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  • 99
    New England Biolabs lambda dna
    Agarose-gel analysis of tagmentation products of phage- <t>λ</t> DNA analyzed on (a) high-resolution and (c) low-resolution ( i.e ., mini) agarose gels. Size-distribution fits for the high-resolution gel (b) and mini gel (d) of the same tagmented λ -DNA sample subjected to increasing numbers of PCR-amplification cycles (lanes 3-5 in (a), lanes 2-4 in (c)): 8 cycles (top plots), 14 cycles (middle plots), and 20 cycles (bottom plots) in both (b) and (d). Vertical dashed lines (light red in (b), (d)) give the positions of maxima in the discrete molecular-weight ladder (blue ROI in (b), (b)).
    Lambda Dna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 528 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 528 article reviews
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    94
    Thermo Fisher lambda dna hindiii marker
    EZ-vision™In-Gel solution. Left: Preload 10x Left Middle: Preload 100x Right Middle: Precast Right: Post-stain.Photographed on a UV transilluminator 365nm with a SYBR™ filter. Lane 1: 1μl of Hyperladder 1kb ™ (Bioline) 2: 1μl of Hyperladder IV ™ (Bioline) 3: 0.3μg <t>Lambda</t> DNA HindIII marker2 ™ (ThermoScientific™) 4: 580ng of PCR product 5: 27ng of PCR product 6: 8ng of PCR product (as measured on a Qubit ™ Fluorometer)
    Lambda Dna Hindiii Marker, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 68 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 94 stars, based on 68 article reviews
    Price from $9.99 to $1999.99
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    99
    Promega unmethylated lambda dna
    eRRBS reveals distribution of cytosine methylations in each sequence context among TKO ES cells with reconstituted expression of either DNMT3A WT or DNMT3A R836A a , The rates of bisulfite conversion for the indicated sequence context in each sample as determined by the unmethylated <t>lambda</t> <t>DNA</t> spike-in control. CpN, all cytosines. b, c , Piecharts showing the percentage of methylated cytosines (total number n shown at the bottom of each plot) identified among the DNMT3A WT or DNMT3A R836A -expressing TKO ES cells in each sequence context. The methylated cytosines were called using a stringent binomial distribution–based filter to eliminate false positives from incomplete bisulfite conversion, with a false discovery rate (FDR) of 1% and 0.1% set for panel b and c , respectively. d , Distribution of methylation levels (% in x-axis) for the indicated sequence context. Insert panels show a closed view of the distribution at sites with intermediate to high levels of cytosine methylation.
    Unmethylated Lambda Dna, supplied by Promega, used in various techniques. Bioz Stars score: 99/100, based on 584 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Promega lambda dna
    (a) Representative fluorescence intensity profile of an individual YOYO-1 stained <t>λ-DNA</t> molecule after injection (red line) and confinement (blue line) in the plasma modified nanochannel filled with 2X TBE buffer. Complete injection into the nanochannel
    Lambda Dna, supplied by Promega, used in various techniques. Bioz Stars score: 99/100, based on 199 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 199 article reviews
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    92
    Thermo Fisher lambda dna
    Double-tethered Soft DNA Curtains with defined orientation.  A)  Cartoon illustrates the printed traptavidin (tAv) line-features that enable specific one-end immobilization of the biotin-λ DNA-digoxigenin (bt-λ DNA-dig, 48.5 kb) molecules. TIRF images shows that in the absence of the buffer flow (-flow), DNA molecules are aligned to the line-features. They are responding to a hydrodynamic force (+flow) by extending parallel to the surface.  B)  To tether the dig-labeled end of bt-λ DNA-dig, continuous slow flow of buffer containing biotinylated anti-dig (bt-anti-dig) antibody is applied and DNA molecules are dragged slightly, but do not reach the neighboring line-feature. At the next step, buffer flow rate is increased and the dig-labeled DNA ends encounter the neighboring line-feature, which is now covered with the bt-anti-dig, and the dig-labeled ends become anchored through dig – anti-dig interaction.  C)  Cartoon illustrates the doubletethered bt-λ DNA-dig molecule after dig-labeled end tethering. TIRF images shows that those DNA molecules that remain stretched without buffer flow (-flow) were successfully both-end tethered.  D)  Cartoon illustrates the DNA immobilization strategy and internal ATTO647N tag, which was located at 14711 bp from the biotinylated DNA end. TIRF images shows SG stained DNA molecules in the absence of buffer flow. Excitation wavelength and emission channel is indicated above each image. Histogram showing the distribution of ATTO647N locations that were determined by fitting the images to 2D Gaussian functions. Si master #8.
    Lambda Dna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 221 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 92 stars, based on 221 article reviews
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    93
    Eppendorf AG lambda dnas
    ( a ) Confocal images of YOYO-1- stained <t>lambda</t> <t>DNAs</t> with different electric potentials (1, 3, 15, and 30 V) for 15 min. ( b ) Relative light intensity of YOYO-1-stained lambda DNAs in the nanochannels. All scale bars are 2 μm.
    Lambda Dnas, supplied by Eppendorf AG, used in various techniques. Bioz Stars score: 93/100, based on 42 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    TaKaRa lambda dna
    Enzymatic analysis of recombinant NucA and NucA‐E104G (A) <t>λ</t> DNA was incubated with rN ucA with or without 1 m m MgCl 2 and 1 m m CaCl 2 . (B) The substrate preference of rN ucA was examined using M13mp18 (single‐stranded circular DNA ), pUC 18 (double‐stranded circular DNA ), and total RNA purified from murine macrophages. (C) λ DNA was incubated with rN ucA with 1 m m MgCl 2 and 1 m m CaCl 2 at different pH . (D) λ DNA was incubated with rN ucA‐E104G with or without 1 m m MgCl 2 and 1 m m CaCl 2 .
    Lambda Dna, supplied by TaKaRa, used in various techniques. Bioz Stars score: 95/100, based on 119 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 95 stars, based on 119 article reviews
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    90
    Promega wizard lambda preps dna purification system
    Enzymatic analysis of recombinant NucA and NucA‐E104G (A) <t>λ</t> DNA was incubated with rN ucA with or without 1 m m MgCl 2 and 1 m m CaCl 2 . (B) The substrate preference of rN ucA was examined using M13mp18 (single‐stranded circular DNA ), pUC 18 (double‐stranded circular DNA ), and total RNA purified from murine macrophages. (C) λ DNA was incubated with rN ucA with 1 m m MgCl 2 and 1 m m CaCl 2 at different pH . (D) λ DNA was incubated with rN ucA‐E104G with or without 1 m m MgCl 2 and 1 m m CaCl 2 .
    Wizard Lambda Preps Dna Purification System, supplied by Promega, used in various techniques. Bioz Stars score: 90/100, based on 162 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/wizard lambda preps dna purification system/product/Promega
    Average 90 stars, based on 162 article reviews
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    88
    Bio-Rad lambda dna ladder
    PFGE of the genomic DNAs of ϕYS40 and ϕTMA. lanes 1 and 5, <t>lambda</t> <t>DNA</t> ladders; lane 2, T4; lane 3, ϕYS40; lane 4, ϕTMA.
    Lambda Dna Ladder, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 88/100, based on 117 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/lambda dna ladder/product/Bio-Rad
    Average 88 stars, based on 117 article reviews
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    92
    Millipore lambda dna
    PFGE of the genomic DNAs of ϕYS40 and ϕTMA. lanes 1 and 5, <t>lambda</t> <t>DNA</t> ladders; lane 2, T4; lane 3, ϕYS40; lane 4, ϕTMA.
    Lambda Dna, supplied by Millipore, used in various techniques. Bioz Stars score: 92/100, based on 60 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/lambda dna/product/Millipore
    Average 92 stars, based on 60 article reviews
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    97
    Millipore lambda phage dna
    Localization and transport of <t>lambda</t> phage <t>DNA</t> molecules from a mature mother to its bud. Phase contrast and fluorescence micrographs of a GV labeled with 0.02 mol% TexasRed-DHPE and encapsulated DNA stained by SYBR Green I. The first image was taken 13 min after the mixing of a dispersion of DNA-containing immature mothers, a catalytic solution (copper (I) chloride, 10 mM; ascorbic acid, 20 mM; and deionized water) and reactive precursors LH (9 mM) and AH/Chol (9/1 mM) ( t = 0 sec). Images were acquired at: ( A ) 13:03 sec, ( B ) 18:23 sec, ( C ) 20:01 sec, ( D ) 20:29 sec, ( E ) 22:06 sec, ( F ) 23:13 sec, ( G ) 35:14 sec, ( H ) 38:18 sec. Scale bar, 10 μm.
    Lambda Phage Dna, supplied by Millipore, used in various techniques. Bioz Stars score: 97/100, based on 40 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/lambda phage dna/product/Millipore
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    97
    New England Biolabs lambda dna n6 methyladenine free
    Localization and transport of <t>lambda</t> phage <t>DNA</t> molecules from a mature mother to its bud. Phase contrast and fluorescence micrographs of a GV labeled with 0.02 mol% TexasRed-DHPE and encapsulated DNA stained by SYBR Green I. The first image was taken 13 min after the mixing of a dispersion of DNA-containing immature mothers, a catalytic solution (copper (I) chloride, 10 mM; ascorbic acid, 20 mM; and deionized water) and reactive precursors LH (9 mM) and AH/Chol (9/1 mM) ( t = 0 sec). Images were acquired at: ( A ) 13:03 sec, ( B ) 18:23 sec, ( C ) 20:01 sec, ( D ) 20:29 sec, ( E ) 22:06 sec, ( F ) 23:13 sec, ( G ) 35:14 sec, ( H ) 38:18 sec. Scale bar, 10 μm.
    Lambda Dna N6 Methyladenine Free, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 97/100, based on 55 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/lambda dna n6 methyladenine free/product/New England Biolabs
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    Image Search Results


    Agarose-gel analysis of tagmentation products of phage- λ DNA analyzed on (a) high-resolution and (c) low-resolution ( i.e ., mini) agarose gels. Size-distribution fits for the high-resolution gel (b) and mini gel (d) of the same tagmented λ -DNA sample subjected to increasing numbers of PCR-amplification cycles (lanes 3-5 in (a), lanes 2-4 in (c)): 8 cycles (top plots), 14 cycles (middle plots), and 20 cycles (bottom plots) in both (b) and (d). Vertical dashed lines (light red in (b), (d)) give the positions of maxima in the discrete molecular-weight ladder (blue ROI in (b), (b)).

    Journal: bioRxiv

    Article Title: Deconvolution of Nucleic-acid Length Distributions: A Gel Electrophoresis Analysis Tool and Applications

    doi: 10.1101/636936

    Figure Lengend Snippet: Agarose-gel analysis of tagmentation products of phage- λ DNA analyzed on (a) high-resolution and (c) low-resolution ( i.e ., mini) agarose gels. Size-distribution fits for the high-resolution gel (b) and mini gel (d) of the same tagmented λ -DNA sample subjected to increasing numbers of PCR-amplification cycles (lanes 3-5 in (a), lanes 2-4 in (c)): 8 cycles (top plots), 14 cycles (middle plots), and 20 cycles (bottom plots) in both (b) and (d). Vertical dashed lines (light red in (b), (d)) give the positions of maxima in the discrete molecular-weight ladder (blue ROI in (b), (b)).

    Article Snippet: A reference mixture of λ -DNA fragments was prepared by digesting λ DNA to completion with 2 units of Aci I (New England Biolabs) per µg of λ DNA (New England Biolabs) for 2 h at 37 °C.

    Techniques: Agarose Gel Electrophoresis, Polymerase Chain Reaction, Amplification, Molecular Weight

    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

    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

    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

    PFGE profiles of total DNA from B. cereus strains restricted by Not I (A), Asc I (B), Sfi I (C), and I- Sce I (D). Y, yeast chromosome marker; λ, lambda ladder marker (New England Biolabs); HS, hot-spot candidate with one single mini-IS Kan r insertion; TS, B. cereus ATCC 14579 type strain; A1 and A2, ade mutants; G1, gua mutant; H1 and H2, his mutants; M1 and M2, met mutants; U1, ura mutant; Aph., aphenotypic double-insertion mutant.

    Journal: Infection and Immunity

    Article Title: Integrated Physical and Genetic Mapping of Bacillus cereus and Other Gram-Positive Bacteria Based on IS231A Transposition Vectors

    doi:

    Figure Lengend Snippet: PFGE profiles of total DNA from B. cereus strains restricted by Not I (A), Asc I (B), Sfi I (C), and I- Sce I (D). Y, yeast chromosome marker; λ, lambda ladder marker (New England Biolabs); HS, hot-spot candidate with one single mini-IS Kan r insertion; TS, B. cereus ATCC 14579 type strain; A1 and A2, ade mutants; G1, gua mutant; H1 and H2, his mutants; M1 and M2, met mutants; U1, ura mutant; Aph., aphenotypic double-insertion mutant.

    Article Snippet: Sizes of the fragments were estimated by using lambda DNA concatemers (size range, 48.5 to 1,018.5 kb) and yeast chromosomes (225 to 1,900 kb) markers (New England Biolabs).

    Techniques: Marker, Mutagenesis

    EZ-vision™In-Gel solution. Left: Preload 10x Left Middle: Preload 100x Right Middle: Precast Right: Post-stain.Photographed on a UV transilluminator 365nm with a SYBR™ filter. Lane 1: 1μl of Hyperladder 1kb ™ (Bioline) 2: 1μl of Hyperladder IV ™ (Bioline) 3: 0.3μg Lambda DNA HindIII marker2 ™ (ThermoScientific™) 4: 580ng of PCR product 5: 27ng of PCR product 6: 8ng of PCR product (as measured on a Qubit ™ Fluorometer)

    Journal: bioRxiv

    Article Title: A comparison of DNA stains and staining methods for Agarose Gel Electrophoresis

    doi: 10.1101/568253

    Figure Lengend Snippet: EZ-vision™In-Gel solution. Left: Preload 10x Left Middle: Preload 100x Right Middle: Precast Right: Post-stain.Photographed on a UV transilluminator 365nm with a SYBR™ filter. Lane 1: 1μl of Hyperladder 1kb ™ (Bioline) 2: 1μl of Hyperladder IV ™ (Bioline) 3: 0.3μg Lambda DNA HindIII marker2 ™ (ThermoScientific™) 4: 580ng of PCR product 5: 27ng of PCR product 6: 8ng of PCR product (as measured on a Qubit ™ Fluorometer)

    Article Snippet: 2μl of SafeWhite was mixed with 1μl each PCR product, and to the Lambda DNA/HindIII marker™ before loading.

    Techniques: Staining, Lambda DNA Preparation, Polymerase Chain Reaction

    Left: EZ-Vision®One Right: SafeWhite. Photographed on a UV transilluminator 365nm with a SYBR™ filter. Lane 1: 1μl of Hyperladder 1kb™ (Bioline) 2: 1μl of Hyperladder IV™ (Bioline) 3: 0.3μg Lambda DNA HindIII marker2 (ThermoScientific™) 4: 580ng of PCR product 5: 27ng of PCR product 6: 8ng of PCR product (as measured on a Qubit ™ Fluorometer)

    Journal: bioRxiv

    Article Title: A comparison of DNA stains and staining methods for Agarose Gel Electrophoresis

    doi: 10.1101/568253

    Figure Lengend Snippet: Left: EZ-Vision®One Right: SafeWhite. Photographed on a UV transilluminator 365nm with a SYBR™ filter. Lane 1: 1μl of Hyperladder 1kb™ (Bioline) 2: 1μl of Hyperladder IV™ (Bioline) 3: 0.3μg Lambda DNA HindIII marker2 (ThermoScientific™) 4: 580ng of PCR product 5: 27ng of PCR product 6: 8ng of PCR product (as measured on a Qubit ™ Fluorometer)

    Article Snippet: 2μl of SafeWhite was mixed with 1μl each PCR product, and to the Lambda DNA/HindIII marker™ before loading.

    Techniques: Lambda DNA Preparation, Polymerase Chain Reaction

    Preload 10x. Top panel: UV transilluminator 365nm with a SYBR™ filter. Centre panel: UV transilluminator 365nm with an EtBr filter. Bottom panel: Invitrogen SafeImager with amber filter. Exposure times vary. Lane 1: 1μl of Hyperladder 1kb™ (Bioline) 2: 1μl of Hyperladder IVTM (Bioline) 3: 0.3μg Lambda DNA HindIII marker2 (ThermoScientific™) 4: 580ng of PCR product 5: 27ng of PCR product 6: 8ng of PCR product

    Journal: bioRxiv

    Article Title: A comparison of DNA stains and staining methods for Agarose Gel Electrophoresis

    doi: 10.1101/568253

    Figure Lengend Snippet: Preload 10x. Top panel: UV transilluminator 365nm with a SYBR™ filter. Centre panel: UV transilluminator 365nm with an EtBr filter. Bottom panel: Invitrogen SafeImager with amber filter. Exposure times vary. Lane 1: 1μl of Hyperladder 1kb™ (Bioline) 2: 1μl of Hyperladder IVTM (Bioline) 3: 0.3μg Lambda DNA HindIII marker2 (ThermoScientific™) 4: 580ng of PCR product 5: 27ng of PCR product 6: 8ng of PCR product

    Article Snippet: 2μl of SafeWhite was mixed with 1μl each PCR product, and to the Lambda DNA/HindIII marker™ before loading.

    Techniques: Lambda DNA Preparation, Polymerase Chain Reaction

    SafeView Left: Preload 10 x Left Middle: Preload 100x Right Middle: Precast Right: Post-stain. Photographed on a UV transilluminator 365nm with an EtBr filter. Lane 1: 1μl of Hyperladder 1kb™ (Bioline) 2: 1μl of Hyperladder IV ™ (Bioline) 3: 0.3μg Lambda DNA HindIII marker2 ™ (ThermoScientific™) 4: 580ng of PCR product 5: 27ng of PCR product 6: 8ng of PCR product (as measured on a Qubit ™ Fluorometer)

    Journal: bioRxiv

    Article Title: A comparison of DNA stains and staining methods for Agarose Gel Electrophoresis

    doi: 10.1101/568253

    Figure Lengend Snippet: SafeView Left: Preload 10 x Left Middle: Preload 100x Right Middle: Precast Right: Post-stain. Photographed on a UV transilluminator 365nm with an EtBr filter. Lane 1: 1μl of Hyperladder 1kb™ (Bioline) 2: 1μl of Hyperladder IV ™ (Bioline) 3: 0.3μg Lambda DNA HindIII marker2 ™ (ThermoScientific™) 4: 580ng of PCR product 5: 27ng of PCR product 6: 8ng of PCR product (as measured on a Qubit ™ Fluorometer)

    Article Snippet: 2μl of SafeWhite was mixed with 1μl each PCR product, and to the Lambda DNA/HindIII marker™ before loading.

    Techniques: Staining, Lambda DNA Preparation, Polymerase Chain Reaction

    SYBR™Safe Left: Preload 10 x Left Middle: Preload 100x Right Middle: Precast Right: Post-stain.Photographed on a UV transilluminator 365nm with a SYBR™ filter. Lane 1: 1μl of Hyperladder 1kb™ (Bioline) 2: 1μl of Hyperladder IV ™ (Bioline) 3: 0.3μg Lambda DNA HindIII marker2 ™ (ThermoScientific™) 4: 580ng of PCR product 5: 27ng of PCR product 6: 8ng of PCR product (as measured on a Qubit ™ Fluorometer)

    Journal: bioRxiv

    Article Title: A comparison of DNA stains and staining methods for Agarose Gel Electrophoresis

    doi: 10.1101/568253

    Figure Lengend Snippet: SYBR™Safe Left: Preload 10 x Left Middle: Preload 100x Right Middle: Precast Right: Post-stain.Photographed on a UV transilluminator 365nm with a SYBR™ filter. Lane 1: 1μl of Hyperladder 1kb™ (Bioline) 2: 1μl of Hyperladder IV ™ (Bioline) 3: 0.3μg Lambda DNA HindIII marker2 ™ (ThermoScientific™) 4: 580ng of PCR product 5: 27ng of PCR product 6: 8ng of PCR product (as measured on a Qubit ™ Fluorometer)

    Article Snippet: 2μl of SafeWhite was mixed with 1μl each PCR product, and to the Lambda DNA/HindIII marker™ before loading.

    Techniques: Staining, Lambda DNA Preparation, Polymerase Chain Reaction

    GelGreen™ Left: Preload 10x Left Middle: Preload 100x Right Middle: Precast Right: Post-stain. Photographed on an Invitrogen SafeImager ™ with an amber filter. Lane 1: 1μl of Hyperladder 1kb™ (Bioline) 2: 1μl of Hyperladder IV ™ (Bioline) 3: 0.3μg Lambda DNA HindIII marker2 ™ (ThermoScientific™) 4: 580ng of PCR product 5: 27ng of PCR product 6: 8ng of PCR product (as measured on a Qubit ™ Fluorometer)

    Journal: bioRxiv

    Article Title: A comparison of DNA stains and staining methods for Agarose Gel Electrophoresis

    doi: 10.1101/568253

    Figure Lengend Snippet: GelGreen™ Left: Preload 10x Left Middle: Preload 100x Right Middle: Precast Right: Post-stain. Photographed on an Invitrogen SafeImager ™ with an amber filter. Lane 1: 1μl of Hyperladder 1kb™ (Bioline) 2: 1μl of Hyperladder IV ™ (Bioline) 3: 0.3μg Lambda DNA HindIII marker2 ™ (ThermoScientific™) 4: 580ng of PCR product 5: 27ng of PCR product 6: 8ng of PCR product (as measured on a Qubit ™ Fluorometer)

    Article Snippet: 2μl of SafeWhite was mixed with 1μl each PCR product, and to the Lambda DNA/HindIII marker™ before loading.

    Techniques: Staining, Lambda DNA Preparation, Polymerase Chain Reaction

    GelRed™ Left: Preload 10x. Left Middle: Preload 100x. Right Middle: Precast. Right: Post-stain. Photographed on a UV transilluminator 365nm with an EtBr filter. Lane 1: 1μl of Hyperladder 1kb™ (Bioline) 2: 1μl of Hyperladder IV ™ (Bioline) 3: 0.3μg Lambda DNA HindIII marker2 ™ (ThermoScientific™) 4: 580ng of PCR product 5: 27ng of PCR product 6: 8ng of PCR product (as measured on a Qubit ™ Fluorometer)

    Journal: bioRxiv

    Article Title: A comparison of DNA stains and staining methods for Agarose Gel Electrophoresis

    doi: 10.1101/568253

    Figure Lengend Snippet: GelRed™ Left: Preload 10x. Left Middle: Preload 100x. Right Middle: Precast. Right: Post-stain. Photographed on a UV transilluminator 365nm with an EtBr filter. Lane 1: 1μl of Hyperladder 1kb™ (Bioline) 2: 1μl of Hyperladder IV ™ (Bioline) 3: 0.3μg Lambda DNA HindIII marker2 ™ (ThermoScientific™) 4: 580ng of PCR product 5: 27ng of PCR product 6: 8ng of PCR product (as measured on a Qubit ™ Fluorometer)

    Article Snippet: 2μl of SafeWhite was mixed with 1μl each PCR product, and to the Lambda DNA/HindIII marker™ before loading.

    Techniques: Staining, Lambda DNA Preparation, Polymerase Chain Reaction

    eRRBS reveals distribution of cytosine methylations in each sequence context among TKO ES cells with reconstituted expression of either DNMT3A WT or DNMT3A R836A a , The rates of bisulfite conversion for the indicated sequence context in each sample as determined by the unmethylated lambda DNA spike-in control. CpN, all cytosines. b, c , Piecharts showing the percentage of methylated cytosines (total number n shown at the bottom of each plot) identified among the DNMT3A WT or DNMT3A R836A -expressing TKO ES cells in each sequence context. The methylated cytosines were called using a stringent binomial distribution–based filter to eliminate false positives from incomplete bisulfite conversion, with a false discovery rate (FDR) of 1% and 0.1% set for panel b and c , respectively. d , Distribution of methylation levels (% in x-axis) for the indicated sequence context. Insert panels show a closed view of the distribution at sites with intermediate to high levels of cytosine methylation.

    Journal: Nature

    Article Title: Structural basis for DNMT3A-mediated de novo DNA methylation

    doi: 10.1038/nature25477

    Figure Lengend Snippet: eRRBS reveals distribution of cytosine methylations in each sequence context among TKO ES cells with reconstituted expression of either DNMT3A WT or DNMT3A R836A a , The rates of bisulfite conversion for the indicated sequence context in each sample as determined by the unmethylated lambda DNA spike-in control. CpN, all cytosines. b, c , Piecharts showing the percentage of methylated cytosines (total number n shown at the bottom of each plot) identified among the DNMT3A WT or DNMT3A R836A -expressing TKO ES cells in each sequence context. The methylated cytosines were called using a stringent binomial distribution–based filter to eliminate false positives from incomplete bisulfite conversion, with a false discovery rate (FDR) of 1% and 0.1% set for panel b and c , respectively. d , Distribution of methylation levels (% in x-axis) for the indicated sequence context. Insert panels show a closed view of the distribution at sites with intermediate to high levels of cytosine methylation.

    Article Snippet: Enhanced Reduced Representation Bisulfite Sequencing (eRRBS) and data analysis Genomic DNA of each sample was added with 0.5% of unmethylated lambda DNA (Promega) as spike-in control and subjected to eRRBS using MethylMidi-seq (Zymo Research) as described before .

    Techniques: Sequencing, Expressing, Lambda DNA Preparation, Methylation

    (a) Representative fluorescence intensity profile of an individual YOYO-1 stained λ-DNA molecule after injection (red line) and confinement (blue line) in the plasma modified nanochannel filled with 2X TBE buffer. Complete injection into the nanochannel

    Journal: The Analyst

    Article Title: Surface Charge, Electroosmotic Flow and DNA Extension in Chemically Modified Thermoplastic Nanoslits and Nanochannels

    doi: 10.1039/c4an01439a

    Figure Lengend Snippet: (a) Representative fluorescence intensity profile of an individual YOYO-1 stained λ-DNA molecule after injection (red line) and confinement (blue line) in the plasma modified nanochannel filled with 2X TBE buffer. Complete injection into the nanochannel

    Article Snippet: To study the electrokinetic parameters and extension length of λ-DNA, 100 × 100 nm nanochannels were used. λ-DNA (Promega Corporation) were stained with the bis-intercalating dye, YOYO-1 (Molecular Probes, Eugene, OR) at a base-pair/dye ratio of 5:1 in an electrolyte solution of 1X TBE (89 mM Tris, 89 mM Borate, 1 mM EDTA) with the addition of 4% v/v β-mercaptoethanol as a radical scavenger to minimize photo-induced damage (photobleaching and/or photonicking).

    Techniques: Fluorescence, Staining, Injection, Modification

    Double-tethered Soft DNA Curtains with defined orientation.  A)  Cartoon illustrates the printed traptavidin (tAv) line-features that enable specific one-end immobilization of the biotin-λ DNA-digoxigenin (bt-λ DNA-dig, 48.5 kb) molecules. TIRF images shows that in the absence of the buffer flow (-flow), DNA molecules are aligned to the line-features. They are responding to a hydrodynamic force (+flow) by extending parallel to the surface.  B)  To tether the dig-labeled end of bt-λ DNA-dig, continuous slow flow of buffer containing biotinylated anti-dig (bt-anti-dig) antibody is applied and DNA molecules are dragged slightly, but do not reach the neighboring line-feature. At the next step, buffer flow rate is increased and the dig-labeled DNA ends encounter the neighboring line-feature, which is now covered with the bt-anti-dig, and the dig-labeled ends become anchored through dig – anti-dig interaction.  C)  Cartoon illustrates the doubletethered bt-λ DNA-dig molecule after dig-labeled end tethering. TIRF images shows that those DNA molecules that remain stretched without buffer flow (-flow) were successfully both-end tethered.  D)  Cartoon illustrates the DNA immobilization strategy and internal ATTO647N tag, which was located at 14711 bp from the biotinylated DNA end. TIRF images shows SG stained DNA molecules in the absence of buffer flow. Excitation wavelength and emission channel is indicated above each image. Histogram showing the distribution of ATTO647N locations that were determined by fitting the images to 2D Gaussian functions. Si master #8.

    Journal: bioRxiv

    Article Title: Oriented Soft DNA Curtains for Single Molecule Imaging

    doi: 10.1101/2020.06.15.151662

    Figure Lengend Snippet: Double-tethered Soft DNA Curtains with defined orientation. A) Cartoon illustrates the printed traptavidin (tAv) line-features that enable specific one-end immobilization of the biotin-λ DNA-digoxigenin (bt-λ DNA-dig, 48.5 kb) molecules. TIRF images shows that in the absence of the buffer flow (-flow), DNA molecules are aligned to the line-features. They are responding to a hydrodynamic force (+flow) by extending parallel to the surface. B) To tether the dig-labeled end of bt-λ DNA-dig, continuous slow flow of buffer containing biotinylated anti-dig (bt-anti-dig) antibody is applied and DNA molecules are dragged slightly, but do not reach the neighboring line-feature. At the next step, buffer flow rate is increased and the dig-labeled DNA ends encounter the neighboring line-feature, which is now covered with the bt-anti-dig, and the dig-labeled ends become anchored through dig – anti-dig interaction. C) Cartoon illustrates the doubletethered bt-λ DNA-dig molecule after dig-labeled end tethering. TIRF images shows that those DNA molecules that remain stretched without buffer flow (-flow) were successfully both-end tethered. D) Cartoon illustrates the DNA immobilization strategy and internal ATTO647N tag, which was located at 14711 bp from the biotinylated DNA end. TIRF images shows SG stained DNA molecules in the absence of buffer flow. Excitation wavelength and emission channel is indicated above each image. Histogram showing the distribution of ATTO647N locations that were determined by fitting the images to 2D Gaussian functions. Si master #8.

    Article Snippet: Production of DNABiotinylated oligonucleotides were annealed to the overhang (cos sequences) at either the left, or both ends of bacteriophage λ DNA (48.5 kb, ThermoFisher Scientific).

    Techniques: Labeling, Staining

    Double-tethered Soft DNA Curtains assay for binding location studies of SpCas9 protein. A) Merged blue and red channel TIRF images representing SG-stained λ DNA (blue) with bound SpCas9 (red). Schematic representation of the assay depicts SpCas9, which was programmed with ATTO647N-labeled crRNA-tracrRNA (Cas9-ATTO647N) targeting site of λ DNA located at 31.1 kb from the biotinylated DNA end. B) Representative kymograms made from individual DNA molecules. C) Histogram of SpCas9-ATTO647N binding events distributions determined by 2D Gaussian fitting. D) SpCas9-ATTO647N binding position vs. dwell time 2D histogram plot. The plot was made from 172 DNA molecules and contains 902 individual binding events. Color code represents the counts.

    Journal: bioRxiv

    Article Title: Oriented Soft DNA Curtains for Single Molecule Imaging

    doi: 10.1101/2020.06.15.151662

    Figure Lengend Snippet: Double-tethered Soft DNA Curtains assay for binding location studies of SpCas9 protein. A) Merged blue and red channel TIRF images representing SG-stained λ DNA (blue) with bound SpCas9 (red). Schematic representation of the assay depicts SpCas9, which was programmed with ATTO647N-labeled crRNA-tracrRNA (Cas9-ATTO647N) targeting site of λ DNA located at 31.1 kb from the biotinylated DNA end. B) Representative kymograms made from individual DNA molecules. C) Histogram of SpCas9-ATTO647N binding events distributions determined by 2D Gaussian fitting. D) SpCas9-ATTO647N binding position vs. dwell time 2D histogram plot. The plot was made from 172 DNA molecules and contains 902 individual binding events. Color code represents the counts.

    Article Snippet: Production of DNABiotinylated oligonucleotides were annealed to the overhang (cos sequences) at either the left, or both ends of bacteriophage λ DNA (48.5 kb, ThermoFisher Scientific).

    Techniques: Binding Assay, Staining, Labeling

    Optimization of DNA arrays fabrication. A) Schematic of the single-tethered Soft DNA Curtains design shows PEG monolayer on a glass coverslip and printed streptavidin (sAv) or traptavidin (tAv) line features, which enables specific one-end immobilization of the biotinylated λ DNA (48.5 kb) molecules. DNA molecules are tethered to the line features and responds to a hydrodynamic force by extending parallel to the surface. B) Effect of printing pressure (PP) on the quality of short DNA molecule arrays. Top panel shows TIRF images of 5 kb long biotinylated DNA molecules stained with SYTOX green (SG), which were immobilized on the sAv line-features fabricated on modified coverslip. PP is indicated above each image. Bottom panel shows AFM images and their line-profiles (1 and 100 pixels) of the sAv line features fabricated on the modified glass coverslip at the same pressure as the TIRF images. [sAv] = 0.02 mg/mL, Si master #1. C) Stability test of single-tethered Soft DNA Curtains – λ DNA molecules immobilized on a sAv (or tAv) array template and stained with SG. Images were acquired every 20 min for a period of 2 h. In between acquisitions, there was no buffer flow applied. During the acquisition, 20 frames were acquired at buffer flow of 1 mL/min and 20 frames without the flow. Graph shows the average number of single-tethered DNA molecules that extended to the full length. Average was taken over line-features and the error bars represents SD. Si master #3.

    Journal: bioRxiv

    Article Title: Oriented Soft DNA Curtains for Single Molecule Imaging

    doi: 10.1101/2020.06.15.151662

    Figure Lengend Snippet: Optimization of DNA arrays fabrication. A) Schematic of the single-tethered Soft DNA Curtains design shows PEG monolayer on a glass coverslip and printed streptavidin (sAv) or traptavidin (tAv) line features, which enables specific one-end immobilization of the biotinylated λ DNA (48.5 kb) molecules. DNA molecules are tethered to the line features and responds to a hydrodynamic force by extending parallel to the surface. B) Effect of printing pressure (PP) on the quality of short DNA molecule arrays. Top panel shows TIRF images of 5 kb long biotinylated DNA molecules stained with SYTOX green (SG), which were immobilized on the sAv line-features fabricated on modified coverslip. PP is indicated above each image. Bottom panel shows AFM images and their line-profiles (1 and 100 pixels) of the sAv line features fabricated on the modified glass coverslip at the same pressure as the TIRF images. [sAv] = 0.02 mg/mL, Si master #1. C) Stability test of single-tethered Soft DNA Curtains – λ DNA molecules immobilized on a sAv (or tAv) array template and stained with SG. Images were acquired every 20 min for a period of 2 h. In between acquisitions, there was no buffer flow applied. During the acquisition, 20 frames were acquired at buffer flow of 1 mL/min and 20 frames without the flow. Graph shows the average number of single-tethered DNA molecules that extended to the full length. Average was taken over line-features and the error bars represents SD. Si master #3.

    Article Snippet: Production of DNABiotinylated oligonucleotides were annealed to the overhang (cos sequences) at either the left, or both ends of bacteriophage λ DNA (48.5 kb, ThermoFisher Scientific).

    Techniques: Staining, Modification

    The construction of mismatched DNA used in single-molecule total internal reflection fluorescence (smTIRF) microscopy a , A schematic illustration for the construction of a 17.3-kb mismatched DNA. L or R (blue) indicates the orientation of the DNA relative to the L and R cos end of λ-phage DNA. P (red) indicates the 5′-phosphate of the DNA. b , A schematic illustration of 17.3-kb mismatched DNA observation by prism-based smTIRF microscopy. c , Representative mismatched DNA visualized by smTIRF microscopy in the absence of flow. The DNA was stained with Sytox Orange and a 40 × 85 µm field of view is shown. d , A schematic illustration of the DNA length determination. e , The length distribution of the mismatched DNA observed by smTIRF microscopy. Gaussian fit of the data are shown along with the mean ± s.d.

    Journal: Nature

    Article Title: Cascading MutS and MutL sliding clamps control DNA diffusion to activate mismatch repair

    doi: 10.1038/nature20562

    Figure Lengend Snippet: The construction of mismatched DNA used in single-molecule total internal reflection fluorescence (smTIRF) microscopy a , A schematic illustration for the construction of a 17.3-kb mismatched DNA. L or R (blue) indicates the orientation of the DNA relative to the L and R cos end of λ-phage DNA. P (red) indicates the 5′-phosphate of the DNA. b , A schematic illustration of 17.3-kb mismatched DNA observation by prism-based smTIRF microscopy. c , Representative mismatched DNA visualized by smTIRF microscopy in the absence of flow. The DNA was stained with Sytox Orange and a 40 × 85 µm field of view is shown. d , A schematic illustration of the DNA length determination. e , The length distribution of the mismatched DNA observed by smTIRF microscopy. Gaussian fit of the data are shown along with the mean ± s.d.

    Article Snippet: λ-phage DNA (3.2 nM, Thermo Scientific) was ligated with the lambda mismatch 1 oligonucleotide (800 nM; , ) at room temperature (22 °C) overnight.

    Techniques: Fluorescence, Microscopy, Flow Cytometry, Staining

    ( a ) Confocal images of YOYO-1- stained lambda DNAs with different electric potentials (1, 3, 15, and 30 V) for 15 min. ( b ) Relative light intensity of YOYO-1-stained lambda DNAs in the nanochannels. All scale bars are 2 μm.

    Journal: Scientific Reports

    Article Title: Controlled generation of nanopatterned electrical DNA interface

    doi: 10.1038/s41598-019-39444-3

    Figure Lengend Snippet: ( a ) Confocal images of YOYO-1- stained lambda DNAs with different electric potentials (1, 3, 15, and 30 V) for 15 min. ( b ) Relative light intensity of YOYO-1-stained lambda DNAs in the nanochannels. All scale bars are 2 μm.

    Article Snippet: A more in-depth examination using the magnification of Channel L4 showed that as the voltage increased, more lambda DNAs accumulated and attached to fill the nanochannel.

    Techniques: Staining

    ( a – c ) SEM images of lambda DNAs detached at −30 V for 0, 5, and 15 min, respectively. All scale bars are 500 nm.

    Journal: Scientific Reports

    Article Title: Controlled generation of nanopatterned electrical DNA interface

    doi: 10.1038/s41598-019-39444-3

    Figure Lengend Snippet: ( a – c ) SEM images of lambda DNAs detached at −30 V for 0, 5, and 15 min, respectively. All scale bars are 500 nm.

    Article Snippet: A more in-depth examination using the magnification of Channel L4 showed that as the voltage increased, more lambda DNAs accumulated and attached to fill the nanochannel.

    Techniques:

    ( a – d ) SEM images of lambda DNAs attached by electrophoresis for 15 min at different electric potentials; 1, 3, 15, and 30 V, respectively. The scale bar is 500 nm. ( e ) Gaps inside nanochannel. ( f ) SEM image of nanochannels with interface showing lambda DNAs attached by electrophoresis at 15 V for 15 min (scale bar =500 nm). ( g ) Ultra high-resolution FE-SEM images of linearly aligned DNAs attachment in nanochannels L 1 , L 2 , L 3 , and L 4 at 15 V for 15 min. All scale bar are 50 nm.

    Journal: Scientific Reports

    Article Title: Controlled generation of nanopatterned electrical DNA interface

    doi: 10.1038/s41598-019-39444-3

    Figure Lengend Snippet: ( a – d ) SEM images of lambda DNAs attached by electrophoresis for 15 min at different electric potentials; 1, 3, 15, and 30 V, respectively. The scale bar is 500 nm. ( e ) Gaps inside nanochannel. ( f ) SEM image of nanochannels with interface showing lambda DNAs attached by electrophoresis at 15 V for 15 min (scale bar =500 nm). ( g ) Ultra high-resolution FE-SEM images of linearly aligned DNAs attachment in nanochannels L 1 , L 2 , L 3 , and L 4 at 15 V for 15 min. All scale bar are 50 nm.

    Article Snippet: A more in-depth examination using the magnification of Channel L4 showed that as the voltage increased, more lambda DNAs accumulated and attached to fill the nanochannel.

    Techniques: Electrophoresis

    Enzymatic analysis of recombinant NucA and NucA‐E104G (A) λ DNA was incubated with rN ucA with or without 1 m m MgCl 2 and 1 m m CaCl 2 . (B) The substrate preference of rN ucA was examined using M13mp18 (single‐stranded circular DNA ), pUC 18 (double‐stranded circular DNA ), and total RNA purified from murine macrophages. (C) λ DNA was incubated with rN ucA with 1 m m MgCl 2 and 1 m m CaCl 2 at different pH . (D) λ DNA was incubated with rN ucA‐E104G with or without 1 m m MgCl 2 and 1 m m CaCl 2 .

    Journal: Molecular Oral Microbiology

    Article Title: Nucleases from Prevotella intermedia can degrade neutrophil extracellular traps

    doi: 10.1111/omi.12171

    Figure Lengend Snippet: Enzymatic analysis of recombinant NucA and NucA‐E104G (A) λ DNA was incubated with rN ucA with or without 1 m m MgCl 2 and 1 m m CaCl 2 . (B) The substrate preference of rN ucA was examined using M13mp18 (single‐stranded circular DNA ), pUC 18 (double‐stranded circular DNA ), and total RNA purified from murine macrophages. (C) λ DNA was incubated with rN ucA with 1 m m MgCl 2 and 1 m m CaCl 2 at different pH . (D) λ DNA was incubated with rN ucA‐E104G with or without 1 m m MgCl 2 and 1 m m CaCl 2 .

    Article Snippet: Biochemical analysis of Pr. intermedia extracellular nuclease To examine the nuclease activity of Pr. intermedia crude nuclease, 0.25 μg of λ DNA (Takara Bio, Shiga, Japan) was incubated with 0.5 μg of crude nuclease in reaction buffer containing 50 mm Tris–HCl (pH 7.0), 150 mm NaCl with or without 1 mm CaCl2 , and 1 mm MgCl2 at 37°C for 10 min.

    Techniques: Recombinant, Incubation, Purification

    Enzymatic analysis of recombinant NucD and NucD‐N229G. (A) λ DNA was incubated with rN ucD with or without 1 m m MgCl 2 and 1 m m CaCl 2 . (B) The substrate preference of rN ucD was examined using M13mp18 (single‐stranded circular DNA ), pUC 18 (double‐stranded circular DNA ), and total RNA purified from murine macrophages. (C) λ DNA was incubated with rN ucD with 1 m m MgCl 2 and 1 m m CaCl 2 at different pH . (D) λ DNA was incubated with rN ucD‐N229G with or without 1 m m MgCl 2 and 1 m m CaCl 2 .

    Journal: Molecular Oral Microbiology

    Article Title: Nucleases from Prevotella intermedia can degrade neutrophil extracellular traps

    doi: 10.1111/omi.12171

    Figure Lengend Snippet: Enzymatic analysis of recombinant NucD and NucD‐N229G. (A) λ DNA was incubated with rN ucD with or without 1 m m MgCl 2 and 1 m m CaCl 2 . (B) The substrate preference of rN ucD was examined using M13mp18 (single‐stranded circular DNA ), pUC 18 (double‐stranded circular DNA ), and total RNA purified from murine macrophages. (C) λ DNA was incubated with rN ucD with 1 m m MgCl 2 and 1 m m CaCl 2 at different pH . (D) λ DNA was incubated with rN ucD‐N229G with or without 1 m m MgCl 2 and 1 m m CaCl 2 .

    Article Snippet: Biochemical analysis of Pr. intermedia extracellular nuclease To examine the nuclease activity of Pr. intermedia crude nuclease, 0.25 μg of λ DNA (Takara Bio, Shiga, Japan) was incubated with 0.5 μg of crude nuclease in reaction buffer containing 50 mm Tris–HCl (pH 7.0), 150 mm NaCl with or without 1 mm CaCl2 , and 1 mm MgCl2 at 37°C for 10 min.

    Techniques: Recombinant, Incubation, Purification

    SDS – PAGE nuclease assay and biochemical analysis of Prevotella intermedia crude nuclease. (A) Pr. intermedia crude nuclease was detected in SDS – PAGE gels containing 0.2 mg ml −1 salmon sperm DNA . After electrophoresis, proteins were renatured. This was followed by incubation in activation buffer containing 1 m m MgCl 2 and 1 m m CaCl 2 for 3 h at 37°C. To visualize DNA degradation, gels were stained with ethidium bromide and examined under ultraviolet light. Two protein bands were observed to possess nuclease activity. (B) λ DNA was incubated with Pr. intermedia crude nuclease with or without 1 m m MgCl 2 and 1 m m CaCl 2 at 37°C for 10 min. Following electrophoresis, DNA was stained with ethidium bromide and visualized under ultraviolet light.

    Journal: Molecular Oral Microbiology

    Article Title: Nucleases from Prevotella intermedia can degrade neutrophil extracellular traps

    doi: 10.1111/omi.12171

    Figure Lengend Snippet: SDS – PAGE nuclease assay and biochemical analysis of Prevotella intermedia crude nuclease. (A) Pr. intermedia crude nuclease was detected in SDS – PAGE gels containing 0.2 mg ml −1 salmon sperm DNA . After electrophoresis, proteins were renatured. This was followed by incubation in activation buffer containing 1 m m MgCl 2 and 1 m m CaCl 2 for 3 h at 37°C. To visualize DNA degradation, gels were stained with ethidium bromide and examined under ultraviolet light. Two protein bands were observed to possess nuclease activity. (B) λ DNA was incubated with Pr. intermedia crude nuclease with or without 1 m m MgCl 2 and 1 m m CaCl 2 at 37°C for 10 min. Following electrophoresis, DNA was stained with ethidium bromide and visualized under ultraviolet light.

    Article Snippet: Biochemical analysis of Pr. intermedia extracellular nuclease To examine the nuclease activity of Pr. intermedia crude nuclease, 0.25 μg of λ DNA (Takara Bio, Shiga, Japan) was incubated with 0.5 μg of crude nuclease in reaction buffer containing 50 mm Tris–HCl (pH 7.0), 150 mm NaCl with or without 1 mm CaCl2 , and 1 mm MgCl2 at 37°C for 10 min.

    Techniques: SDS Page, Nuclease Assay, Electrophoresis, Incubation, Activation Assay, Staining, Activity Assay

    PFGE of the genomic DNAs of ϕYS40 and ϕTMA. lanes 1 and 5, lambda DNA ladders; lane 2, T4; lane 3, ϕYS40; lane 4, ϕTMA.

    Journal: Bacteriophage

    Article Title: Genomic and proteomic characterization of the large Myoviridae bacteriophage \u03d5TMA of the extreme thermophile Thermus thermophilus

    doi: 10.4161/bact.1.3.16712

    Figure Lengend Snippet: PFGE of the genomic DNAs of ϕYS40 and ϕTMA. lanes 1 and 5, lambda DNA ladders; lane 2, T4; lane 3, ϕYS40; lane 4, ϕTMA.

    Article Snippet: Lambda-DNA ladder (BioRad, 170-3635) was used as the size marker.

    Techniques: Lambda DNA Preparation

    Localization and transport of lambda phage DNA molecules from a mature mother to its bud. Phase contrast and fluorescence micrographs of a GV labeled with 0.02 mol% TexasRed-DHPE and encapsulated DNA stained by SYBR Green I. The first image was taken 13 min after the mixing of a dispersion of DNA-containing immature mothers, a catalytic solution (copper (I) chloride, 10 mM; ascorbic acid, 20 mM; and deionized water) and reactive precursors LH (9 mM) and AH/Chol (9/1 mM) ( t = 0 sec). Images were acquired at: ( A ) 13:03 sec, ( B ) 18:23 sec, ( C ) 20:01 sec, ( D ) 20:29 sec, ( E ) 22:06 sec, ( F ) 23:13 sec, ( G ) 35:14 sec, ( H ) 38:18 sec. Scale bar, 10 μm.

    Journal: Scientific Reports

    Article Title: Budding and Division of Giant Vesicles Linked to Phospholipid Production

    doi: 10.1038/s41598-018-36183-9

    Figure Lengend Snippet: Localization and transport of lambda phage DNA molecules from a mature mother to its bud. Phase contrast and fluorescence micrographs of a GV labeled with 0.02 mol% TexasRed-DHPE and encapsulated DNA stained by SYBR Green I. The first image was taken 13 min after the mixing of a dispersion of DNA-containing immature mothers, a catalytic solution (copper (I) chloride, 10 mM; ascorbic acid, 20 mM; and deionized water) and reactive precursors LH (9 mM) and AH/Chol (9/1 mM) ( t = 0 sec). Images were acquired at: ( A ) 13:03 sec, ( B ) 18:23 sec, ( C ) 20:01 sec, ( D ) 20:29 sec, ( E ) 22:06 sec, ( F ) 23:13 sec, ( G ) 35:14 sec, ( H ) 38:18 sec. Scale bar, 10 μm.

    Article Snippet: Lambda phage DNA (48502-base pair) methylated from Escherichia coli host strain W3110 was purchased from Sigma-Aldrich (St. Louis, MO, USA).

    Techniques: Fluorescence, Labeling, Staining, SYBR Green Assay, Size-exclusion Chromatography