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    New England Biolabs lambda phage dna
    Assessment of 5-hmC labeling efficiency. <t>Lambda</t> <t>DNA</t> was nicked with Nt.BspQI (nine expected labeling spots) and labeled with either 5-hmC or fluorescent dUTP. 5-hmC was labeled according to our labeling scheme, and the samples were mixed and imaged together in order to evaluate the labeling efficiency. (A) Representative field of view showing a mixed population of green (nicking) and red (5-hmC) labeled molecules. (B) Histograms showing the number of labels per molecule for 5-hmC labeling (top) and nicking (bottom).
    Lambda Phage Dna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 161 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/lambda phage dna/product/New England Biolabs
    Average 99 stars, based on 161 article reviews
    Price from $9.99 to $1999.99
    lambda phage dna - by Bioz Stars, 2020-05
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    94
    New England Biolabs phage lambda pfge ladder
    <t>S1-PFGE</t> and southern hybridization of 16SrRNA, oqxA , and aac(6 ′ )Ib-cr on two oqxAB-positive isolates. Arrows indicated chromosomal DNA or plasmids harboring oqxAB and aac(6 ′ )Ib-cr . 06–53 and 10–63 are oqxAB -positive S. typhimurium clinical isolates; M, <t>Lambda</t> PFGE marker.
    Phage Lambda Pfge Ladder, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/phage lambda pfge ladder/product/New England Biolabs
    Average 94 stars, based on 14 article reviews
    Price from $9.99 to $1999.99
    phage lambda pfge ladder - by Bioz Stars, 2020-05
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      Buy from Supplier

    Image Search Results


    Assessment of 5-hmC labeling efficiency. Lambda DNA was nicked with Nt.BspQI (nine expected labeling spots) and labeled with either 5-hmC or fluorescent dUTP. 5-hmC was labeled according to our labeling scheme, and the samples were mixed and imaged together in order to evaluate the labeling efficiency. (A) Representative field of view showing a mixed population of green (nicking) and red (5-hmC) labeled molecules. (B) Histograms showing the number of labels per molecule for 5-hmC labeling (top) and nicking (bottom).

    Journal: ACS Nano

    Article Title: Epigenetic Optical Mapping of 5-Hydroxymethylcytosine in Nanochannel Arrays

    doi: 10.1021/acsnano.8b03023

    Figure Lengend Snippet: Assessment of 5-hmC labeling efficiency. Lambda DNA was nicked with Nt.BspQI (nine expected labeling spots) and labeled with either 5-hmC or fluorescent dUTP. 5-hmC was labeled according to our labeling scheme, and the samples were mixed and imaged together in order to evaluate the labeling efficiency. (A) Representative field of view showing a mixed population of green (nicking) and red (5-hmC) labeled molecules. (B) Histograms showing the number of labels per molecule for 5-hmC labeling (top) and nicking (bottom).

    Article Snippet: For the nicking reaction, 900 ng of lambda phage DNA (New England Biolabs) was digested with 30 units of Nt.BspQI nicking enzyme (New England Biolabs) for 2 h at 50 °C in the presence of 3 μL of 10× buffer 3.1 (New England Biolabs) and ultrapure water to a total volume of 30 μL.

    Techniques: Labeling, Lambda DNA Preparation

    ( a ) Side view of the flow cell showing the trapping and excitation laser beams. ( b ) Top view of the flow cell. An individual DNA molecule held by an optical trap ( orange ) via its attached bead, and extended by flowing buffer, is moved into protein solution by translating the stage holding the flow cell perpendicular to the direction of flow. DNA was stained with YOYO-1 dye, allowing the compaction to be observed using fluorescence microscopy. The molecule was then moved back to the DNA side of the flow cell (which was protein-free), and the decompaction of the molecule was observed as protein left it, ultimately returning to its original length. ( c ) Time-lapse images of a lambda-phage DNA dimer (35 μ m contour length) undergoing compaction by Abf2p. The Abf2p concentration is 2 μ M. The time interval between successive frames is 0.5 s. The buffer flow speed is 63 μ m/s.

    Journal: Biophysical Journal

    Article Title: Packaging of Single DNA Molecules by the Yeast Mitochondrial Protein Abf2p

    doi:

    Figure Lengend Snippet: ( a ) Side view of the flow cell showing the trapping and excitation laser beams. ( b ) Top view of the flow cell. An individual DNA molecule held by an optical trap ( orange ) via its attached bead, and extended by flowing buffer, is moved into protein solution by translating the stage holding the flow cell perpendicular to the direction of flow. DNA was stained with YOYO-1 dye, allowing the compaction to be observed using fluorescence microscopy. The molecule was then moved back to the DNA side of the flow cell (which was protein-free), and the decompaction of the molecule was observed as protein left it, ultimately returning to its original length. ( c ) Time-lapse images of a lambda-phage DNA dimer (35 μ m contour length) undergoing compaction by Abf2p. The Abf2p concentration is 2 μ M. The time interval between successive frames is 0.5 s. The buffer flow speed is 63 μ m/s.

    Article Snippet: DNA binding activity was established with a gel-retardation assay ( ) using either supercoiled pLitmus-38(+) or linear lambda-phage DNA (New England BioLabs, Beverly, MA) as a substrate.

    Techniques: Flow Cytometry, Staining, Fluorescence, Microscopy, Concentration Assay

    Schematic of DNA curtain assay with quantum dot (Qdot)-conjugated XPC and initial binding position on undamaged lambda (λ) DNA. ( A ) Schematic of DNA curtains. Top left: top view of DNA curtains, bottom left: side-view of DNA curtains, and right: Qdot-conjugated XPC. The structure of XPC is adopted from yeast Rad4-Rad23 ( 10 ). ( B ) Histogram for the initial binding positions of XPC-RAD23B on undamaged λ-DNA. The error bars were obtained by bootstrapping with 70% confidence interval.

    Journal: Nucleic Acids Research

    Article Title: Single-molecule visualization reveals the damage search mechanism for the human NER protein XPC-RAD23B

    doi: 10.1093/nar/gkz629

    Figure Lengend Snippet: Schematic of DNA curtain assay with quantum dot (Qdot)-conjugated XPC and initial binding position on undamaged lambda (λ) DNA. ( A ) Schematic of DNA curtains. Top left: top view of DNA curtains, bottom left: side-view of DNA curtains, and right: Qdot-conjugated XPC. The structure of XPC is adopted from yeast Rad4-Rad23 ( 10 ). ( B ) Histogram for the initial binding positions of XPC-RAD23B on undamaged λ-DNA. The error bars were obtained by bootstrapping with 70% confidence interval.

    Article Snippet: Lambda phage (λ) DNA for the undamaged DNA substrate was purchased from New England Biolabs.

    Techniques: Binding Assay

    PFGE of undigested DNAs from B. cereus and B. thuringiensis . (A) The electrophoresis was run on a Beckman apparatus with 4-s pulses for 10 min at 170 mA and 30-s pulses for 20 h at 150 mA. (B) Hybridization of extrachromosomal DNA of 300 kb from AH 818. Lanes 1 to 7 and 10 to 13 are of ETs 24 and 25. Lanes: 1, AH 825; 2, AH 827; 3, AH 828; 4, AH 831; 5, AH 829; 6 AH 826; 7, AH 818; 8, S. cerevisiae chromosomes; 9, lambda concatemers; 10, AH 817; 11, AH 819; 12, AH 823; 13, AH 818; 14, AH 812 (ETs 22 and 23); 15, AH 810 (ET 21); 16, AH 814 (ET 41); 17, S. cerevisiae chromosomes; 18, lambda concatemers; 19, AH 725 (ET 41); 20, AH 814 (ET 41); 21, AH 718 (ET 41); 22, AH 811 (ET 40); 23, AH 815 (ET 39); 24, AH 601 (ET 44); 25, AH 818; 26, S. cerevisiae chromosomes; 27, lambda concatemers; 28, AH 407 (ET 6); 29, AH 406 (ET 7); 30, AH 610 (ET 1); 31, AH 612 (ET 5); 32, AH 608 (ET 31); 33, AH 818; 34, AH 722 (ET 34). Isolate AH 818 is used as a control in lanes 13, 25, and 33. Symbols indicate strains isolated from patients (▴) or dairies (■).

    Journal: Journal of Clinical Microbiology

    Article Title: Genetic Structure of Population of Bacillus cereus and B. thuringiensis Isolates Associated with Periodontitis and Other Human Infections

    doi:

    Figure Lengend Snippet: PFGE of undigested DNAs from B. cereus and B. thuringiensis . (A) The electrophoresis was run on a Beckman apparatus with 4-s pulses for 10 min at 170 mA and 30-s pulses for 20 h at 150 mA. (B) Hybridization of extrachromosomal DNA of 300 kb from AH 818. Lanes 1 to 7 and 10 to 13 are of ETs 24 and 25. Lanes: 1, AH 825; 2, AH 827; 3, AH 828; 4, AH 831; 5, AH 829; 6 AH 826; 7, AH 818; 8, S. cerevisiae chromosomes; 9, lambda concatemers; 10, AH 817; 11, AH 819; 12, AH 823; 13, AH 818; 14, AH 812 (ETs 22 and 23); 15, AH 810 (ET 21); 16, AH 814 (ET 41); 17, S. cerevisiae chromosomes; 18, lambda concatemers; 19, AH 725 (ET 41); 20, AH 814 (ET 41); 21, AH 718 (ET 41); 22, AH 811 (ET 40); 23, AH 815 (ET 39); 24, AH 601 (ET 44); 25, AH 818; 26, S. cerevisiae chromosomes; 27, lambda concatemers; 28, AH 407 (ET 6); 29, AH 406 (ET 7); 30, AH 610 (ET 1); 31, AH 612 (ET 5); 32, AH 608 (ET 31); 33, AH 818; 34, AH 722 (ET 34). Isolate AH 818 is used as a control in lanes 13, 25, and 33. Symbols indicate strains isolated from patients (▴) or dairies (■).

    Article Snippet: Size markers used were Saccharomyces cerevisiae chromosomes (New England BioLabs) and a mixture of phage lambda DNA concatemers and Hin dIII fragments of lambda (New England BioLabs).

    Techniques: Electrophoresis, Hybridization, Isolation

    Representative PFGE of selected strains. All lanes are from the same gel. The positions of migration of the λ DNA concatamers are shown to the left of the gel, and their sizes are indicated in kilobases. HOS., hospital; PFGE, PFGE pattern similarity cluster; STR., strain number; —, strain not belonging to a PFGE pattern similarity cluster.

    Journal: Journal of Clinical Microbiology

    Article Title: Emergence of Multidrug Resistance in Ubiquitous and Dominant Pseudomonas aeruginosa Serogroup O:11

    doi:

    Figure Lengend Snippet: Representative PFGE of selected strains. All lanes are from the same gel. The positions of migration of the λ DNA concatamers are shown to the left of the gel, and their sizes are indicated in kilobases. HOS., hospital; PFGE, PFGE pattern similarity cluster; STR., strain number; —, strain not belonging to a PFGE pattern similarity cluster.

    Article Snippet: The gels were run at 14°C, 6 V cm−1 , and a 120° switch angle, for 18 h, with a linear switch time ramp of 0.5 to 20 s. Lambda phage DNA concatamers (New England Biolabs) were used as DNA size markers.

    Techniques: Migration

    Effect of BAY 38-4766 on concatemer processing of HCMV DNA. HELF were infected with AD169-wt and AD169-rt at an MOI of 1 and were cultivated in the absence (−) or presence of selected inhibitor concentrations. At 3 to 4 days p.i., cells were embedded in agarose plugs and digested with proteinase K. After electrophoretic separation, genomic DNA was subjected to Southern blot analysis using a DIG-labeled DNA probe synthesized with Hin dIII-digested AD169 DNA template fragments. MW, molecular weights derived from concatemeric phage lambda genomic DNA; polymer, wild-type replicative concatemers; monomer, monomeric genome lengths; +, monomer+ form of HCMV DNA (270 kb).

    Journal: Journal of Virology

    Article Title: A Novel Nonnucleoside Inhibitor Specifically Targets Cytomegalovirus DNA Maturation via the UL89 and UL56 Gene Products

    doi: 10.1128/JVI.75.19.9077-9086.2001

    Figure Lengend Snippet: Effect of BAY 38-4766 on concatemer processing of HCMV DNA. HELF were infected with AD169-wt and AD169-rt at an MOI of 1 and were cultivated in the absence (−) or presence of selected inhibitor concentrations. At 3 to 4 days p.i., cells were embedded in agarose plugs and digested with proteinase K. After electrophoretic separation, genomic DNA was subjected to Southern blot analysis using a DIG-labeled DNA probe synthesized with Hin dIII-digested AD169 DNA template fragments. MW, molecular weights derived from concatemeric phage lambda genomic DNA; polymer, wild-type replicative concatemers; monomer, monomeric genome lengths; +, monomer+ form of HCMV DNA (270 kb).

    Article Snippet: Lambda phage DNA concatemers (New England Biolabs, Frankfurt am Main, Germany) were used as molecular size standards.

    Techniques: Infection, Southern Blot, Labeling, Synthesized, Derivative Assay

    DNA extension versus time of λ-DNA treated with Pt(R,R-DACH) or Pt(S,S-DACH). Each data curve was the average of at least three independent measurements.

    Journal: PLoS ONE

    Article Title: Oxaliplatin and Its Enantiomer Induce Different Condensation Dynamics of Single DNA Molecules

    doi: 10.1371/journal.pone.0071556

    Figure Lengend Snippet: DNA extension versus time of λ-DNA treated with Pt(R,R-DACH) or Pt(S,S-DACH). Each data curve was the average of at least three independent measurements.

    Article Snippet: λ-DNA Preparation for Magnetic Tweezers Study The bacteriophage λ-DNA (New England Biolabs), which has two 12-nt cohesive termini, was separately annealed with two 12-nt labeled oligomers (labeled by biotin and digoxigenin, respectively).

    Techniques:

    Force-extension curves and persistence length as a function of incubation time. (A) The force-extension curves of λ-DNA without drug ( L = 16.5±0.04 µm, P = 44.0±2.1 nm), with 60 µM Pt(S,S-DACH) incubated for 3 h ( L = 17.3±0.08 µm, P = 16.5±1.0 nm ) and 60 µM Pt(R,R-DACH) incubated for 3 h ( L = 17.1±0.09 µm, P = 12.9±0.7 nm ). The data were fitted by the WLC model (Eq. 1). (B) The persistence lengths of λ-DNA treated with 60 µM Pt(R,R-DACH) or Pt(S,S-DACH) for different incubation times. Each data point was the mean of twenty independent measurements. The error bars corresponded to 95% confidence intervals. The difference was considered statistically significant when the p value of two-sample t-test was less than 0.05.

    Journal: PLoS ONE

    Article Title: Oxaliplatin and Its Enantiomer Induce Different Condensation Dynamics of Single DNA Molecules

    doi: 10.1371/journal.pone.0071556

    Figure Lengend Snippet: Force-extension curves and persistence length as a function of incubation time. (A) The force-extension curves of λ-DNA without drug ( L = 16.5±0.04 µm, P = 44.0±2.1 nm), with 60 µM Pt(S,S-DACH) incubated for 3 h ( L = 17.3±0.08 µm, P = 16.5±1.0 nm ) and 60 µM Pt(R,R-DACH) incubated for 3 h ( L = 17.1±0.09 µm, P = 12.9±0.7 nm ). The data were fitted by the WLC model (Eq. 1). (B) The persistence lengths of λ-DNA treated with 60 µM Pt(R,R-DACH) or Pt(S,S-DACH) for different incubation times. Each data point was the mean of twenty independent measurements. The error bars corresponded to 95% confidence intervals. The difference was considered statistically significant when the p value of two-sample t-test was less than 0.05.

    Article Snippet: λ-DNA Preparation for Magnetic Tweezers Study The bacteriophage λ-DNA (New England Biolabs), which has two 12-nt cohesive termini, was separately annealed with two 12-nt labeled oligomers (labeled by biotin and digoxigenin, respectively).

    Techniques: Incubation

    Digestion of phage λ DNA by wild-type and mutant M. bovis cells. Sampling time points were 15 min (a), 30 min (b), and 60 min (c). Lane M, molecular mass markers (Bioline Hyperladder I); lanes 1, nuclease-free water (negative control); lanes 2,

    Journal: Journal of Bacteriology

    Article Title: Disruption of the Membrane Nuclease Gene (MBOVPG45_0215) of Mycoplasma bovis Greatly Reduces Cellular Nuclease Activity

    doi: 10.1128/JB.00034-15

    Figure Lengend Snippet: Digestion of phage λ DNA by wild-type and mutant M. bovis cells. Sampling time points were 15 min (a), 30 min (b), and 60 min (c). Lane M, molecular mass markers (Bioline Hyperladder I); lanes 1, nuclease-free water (negative control); lanes 2,

    Article Snippet: The exonuclease and endonuclease activities of the cells were determined by incubating proteins from cells from late-log-phase cultures suspended in 50 μl of nuclease reaction buffer (25 mM Tris-HCl, pH 8.8, 10 mM CaCl2 , 10 mM MgCl2 ) at 37°C with 500 ng of double-stranded phage λ DNA (New England BioLabs) or 2.0 μg of closed circular plasmid DNA (plasmid pRecAGKIRRPG2, which was generated to disrupt a specific gene target by homologous recombination in M. bovis ) as the substrates.

    Techniques: Mutagenesis, Sampling, Negative Control

    Components of the Platform ACE System. ( A ) Platform ACE is a murine artificial chromosome pre-engineered to contain multiple recombination acceptor att P sites. ( B ) ACE Integrase is based on the enzyme lambda integrase, which has been modified as described in the text. The modification renders the integrase functionally independent of bacterial host cell factors and capable of operating in a mammalian context. In the Platform ACE system, an ACE Integrase expression vector is co-transfected with a targeting vector (see below) into a cell line harboring the Platform ACE. The transiently expressed ACE Integrase then catalyses the integration of the targeting vector onto the Platform ACE. ( C ) The ATV is a plasmid-based shuttle vector that conveys a gene(s) of interest onto the Platform ACE by means of targeted recombination between the recombination acceptor att P sites present on the Platform ACE and the recombination donor att B site of the ATV, catalyzed by the ACE Integrase. The presence of a promoterless antibiotic resistance gene downstream of the att B donor site allows for selection of targeted integration events. ( D ) A representation of a ‘loaded’ recombination acceptor site on the Platform ACE. Note that the targeted integration of the targeting vector has resulted in the activation of the promoterless antibiotic resistance gene by virtue of its in frame insertion downstream of the SV40 promoter present in the ACE acceptor site. ( E ) Southern-blot analysis of Platform ACE. Genomic DNA was hybridized with a labeled probe encoding the SV40 promoter and att P site. Lanes 1–3: copy number controls: 50 copies (lane 1), 100 copies (lane 2), 250 copies (lane 3); LMTK − negative control (without ACE, Lane 4) and CHR1 cell line (containing Platform ACE, Lane 5). See Materials and Methods for details.

    Journal: Nucleic Acids Research

    Article Title: A mammalian artificial chromosome engineering system (ACE System) applicable to biopharmaceutical protein production, transgenesis and gene-based cell therapy

    doi: 10.1093/nar/gnh169

    Figure Lengend Snippet: Components of the Platform ACE System. ( A ) Platform ACE is a murine artificial chromosome pre-engineered to contain multiple recombination acceptor att P sites. ( B ) ACE Integrase is based on the enzyme lambda integrase, which has been modified as described in the text. The modification renders the integrase functionally independent of bacterial host cell factors and capable of operating in a mammalian context. In the Platform ACE system, an ACE Integrase expression vector is co-transfected with a targeting vector (see below) into a cell line harboring the Platform ACE. The transiently expressed ACE Integrase then catalyses the integration of the targeting vector onto the Platform ACE. ( C ) The ATV is a plasmid-based shuttle vector that conveys a gene(s) of interest onto the Platform ACE by means of targeted recombination between the recombination acceptor att P sites present on the Platform ACE and the recombination donor att B site of the ATV, catalyzed by the ACE Integrase. The presence of a promoterless antibiotic resistance gene downstream of the att B donor site allows for selection of targeted integration events. ( D ) A representation of a ‘loaded’ recombination acceptor site on the Platform ACE. Note that the targeted integration of the targeting vector has resulted in the activation of the promoterless antibiotic resistance gene by virtue of its in frame insertion downstream of the SV40 promoter present in the ACE acceptor site. ( E ) Southern-blot analysis of Platform ACE. Genomic DNA was hybridized with a labeled probe encoding the SV40 promoter and att P site. Lanes 1–3: copy number controls: 50 copies (lane 1), 100 copies (lane 2), 250 copies (lane 3); LMTK − negative control (without ACE, Lane 4) and CHR1 cell line (containing Platform ACE, Lane 5). See Materials and Methods for details.

    Article Snippet: The lambda integrase gene was amplified by PCR from bacteriophage lambda DNA (cI857 ind 1 Sam 7, New England Biolabs) using the LamInt primer pair (see Supplementary Material, Primer Table.pdf).

    Techniques: Modification, Expressing, Plasmid Preparation, Transfection, Selection, Activation Assay, Southern Blot, Labeling, Negative Control

    S1-PFGE and southern hybridization of 16SrRNA, oqxA , and aac(6 ′ )Ib-cr on two oqxAB-positive isolates. Arrows indicated chromosomal DNA or plasmids harboring oqxAB and aac(6 ′ )Ib-cr . 06–53 and 10–63 are oqxAB -positive S. typhimurium clinical isolates; M, Lambda PFGE marker.

    Journal: Frontiers in Microbiology

    Article Title: PMQR genes oqxAB and aac(6′)Ib-cr accelerate the development of fluoroquinolone resistance in Salmonella typhimurium

    doi: 10.3389/fmicb.2014.00521

    Figure Lengend Snippet: S1-PFGE and southern hybridization of 16SrRNA, oqxA , and aac(6 ′ )Ib-cr on two oqxAB-positive isolates. Arrows indicated chromosomal DNA or plasmids harboring oqxAB and aac(6 ′ )Ib-cr . 06–53 and 10–63 are oqxAB -positive S. typhimurium clinical isolates; M, Lambda PFGE marker.

    Article Snippet: Briefly, agarose-embedded DNA was digested with S1 nuclease (New England BioLab) at 37°C for 1 h. The restriction fragments were separated by electrophoresis in 0.5 Tris-borate-EDTA buffer at 14°C for 18 h using a Chef Mapper electrophoresis system (Bio-Rad, Hercules, CA, USA) with pulse times of 2.16 to 63.8 s. Phage Lambda PFGE ladder (New England BioLab) was used as DNA size marker.

    Techniques: Hybridization, Marker