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Promega lambda phage dna
Lambda Phage Dna, supplied by Promega, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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DNA Extraction:

Article Title: Isolation, Characterization, and Ecology of Sulfur-Respiring Crenarchaea Inhabiting Acid-Sulfate-Chloride-Containing Geothermal Springs in Yellowstone National Park ▿ Inhabiting Acid-Sulfate-Chloride-Containing Geothermal Springs in Yellowstone National Park ▿ †
Article Snippet: At the laboratory, samples of S0 floc were treated to remove residual S0 and subjected to total DNA extraction as described above for DGGE analysis. .. DNA was quantified using the nucleic acid binding fluorochrome SYBR Green I (Invitrogen) added to achieve a final concentration of 1/1,000 (vol/vol), an ND-3300 Fluorospectrometer (NanoDrop Technologies, Wilmington, DE), and lambda phage DNA (Promega) as the standard.

SYBR Green Assay:

Article Title: Isolation, Characterization, and Ecology of Sulfur-Respiring Crenarchaea Inhabiting Acid-Sulfate-Chloride-Containing Geothermal Springs in Yellowstone National Park ▿ Inhabiting Acid-Sulfate-Chloride-Containing Geothermal Springs in Yellowstone National Park ▿ †
Article Snippet: .. DNA was quantified using the nucleic acid binding fluorochrome SYBR Green I (Invitrogen) added to achieve a final concentration of 1/1,000 (vol/vol), an ND-3300 Fluorospectrometer (NanoDrop Technologies, Wilmington, DE), and lambda phage DNA (Promega) as the standard. ..

Positron Emission Tomography:

Article Title: Increasing the accuracy of nanopore DNA sequencing using a time-varying cross membrane voltage
Article Snippet: The lambda phage DNA (GenBank J02459.1 ) was obtained from Promega. .. The pET-28a DNA was obtained from collaborators who used it as an expression vector for another DNA sequence not used in this work.

Binding Assay:

Article Title: Isolation, Characterization, and Ecology of Sulfur-Respiring Crenarchaea Inhabiting Acid-Sulfate-Chloride-Containing Geothermal Springs in Yellowstone National Park ▿ Inhabiting Acid-Sulfate-Chloride-Containing Geothermal Springs in Yellowstone National Park ▿ †
Article Snippet: .. DNA was quantified using the nucleic acid binding fluorochrome SYBR Green I (Invitrogen) added to achieve a final concentration of 1/1,000 (vol/vol), an ND-3300 Fluorospectrometer (NanoDrop Technologies, Wilmington, DE), and lambda phage DNA (Promega) as the standard. ..

Synthesized:

Article Title: Increasing the accuracy of nanopore DNA sequencing using a time-varying cross membrane voltage
Article Snippet: DNA Sequences and Constructs Short DNA oligonucleotides were synthesized and purified using column purification methods at Stanford University Protein and Nucleic Acid Facility. .. The lambda phage DNA (GenBank J02459.1 ) was obtained from Promega.

Flocculation:

Article Title: Isolation, Characterization, and Ecology of Sulfur-Respiring Crenarchaea Inhabiting Acid-Sulfate-Chloride-Containing Geothermal Springs in Yellowstone National Park ▿ Inhabiting Acid-Sulfate-Chloride-Containing Geothermal Springs in Yellowstone National Park ▿ †
Article Snippet: At the laboratory, samples of S0 floc were treated to remove residual S0 and subjected to total DNA extraction as described above for DGGE analysis. .. DNA was quantified using the nucleic acid binding fluorochrome SYBR Green I (Invitrogen) added to achieve a final concentration of 1/1,000 (vol/vol), an ND-3300 Fluorospectrometer (NanoDrop Technologies, Wilmington, DE), and lambda phage DNA (Promega) as the standard.

Construct:

Article Title: Increasing the accuracy of nanopore DNA sequencing using a time-varying cross membrane voltage
Article Snippet: Paragraph title: DNA Sequences and Constructs ... The lambda phage DNA (GenBank J02459.1 ) was obtained from Promega.

Purification:

Article Title: A Comprehensive Genetic Study of Streptococcal Immunoglobulin A1 Proteases: Evidence for Recombination within and between Species
Article Snippet: .. Lambda phage DNA prepared as described previously ( ) and PCR products were purified with Wizard Minicolumns (Promega, Madison, Wis.). .. Individual sequence reactions were done with a Taq DyeDeoxy-Terminator cycle sequencing kit (Perkin-Elmer, Foster City, Calif.) and analyzed with an Applied Biosystem DNA sequencer (Perkin-Elmer).

Article Title: Increasing the accuracy of nanopore DNA sequencing using a time-varying cross membrane voltage
Article Snippet: DNA Sequences and Constructs Short DNA oligonucleotides were synthesized and purified using column purification methods at Stanford University Protein and Nucleic Acid Facility. .. The lambda phage DNA (GenBank J02459.1 ) was obtained from Promega.

Real-time Polymerase Chain Reaction:

Article Title: Isolation, Characterization, and Ecology of Sulfur-Respiring Crenarchaea Inhabiting Acid-Sulfate-Chloride-Containing Geothermal Springs in Yellowstone National Park ▿ Inhabiting Acid-Sulfate-Chloride-Containing Geothermal Springs in Yellowstone National Park ▿ †
Article Snippet: Paragraph title: qPCR analysis. ... DNA was quantified using the nucleic acid binding fluorochrome SYBR Green I (Invitrogen) added to achieve a final concentration of 1/1,000 (vol/vol), an ND-3300 Fluorospectrometer (NanoDrop Technologies, Wilmington, DE), and lambda phage DNA (Promega) as the standard.

Concentration Assay:

Article Title: Isolation, Characterization, and Ecology of Sulfur-Respiring Crenarchaea Inhabiting Acid-Sulfate-Chloride-Containing Geothermal Springs in Yellowstone National Park ▿ Inhabiting Acid-Sulfate-Chloride-Containing Geothermal Springs in Yellowstone National Park ▿ †
Article Snippet: .. DNA was quantified using the nucleic acid binding fluorochrome SYBR Green I (Invitrogen) added to achieve a final concentration of 1/1,000 (vol/vol), an ND-3300 Fluorospectrometer (NanoDrop Technologies, Wilmington, DE), and lambda phage DNA (Promega) as the standard. ..

Generated:

Article Title: Isolation, Characterization, and Ecology of Sulfur-Respiring Crenarchaea Inhabiting Acid-Sulfate-Chloride-Containing Geothermal Springs in Yellowstone National Park ▿ Inhabiting Acid-Sulfate-Chloride-Containing Geothermal Springs in Yellowstone National Park ▿ †
Article Snippet: DNA was quantified using the nucleic acid binding fluorochrome SYBR Green I (Invitrogen) added to achieve a final concentration of 1/1,000 (vol/vol), an ND-3300 Fluorospectrometer (NanoDrop Technologies, Wilmington, DE), and lambda phage DNA (Promega) as the standard. .. To ensure that qPCR amplicons generated in each reaction arose from the template of either isolate 18U65 or 18D70, forward primers were designed to contain 3- to 4-bp sequence mismatches compared to the 16S rRNA gene sequence of A. aceticus and Caldisphaera lagunensis , respectively.

Polymerase Chain Reaction:

Article Title: A Comprehensive Genetic Study of Streptococcal Immunoglobulin A1 Proteases: Evidence for Recombination within and between Species
Article Snippet: .. Lambda phage DNA prepared as described previously ( ) and PCR products were purified with Wizard Minicolumns (Promega, Madison, Wis.). .. Individual sequence reactions were done with a Taq DyeDeoxy-Terminator cycle sequencing kit (Perkin-Elmer, Foster City, Calif.) and analyzed with an Applied Biosystem DNA sequencer (Perkin-Elmer).

DNA Sequencing:

Article Title: A Comprehensive Genetic Study of Streptococcal Immunoglobulin A1 Proteases: Evidence for Recombination within and between Species
Article Snippet: Paragraph title: DNA sequencing. ... Lambda phage DNA prepared as described previously ( ) and PCR products were purified with Wizard Minicolumns (Promega, Madison, Wis.).

Expressing:

Article Title: Increasing the accuracy of nanopore DNA sequencing using a time-varying cross membrane voltage
Article Snippet: The lambda phage DNA (GenBank J02459.1 ) was obtained from Promega. .. The pET-28a DNA was obtained from collaborators who used it as an expression vector for another DNA sequence not used in this work.

Sequencing:

Article Title: A Comprehensive Genetic Study of Streptococcal Immunoglobulin A1 Proteases: Evidence for Recombination within and between Species
Article Snippet: DNAs from M13 phages were prepared as described previously , whereas plasmid DNAs were prepared as recommended by the supplier of the sequencing kit. .. Lambda phage DNA prepared as described previously ( ) and PCR products were purified with Wizard Minicolumns (Promega, Madison, Wis.).

Article Title: Increasing the accuracy of nanopore DNA sequencing using a time-varying cross membrane voltage
Article Snippet: The ΦX-174 DNA (NCBI reference sequence NC_001422.1) was obtained from New England Biolabs. .. The lambda phage DNA (GenBank J02459.1 ) was obtained from Promega.

Article Title: Isolation, Characterization, and Ecology of Sulfur-Respiring Crenarchaea Inhabiting Acid-Sulfate-Chloride-Containing Geothermal Springs in Yellowstone National Park ▿ Inhabiting Acid-Sulfate-Chloride-Containing Geothermal Springs in Yellowstone National Park ▿ †
Article Snippet: DNA was quantified using the nucleic acid binding fluorochrome SYBR Green I (Invitrogen) added to achieve a final concentration of 1/1,000 (vol/vol), an ND-3300 Fluorospectrometer (NanoDrop Technologies, Wilmington, DE), and lambda phage DNA (Promega) as the standard. .. To ensure that qPCR amplicons generated in each reaction arose from the template of either isolate 18U65 or 18D70, forward primers were designed to contain 3- to 4-bp sequence mismatches compared to the 16S rRNA gene sequence of A. aceticus and Caldisphaera lagunensis , respectively.

Denaturing Gradient Gel Electrophoresis:

Article Title: Isolation, Characterization, and Ecology of Sulfur-Respiring Crenarchaea Inhabiting Acid-Sulfate-Chloride-Containing Geothermal Springs in Yellowstone National Park ▿ Inhabiting Acid-Sulfate-Chloride-Containing Geothermal Springs in Yellowstone National Park ▿ †
Article Snippet: At the laboratory, samples of S0 floc were treated to remove residual S0 and subjected to total DNA extraction as described above for DGGE analysis. .. DNA was quantified using the nucleic acid binding fluorochrome SYBR Green I (Invitrogen) added to achieve a final concentration of 1/1,000 (vol/vol), an ND-3300 Fluorospectrometer (NanoDrop Technologies, Wilmington, DE), and lambda phage DNA (Promega) as the standard.

Plasmid Preparation:

Article Title: A Comprehensive Genetic Study of Streptococcal Immunoglobulin A1 Proteases: Evidence for Recombination within and between Species
Article Snippet: DNAs from M13 phages were prepared as described previously , whereas plasmid DNAs were prepared as recommended by the supplier of the sequencing kit. .. Lambda phage DNA prepared as described previously ( ) and PCR products were purified with Wizard Minicolumns (Promega, Madison, Wis.).

Article Title: Increasing the accuracy of nanopore DNA sequencing using a time-varying cross membrane voltage
Article Snippet: The lambda phage DNA (GenBank J02459.1 ) was obtained from Promega. .. The pET-28a DNA was obtained from collaborators who used it as an expression vector for another DNA sequence not used in this work.

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  • 93
    Promega phage dna
    Agarose gel electrophoresis and Southern blot hybridization of phage DNAs. (A) Agarose gel electrophoresis of Sma I-digested DNAs of phages <t>φSC370,</t> φLC159, and 933W. The molecular weight marker was bacteriophage lambda <t>DNA</t> digested with Eco RI and Hin dIII. (B) Hybridization with lambda marker as the gene probe. (C) Hybridization with Sma I-digested DNA of phage φLC159 as the gene probe. (D) Hybridization with Sma I-digested DNA of phage φSC370 as the gene probe.
    Phage Dna, supplied by Promega, used in various techniques. Bioz Stars score: 93/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/phage dna/product/Promega
    Average 93 stars, based on 14 article reviews
    Price from $9.99 to $1999.99
    phage dna - by Bioz Stars, 2020-02
    93/100 stars
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    90
    Promega phage dna isolation
    Genome maps of <t>DLP1</t> and DLP2. The scale (in kbp) is shown above the DLP1 and DLP2 genomic maps. The assigned function of the predicted proteins encoded by each open reading frame is as follows: grey - unknown function; purple - lysis; green - virion morphogenesis; blue - <t>DNA</t> replication/repair. Numbers within the larger ORFs relate to gene product number
    Phage Dna Isolation, supplied by Promega, used in various techniques. Bioz Stars score: 90/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/phage dna isolation/product/Promega
    Average 90 stars, based on 5 article reviews
    Price from $9.99 to $1999.99
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    78
    Promega three dimensional nanofunnels lambda phage dna
    Residence time measurements and threshold electric field reduction. a Mean residence times measured at various nanochannel electric field strengths, E , in three different <t>nanofunnels</t> (defined by α = 0.78, α = 0.45, and α = 0; see Eq. 2 ) and in the absence of a nanofunnel. Each dataset is associated with the nanofunnel indicated directly above it in the figure and is color coded accordingly. Data were collected using stained λ-phage (48.5 kbp, open circles) and T4-phage (165.6 kbp, filled squares) <t>DNA</t> molecules. The error bars indicate the standard deviations of at least 20 independent measurements per experimental data point. The curves represent the best-fit of the theoretical model to these experimental data. b Extrapolating the experimental electric field data in ( a ) to τ 0 = 6 ms results in the characteristic threshold electric field strength, E 0 (normalized to the threshold electric field strength measured in the absence of a nanofunnel E 0 (no funnel)) for each of the three nanofunnels (red, green, and blue symbols obtained from the data in ( a ) of the same colors). τ 0 = 6 ms corresponds to the Zimm relaxation time of the leading portion (~3000 bp) of the nanofunnel-confined molecule 23 , 24 . This 3000-bp segment is the length of DNA that must enter the nanochannel to initiate threading, as determined from the theoretical monomer concentration profiles shown in Supplementary Fig. 7b . The experimental values in ( b ) for the α = 1.46 and α = 1.89 nanofunnels were determined as described in the Supplementary Methods. The solid and dashed black lines are interpolations of theoretical values calculated for T4-phage and λ-phage DNA, respectively, over a wider range of α values. The error bars indicate the 1 σ confidence level of the threshold electric field strengths determined from the experimental data and are smaller than the symbols for the results from nanofunnels where α > 0.45
    Three Dimensional Nanofunnels Lambda Phage Dna, supplied by Promega, used in various techniques. Bioz Stars score: 78/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/three dimensional nanofunnels lambda phage dna/product/Promega
    Average 78 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    three dimensional nanofunnels lambda phage dna - by Bioz Stars, 2020-02
    78/100 stars
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    90
    Promega unmethylated bacteriophage lambda dna
    Characterization of the Ae. aegypti methylome by whole-genome bisulfite sequencing. ( A ) Average methylation levels were determined for all cytosine residues and then distributed into bins with increasing methylation ratios. For comparison, the corresponding data is also shown for bacteriophage <t>lambda</t> (negative control) and human blood (positive control) <t>DNA</t> that was spiked into the Ae. aegypti sample prior to bisulfite conversion. The actual numerical values of the first bins are indicated above the corresponding bars. ( B ) Dinucleotide sequence context of unconverted cytosines. No unconverted cytosines were found in the lambda dataset.
    Unmethylated Bacteriophage Lambda Dna, supplied by Promega, used in various techniques. Bioz Stars score: 90/100, based on 0 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/unmethylated bacteriophage lambda dna/product/Promega
    Average 90 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
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    Agarose gel electrophoresis and Southern blot hybridization of phage DNAs. (A) Agarose gel electrophoresis of Sma I-digested DNAs of phages φSC370, φLC159, and 933W. The molecular weight marker was bacteriophage lambda DNA digested with Eco RI and Hin dIII. (B) Hybridization with lambda marker as the gene probe. (C) Hybridization with Sma I-digested DNA of phage φLC159 as the gene probe. (D) Hybridization with Sma I-digested DNA of phage φSC370 as the gene probe.

    Journal: Infection and Immunity

    Article Title: Shiga Toxin 2-Converting Bacteriophages Associated with Clonal Variability in Escherichia coli O157:H7 Strains of Human Origin Isolated from a Single Outbreak

    doi: 10.1128/IAI.71.8.4554-4562.2003

    Figure Lengend Snippet: Agarose gel electrophoresis and Southern blot hybridization of phage DNAs. (A) Agarose gel electrophoresis of Sma I-digested DNAs of phages φSC370, φLC159, and 933W. The molecular weight marker was bacteriophage lambda DNA digested with Eco RI and Hin dIII. (B) Hybridization with lambda marker as the gene probe. (C) Hybridization with Sma I-digested DNA of phage φLC159 as the gene probe. (D) Hybridization with Sma I-digested DNA of phage φSC370 as the gene probe.

    Article Snippet: When the production of phage did not result in a high concentration of DNA, as observed for phage φSC370, phage DNA was purified from 500 ml of induced bacterial cultures and digested with various restriction enzymes, including Bam HI, Cla I, Eco RI, Eco RV, Kpn I, Pst I, Sal I, and Sma I (Promega Co.).

    Techniques: Agarose Gel Electrophoresis, Southern Blot, Hybridization, Molecular Weight, Marker, Lambda DNA Preparation

    Genome maps of DLP1 and DLP2. The scale (in kbp) is shown above the DLP1 and DLP2 genomic maps. The assigned function of the predicted proteins encoded by each open reading frame is as follows: grey - unknown function; purple - lysis; green - virion morphogenesis; blue - DNA replication/repair. Numbers within the larger ORFs relate to gene product number

    Journal: BMC Genomics

    Article Title: The isolation and characterization of two Stenotrophomonas maltophilia bacteriophages capable of cross-taxonomic order infectivity

    doi: 10.1186/s12864-015-1848-y

    Figure Lengend Snippet: Genome maps of DLP1 and DLP2. The scale (in kbp) is shown above the DLP1 and DLP2 genomic maps. The assigned function of the predicted proteins encoded by each open reading frame is as follows: grey - unknown function; purple - lysis; green - virion morphogenesis; blue - DNA replication/repair. Numbers within the larger ORFs relate to gene product number

    Article Snippet: Phage DNA isolation, RFLP analysis and sequencing DLP1 and DLP2 genomic DNA was isolated from bacteriophage lysate using the Wizard Lambda DNA purification system (Promega Corp., Madison, WI) with a modified protocol [ , ].

    Techniques: Lysis

    Restriction fragment length polymorphism of DLP1 and DLP2 genomic DNA. 1 μg of phage genomic DNA was digested 5 min with EcoRI and separated on a 1 % agarose gel. L: 1 Kb Plus DNA Ladder (Invitrogen). Several differences in banding pattern between the genomic DNAs isolated from the two phages is apparent

    Journal: BMC Genomics

    Article Title: The isolation and characterization of two Stenotrophomonas maltophilia bacteriophages capable of cross-taxonomic order infectivity

    doi: 10.1186/s12864-015-1848-y

    Figure Lengend Snippet: Restriction fragment length polymorphism of DLP1 and DLP2 genomic DNA. 1 μg of phage genomic DNA was digested 5 min with EcoRI and separated on a 1 % agarose gel. L: 1 Kb Plus DNA Ladder (Invitrogen). Several differences in banding pattern between the genomic DNAs isolated from the two phages is apparent

    Article Snippet: Phage DNA isolation, RFLP analysis and sequencing DLP1 and DLP2 genomic DNA was isolated from bacteriophage lysate using the Wizard Lambda DNA purification system (Promega Corp., Madison, WI) with a modified protocol [ , ].

    Techniques: Agarose Gel Electrophoresis, Isolation

    PCR confirmation of P. aeruginosa infections by DLP1 and DLP2. Lanes 1 and 9: 1 Kb Plus DNA ladder (Invitrogen), lane 2: DLP1 phage DNA, lane 3: DLP1 negative control, lane 4: DLP1 phage lysate, lane 5: DLP2 phage DNA, lane 6: DLP1 phage lysate from PA01 infection, lane 7: DLP1 phage lysate from ENV009 infection, lane 8: blank, lane 10: DLP2 phage DNA, lane 11: DLP2 negative control, lane 12: DLP2 phage lysate, lane 13: DLP1 phage lysate, lane 14: DLP2 phage lysate from HER004 infection, lane 15: DLP2 phage lysate from 14,715 infection. The size of the markers (in Kbp) is shown on the left

    Journal: BMC Genomics

    Article Title: The isolation and characterization of two Stenotrophomonas maltophilia bacteriophages capable of cross-taxonomic order infectivity

    doi: 10.1186/s12864-015-1848-y

    Figure Lengend Snippet: PCR confirmation of P. aeruginosa infections by DLP1 and DLP2. Lanes 1 and 9: 1 Kb Plus DNA ladder (Invitrogen), lane 2: DLP1 phage DNA, lane 3: DLP1 negative control, lane 4: DLP1 phage lysate, lane 5: DLP2 phage DNA, lane 6: DLP1 phage lysate from PA01 infection, lane 7: DLP1 phage lysate from ENV009 infection, lane 8: blank, lane 10: DLP2 phage DNA, lane 11: DLP2 negative control, lane 12: DLP2 phage lysate, lane 13: DLP1 phage lysate, lane 14: DLP2 phage lysate from HER004 infection, lane 15: DLP2 phage lysate from 14,715 infection. The size of the markers (in Kbp) is shown on the left

    Article Snippet: Phage DNA isolation, RFLP analysis and sequencing DLP1 and DLP2 genomic DNA was isolated from bacteriophage lysate using the Wizard Lambda DNA purification system (Promega Corp., Madison, WI) with a modified protocol [ , ].

    Techniques: Polymerase Chain Reaction, Negative Control, Infection

    Residence time measurements and threshold electric field reduction. a Mean residence times measured at various nanochannel electric field strengths, E , in three different nanofunnels (defined by α = 0.78, α = 0.45, and α = 0; see Eq. 2 ) and in the absence of a nanofunnel. Each dataset is associated with the nanofunnel indicated directly above it in the figure and is color coded accordingly. Data were collected using stained λ-phage (48.5 kbp, open circles) and T4-phage (165.6 kbp, filled squares) DNA molecules. The error bars indicate the standard deviations of at least 20 independent measurements per experimental data point. The curves represent the best-fit of the theoretical model to these experimental data. b Extrapolating the experimental electric field data in ( a ) to τ 0 = 6 ms results in the characteristic threshold electric field strength, E 0 (normalized to the threshold electric field strength measured in the absence of a nanofunnel E 0 (no funnel)) for each of the three nanofunnels (red, green, and blue symbols obtained from the data in ( a ) of the same colors). τ 0 = 6 ms corresponds to the Zimm relaxation time of the leading portion (~3000 bp) of the nanofunnel-confined molecule 23 , 24 . This 3000-bp segment is the length of DNA that must enter the nanochannel to initiate threading, as determined from the theoretical monomer concentration profiles shown in Supplementary Fig. 7b . The experimental values in ( b ) for the α = 1.46 and α = 1.89 nanofunnels were determined as described in the Supplementary Methods. The solid and dashed black lines are interpolations of theoretical values calculated for T4-phage and λ-phage DNA, respectively, over a wider range of α values. The error bars indicate the 1 σ confidence level of the threshold electric field strengths determined from the experimental data and are smaller than the symbols for the results from nanofunnels where α > 0.45

    Journal: Nature Communications

    Article Title: Enhanced nanochannel translocation and localization of genomic DNA molecules using three-dimensional nanofunnels

    doi: 10.1038/s41467-017-00951-4

    Figure Lengend Snippet: Residence time measurements and threshold electric field reduction. a Mean residence times measured at various nanochannel electric field strengths, E , in three different nanofunnels (defined by α = 0.78, α = 0.45, and α = 0; see Eq. 2 ) and in the absence of a nanofunnel. Each dataset is associated with the nanofunnel indicated directly above it in the figure and is color coded accordingly. Data were collected using stained λ-phage (48.5 kbp, open circles) and T4-phage (165.6 kbp, filled squares) DNA molecules. The error bars indicate the standard deviations of at least 20 independent measurements per experimental data point. The curves represent the best-fit of the theoretical model to these experimental data. b Extrapolating the experimental electric field data in ( a ) to τ 0 = 6 ms results in the characteristic threshold electric field strength, E 0 (normalized to the threshold electric field strength measured in the absence of a nanofunnel E 0 (no funnel)) for each of the three nanofunnels (red, green, and blue symbols obtained from the data in ( a ) of the same colors). τ 0 = 6 ms corresponds to the Zimm relaxation time of the leading portion (~3000 bp) of the nanofunnel-confined molecule 23 , 24 . This 3000-bp segment is the length of DNA that must enter the nanochannel to initiate threading, as determined from the theoretical monomer concentration profiles shown in Supplementary Fig. 7b . The experimental values in ( b ) for the α = 1.46 and α = 1.89 nanofunnels were determined as described in the Supplementary Methods. The solid and dashed black lines are interpolations of theoretical values calculated for T4-phage and λ-phage DNA, respectively, over a wider range of α values. The error bars indicate the 1 σ confidence level of the threshold electric field strengths determined from the experimental data and are smaller than the symbols for the results from nanofunnels where α > 0.45

    Article Snippet: Measuring DNA molecules in three-dimensional nanofunnels Lambda-phage DNA (Promega) or T4-phage DNA (Nippon Gene) in 2X TBE was stained with the intercalating dye, YOYO-1 (Invitrogen), at a base-pair:dye ratio of 5:1.

    Techniques: Staining, Mass Spectrometry, Concentration Assay

    Characterization of the Ae. aegypti methylome by whole-genome bisulfite sequencing. ( A ) Average methylation levels were determined for all cytosine residues and then distributed into bins with increasing methylation ratios. For comparison, the corresponding data is also shown for bacteriophage lambda (negative control) and human blood (positive control) DNA that was spiked into the Ae. aegypti sample prior to bisulfite conversion. The actual numerical values of the first bins are indicated above the corresponding bars. ( B ) Dinucleotide sequence context of unconverted cytosines. No unconverted cytosines were found in the lambda dataset.

    Journal: Scientific Reports

    Article Title: Comprehensive DNA methylation analysis of the Aedes aegypti genome

    doi: 10.1038/srep36444

    Figure Lengend Snippet: Characterization of the Ae. aegypti methylome by whole-genome bisulfite sequencing. ( A ) Average methylation levels were determined for all cytosine residues and then distributed into bins with increasing methylation ratios. For comparison, the corresponding data is also shown for bacteriophage lambda (negative control) and human blood (positive control) DNA that was spiked into the Ae. aegypti sample prior to bisulfite conversion. The actual numerical values of the first bins are indicated above the corresponding bars. ( B ) Dinucleotide sequence context of unconverted cytosines. No unconverted cytosines were found in the lambda dataset.

    Article Snippet: As a spike-in control, unmethylated bacteriophage lambda DNA (Promega) and genomic DNA extracted from human blood (Blood & Cell Culture DNA Kit, Qiagen) were used.

    Techniques: Methylation Sequencing, Methylation, Negative Control, Positive Control, Sequencing