DNA cleavage by <t>BamHI</t> (300 nM) on the pCco5 derivative containing a single recognition site (squares, 78 events) and on Lambda phage DNA with five BamHI sites (triangles, 28 events) using 2.5 nM BamHI. Each point consists of at least 6 cleavage events. Vertical error bars represent the standard error of the mean rate. Horizontal error bars are the standard deviation of the combined DNA tensions (a result of the binning). The data in (a and b) are fitted to the described model (normalized χ 2 are 0.6 and 0.2, respectively). The BamHI rates in (c) do not significantly vary with DNA tension and were fitted with constant values [normalized χ 2 are 0.8 (hydrolysis, green line) and 1.6 (diffusion, blue line)].
Ecorv, supplied by Roche, used in various techniques. Bioz Stars score: 92/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Images

1) Product Images from "DNA-tension dependence of restriction enzyme activity reveals mechanochemical properties of the reaction pathway"

Article Title: DNA-tension dependence of restriction enzyme activity reveals mechanochemical properties of the reaction pathway

Journal: Nucleic Acids Research

doi: 10.1093/nar/gki565

Measured cleavage rate versus DNA tension. ( a ) The effect of tension on cleavage of linearized pCco5 by EcoRV (number of recognition sites n = 1). EcoRV concentration was 25 nM in terms of dimers. The total amount of cutting events was 68. ( b ) EcoRV on Lambda phage DNA ( n = 21), 32 cutting events. ( c ) Tension dependence on DNA cleavage by BamHI (300 nM) on the pCco5 derivative containing a single recognition site (squares, 78 events) and on Lambda phage DNA with five BamHI sites (triangles, 28 events) using 2.5 nM BamHI. Each point consists of at least 6 cleavage events. Vertical error bars represent the standard error of the mean rate. Horizontal error bars are the standard deviation of the combined DNA tensions (a result of the binning). The data in (a and b) are fitted to the described model (normalized χ 2 are 0.6 and 0.2, respectively). The BamHI rates in (c) do not significantly vary with DNA tension and were fitted with constant values [normalized χ 2 are 0.8 (hydrolysis, green line) and 1.6 (diffusion, blue line)].
Figure Legend Snippet: Measured cleavage rate versus DNA tension. ( a ) The effect of tension on cleavage of linearized pCco5 by EcoRV (number of recognition sites n = 1). EcoRV concentration was 25 nM in terms of dimers. The total amount of cutting events was 68. ( b ) EcoRV on Lambda phage DNA ( n = 21), 32 cutting events. ( c ) Tension dependence on DNA cleavage by BamHI (300 nM) on the pCco5 derivative containing a single recognition site (squares, 78 events) and on Lambda phage DNA with five BamHI sites (triangles, 28 events) using 2.5 nM BamHI. Each point consists of at least 6 cleavage events. Vertical error bars represent the standard error of the mean rate. Horizontal error bars are the standard deviation of the combined DNA tensions (a result of the binning). The data in (a and b) are fitted to the described model (normalized χ 2 are 0.6 and 0.2, respectively). The BamHI rates in (c) do not significantly vary with DNA tension and were fitted with constant values [normalized χ 2 are 0.8 (hydrolysis, green line) and 1.6 (diffusion, blue line)].

Techniques Used: Concentration Assay, Standard Deviation, Diffusion-based Assay

Crystal structures of specific enzyme–DNA complexes of BamHI (1) ( 23 ) and EcoRV (2) ( 2 , 18 ). The DNA configuration within both complexes is shown separately, (3) and (4), respectively. While BamHI does not distort its recognition site, EcoRV induces a 50° kink located at the center base pair step.
Figure Legend Snippet: Crystal structures of specific enzyme–DNA complexes of BamHI (1) ( 23 ) and EcoRV (2) ( 2 , 18 ). The DNA configuration within both complexes is shown separately, (3) and (4), respectively. While BamHI does not distort its recognition site, EcoRV induces a 50° kink located at the center base pair step.

Techniques Used:

2) Product Images from "BDNF-Live-Exon-Visualization (BLEV) Allows Differential Detection of BDNF Transcripts in vitro and in vivo"

Article Title: BDNF-Live-Exon-Visualization (BLEV) Allows Differential Detection of BDNF Transcripts in vitro and in vivo

Journal: Frontiers in Molecular Neuroscience

doi: 10.3389/fnmol.2018.00325

Generation of the BLEV reporter mouse. (A) Schematic drawing of the Bdnf gene (Aid et al., 2007 ) and the BDNF vector construct used for homologous recombination. Crossing-over events are indicated by red dotted lines and crosses. The 5' and 3' parts for homologous recombination are marked in red. (B) Bdnf gene construct depicting insertion sites of the BLEV construct. Arrows indicate the EcoRV restriction sites (RS) used for Southern blot. Black arrows indicate EcoRV RS cutting the WT and the transgenic sequence, red arrows cut only the transgenic sequence. (C) Southern blot of a positively transfected ES cell clone. The positions of the four Southern blot probes (colored lines: green, blue, orange, and pink) are shown under the schematic drawing of the BDNF construct. Probe 1, specific for the 5′-end: WT band 9.8 kb, transgenic allele 3 kb; probe 2, covering parts of exon-IV transgene: WT band 9.8 kb, transgenic allele 5.3 kb; probe 3, covering parts of the exon-VI transgene: WT band 9.8 kb, transgenic allele 6.3 kb; probe 4, specific for the 3′-end: WT and transgenic allele 12.7 kb. Note that the size of the drawn construct and probes does not reflect the real size of the DNA fragments obtained by Southern blot. For original Blots see Supplementary Figure 1 .
Figure Legend Snippet: Generation of the BLEV reporter mouse. (A) Schematic drawing of the Bdnf gene (Aid et al., 2007 ) and the BDNF vector construct used for homologous recombination. Crossing-over events are indicated by red dotted lines and crosses. The 5' and 3' parts for homologous recombination are marked in red. (B) Bdnf gene construct depicting insertion sites of the BLEV construct. Arrows indicate the EcoRV restriction sites (RS) used for Southern blot. Black arrows indicate EcoRV RS cutting the WT and the transgenic sequence, red arrows cut only the transgenic sequence. (C) Southern blot of a positively transfected ES cell clone. The positions of the four Southern blot probes (colored lines: green, blue, orange, and pink) are shown under the schematic drawing of the BDNF construct. Probe 1, specific for the 5′-end: WT band 9.8 kb, transgenic allele 3 kb; probe 2, covering parts of exon-IV transgene: WT band 9.8 kb, transgenic allele 5.3 kb; probe 3, covering parts of the exon-VI transgene: WT band 9.8 kb, transgenic allele 6.3 kb; probe 4, specific for the 3′-end: WT and transgenic allele 12.7 kb. Note that the size of the drawn construct and probes does not reflect the real size of the DNA fragments obtained by Southern blot. For original Blots see Supplementary Figure 1 .

Techniques Used: Plasmid Preparation, Construct, Homologous Recombination, Southern Blot, Transgenic Assay, Sequencing, Transfection

3) Product Images from "Characterization of Integrative and Conjugative Element ICEKp1-Associated Genomic Heterogeneity in a Klebsiella pneumoniae Strain Isolated from a Primary Liver Abscess ▿"

Article Title: Characterization of Integrative and Conjugative Element ICEKp1-Associated Genomic Heterogeneity in a Klebsiella pneumoniae Strain Isolated from a Primary Liver Abscess ▿

Journal:

doi: 10.1128/JB.01219-07

Mobility of ICE Kp1 in strain NTUH-K2044. (A) PCR analysis of the location of ICE Kp1 in strains NTUH-K2044 and NTUH-K2044 ICE Kp1 − . (B) Southern hybridization of EcoRV-digested DNA from strains NTUH-K2044 and NTUH-K2044 ICE Kp1 − with asn
Figure Legend Snippet: Mobility of ICE Kp1 in strain NTUH-K2044. (A) PCR analysis of the location of ICE Kp1 in strains NTUH-K2044 and NTUH-K2044 ICE Kp1 − . (B) Southern hybridization of EcoRV-digested DNA from strains NTUH-K2044 and NTUH-K2044 ICE Kp1 − with asn

Techniques Used: Polymerase Chain Reaction, Hybridization

Related Articles

Clone Assay:

Article Title: A deletion defining a common Asian lineage of Mycobacterium tuberculosis associates with immune subversion
Article Snippet: .. All digested products were ultimately cloned into BamHI, or BamHI and EcoRV were linearized pSMT3 by using a rapid ligation kit (Roche). .. The pSMT3 vector carries a pUC19 backbone with a pAL5000-based mycobacterial origin of replication and bears hygromycin resistance.

Immunohistochemistry:

Article Title: Localization of the Brainstem GABAergic Neurons Controlling Paradoxical (REM) Sleep
Article Snippet: .. Fos immunohistochemistry combined with GAD67 mRNA in situ hybridization As described before , the recombinant plasmid containing the GAD67 cDNA was linearised using EcoRV and transcribed using SP6 RNA polymerase and a nonradioactive RNA labeling kit (Roche Diagnostic, Mannheim, Germany) for the antisense probe. .. The brain sections were successively incubated in a rabbit antiserum to Fos (1∶4000; Ab-5; Oncogene, CA, USA) in 10 mM PB containing 0.9% NaCl and 0.3% Triton-100× (PBST) for 18 h at room temperature; a biotinylated goat antirabbit IgG solution (1∶1000; Vector Laboratories, Burlingame, CA, USA); and an ABC-HRP solution (1∶1000; Elite kit, Vector Laboratories) both for 90 min at room temperature.

Southern Blot:

Article Title: The malaria circumsporozoite protein has two functional domains, each with distinct roles as sporozoites journey from mosquito to mammalian host
Article Snippet: .. Southern blotting was performed with genomic DNA from erythrocytic stage parasites digested with EcoRV and probed with the 873-bp PmlI–PacI fragment of CSP , which was labeled with digoxigenin-dUTP by random priming and detected using the DIG High Prime DNA Labeling and Detection kit (Roche). .. In addition, the CSP coding sequence of each clone was amplified using primers P3 (5′-GAGCTATGTTACAATGAAGG-3′) and P4 (5′-AAATTCTAGTATTTTTTCCGCGC-3′) and sequenced to confirm that the deletion was not corrected.

Ligation:

Article Title: A deletion defining a common Asian lineage of Mycobacterium tuberculosis associates with immune subversion
Article Snippet: .. All digested products were ultimately cloned into BamHI, or BamHI and EcoRV were linearized pSMT3 by using a rapid ligation kit (Roche). .. The pSMT3 vector carries a pUC19 backbone with a pAL5000-based mycobacterial origin of replication and bears hygromycin resistance.

Mutagenesis:

Article Title: Mechanisms of Azole Resistance in Petite Mutants of Candida glabrata
Article Snippet: .. The mtDNA of parent and mutant cells was analyzed after digestion by EcoRV (Roche Diagnostics GmbH, Mannheim, Germany), and the presence of mitochondria was investigated by transmission electron microscopy as previously described ( ). .. Mutation rates in the presence of azoles were evaluated for both clinical isolates on Casitone agar plates containing an inhibitory concentration of drug.

Isolation:

Article Title: BDNF-Live-Exon-Visualization (BLEV) Allows Differential Detection of BDNF Transcripts in vitro and in vivo
Article Snippet: .. In brief, isolated DNA was digested using EcoRV and SalI (Roche). .. DNA fragments were separated on a 0.8% agarose gel.

DNA Labeling:

Article Title: The malaria circumsporozoite protein has two functional domains, each with distinct roles as sporozoites journey from mosquito to mammalian host
Article Snippet: .. Southern blotting was performed with genomic DNA from erythrocytic stage parasites digested with EcoRV and probed with the 873-bp PmlI–PacI fragment of CSP , which was labeled with digoxigenin-dUTP by random priming and detected using the DIG High Prime DNA Labeling and Detection kit (Roche). .. In addition, the CSP coding sequence of each clone was amplified using primers P3 (5′-GAGCTATGTTACAATGAAGG-3′) and P4 (5′-AAATTCTAGTATTTTTTCCGCGC-3′) and sequenced to confirm that the deletion was not corrected.

Labeling:

Article Title: Localization of the Brainstem GABAergic Neurons Controlling Paradoxical (REM) Sleep
Article Snippet: .. Fos immunohistochemistry combined with GAD67 mRNA in situ hybridization As described before , the recombinant plasmid containing the GAD67 cDNA was linearised using EcoRV and transcribed using SP6 RNA polymerase and a nonradioactive RNA labeling kit (Roche Diagnostic, Mannheim, Germany) for the antisense probe. .. The brain sections were successively incubated in a rabbit antiserum to Fos (1∶4000; Ab-5; Oncogene, CA, USA) in 10 mM PB containing 0.9% NaCl and 0.3% Triton-100× (PBST) for 18 h at room temperature; a biotinylated goat antirabbit IgG solution (1∶1000; Vector Laboratories, Burlingame, CA, USA); and an ABC-HRP solution (1∶1000; Elite kit, Vector Laboratories) both for 90 min at room temperature.

Article Title: Neuroglobin expression in the mammalian auditory system
Article Snippet: .. Sense and antisense Ngb probes were generated by linearizing the subclone with HindIII or EcoRV, respectively, followed by labeling using the DIG RNA labeling kit (Roche, Indianapolis, IN) according to the manufacturer’s protocol. .. Paraffin embedded sections were deparaffinized in CitriSolve (Fisher Scientific, Waltham, MA), hydrated in graded alcohols, and rinsed 2× in 1×PBS for 5 min prior to prehybridization.

Article Title: The malaria circumsporozoite protein has two functional domains, each with distinct roles as sporozoites journey from mosquito to mammalian host
Article Snippet: .. Southern blotting was performed with genomic DNA from erythrocytic stage parasites digested with EcoRV and probed with the 873-bp PmlI–PacI fragment of CSP , which was labeled with digoxigenin-dUTP by random priming and detected using the DIG High Prime DNA Labeling and Detection kit (Roche). .. In addition, the CSP coding sequence of each clone was amplified using primers P3 (5′-GAGCTATGTTACAATGAAGG-3′) and P4 (5′-AAATTCTAGTATTTTTTCCGCGC-3′) and sequenced to confirm that the deletion was not corrected.

Generated:

Article Title: Neuroglobin expression in the mammalian auditory system
Article Snippet: .. Sense and antisense Ngb probes were generated by linearizing the subclone with HindIII or EcoRV, respectively, followed by labeling using the DIG RNA labeling kit (Roche, Indianapolis, IN) according to the manufacturer’s protocol. .. Paraffin embedded sections were deparaffinized in CitriSolve (Fisher Scientific, Waltham, MA), hydrated in graded alcohols, and rinsed 2× in 1×PBS for 5 min prior to prehybridization.

Electron Microscopy:

Article Title: Mechanisms of Azole Resistance in Petite Mutants of Candida glabrata
Article Snippet: .. The mtDNA of parent and mutant cells was analyzed after digestion by EcoRV (Roche Diagnostics GmbH, Mannheim, Germany), and the presence of mitochondria was investigated by transmission electron microscopy as previously described ( ). .. Mutation rates in the presence of azoles were evaluated for both clinical isolates on Casitone agar plates containing an inhibitory concentration of drug.

Transmission Assay:

Article Title: Mechanisms of Azole Resistance in Petite Mutants of Candida glabrata
Article Snippet: .. The mtDNA of parent and mutant cells was analyzed after digestion by EcoRV (Roche Diagnostics GmbH, Mannheim, Germany), and the presence of mitochondria was investigated by transmission electron microscopy as previously described ( ). .. Mutation rates in the presence of azoles were evaluated for both clinical isolates on Casitone agar plates containing an inhibitory concentration of drug.

Recombinant:

Article Title: Localization of the Brainstem GABAergic Neurons Controlling Paradoxical (REM) Sleep
Article Snippet: .. Fos immunohistochemistry combined with GAD67 mRNA in situ hybridization As described before , the recombinant plasmid containing the GAD67 cDNA was linearised using EcoRV and transcribed using SP6 RNA polymerase and a nonradioactive RNA labeling kit (Roche Diagnostic, Mannheim, Germany) for the antisense probe. .. The brain sections were successively incubated in a rabbit antiserum to Fos (1∶4000; Ab-5; Oncogene, CA, USA) in 10 mM PB containing 0.9% NaCl and 0.3% Triton-100× (PBST) for 18 h at room temperature; a biotinylated goat antirabbit IgG solution (1∶1000; Vector Laboratories, Burlingame, CA, USA); and an ABC-HRP solution (1∶1000; Elite kit, Vector Laboratories) both for 90 min at room temperature.

In Situ Hybridization:

Article Title: Localization of the Brainstem GABAergic Neurons Controlling Paradoxical (REM) Sleep
Article Snippet: .. Fos immunohistochemistry combined with GAD67 mRNA in situ hybridization As described before , the recombinant plasmid containing the GAD67 cDNA was linearised using EcoRV and transcribed using SP6 RNA polymerase and a nonradioactive RNA labeling kit (Roche Diagnostic, Mannheim, Germany) for the antisense probe. .. The brain sections were successively incubated in a rabbit antiserum to Fos (1∶4000; Ab-5; Oncogene, CA, USA) in 10 mM PB containing 0.9% NaCl and 0.3% Triton-100× (PBST) for 18 h at room temperature; a biotinylated goat antirabbit IgG solution (1∶1000; Vector Laboratories, Burlingame, CA, USA); and an ABC-HRP solution (1∶1000; Elite kit, Vector Laboratories) both for 90 min at room temperature.

Plasmid Preparation:

Article Title: Localization of the Brainstem GABAergic Neurons Controlling Paradoxical (REM) Sleep
Article Snippet: .. Fos immunohistochemistry combined with GAD67 mRNA in situ hybridization As described before , the recombinant plasmid containing the GAD67 cDNA was linearised using EcoRV and transcribed using SP6 RNA polymerase and a nonradioactive RNA labeling kit (Roche Diagnostic, Mannheim, Germany) for the antisense probe. .. The brain sections were successively incubated in a rabbit antiserum to Fos (1∶4000; Ab-5; Oncogene, CA, USA) in 10 mM PB containing 0.9% NaCl and 0.3% Triton-100× (PBST) for 18 h at room temperature; a biotinylated goat antirabbit IgG solution (1∶1000; Vector Laboratories, Burlingame, CA, USA); and an ABC-HRP solution (1∶1000; Elite kit, Vector Laboratories) both for 90 min at room temperature.

Article Title: DNA-tension dependence of restriction enzyme activity reveals mechanochemical properties of the reaction pathway
Article Snippet: .. Plasmid pCco5 DNA (6538 bp; gift from W. Reijnders, Vrije Universiteit, Amsterdam) was utilized for the single cleavage site experiments on EcoRV and BamHI, whereas for the multiple site experiments Lambda phage DNA (48 502 bp; Roche GmbH, Germany) was used. .. The pCco5 plasmid was linearized by SpeI digestion (New England Biolabs) and extracted from 0.7% agarose gel using a QIAEX II kit (Qiagen).

Hybridization:

Article Title: Characterization of Integrative and Conjugative Element ICEKp1-Associated Genomic Heterogeneity in a Klebsiella pneumoniae Strain Isolated from a Primary Liver Abscess ▿
Article Snippet: .. Approximately 5-μg portions of genomic DNA from various K. pneumoniae strains were digested by EcoRV and subjected to Southern hybridization according to manufacturer's instructions (Roche Molecular Biochemicals, Mannheim, Germany). .. Primers (asn-F and asn-R primers [Table ]) were designed to generate the digoxigenin-labeled asn tRNA gene probe by PCR.

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    Roche ecorv
    Measured cleavage rate versus DNA tension. ( a ) The effect of tension on cleavage of linearized pCco5 by <t>EcoRV</t> (number of recognition sites n = 1). EcoRV concentration was 25 nM in terms of dimers. The total amount of cutting events was 68. ( b ) EcoRV on Lambda phage DNA ( n = 21), 32 cutting events. ( c ) Tension dependence on DNA cleavage by <t>BamHI</t> (300 nM) on the pCco5 derivative containing a single recognition site (squares, 78 events) and on Lambda phage DNA with five BamHI sites (triangles, 28 events) using 2.5 nM BamHI. Each point consists of at least 6 cleavage events. Vertical error bars represent the standard error of the mean rate. Horizontal error bars are the standard deviation of the combined DNA tensions (a result of the binning). The data in (a and b) are fitted to the described model (normalized χ 2 are 0.6 and 0.2, respectively). The BamHI rates in (c) do not significantly vary with DNA tension and were fitted with constant values [normalized χ 2 are 0.8 (hydrolysis, green line) and 1.6 (diffusion, blue line)].
    Ecorv, supplied by Roche, used in various techniques. Bioz Stars score: 92/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Measured cleavage rate versus DNA tension. ( a ) The effect of tension on cleavage of linearized pCco5 by EcoRV (number of recognition sites n = 1). EcoRV concentration was 25 nM in terms of dimers. The total amount of cutting events was 68. ( b ) EcoRV on Lambda phage DNA ( n = 21), 32 cutting events. ( c ) Tension dependence on DNA cleavage by BamHI (300 nM) on the pCco5 derivative containing a single recognition site (squares, 78 events) and on Lambda phage DNA with five BamHI sites (triangles, 28 events) using 2.5 nM BamHI. Each point consists of at least 6 cleavage events. Vertical error bars represent the standard error of the mean rate. Horizontal error bars are the standard deviation of the combined DNA tensions (a result of the binning). The data in (a and b) are fitted to the described model (normalized χ 2 are 0.6 and 0.2, respectively). The BamHI rates in (c) do not significantly vary with DNA tension and were fitted with constant values [normalized χ 2 are 0.8 (hydrolysis, green line) and 1.6 (diffusion, blue line)].

    Journal: Nucleic Acids Research

    Article Title: DNA-tension dependence of restriction enzyme activity reveals mechanochemical properties of the reaction pathway

    doi: 10.1093/nar/gki565

    Figure Lengend Snippet: Measured cleavage rate versus DNA tension. ( a ) The effect of tension on cleavage of linearized pCco5 by EcoRV (number of recognition sites n = 1). EcoRV concentration was 25 nM in terms of dimers. The total amount of cutting events was 68. ( b ) EcoRV on Lambda phage DNA ( n = 21), 32 cutting events. ( c ) Tension dependence on DNA cleavage by BamHI (300 nM) on the pCco5 derivative containing a single recognition site (squares, 78 events) and on Lambda phage DNA with five BamHI sites (triangles, 28 events) using 2.5 nM BamHI. Each point consists of at least 6 cleavage events. Vertical error bars represent the standard error of the mean rate. Horizontal error bars are the standard deviation of the combined DNA tensions (a result of the binning). The data in (a and b) are fitted to the described model (normalized χ 2 are 0.6 and 0.2, respectively). The BamHI rates in (c) do not significantly vary with DNA tension and were fitted with constant values [normalized χ 2 are 0.8 (hydrolysis, green line) and 1.6 (diffusion, blue line)].

    Article Snippet: Plasmid pCco5 DNA (6538 bp; gift from W. Reijnders, Vrije Universiteit, Amsterdam) was utilized for the single cleavage site experiments on EcoRV and BamHI, whereas for the multiple site experiments Lambda phage DNA (48 502 bp; Roche GmbH, Germany) was used.

    Techniques: Concentration Assay, Standard Deviation, Diffusion-based Assay

    Crystal structures of specific enzyme–DNA complexes of BamHI (1) ( 23 ) and EcoRV (2) ( 2 , 18 ). The DNA configuration within both complexes is shown separately, (3) and (4), respectively. While BamHI does not distort its recognition site, EcoRV induces a 50° kink located at the center base pair step.

    Journal: Nucleic Acids Research

    Article Title: DNA-tension dependence of restriction enzyme activity reveals mechanochemical properties of the reaction pathway

    doi: 10.1093/nar/gki565

    Figure Lengend Snippet: Crystal structures of specific enzyme–DNA complexes of BamHI (1) ( 23 ) and EcoRV (2) ( 2 , 18 ). The DNA configuration within both complexes is shown separately, (3) and (4), respectively. While BamHI does not distort its recognition site, EcoRV induces a 50° kink located at the center base pair step.

    Article Snippet: Plasmid pCco5 DNA (6538 bp; gift from W. Reijnders, Vrije Universiteit, Amsterdam) was utilized for the single cleavage site experiments on EcoRV and BamHI, whereas for the multiple site experiments Lambda phage DNA (48 502 bp; Roche GmbH, Germany) was used.

    Techniques:

    Generation of the BLEV reporter mouse. (A) Schematic drawing of the Bdnf gene (Aid et al., 2007 ) and the BDNF vector construct used for homologous recombination. Crossing-over events are indicated by red dotted lines and crosses. The 5' and 3' parts for homologous recombination are marked in red. (B) Bdnf gene construct depicting insertion sites of the BLEV construct. Arrows indicate the EcoRV restriction sites (RS) used for Southern blot. Black arrows indicate EcoRV RS cutting the WT and the transgenic sequence, red arrows cut only the transgenic sequence. (C) Southern blot of a positively transfected ES cell clone. The positions of the four Southern blot probes (colored lines: green, blue, orange, and pink) are shown under the schematic drawing of the BDNF construct. Probe 1, specific for the 5′-end: WT band 9.8 kb, transgenic allele 3 kb; probe 2, covering parts of exon-IV transgene: WT band 9.8 kb, transgenic allele 5.3 kb; probe 3, covering parts of the exon-VI transgene: WT band 9.8 kb, transgenic allele 6.3 kb; probe 4, specific for the 3′-end: WT and transgenic allele 12.7 kb. Note that the size of the drawn construct and probes does not reflect the real size of the DNA fragments obtained by Southern blot. For original Blots see Supplementary Figure 1 .

    Journal: Frontiers in Molecular Neuroscience

    Article Title: BDNF-Live-Exon-Visualization (BLEV) Allows Differential Detection of BDNF Transcripts in vitro and in vivo

    doi: 10.3389/fnmol.2018.00325

    Figure Lengend Snippet: Generation of the BLEV reporter mouse. (A) Schematic drawing of the Bdnf gene (Aid et al., 2007 ) and the BDNF vector construct used for homologous recombination. Crossing-over events are indicated by red dotted lines and crosses. The 5' and 3' parts for homologous recombination are marked in red. (B) Bdnf gene construct depicting insertion sites of the BLEV construct. Arrows indicate the EcoRV restriction sites (RS) used for Southern blot. Black arrows indicate EcoRV RS cutting the WT and the transgenic sequence, red arrows cut only the transgenic sequence. (C) Southern blot of a positively transfected ES cell clone. The positions of the four Southern blot probes (colored lines: green, blue, orange, and pink) are shown under the schematic drawing of the BDNF construct. Probe 1, specific for the 5′-end: WT band 9.8 kb, transgenic allele 3 kb; probe 2, covering parts of exon-IV transgene: WT band 9.8 kb, transgenic allele 5.3 kb; probe 3, covering parts of the exon-VI transgene: WT band 9.8 kb, transgenic allele 6.3 kb; probe 4, specific for the 3′-end: WT and transgenic allele 12.7 kb. Note that the size of the drawn construct and probes does not reflect the real size of the DNA fragments obtained by Southern blot. For original Blots see Supplementary Figure 1 .

    Article Snippet: In brief, isolated DNA was digested using EcoRV and SalI (Roche).

    Techniques: Plasmid Preparation, Construct, Homologous Recombination, Southern Blot, Transgenic Assay, Sequencing, Transfection

    Mobility of ICE Kp1 in strain NTUH-K2044. (A) PCR analysis of the location of ICE Kp1 in strains NTUH-K2044 and NTUH-K2044 ICE Kp1 − . (B) Southern hybridization of EcoRV-digested DNA from strains NTUH-K2044 and NTUH-K2044 ICE Kp1 − with asn

    Journal:

    Article Title: Characterization of Integrative and Conjugative Element ICEKp1-Associated Genomic Heterogeneity in a Klebsiella pneumoniae Strain Isolated from a Primary Liver Abscess ▿

    doi: 10.1128/JB.01219-07

    Figure Lengend Snippet: Mobility of ICE Kp1 in strain NTUH-K2044. (A) PCR analysis of the location of ICE Kp1 in strains NTUH-K2044 and NTUH-K2044 ICE Kp1 − . (B) Southern hybridization of EcoRV-digested DNA from strains NTUH-K2044 and NTUH-K2044 ICE Kp1 − with asn

    Article Snippet: Approximately 5-μg portions of genomic DNA from various K. pneumoniae strains were digested by EcoRV and subjected to Southern hybridization according to manufacturer's instructions (Roche Molecular Biochemicals, Mannheim, Germany).

    Techniques: Polymerase Chain Reaction, Hybridization