bamhi restriction enzymes  (New England Biolabs)


Bioz Verified Symbol New England Biolabs is a verified supplier
Bioz Manufacturer Symbol New England Biolabs manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 99
    Name:
    BamHI
    Description:
    BamHI 50 000 units
    Catalog Number:
    R0136L
    Price:
    249
    Category:
    Restriction Enzymes
    Size:
    50 000 units
    Buy from Supplier


    Structured Review

    New England Biolabs bamhi restriction enzymes
    BamHI
    BamHI 50 000 units
    https://www.bioz.com/result/bamhi restriction enzymes/product/New England Biolabs
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    bamhi restriction enzymes - by Bioz Stars, 2021-05
    99/100 stars

    Images

    Related Articles

    In Vitro:

    Article Title: Direct detection of methylation in genomic DNA
    Article Snippet: Chromosomal DNA of H.pylori strain 1061 was isolated as described earlier ( ). pUC19 plasmid DNA was isolated from E.coli DH5α using the Wizard plus SV miniprep kit (Promega). .. In vitro methylation of pUC19 DNA was performed with M.EcoRI (N 6 -methyladenine), M.HaeIII (5-methylcytosine) or M.BamHI (N 4 -methylcytosine) obtained from New England Biolabs according to the manufacturer's instructions. .. Complete methylation was subsequently confirmed by incubation of methylated DNA with the corresponding restriction endonucleases (Roche), separation by agarose gel electrophoresis and visualization by ethidium bromide staining.

    Methylation:

    Article Title: Direct detection of methylation in genomic DNA
    Article Snippet: Chromosomal DNA of H.pylori strain 1061 was isolated as described earlier ( ). pUC19 plasmid DNA was isolated from E.coli DH5α using the Wizard plus SV miniprep kit (Promega). .. In vitro methylation of pUC19 DNA was performed with M.EcoRI (N 6 -methyladenine), M.HaeIII (5-methylcytosine) or M.BamHI (N 4 -methylcytosine) obtained from New England Biolabs according to the manufacturer's instructions. .. Complete methylation was subsequently confirmed by incubation of methylated DNA with the corresponding restriction endonucleases (Roche), separation by agarose gel electrophoresis and visualization by ethidium bromide staining.

    Incubation:

    Article Title: Topoisomerase 2 Is Dispensable for the Replication and Segregation of Small Yeast Artificial Chromosomes (YACs)
    Article Snippet: .. DNA treatments DNA was digested with BamHI, EcoRV, KpnI, NsiI, PvuI, PvuII, SalI, SwaI, XhoI, (New England Biolabs) and Nt.Bpu10I (Thermo Scientific) for at least 2 hours at 37°C except for SwaI that was incubated at 25°C. .. 2D agarose gel electrophoresis and southern transfer The first dimension was in a 0.35–0.5% agarose gel (Seakem; FMC Bioproducts) in TBE buffer (89 mM Tris-borate, 2 mM EDTA) at 0.9 V/cm at room temperature for 27–38 h. The second dimension was in a 0.9–1.2% agarose gel in TBE buffer and was run perpendicular to the first dimension.

    Article Title: Comparative analysis of linker histone H1, MeCP2, and HMGD1 on nucleosome stability and target site accessibility
    Article Snippet: The DNA was run on a 1% agarose gel with 0.2× GelStar in 1× TAE (Tris-Acetic Acid-EDTA) at 100 volts for 1 h. .. Chromatin remodeling reactions For probing nucleosomal array accessibility, 25 ng of chromatin or chromatosome arrays (based on DNA) were incubated with +/−300 nM of ISWI and 2 mM ATP in 100 mM NaCl, 50 mM Tris-HCl pH 8.0, 1 mM DTT, and 1 mM MgCl2 for 1 h at 27 °C, followed by adding either 40 U of BamHI (NEB) or PstI (NEB) and allowed to digest for 1 h or 15 min respectively at 37 °C. ..

    Generated:

    Article Title: A domain insertion in Escherichia coli GyrB adopts a novel fold that plays a critical role in gyrase function
    Article Snippet: Gels were run at 1.5 V/ cm for 14–18 h and stained with 0.5 μg/ml EtBr in 0.5 × TBE for 30 min. Gels were then destained briefly in 0.5 × TBE and bands visualized by UV transillumination. .. A linearized pBSK standard was generated by cleaving the negatively-supercoiled DNA with BamHI (New England Biolabs). .. DNA-binding assays DNA binding was visualized by electrophoretic mobility shift assays (EMSAs).

    Plasmid Preparation:

    Article Title: Enhanced antifungal activity of bovine lactoferrin-producing probiotic Lactobacillus casei in the murine model of vulvovaginal candidiasis
    Article Snippet: Plasmid pUC57-BLF was amplified in E. coli DH5α and purified using the E.Z.N.A plasmid mini kit (Omega Bio-tek, Inc., Norcross, GA, USA). .. The BLF fragment was retrieved from the pUC57-BLF using BamHI and XhoI enzymes (New England Biolabs Inc., Ipswich, MA, USA) and ligated into the corresponding sites of pPG612.1, generating the plasmid pPG612.1-BLF. .. The ligation reaction mix was used to transform E. coli DH5α and the resulting transformants were confirmed by PCR amplification and sequencing (Table ).

    Agarose Gel Electrophoresis:

    Article Title: Simple and Cost-Effective Restriction Endonuclease Analysis of Human Adenoviruses
    Article Snippet: The electrophoresis was performed in TAE buffer at 100 V for 50 minutes (Mupid, Advance, Tokyo, Japan). .. DNA Restriction Endonuclease Analysis and Agarose Gel Electrophoresis Both usual RE and RE fast digestion of HAdV-1p, HAdV-3p, HAdV-4p, and HAdV-37p were performed with usual REs and high fidelity (HF) REs, such as BamHI , BglII , and HindIII (New England Biolabs), which have the power to complete digestion within 5–15 minutes. ..

    Amplification:

    Article Title: Development of a Tet-On inducible expression system for the anhydrobiotic cell line, Pv11
    Article Snippet: A DNA fragment for the AMV RTα gene was synthesized by Eurofins Genomics K.K, Tokyo, Japan. .. The AMV RTα gene was then amplified by PCR with specific primers ( ) and inserted into pPv121-MCS digested with BamHI and SacII using NEBuilder HiFi DNA Assembly Mater Mix. .. For the pTetO-202bp-AMV RTα expression vector, the AMV RTα sequence was amplified and inserted into pTetO-202bp-Nluc digested with SalI and BglII using NEBuilder HiFi DNA Assembly Master Mix.

    Polymerase Chain Reaction:

    Article Title: Development of a Tet-On inducible expression system for the anhydrobiotic cell line, Pv11
    Article Snippet: A DNA fragment for the AMV RTα gene was synthesized by Eurofins Genomics K.K, Tokyo, Japan. .. The AMV RTα gene was then amplified by PCR with specific primers ( ) and inserted into pPv121-MCS digested with BamHI and SacII using NEBuilder HiFi DNA Assembly Mater Mix. .. For the pTetO-202bp-AMV RTα expression vector, the AMV RTα sequence was amplified and inserted into pTetO-202bp-Nluc digested with SalI and BglII using NEBuilder HiFi DNA Assembly Master Mix.

    Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 99
    New England Biolabs bamhi
    Construction and expression of the secretion plasmid <t>pPG612.1-BLF</t> in L.casei . a The synthetic BLF gene fragment (2.1kp) was digested with restriction enzymes <t>BamHI</t> and XhoI, and ligated into the sticky end of the plasmid pPG612.1 which was also digested with the same restriction enzyme, resulting in the plasmid pPG612.1-BLF (5.6kp). b The plasmid pPG612.1-BLF was electroporated into L.casei using a BioRad GenePulser with single electric pulse (voltage, 1.5 kV; capacitance, 25 μF; and resistance, 400 Ω.). PCR amplification of the BamHI site and XhoI site of the plasmid pPG612.1-BLF which was extracted from the L.casei /pPG612.1-BLF strain resulted in 500 bp and 800 bp products, respectively. Lane 1, PCR product of XhoI site; Lane 2, PCR product of BamHI site. M, DNA maker. c BLF was detected in the supernatant and pellet of L.casei /pPG612.1-BLF culture by Western blotting, indicating the expression and secretion of BLF by L.casei /pPG612.1-BLF. Lane 1, supernatant of L.casei /pPG612.1-BLF culture; Lane 2, pellet of L.casei /pPG612.1-BLF culture; Lane 3, supernatant of L.casei /pPG612.1 culture; Lane 4, pellet of L.casei /pPG612.1 culture
    Bamhi, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bamhi/product/New England Biolabs
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    bamhi - by Bioz Stars, 2021-05
    99/100 stars
      Buy from Supplier

    99
    New England Biolabs recombinant restriction enzyme bamhi hf
    Overview of the proposed ONS-based protocol for mtDNA methylation calling a ) Log-likelihood ratio values of methylation calculated by Nanopolish, using the positive and negative controls. The log-likelihood range between −20 and 20 (used to build the ROC curve) is shown. b ) Receiver operating characteristic (ROC) curve calculated by changing the methylation call log-likelihood ratio threshold from a value of −20 to 20, with a step of 0.25. The dash lines are drawn at FPR (False Positive Rate) and TPR (True Positive Rate) values obtained by setting the ratio equal to 5. AUC = area under the curve. c ) Methylation call accuracy calculated at increasing values of log-likelihood ratio (ranging between 0 and 10). The dash line indicates the accuracy achieved at the ratio equal to 5 (accuracy = 0.99). d) Overview of the workflow used to process samples using (left) standard ONT fragmentation protocol and (right) <t>BamHI-based</t> protocol. e) Ratio of signal from the mitochondrial MT-ND1 over RNASE P ddPCR probes in undigested genomic <t>DNA</t> and BamHI-digested genomic DNA. N = 4 for each protocol used. Star indicates significance (*: two-sided P = ≤ 0.05, Wilcoxon test). f) Distributions of the total sequenced reads in 3 samples prepared with either fragmentation or BamHI-based protocols. Reads from Rho 0 cells (treated with BamHI) are highlighted in yellow. Blue dashed lines correspond to the chosen cutoff for read filtering at 4000bp and 17000 bp. The red dashed line corresponds to the human mtDNA genome length (16.5 Kbp). g) Distribution of the aligned reads filtered by length (4000bp −17000 bp) on the human mtDNA reference sequence in 3 samples prepared with either fragmentation or BamHI-based protocols. Reads from Rho 0 cells (treated with BamHI) are highlighted in yellow.
    Recombinant Restriction Enzyme Bamhi Hf, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/recombinant restriction enzyme bamhi hf/product/New England Biolabs
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    recombinant restriction enzyme bamhi hf - by Bioz Stars, 2021-05
    99/100 stars
      Buy from Supplier

    86
    New England Biolabs restriction endonucleases bamhi
    Genetic map, 2D gel analysis of linear fragments corresponding to pYAC_MEM_3rRFBs+ and densitometry of the spots accumulated on the simple-Y arc. ( A ) Genetic map of pYAC_MEM_3rRFBs+ (8908 bp) showing its most relevant features (for further details see the legend of Figure 3 ). Note the insertion of an EcoRI fragment containing the three putative Fob1 binding sites expected to act as RFBs (indicated in red), described by Kobayashi ( 20 ). ( B ) Map of the 3708 bp linear fragment generated by digestion of pYAC_MEM_3rRFBs+ with SwaI and <t>BamHI</t> showing the relative position of the three putative RFBs. ( C ) Map of the 5186 bp linear fragment generated by digestion of pYAC_MEM_3rRFBs+ with <t>EcoRV</t> and MluI showing the relative position of the three putative RFBs. ( D ) 2D gel immunogram of the RIs corresponding to the SwaI-BamHI 3708 bp linear fragment with its diagrammatic interpretation in ( E ). The 2D gel immunogram of the RIs corresponding to the EcoRV-MluI 5186-bp linear fragment is shown in ( F ) with its diagrammatic interpretation in ( G ). The densitometric profile corresponding to the spots observed on the simple-Y arc shown in (D) is presented in ( H ) indicating the height of the peaks and the distance separating them.
    Restriction Endonucleases Bamhi, 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
    https://www.bioz.com/result/restriction endonucleases bamhi/product/New England Biolabs
    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    restriction endonucleases bamhi - by Bioz Stars, 2021-05
    86/100 stars
      Buy from Supplier

    Image Search Results


    Construction and expression of the secretion plasmid pPG612.1-BLF in L.casei . a The synthetic BLF gene fragment (2.1kp) was digested with restriction enzymes BamHI and XhoI, and ligated into the sticky end of the plasmid pPG612.1 which was also digested with the same restriction enzyme, resulting in the plasmid pPG612.1-BLF (5.6kp). b The plasmid pPG612.1-BLF was electroporated into L.casei using a BioRad GenePulser with single electric pulse (voltage, 1.5 kV; capacitance, 25 μF; and resistance, 400 Ω.). PCR amplification of the BamHI site and XhoI site of the plasmid pPG612.1-BLF which was extracted from the L.casei /pPG612.1-BLF strain resulted in 500 bp and 800 bp products, respectively. Lane 1, PCR product of XhoI site; Lane 2, PCR product of BamHI site. M, DNA maker. c BLF was detected in the supernatant and pellet of L.casei /pPG612.1-BLF culture by Western blotting, indicating the expression and secretion of BLF by L.casei /pPG612.1-BLF. Lane 1, supernatant of L.casei /pPG612.1-BLF culture; Lane 2, pellet of L.casei /pPG612.1-BLF culture; Lane 3, supernatant of L.casei /pPG612.1 culture; Lane 4, pellet of L.casei /pPG612.1 culture

    Journal: BMC Microbiology

    Article Title: Enhanced antifungal activity of bovine lactoferrin-producing probiotic Lactobacillus casei in the murine model of vulvovaginal candidiasis

    doi: 10.1186/s12866-018-1370-x

    Figure Lengend Snippet: Construction and expression of the secretion plasmid pPG612.1-BLF in L.casei . a The synthetic BLF gene fragment (2.1kp) was digested with restriction enzymes BamHI and XhoI, and ligated into the sticky end of the plasmid pPG612.1 which was also digested with the same restriction enzyme, resulting in the plasmid pPG612.1-BLF (5.6kp). b The plasmid pPG612.1-BLF was electroporated into L.casei using a BioRad GenePulser with single electric pulse (voltage, 1.5 kV; capacitance, 25 μF; and resistance, 400 Ω.). PCR amplification of the BamHI site and XhoI site of the plasmid pPG612.1-BLF which was extracted from the L.casei /pPG612.1-BLF strain resulted in 500 bp and 800 bp products, respectively. Lane 1, PCR product of XhoI site; Lane 2, PCR product of BamHI site. M, DNA maker. c BLF was detected in the supernatant and pellet of L.casei /pPG612.1-BLF culture by Western blotting, indicating the expression and secretion of BLF by L.casei /pPG612.1-BLF. Lane 1, supernatant of L.casei /pPG612.1-BLF culture; Lane 2, pellet of L.casei /pPG612.1-BLF culture; Lane 3, supernatant of L.casei /pPG612.1 culture; Lane 4, pellet of L.casei /pPG612.1 culture

    Article Snippet: The BLF fragment was retrieved from the pUC57-BLF using BamHI and XhoI enzymes (New England Biolabs Inc., Ipswich, MA, USA) and ligated into the corresponding sites of pPG612.1, generating the plasmid pPG612.1-BLF.

    Techniques: Expressing, Plasmid Preparation, Polymerase Chain Reaction, Amplification, Western Blot

    BamHI digestion prior to bisulfite sequencing decreases cytosine unconvertion rate. Targeted bisulfite sequencing was used to compare undigested and digested DNA methylation levels at five different regions of the mtDNA from human muscle cells and SKOV3 cells ( N = 3). (A) Drawing displays the mtDNA regions investigated by targeted bisulfite sequencing. (B) Percentage methylation for undigested and digested mtDNA. Full circle represents cytosines in CpG context whereas open circle is cytosines in non-CpG context. Results are presented with a min-max interval and a sign test was used to test for significant methylation differences. D-loop (6–298) P = 2.02E-41 (Lonza) and P = 1.40E-24 (SKOV3); D-loop (279–458): P = 5.00E-12 (Lonza) and P = 8.20E-08 (SKOV3); tRNA-F+12S: P = 9.22E-15 (Lonza) and P = 1.29E-9 (SKOV3); 16S: P = 6.50E-05; ND5: P = 1.70E-05 (Lonza) and P = 9.97E-13 (SKOV3); CYTB: P = 2.96E-09 (Lonza), and P = 6.68E-13 (SKOV3). D-loop (6–298) includes origin of replication and tRNA-F+12S includes heavy strand promoter 2. P H1 : heavy-strand promoter 1; P H2 : Heavy-strand promote 2; P L : Light-strand promoter; OH: Origin of replication from heavy-strand; O L : Origin of replication from light-strand. ND: not determined.

    Journal: Frontiers in Genetics

    Article Title: Evidence Suggesting Absence of Mitochondrial DNA Methylation

    doi: 10.3389/fgene.2017.00166

    Figure Lengend Snippet: BamHI digestion prior to bisulfite sequencing decreases cytosine unconvertion rate. Targeted bisulfite sequencing was used to compare undigested and digested DNA methylation levels at five different regions of the mtDNA from human muscle cells and SKOV3 cells ( N = 3). (A) Drawing displays the mtDNA regions investigated by targeted bisulfite sequencing. (B) Percentage methylation for undigested and digested mtDNA. Full circle represents cytosines in CpG context whereas open circle is cytosines in non-CpG context. Results are presented with a min-max interval and a sign test was used to test for significant methylation differences. D-loop (6–298) P = 2.02E-41 (Lonza) and P = 1.40E-24 (SKOV3); D-loop (279–458): P = 5.00E-12 (Lonza) and P = 8.20E-08 (SKOV3); tRNA-F+12S: P = 9.22E-15 (Lonza) and P = 1.29E-9 (SKOV3); 16S: P = 6.50E-05; ND5: P = 1.70E-05 (Lonza) and P = 9.97E-13 (SKOV3); CYTB: P = 2.96E-09 (Lonza), and P = 6.68E-13 (SKOV3). D-loop (6–298) includes origin of replication and tRNA-F+12S includes heavy strand promoter 2. P H1 : heavy-strand promoter 1; P H2 : Heavy-strand promote 2; P L : Light-strand promoter; OH: Origin of replication from heavy-strand; O L : Origin of replication from light-strand. ND: not determined.

    Article Snippet: We tested the hypothesis that mtDNA supercoils can be a source of overestimation of methylation by subjecting DNA to digestion with the BamHI restriction enzyme prior to targeted bisulfite sequencing to remove any secondary structure and linearize mtDNA.

    Techniques: Methylation Sequencing, DNA Methylation Assay, Methylation

    Overview of the proposed ONS-based protocol for mtDNA methylation calling a ) Log-likelihood ratio values of methylation calculated by Nanopolish, using the positive and negative controls. The log-likelihood range between −20 and 20 (used to build the ROC curve) is shown. b ) Receiver operating characteristic (ROC) curve calculated by changing the methylation call log-likelihood ratio threshold from a value of −20 to 20, with a step of 0.25. The dash lines are drawn at FPR (False Positive Rate) and TPR (True Positive Rate) values obtained by setting the ratio equal to 5. AUC = area under the curve. c ) Methylation call accuracy calculated at increasing values of log-likelihood ratio (ranging between 0 and 10). The dash line indicates the accuracy achieved at the ratio equal to 5 (accuracy = 0.99). d) Overview of the workflow used to process samples using (left) standard ONT fragmentation protocol and (right) BamHI-based protocol. e) Ratio of signal from the mitochondrial MT-ND1 over RNASE P ddPCR probes in undigested genomic DNA and BamHI-digested genomic DNA. N = 4 for each protocol used. Star indicates significance (*: two-sided P = ≤ 0.05, Wilcoxon test). f) Distributions of the total sequenced reads in 3 samples prepared with either fragmentation or BamHI-based protocols. Reads from Rho 0 cells (treated with BamHI) are highlighted in yellow. Blue dashed lines correspond to the chosen cutoff for read filtering at 4000bp and 17000 bp. The red dashed line corresponds to the human mtDNA genome length (16.5 Kbp). g) Distribution of the aligned reads filtered by length (4000bp −17000 bp) on the human mtDNA reference sequence in 3 samples prepared with either fragmentation or BamHI-based protocols. Reads from Rho 0 cells (treated with BamHI) are highlighted in yellow.

    Journal: bioRxiv

    Article Title: Oxford Nanopore sequencing-based protocol to detect CpG methylation in human mitochondrial DNA

    doi: 10.1101/2021.02.20.432086

    Figure Lengend Snippet: Overview of the proposed ONS-based protocol for mtDNA methylation calling a ) Log-likelihood ratio values of methylation calculated by Nanopolish, using the positive and negative controls. The log-likelihood range between −20 and 20 (used to build the ROC curve) is shown. b ) Receiver operating characteristic (ROC) curve calculated by changing the methylation call log-likelihood ratio threshold from a value of −20 to 20, with a step of 0.25. The dash lines are drawn at FPR (False Positive Rate) and TPR (True Positive Rate) values obtained by setting the ratio equal to 5. AUC = area under the curve. c ) Methylation call accuracy calculated at increasing values of log-likelihood ratio (ranging between 0 and 10). The dash line indicates the accuracy achieved at the ratio equal to 5 (accuracy = 0.99). d) Overview of the workflow used to process samples using (left) standard ONT fragmentation protocol and (right) BamHI-based protocol. e) Ratio of signal from the mitochondrial MT-ND1 over RNASE P ddPCR probes in undigested genomic DNA and BamHI-digested genomic DNA. N = 4 for each protocol used. Star indicates significance (*: two-sided P = ≤ 0.05, Wilcoxon test). f) Distributions of the total sequenced reads in 3 samples prepared with either fragmentation or BamHI-based protocols. Reads from Rho 0 cells (treated with BamHI) are highlighted in yellow. Blue dashed lines correspond to the chosen cutoff for read filtering at 4000bp and 17000 bp. The red dashed line corresponds to the human mtDNA genome length (16.5 Kbp). g) Distribution of the aligned reads filtered by length (4000bp −17000 bp) on the human mtDNA reference sequence in 3 samples prepared with either fragmentation or BamHI-based protocols. Reads from Rho 0 cells (treated with BamHI) are highlighted in yellow.

    Article Snippet: Mitochondrial DNA enrichment for single-molecule sequencing1 µg of genomic DNA (nuclear + mitochondrial DNA) per 50 µl reactions was digested with 40 units of the recombinant restriction enzyme BamHI-HF (NEB) for 1 hour at 37°C in the presence of CutSmart buffer (NEB).

    Techniques: Methylation, Sequencing

    Genetic map, 2D gel analysis of linear fragments corresponding to pYAC_MEM_3rRFBs+ and densitometry of the spots accumulated on the simple-Y arc. ( A ) Genetic map of pYAC_MEM_3rRFBs+ (8908 bp) showing its most relevant features (for further details see the legend of Figure 3 ). Note the insertion of an EcoRI fragment containing the three putative Fob1 binding sites expected to act as RFBs (indicated in red), described by Kobayashi ( 20 ). ( B ) Map of the 3708 bp linear fragment generated by digestion of pYAC_MEM_3rRFBs+ with SwaI and BamHI showing the relative position of the three putative RFBs. ( C ) Map of the 5186 bp linear fragment generated by digestion of pYAC_MEM_3rRFBs+ with EcoRV and MluI showing the relative position of the three putative RFBs. ( D ) 2D gel immunogram of the RIs corresponding to the SwaI-BamHI 3708 bp linear fragment with its diagrammatic interpretation in ( E ). The 2D gel immunogram of the RIs corresponding to the EcoRV-MluI 5186-bp linear fragment is shown in ( F ) with its diagrammatic interpretation in ( G ). The densitometric profile corresponding to the spots observed on the simple-Y arc shown in (D) is presented in ( H ) indicating the height of the peaks and the distance separating them.

    Journal: Nucleic Acids Research

    Article Title: The abundance of Fob1 modulates the efficiency of rRFBs to stall replication forks

    doi: 10.1093/nar/gkx655

    Figure Lengend Snippet: Genetic map, 2D gel analysis of linear fragments corresponding to pYAC_MEM_3rRFBs+ and densitometry of the spots accumulated on the simple-Y arc. ( A ) Genetic map of pYAC_MEM_3rRFBs+ (8908 bp) showing its most relevant features (for further details see the legend of Figure 3 ). Note the insertion of an EcoRI fragment containing the three putative Fob1 binding sites expected to act as RFBs (indicated in red), described by Kobayashi ( 20 ). ( B ) Map of the 3708 bp linear fragment generated by digestion of pYAC_MEM_3rRFBs+ with SwaI and BamHI showing the relative position of the three putative RFBs. ( C ) Map of the 5186 bp linear fragment generated by digestion of pYAC_MEM_3rRFBs+ with EcoRV and MluI showing the relative position of the three putative RFBs. ( D ) 2D gel immunogram of the RIs corresponding to the SwaI-BamHI 3708 bp linear fragment with its diagrammatic interpretation in ( E ). The 2D gel immunogram of the RIs corresponding to the EcoRV-MluI 5186-bp linear fragment is shown in ( F ) with its diagrammatic interpretation in ( G ). The densitometric profile corresponding to the spots observed on the simple-Y arc shown in (D) is presented in ( H ) indicating the height of the peaks and the distance separating them.

    Article Snippet: DNA treatments DNA was digested with the restriction endonucleases BamHI, EcoRV, SwaI, FspI and MluI (New England Biolabs) for at least 2 h at 37°C except for SwaI that was digested at 25°C.

    Techniques: Two-Dimensional Gel Electrophoresis, Binding Assay, Activated Clotting Time Assay, Generated

    Genetic map, 2D gel analysis of linear fragments corresponding to pYAC_AC_3′rRFBs+ and densitometry of the spots accumulated on the simple-Y arc. ( A ) Genetic map of pYAC_AC_3′rRFBs+ (8175 bp) showing its most relevant features (for further details see the legend of Figure 3 ). Note that here the three putative Fob1 binding sites expected to act as RFBs (indicated in red and white), described by Kobayashi ( 20 ), are equally distanced. ( B ) Map of the 3710-bp linear fragment generated by digestion of pYAC_AC_3′rRFBs+ with FspI and BamHI showing the relative position of the three putative RFBs. ( C ) Map of the 4454-bp linear fragment generated by digestion of pYAC_AC_3′rRFBs+ with EcoRV and MluI showing the relative position of the three putative RFBs. ( D ) 2D gel immunogram of the RIs corresponding to the FspI-BamHI 3710-bp linear fragment with its diagrammatic interpretation in ( E ). The 2D gel immunogram of the RIs corresponding to the EcoRV-MluI 4454-bp linear fragment is shown in ( F ) with its diagrammatic interpretation in ( G ). The densitometric profile corresponding to the spots observed on the simple-Y arc shown in (D) is presented in ( H ) indicating the height of the peaks and the distance separating them. For comparison, the densitometric profile corresponding to pYAC_MEM_3rRFBs shown in Figure 4H is presented on top.

    Journal: Nucleic Acids Research

    Article Title: The abundance of Fob1 modulates the efficiency of rRFBs to stall replication forks

    doi: 10.1093/nar/gkx655

    Figure Lengend Snippet: Genetic map, 2D gel analysis of linear fragments corresponding to pYAC_AC_3′rRFBs+ and densitometry of the spots accumulated on the simple-Y arc. ( A ) Genetic map of pYAC_AC_3′rRFBs+ (8175 bp) showing its most relevant features (for further details see the legend of Figure 3 ). Note that here the three putative Fob1 binding sites expected to act as RFBs (indicated in red and white), described by Kobayashi ( 20 ), are equally distanced. ( B ) Map of the 3710-bp linear fragment generated by digestion of pYAC_AC_3′rRFBs+ with FspI and BamHI showing the relative position of the three putative RFBs. ( C ) Map of the 4454-bp linear fragment generated by digestion of pYAC_AC_3′rRFBs+ with EcoRV and MluI showing the relative position of the three putative RFBs. ( D ) 2D gel immunogram of the RIs corresponding to the FspI-BamHI 3710-bp linear fragment with its diagrammatic interpretation in ( E ). The 2D gel immunogram of the RIs corresponding to the EcoRV-MluI 4454-bp linear fragment is shown in ( F ) with its diagrammatic interpretation in ( G ). The densitometric profile corresponding to the spots observed on the simple-Y arc shown in (D) is presented in ( H ) indicating the height of the peaks and the distance separating them. For comparison, the densitometric profile corresponding to pYAC_MEM_3rRFBs shown in Figure 4H is presented on top.

    Article Snippet: DNA treatments DNA was digested with the restriction endonucleases BamHI, EcoRV, SwaI, FspI and MluI (New England Biolabs) for at least 2 h at 37°C except for SwaI that was digested at 25°C.

    Techniques: Two-Dimensional Gel Electrophoresis, Binding Assay, Activated Clotting Time Assay, Generated

    Genetic map and 2D gel analysis of linear fragments corresponding to pYAC_MEM. ( A ) Genetic map of pYAC_MEM (7966 bp) showing its most relevant features: clockwise starting with the replication origin ARS4 (indicated in green), URA3 gene active in Saccharomyces cerevisiae (indicated in light blue), L1 lambda DNA used for hybridization (indicated in yellow), HIS3 gene active in S. cerevisiae (indicated in light blue), L2 lambda DNA used for hybridization (indicated in yellow), the ColE1 replication origin active only in Escherichia coli (indicated in gray), the ampicillin resistance gene active only in E. coli (indicated in gray) and the budding yeast centromeric sequence CEN6 (indicated in orange). The sites for specific restriction endonucleases are indicated outside the map. In addition, a magenta triangle points the position located 180° apart from the replication origin ARS4. ( B ) Map of the 2764-bp linear fragment generated by digestion of pYAC_MEM with SwaI and BamHI. ( C ) Map of the 4245-bp linear fragment generated by digestion of pYAC_MEM with EcoRV and MluI. ( D ) 2D gel immunogram of the RIs corresponding to the SwaI-BamHI 2764 bp linear fragment with its diagrammatic interpretation in ( E ). The 2D gel immunogram of the RIs corresponding to the EcoRV-MluI 4245-bp linear fragment is shown in ( F ) with its diagrammatic interpretation in ( G ). De-localized termination signals are indicated in magenta.

    Journal: Nucleic Acids Research

    Article Title: The abundance of Fob1 modulates the efficiency of rRFBs to stall replication forks

    doi: 10.1093/nar/gkx655

    Figure Lengend Snippet: Genetic map and 2D gel analysis of linear fragments corresponding to pYAC_MEM. ( A ) Genetic map of pYAC_MEM (7966 bp) showing its most relevant features: clockwise starting with the replication origin ARS4 (indicated in green), URA3 gene active in Saccharomyces cerevisiae (indicated in light blue), L1 lambda DNA used for hybridization (indicated in yellow), HIS3 gene active in S. cerevisiae (indicated in light blue), L2 lambda DNA used for hybridization (indicated in yellow), the ColE1 replication origin active only in Escherichia coli (indicated in gray), the ampicillin resistance gene active only in E. coli (indicated in gray) and the budding yeast centromeric sequence CEN6 (indicated in orange). The sites for specific restriction endonucleases are indicated outside the map. In addition, a magenta triangle points the position located 180° apart from the replication origin ARS4. ( B ) Map of the 2764-bp linear fragment generated by digestion of pYAC_MEM with SwaI and BamHI. ( C ) Map of the 4245-bp linear fragment generated by digestion of pYAC_MEM with EcoRV and MluI. ( D ) 2D gel immunogram of the RIs corresponding to the SwaI-BamHI 2764 bp linear fragment with its diagrammatic interpretation in ( E ). The 2D gel immunogram of the RIs corresponding to the EcoRV-MluI 4245-bp linear fragment is shown in ( F ) with its diagrammatic interpretation in ( G ). De-localized termination signals are indicated in magenta.

    Article Snippet: DNA treatments DNA was digested with the restriction endonucleases BamHI, EcoRV, SwaI, FspI and MluI (New England Biolabs) for at least 2 h at 37°C except for SwaI that was digested at 25°C.

    Techniques: Two-Dimensional Gel Electrophoresis, Lambda DNA Preparation, Hybridization, Sequencing, Generated

    Genetic map, 2D gel analysis of linear fragments corresponding to pYAC_AC_10rRFBs+ isolated from cells that overexpress Fob1 and densitometry of the spots accumulated on the simple-Y arc. ( A ) Genetic map of pYAC_AC_10rRFBs+ (8916 bp) showing its most relevant features (for further details see the legend of Figure 3 ). Note that here the fragment inserted at the unique SalI site of pYAC_MEM contained the 10 Fob1 binding sites described by Kobayashi ( 20 ) that were confirmed to act as RFBs in vivo (See Figures 4 and 5 ). ( B ) Map of the 3705-bp linear fragment generated by digestion of pYAC_AC_10rRFBs+ with SwaI and BamHI showing the relative position of the ten putative RFBs. ( C ) Map of the 5194-bp linear fragment generated by digestion of pYAC_AC_10rRFBs+ with EcoRV and MluI showing the relative position of the 10 putative RFBs. ( D ) 2D gel immunogram of the RIs corresponding to the SwaI-BamHI 3705 bp linear fragment with its diagrammatic interpretation in ( E ). The 2D gel immunogram of the RIs corresponding to the EcoRV-MluI 5194 bp linear fragment is shown in ( F ) with its diagrammatic interpretation in ( G ). The densitometric profile corresponding to the six most distal spots observed on the simple-Y arc shown in ( D ) is presented in ( H ) indicating the height of the peaks. For comparison, the densitometric profile corresponding to the 3705-bp SwaI-BamHI of pYAC_AC_10rRFBs isolated from the top2-td strain shown in Figure 4H is presented on top.

    Journal: Nucleic Acids Research

    Article Title: The abundance of Fob1 modulates the efficiency of rRFBs to stall replication forks

    doi: 10.1093/nar/gkx655

    Figure Lengend Snippet: Genetic map, 2D gel analysis of linear fragments corresponding to pYAC_AC_10rRFBs+ isolated from cells that overexpress Fob1 and densitometry of the spots accumulated on the simple-Y arc. ( A ) Genetic map of pYAC_AC_10rRFBs+ (8916 bp) showing its most relevant features (for further details see the legend of Figure 3 ). Note that here the fragment inserted at the unique SalI site of pYAC_MEM contained the 10 Fob1 binding sites described by Kobayashi ( 20 ) that were confirmed to act as RFBs in vivo (See Figures 4 and 5 ). ( B ) Map of the 3705-bp linear fragment generated by digestion of pYAC_AC_10rRFBs+ with SwaI and BamHI showing the relative position of the ten putative RFBs. ( C ) Map of the 5194-bp linear fragment generated by digestion of pYAC_AC_10rRFBs+ with EcoRV and MluI showing the relative position of the 10 putative RFBs. ( D ) 2D gel immunogram of the RIs corresponding to the SwaI-BamHI 3705 bp linear fragment with its diagrammatic interpretation in ( E ). The 2D gel immunogram of the RIs corresponding to the EcoRV-MluI 5194 bp linear fragment is shown in ( F ) with its diagrammatic interpretation in ( G ). The densitometric profile corresponding to the six most distal spots observed on the simple-Y arc shown in ( D ) is presented in ( H ) indicating the height of the peaks. For comparison, the densitometric profile corresponding to the 3705-bp SwaI-BamHI of pYAC_AC_10rRFBs isolated from the top2-td strain shown in Figure 4H is presented on top.

    Article Snippet: DNA treatments DNA was digested with the restriction endonucleases BamHI, EcoRV, SwaI, FspI and MluI (New England Biolabs) for at least 2 h at 37°C except for SwaI that was digested at 25°C.

    Techniques: Two-Dimensional Gel Electrophoresis, Isolation, Binding Assay, Activated Clotting Time Assay, In Vivo, Generated

    Genetic map, 2D gel analysis of linear fragments corresponding to pYAC_AC_10rRFBs+ and densitometry of the spots accumulated on the simple-Y arc. ( A ) Genetic map of pYAC_AC_10rRFBs+ (8916 bp) showing its most relevant features (for further details see the legend of Figure 3 ). Note that here the fragment inserted at the unique SalI site of pYAC_MEM contained the 10 Fob1 binding sites described by Kobayashi ( 20 ) that were confirmed to act as RFBs in vivo (See Figures 4 and 5 ). ( B ) Map of the 3705-bp linear fragment generated by digestion of pYAC_AC_10rRFBs+ with SwaI and BamHI showing the relative position of the 10 putative RFBs. ( C ) Map of the 5194-bp linear fragment generated by digestion of pYAC_AC_10rRFBs+ with EcoRV and MluI showing the relative position of the 10 putative RFBs. ( D ) 2D gel immunogram of the RIs corresponding to the SwaI-BamHI 3705-bp linear fragment with its diagrammatic interpretation in ( E ). The 2D gel immunogram of the RIs corresponding to the EcoRV-MluI 5194-bp linear fragment is shown in ( F ) with its diagrammatic interpretation in ( G ). The densitometric profile corresponding to the six most distal spots observed on the simple-Y arc shown in (D) is presented in ( H ) indicating the height of the peaks.

    Journal: Nucleic Acids Research

    Article Title: The abundance of Fob1 modulates the efficiency of rRFBs to stall replication forks

    doi: 10.1093/nar/gkx655

    Figure Lengend Snippet: Genetic map, 2D gel analysis of linear fragments corresponding to pYAC_AC_10rRFBs+ and densitometry of the spots accumulated on the simple-Y arc. ( A ) Genetic map of pYAC_AC_10rRFBs+ (8916 bp) showing its most relevant features (for further details see the legend of Figure 3 ). Note that here the fragment inserted at the unique SalI site of pYAC_MEM contained the 10 Fob1 binding sites described by Kobayashi ( 20 ) that were confirmed to act as RFBs in vivo (See Figures 4 and 5 ). ( B ) Map of the 3705-bp linear fragment generated by digestion of pYAC_AC_10rRFBs+ with SwaI and BamHI showing the relative position of the 10 putative RFBs. ( C ) Map of the 5194-bp linear fragment generated by digestion of pYAC_AC_10rRFBs+ with EcoRV and MluI showing the relative position of the 10 putative RFBs. ( D ) 2D gel immunogram of the RIs corresponding to the SwaI-BamHI 3705-bp linear fragment with its diagrammatic interpretation in ( E ). The 2D gel immunogram of the RIs corresponding to the EcoRV-MluI 5194-bp linear fragment is shown in ( F ) with its diagrammatic interpretation in ( G ). The densitometric profile corresponding to the six most distal spots observed on the simple-Y arc shown in (D) is presented in ( H ) indicating the height of the peaks.

    Article Snippet: DNA treatments DNA was digested with the restriction endonucleases BamHI, EcoRV, SwaI, FspI and MluI (New England Biolabs) for at least 2 h at 37°C except for SwaI that was digested at 25°C.

    Techniques: Two-Dimensional Gel Electrophoresis, Binding Assay, Activated Clotting Time Assay, In Vivo, Generated