bacteriophage λ double stranded dna Search Results


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  • 99
    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 306 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 306 article reviews
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    99
    Thermo Fisher bacteriophage λ 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.
    Bacteriophage λ Dna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 95 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 95 article reviews
    Price from $9.99 to $1999.99
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    99
    Millipore agarose gel electrophoresis
    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.
    Agarose Gel Electrophoresis, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 968 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Promega lambda phage 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 Phage Dna, supplied by Promega, used in various techniques. Bioz Stars score: 99/100, based on 95 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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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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    98
    Millipore escherichia coli strains
    Radioactive signal for increasing amounts of <t>DNA</t> added to 10 ng of radiolabeled <t>RNA</t> and for DNA alone. The signal is expressed as the SAB.
    Escherichia Coli Strains, supplied by Millipore, used in various techniques. Bioz Stars score: 98/100, based on 192 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Promega unmethylated lambda dna
    Radioactive signal for increasing amounts of <t>DNA</t> added to 10 ng of radiolabeled <t>RNA</t> and for DNA alone. The signal is expressed as the SAB.
    Unmethylated Lambda Dna, supplied by Promega, used in various techniques. Bioz Stars score: 91/100, based on 569 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Millipore expand long template pcr system
    Radioactive signal for increasing amounts of <t>DNA</t> added to 10 ng of radiolabeled <t>RNA</t> and for DNA alone. The signal is expressed as the SAB.
    Expand Long Template Pcr System, supplied by Millipore, used in various techniques. Bioz Stars score: 94/100, based on 32 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    New England Biolabs bacteriophage lambda ladder pfge marker
    Radioactive signal for increasing amounts of <t>DNA</t> added to 10 ng of radiolabeled <t>RNA</t> and for DNA alone. The signal is expressed as the SAB.
    Bacteriophage Lambda Ladder Pfge Marker, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 30 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bacteriophage lambda ladder pfge marker/product/New England Biolabs
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    88
    Stratagene lambda dash ii bacteriophage dna
    Radioactive signal for increasing amounts of <t>DNA</t> added to 10 ng of radiolabeled <t>RNA</t> and for DNA alone. The signal is expressed as the SAB.
    Lambda Dash Ii Bacteriophage Dna, supplied by Stratagene, used in various techniques. Bioz Stars score: 88/100, based on 28 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    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

    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

    Photon count, length, and folding. In a 1 min run, 416 molecules from a λ -bacteriophage DNA sample are analyzed. The average molecule speed is at a device bias of U = 50 V. ( A ) Distribution of the apparent length ( B ) Distribution of the real length ( C ) Schematic defining apparent length real length free length and folded (looped) length for a molecule with a single loop. ( D ) Photon counts (cnts) per molecule versus apparent length ( E ) Photon counts per molecule versus real length The linear fit passing through the origin has a slope of ( F ) Distribution of the photon count per molecule. A comparison of D and E shows that folding explains the distribution of molecules with the same photon count over different apparent lengths. Fitting the photon count ( F ) and real length distributions ( C ) with Gaussian distributions leads to a mean photon count of photons and a real length of for intact λ -DNA molecules. All molecules within two standard deviations of the mean photon count and the mean real length are considered to be intact ( horizontal and vertical arrows indicate region). This accounts for 52% of the molecules analyzed, whereas the rest of the molecules are interpreted as fragments or concatemers. ( E , inset ) Distribution of the free length/real length ratio for all intact molecules; 79% of the intact molecules have

    Journal: Biophysical Journal

    Article Title: Conformation, Length, and Speed Measurements of Electrodynamically Stretched DNA in Nanochannels

    doi: 10.1529/biophysj.107.121020

    Figure Lengend Snippet: Photon count, length, and folding. In a 1 min run, 416 molecules from a λ -bacteriophage DNA sample are analyzed. The average molecule speed is at a device bias of U = 50 V. ( A ) Distribution of the apparent length ( B ) Distribution of the real length ( C ) Schematic defining apparent length real length free length and folded (looped) length for a molecule with a single loop. ( D ) Photon counts (cnts) per molecule versus apparent length ( E ) Photon counts per molecule versus real length The linear fit passing through the origin has a slope of ( F ) Distribution of the photon count per molecule. A comparison of D and E shows that folding explains the distribution of molecules with the same photon count over different apparent lengths. Fitting the photon count ( F ) and real length distributions ( C ) with Gaussian distributions leads to a mean photon count of photons and a real length of for intact λ -DNA molecules. All molecules within two standard deviations of the mean photon count and the mean real length are considered to be intact ( horizontal and vertical arrows indicate region). This accounts for 52% of the molecules analyzed, whereas the rest of the molecules are interpreted as fragments or concatemers. ( E , inset ) Distribution of the free length/real length ratio for all intact molecules; 79% of the intact molecules have

    Article Snippet: A Hin dIII digest of λ -bacteriophage DNA (New England Biolabs) was prepared in a similar manner with the exception that it was heated to 60°C.

    Techniques:

    Photon count, length, speed, and size. Analysis of a sample containing a mixture of λ -bacteriophage DNA and its Hin dIII digest. In 2 min, 16,315 molecules were detected with an average speed ( A ) Distribution of the real length The peaks are shown fitted to nine modified Gaussians ( red ). ( B ) Real length versus number of basepairs. ( C ) Photon count (cnts) per molecule versus the number of basepairs. A linear fit yields a slope of ( D ) Distribution of photon counts cnts per molecule versus real length ( E ) Distribution of the photon counts per molecule. The peaks are fitted to eight modified Gaussians ( red ). The peaks in A and E are interpreted as the following DNA strand sizes, in number of basepairs: 125, 564, (2027 + 2322)/2, 4361, 6557, 9416, 23,130, 23,130 + 4361, 48,502. Whereas peaks 7 and 8 are resolved separately in A , they are combined in E . The values plotted in B and C are the mean values resulting from the Gaussian fits from A and E , respectively. ( F ) Distribution of molecule speed versus real length DNA speed is essentially constant with length, showing only a slight decrease for the shortest fragment.

    Journal: Biophysical Journal

    Article Title: Conformation, Length, and Speed Measurements of Electrodynamically Stretched DNA in Nanochannels

    doi: 10.1529/biophysj.107.121020

    Figure Lengend Snippet: Photon count, length, speed, and size. Analysis of a sample containing a mixture of λ -bacteriophage DNA and its Hin dIII digest. In 2 min, 16,315 molecules were detected with an average speed ( A ) Distribution of the real length The peaks are shown fitted to nine modified Gaussians ( red ). ( B ) Real length versus number of basepairs. ( C ) Photon count (cnts) per molecule versus the number of basepairs. A linear fit yields a slope of ( D ) Distribution of photon counts cnts per molecule versus real length ( E ) Distribution of the photon counts per molecule. The peaks are fitted to eight modified Gaussians ( red ). The peaks in A and E are interpreted as the following DNA strand sizes, in number of basepairs: 125, 564, (2027 + 2322)/2, 4361, 6557, 9416, 23,130, 23,130 + 4361, 48,502. Whereas peaks 7 and 8 are resolved separately in A , they are combined in E . The values plotted in B and C are the mean values resulting from the Gaussian fits from A and E , respectively. ( F ) Distribution of molecule speed versus real length DNA speed is essentially constant with length, showing only a slight decrease for the shortest fragment.

    Article Snippet: A Hin dIII digest of λ -bacteriophage DNA (New England Biolabs) was prepared in a similar manner with the exception that it was heated to 60°C.

    Techniques: 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

    Types of data output provided by the custom analysis software of the real-time digital nucleic acid amplification instrument after a multivolume PCR reaction using lambda DNA on a multivolume SlipChip device with a 15 s exposure time. Each graph (B–D) was exported as line art and scaled. (A) An image depicting the mask created to define the locations of each compartmentalized reaction on a multivolume microfluidic device. (B) Baseline-corrected amplification traces from each of the reaction wells on the microfluidic device. Two intensity groups result because in this multivolume microfluidic device there are two well depths (the two larger volumes are 100 μm deep and the two smaller volumes are 50 μm deep) [ 20 ]. The arrow shows the correlation of a single compartmentalized reaction (A) to its real-time trace (B). (C) A graph depicting the number of positive reactions as a function of amplification cycle from the data generated in (B). (D) A graph depicting the negative derivative of the collected melt curve traces from each of the positive reactions. (E) A screenshot of the analysis software analyzing the real-time data shown in panel (B).

    Journal: PLoS ONE

    Article Title: Instrument for Real-Time Digital Nucleic Acid Amplification on Custom Microfluidic Devices

    doi: 10.1371/journal.pone.0163060

    Figure Lengend Snippet: Types of data output provided by the custom analysis software of the real-time digital nucleic acid amplification instrument after a multivolume PCR reaction using lambda DNA on a multivolume SlipChip device with a 15 s exposure time. Each graph (B–D) was exported as line art and scaled. (A) An image depicting the mask created to define the locations of each compartmentalized reaction on a multivolume microfluidic device. (B) Baseline-corrected amplification traces from each of the reaction wells on the microfluidic device. Two intensity groups result because in this multivolume microfluidic device there are two well depths (the two larger volumes are 100 μm deep and the two smaller volumes are 50 μm deep) [ 20 ]. The arrow shows the correlation of a single compartmentalized reaction (A) to its real-time trace (B). (C) A graph depicting the number of positive reactions as a function of amplification cycle from the data generated in (B). (D) A graph depicting the negative derivative of the collected melt curve traces from each of the positive reactions. (E) A screenshot of the analysis software analyzing the real-time data shown in panel (B).

    Article Snippet: Bio-Rad (Hercules, CA, USA) SsoFast Evagreen Supermix, Phage lambda DNA (500 μg), SUPERase In RNase Inhibitor (20 U/μL), mineral oil (DNase, RNase, and Protease free), and tetradecane were purchased from Thermo Fisher Scientific (Hanover Park, IL, USA).

    Techniques: Software, Amplification, Polymerase Chain Reaction, Lambda DNA Preparation, Generated

    Low Ionic Strength Destabilizes Chromatin. (a–c) AFM images of chromatin assembled from lambda phage DNA in 2-fold diluted egg extract in XB2 buffer and digested with restriction enzyme Alu I. The final buffer is (a) XB2 buffer, (b) 10 mM HEPES

    Journal: Chromosoma

    Article Title: Atomic Force Microscope Imaging of Chromatin Assembled in Xenopus laevis Egg Extract

    doi: 10.1007/s00412-010-0307-4

    Figure Lengend Snippet: Low Ionic Strength Destabilizes Chromatin. (a–c) AFM images of chromatin assembled from lambda phage DNA in 2-fold diluted egg extract in XB2 buffer and digested with restriction enzyme Alu I. The final buffer is (a) XB2 buffer, (b) 10 mM HEPES

    Article Snippet: In order to estimate the tip-induced-width-increase in width measurement, we imaged lambda-phage DNA (Fermentas) on 0.1% glutaraldehyde mica surface using three different AFM probes.

    Techniques:

    Direct Imaging Method for AFM of Higher-Order Structures. AFM images of chromatin assembled from lambda phage DNA in Xenopus laevis egg extract on streptavidin-coated surface and imaged directly on the same surface. (a) The control surface without DNA

    Journal: Chromosoma

    Article Title: Atomic Force Microscope Imaging of Chromatin Assembled in Xenopus laevis Egg Extract

    doi: 10.1007/s00412-010-0307-4

    Figure Lengend Snippet: Direct Imaging Method for AFM of Higher-Order Structures. AFM images of chromatin assembled from lambda phage DNA in Xenopus laevis egg extract on streptavidin-coated surface and imaged directly on the same surface. (a) The control surface without DNA

    Article Snippet: In order to estimate the tip-induced-width-increase in width measurement, we imaged lambda-phage DNA (Fermentas) on 0.1% glutaraldehyde mica surface using three different AFM probes.

    Techniques: Imaging

    Diluted Extracts Produce Mixed Chromatin and DNA Structures. AFM images of chromatin assembled from lambda phage DNA in (a) 2-fold, (b) 20-fold and (c) 100-fold diluted egg extract digested with restriction enzyme Alu I in XB2 buffer. The final solution

    Journal: Chromosoma

    Article Title: Atomic Force Microscope Imaging of Chromatin Assembled in Xenopus laevis Egg Extract

    doi: 10.1007/s00412-010-0307-4

    Figure Lengend Snippet: Diluted Extracts Produce Mixed Chromatin and DNA Structures. AFM images of chromatin assembled from lambda phage DNA in (a) 2-fold, (b) 20-fold and (c) 100-fold diluted egg extract digested with restriction enzyme Alu I in XB2 buffer. The final solution

    Article Snippet: In order to estimate the tip-induced-width-increase in width measurement, we imaged lambda-phage DNA (Fermentas) on 0.1% glutaraldehyde mica surface using three different AFM probes.

    Techniques:

    PFGE separation of Spe I-digested chromosomal DNA from A. hydrophila . Lane 1, A136; lane 2, A136m; lane 3, A139; lanes 4 and 5, two clinical strains of A. hydrophila , A2866 and A4252, respectively; lane 6, CCRC 13018; lane 7, CCRC 13881; lane M, bacteriophage lambda DNA concatemers.

    Journal: Journal of Clinical Microbiology

    Article Title: Inducible ?-Lactam Resistance in Aeromonas hydrophila: Therapeutic Challenge for Antimicrobial Therapy

    doi:

    Figure Lengend Snippet: PFGE separation of Spe I-digested chromosomal DNA from A. hydrophila . Lane 1, A136; lane 2, A136m; lane 3, A139; lanes 4 and 5, two clinical strains of A. hydrophila , A2866 and A4252, respectively; lane 6, CCRC 13018; lane 7, CCRC 13881; lane M, bacteriophage lambda DNA concatemers.

    Article Snippet: Bacteriophage lambda DNA concatemers (Gibco BRL, Gaithersburg, Md.) were used as size standards.

    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

    Fluorescence intensity and applied electrical potential vs time during electrokinetic injection of 5 μg∕mL YOYO-1 labeled λ-phage DNA in 40 mM TAE buffer across a single 300 nm diam×10 μm long PDMS nanopore.

    Journal: Biomicrofluidics

    Article Title: Single nanopore transport of synthetic and biological polyelectrolytes in three-dimensional hybrid microfluidic/nanofluidic devices

    doi: 10.1063/1.3059546

    Figure Lengend Snippet: Fluorescence intensity and applied electrical potential vs time during electrokinetic injection of 5 μg∕mL YOYO-1 labeled λ-phage DNA in 40 mM TAE buffer across a single 300 nm diam×10 μm long PDMS nanopore.

    Article Snippet: Polystyrene sulfonate sodium salt (PSS), polyallylamine chloride salt (PAA), tris(hydroxymethyl)aminomethane (TRIS), ethylenediaminetetraacetic (EDTA), λ-phage DNA, and acetic acid (Sigma Aldrich Co., St. Louis, MO) and YOYO-1 (Invitrogen, Carlsbad, CA) were used as received.

    Techniques: Fluorescence, Injection, Labeling

    Radioactive signal for increasing amounts of DNA added to 10 ng of radiolabeled RNA and for DNA alone. The signal is expressed as the SAB.

    Journal: Applied and Environmental Microbiology

    Article Title: The Presence of Humic Substances and DNA in RNA Extracts Affects Hybridization Results

    doi:

    Figure Lengend Snippet: Radioactive signal for increasing amounts of DNA added to 10 ng of radiolabeled RNA and for DNA alone. The signal is expressed as the SAB.

    Article Snippet: To evaluate the effect of the presence of DNA in RNA extracts on membrane hybridizations, RNA was removed from E. coli DNA (catalog no. D-2001; Sigma, St. Louis, Mo.) by RNase digestion (Ribonuclease 1 A; Pharmacia).

    Techniques:

    Hybridization response for RNA amended with DNA and for DNA alone. The hybridization response is expressed as a percentage of the hybridization response obtained with RNA only.

    Journal: Applied and Environmental Microbiology

    Article Title: The Presence of Humic Substances and DNA in RNA Extracts Affects Hybridization Results

    doi:

    Figure Lengend Snippet: Hybridization response for RNA amended with DNA and for DNA alone. The hybridization response is expressed as a percentage of the hybridization response obtained with RNA only.

    Article Snippet: To evaluate the effect of the presence of DNA in RNA extracts on membrane hybridizations, RNA was removed from E. coli DNA (catalog no. D-2001; Sigma, St. Louis, Mo.) by RNase digestion (Ribonuclease 1 A; Pharmacia).

    Techniques: Hybridization