lambda phage dna  (New England Biolabs)


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  • 99
    Name:
    Lambda DNA
    Description:
    Lambda DNA 1 250 ug
    Catalog Number:
    N3011L
    Price:
    270
    Size:
    1 250 ug
    Category:
    Genomic DNA
    Score:
    85
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    Structured Review

    New England Biolabs lambda phage dna
    Lambda DNA
    Lambda DNA 1 250 ug
    https://www.bioz.com/result/lambda phage dna/product/New England Biolabs
    Average 99 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
    lambda phage dna - by Bioz Stars, 2019-10
    99/100 stars

    Images

    1) Product Images from "Quantification of Trace-Level DNA by Real-Time Whole Genome Amplification"

    Article Title: Quantification of Trace-Level DNA by Real-Time Whole Genome Amplification

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0028661

    Application of the real-time DOP-PCR to diverse DNA species. Amplification profiles and their standard curves were obtained from human placental DNA (HPD; A), calf thymus DNA (CTD; B), E. coli DNA (C), and lambda phage DNA (D). Standard DNA samples from 80 fg to 80 ng and a no-template control were amplified. Six independent experiments each comprising triplicate reactions were performed, and typical results of one experiment are presented. Data for 80 ng and NTC were omitted for the plotting of standard curves.
    Figure Legend Snippet: Application of the real-time DOP-PCR to diverse DNA species. Amplification profiles and their standard curves were obtained from human placental DNA (HPD; A), calf thymus DNA (CTD; B), E. coli DNA (C), and lambda phage DNA (D). Standard DNA samples from 80 fg to 80 ng and a no-template control were amplified. Six independent experiments each comprising triplicate reactions were performed, and typical results of one experiment are presented. Data for 80 ng and NTC were omitted for the plotting of standard curves.

    Techniques Used: Degenerate Oligonucleotide–primed Polymerase Chain Reaction, Amplification

    2) Product Images from "Conserved linear dynamics of single-molecule Brownian motion"

    Article Title: Conserved linear dynamics of single-molecule Brownian motion

    Journal: Nature Communications

    doi: 10.1038/ncomms15675

    Lattice occupancy analysis of lambda DNA. ( a ) MSD-Δ t profile of lambda DNA (Δ t =6.4 ms). The red line shows the theoretical MSD-Δ t profile. ( b ) Frequency histogram of the HE-1Δ t distribution of the experimental (top) and the S r A r simulated replicates (bottom) of lambda DNA. ( c ) Averaged MSD-Δ t profiles of the sub-trajectories captured in the same way as in Fig. 7a (red) and Fig. 7b (blue). The red and blue lines are the theoretical MSD-Δ t profiles. The green line shows the overall, theoretical MSD-Δ t profile of the experimental replicates.
    Figure Legend Snippet: Lattice occupancy analysis of lambda DNA. ( a ) MSD-Δ t profile of lambda DNA (Δ t =6.4 ms). The red line shows the theoretical MSD-Δ t profile. ( b ) Frequency histogram of the HE-1Δ t distribution of the experimental (top) and the S r A r simulated replicates (bottom) of lambda DNA. ( c ) Averaged MSD-Δ t profiles of the sub-trajectories captured in the same way as in Fig. 7a (red) and Fig. 7b (blue). The red and blue lines are the theoretical MSD-Δ t profiles. The green line shows the overall, theoretical MSD-Δ t profile of the experimental replicates.

    Techniques Used: Lambda DNA Preparation, Mass Spectrometry

    3) Product Images from "Quantification of Trace-Level DNA by Real-Time Whole Genome Amplification"

    Article Title: Quantification of Trace-Level DNA by Real-Time Whole Genome Amplification

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0028661

    Application of the real-time DOP-PCR to diverse DNA species. Amplification profiles and their standard curves were obtained from human placental DNA (HPD; A), calf thymus DNA (CTD; B), E. coli DNA (C), and lambda phage DNA (D). Standard DNA samples from 80 fg to 80 ng and a no-template control were amplified. Six independent experiments each comprising triplicate reactions were performed, and typical results of one experiment are presented. Data for 80 ng and NTC were omitted for the plotting of standard curves.
    Figure Legend Snippet: Application of the real-time DOP-PCR to diverse DNA species. Amplification profiles and their standard curves were obtained from human placental DNA (HPD; A), calf thymus DNA (CTD; B), E. coli DNA (C), and lambda phage DNA (D). Standard DNA samples from 80 fg to 80 ng and a no-template control were amplified. Six independent experiments each comprising triplicate reactions were performed, and typical results of one experiment are presented. Data for 80 ng and NTC were omitted for the plotting of standard curves.

    Techniques Used: Degenerate Oligonucleotide–primed Polymerase Chain Reaction, Amplification

    4) Product Images from "Epigenetic Optical Mapping of 5-Hydroxymethylcytosine in Nanochannel Arrays"

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

    Journal: ACS Nano

    doi: 10.1021/acsnano.8b03023

    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).
    Figure Legend 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).

    Techniques Used: Labeling, Lambda DNA Preparation

    5) Product Images from "Development of single-cell array for large-scale DNA fluorescence in situ hybridization"

    Article Title: Development of single-cell array for large-scale DNA fluorescence in situ hybridization

    Journal:

    doi: 10.1039/c2lc40364a

    (a) Phase-contrast micrograph of 10-μm-wide circular PVA dots (black) printed on an APTES-coated glass slide. (b) Height atomic-force microscopy image of a PVA dot on APTES (upper panel) and its line profile (lower panel). Fluorescence micrograph of APTES islands stained with fluorescent rhodamine-B-isothiocyanate (RITC) (c) and YOYO-1–labelled lambda DNA (d).
    Figure Legend Snippet: (a) Phase-contrast micrograph of 10-μm-wide circular PVA dots (black) printed on an APTES-coated glass slide. (b) Height atomic-force microscopy image of a PVA dot on APTES (upper panel) and its line profile (lower panel). Fluorescence micrograph of APTES islands stained with fluorescent rhodamine-B-isothiocyanate (RITC) (c) and YOYO-1–labelled lambda DNA (d).

    Techniques Used: Microscopy, Fluorescence, Staining, Lambda DNA Preparation

    Related Articles

    Clone Assay:

    Article Title: Genomic and proteomic characterization of SuMu, a Mu-like bacteriophage infecting Haemophilus parasuis
    Article Snippet: Paragraph title: Cloning, DNA sequencing, and data analysis ... The size of the amplified DNA was compared to amplified Lambda kit control DNA, Lambda DNA (New England Biolabs (NEB), Ipswich, MA), and Hin d III-digested Lambda DNA (NEB).

    Centrifugation:

    Article Title: Genomic and proteomic characterization of SuMu, a Mu-like bacteriophage infecting Haemophilus parasuis
    Article Snippet: Fifty μl of dialyzed bacteriophage preparation obtained by centrifugation at 145,000 × g was treated with 0.5 units each of DNase and RNase for 30 min at 37°C, then 20 units of proteinase K (BRL) and 1% SDS for 1 h at 65°C. .. The size of the amplified DNA was compared to amplified Lambda kit control DNA, Lambda DNA (New England Biolabs (NEB), Ipswich, MA), and Hin d III-digested Lambda DNA (NEB).

    Amplification:

    Article Title: Genomic and proteomic characterization of SuMu, a Mu-like bacteriophage infecting Haemophilus parasuis
    Article Snippet: The amplified product was heat-inactivated and precipitated with ethanol containing 0.15 M sodium acetate, 25 mM EDTA, reconstituted in buffer EB (Qiagen, Valencia, CA), and separated by electrophoresis on a 0.6% gel at 100 V for 60 min. .. The size of the amplified DNA was compared to amplified Lambda kit control DNA, Lambda DNA (New England Biolabs (NEB), Ipswich, MA), and Hin d III-digested Lambda DNA (NEB). .. The amplified DNA was resolved by electrophoresis on a 0.8% agarose gel and DNA fragments between 2–23 kb were eluted from the gel using a Qiaquick kit (Qiagen).

    Synthesized:

    Article Title: RecA protein promotes the regression of stalled replication forks in vitro
    Article Snippet: Restriction enzymes, λ DNA- Bst EII digest marker, and T4 DNA ligase were purchased from New England Biolabs, Tris buffer from Fisher Scientific, and ATP, dATP, phosphocreatine, and creatine phosphokinase (lot no. 78H 7824) from Sigma. .. Restriction enzymes, λ DNA- Bst EII digest marker, and T4 DNA ligase were purchased from New England Biolabs, Tris buffer from Fisher Scientific, and ATP, dATP, phosphocreatine, and creatine phosphokinase (lot no. 78H 7824) from Sigma.

    Lambda DNA Preparation:

    Article Title: Genomic and proteomic characterization of SuMu, a Mu-like bacteriophage infecting Haemophilus parasuis
    Article Snippet: The amplified product was heat-inactivated and precipitated with ethanol containing 0.15 M sodium acetate, 25 mM EDTA, reconstituted in buffer EB (Qiagen, Valencia, CA), and separated by electrophoresis on a 0.6% gel at 100 V for 60 min. .. The size of the amplified DNA was compared to amplified Lambda kit control DNA, Lambda DNA (New England Biolabs (NEB), Ipswich, MA), and Hin d III-digested Lambda DNA (NEB). .. The amplified DNA was resolved by electrophoresis on a 0.8% agarose gel and DNA fragments between 2–23 kb were eluted from the gel using a Qiaquick kit (Qiagen).

    Article Title: SIRT6 exhibits nucleosome-dependent deacetylase activity
    Article Snippet: Pure chicken histone octamers (Abcam cat-ab45275) were subjected to the standard salt dialysis protocol, as described ( ). .. Briefly, 12 µg of pure chicken octamers and 15 µg of sonicated phage lambda DNA (NEB) were incubated for 30 min in a 2 M dialysis buffer (2 M NaCl, 20 mM Tris–HCl, pH = 7.2) in 700 µl of reaction volume. .. The mixture was dialyzed against descending concentrations of NaCl (1.2 M, 1 M, 0.8 M and 0.6 M) for 2 h each at 4 C. Finally, the complexes were dialyzed overnight in 10 mM Tris, pH = 7.2, without NaCl.

    Article Title: DNA Unwinding Heterogeneity by RecBCD Results from Static Molecules Able to Equilibrate
    Article Snippet: The two mutant enzymes, RecBCDK177Q (RecBCD* ) and RecBK29Q CD (RecB* CD), were purified as described . .. Bacteriophage λ DNA (N -methyladenine-free lambda DNA, New England Biolabs) was biotinylated by ligation to a 3’-biotinylated 12-mer oligonucleotide (cosA : 5’-GGGCGGCGACCT-3’ or cosB : 5’-AGGTCGCCGCCC-3’, Operon Technologies) that is complementary to one of the cohesive ends of λ DNA ; except for the thermal reannealing and control experiments, where cosA was used, all other experiments used the cosB oligonucleotide. .. The pUC19 plasmid DNA was purified by cesium chloride gradient centrifugation.

    Article Title: BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies
    Article Snippet: Oligonucleotides were purchased from Eurogentec S.A. (Brussels, Belgium). .. Taq polymerase was supplied from Promega, Terminal Transferase, BbvI and bacteriophage lambda DNA were from New England Biolabs. .. Microscope glass slides (76 × 26 × 1 mm3 , Knittel, Merck, ABS Postfach, Germany) were obtained from commercial sources.

    Article Title: Follicular Conjunctivitis due to Chlamydia felis—Case Report, Review of the Literature and Improved Molecular Diagnostics
    Article Snippet: DNA was prepared from 200 µl transport medium using the High Pure PCR Preparation Kit (Roche Diagnostics, Mannheim, Germany). .. Prior to DNA preparation, 150,000 copies of bacteriophage Lambda DNA (New England Biolabs, Frankfurt, Germany) were added to the sample for internal inhibition control. .. Real-time PCR for specific detection of C. trachomatis cryptic plasmid was performed as described by Jaton et al. ( ).

    End-sequence Profiling:

    Article Title: A Novel Nonnucleoside Inhibitor Specifically Targets Cytomegalovirus DNA Maturation via the UL89 and UL56 Gene Products
    Article Snippet: Blocks were incubated twice for 24 h at 50°C in 1 ml of ESP buffer (0.5 M EDTA [pH 9.5], 1% sodium lauryl sarcosine, 0.1% proteinase K), washed three times for 2 h in 15 ml of TE buffer (0.1 M Tris-Cl [pH 8], 1 mM EDTA), and stored at 4°C until use. .. Lambda phage DNA concatemers (New England Biolabs, Frankfurt am Main, Germany) were used as molecular size standards.

    Electrophoresis:

    Article Title: Comparison of Pulsed-Field Gel Electrophoresis and Coagulase Gene Restriction Profile Analysis Techniques in the Molecular Typing of Staphylococcus aureus
    Article Snippet: DNA fragments were separated in 0.9% agarose gels at 13°C with a Rotaphor type V apparatus (Biometra, Göttingen, Germany) in 0.5× TBE buffer (0.045 M Tris-borate, 0.1 mM EDTA [pH 8.3]). .. Electrophoresis was performed at a fixed voltage (190 V), at a 120° fixed angle, and with pulse time intervals from 8 to 14 s for 10 h and then from 19 to 28 s for 12 h. A ladder of bacteriophage λ DNA concatemers (New England BioLabs, Inc., Beverly, Mass.) was included to estimate the sizes of the DNA fragments. .. The PFGE pattern was interpreted in accordance with a previously published guideline ( ).

    Article Title: Genomic and proteomic characterization of SuMu, a Mu-like bacteriophage infecting Haemophilus parasuis
    Article Snippet: The amplified product was heat-inactivated and precipitated with ethanol containing 0.15 M sodium acetate, 25 mM EDTA, reconstituted in buffer EB (Qiagen, Valencia, CA), and separated by electrophoresis on a 0.6% gel at 100 V for 60 min. .. The size of the amplified DNA was compared to amplified Lambda kit control DNA, Lambda DNA (New England Biolabs (NEB), Ipswich, MA), and Hin d III-digested Lambda DNA (NEB).

    Article Title: DNA Unwinding Heterogeneity by RecBCD Results from Static Molecules Able to Equilibrate
    Article Snippet: After electrophoresis, the gel was imaged using an AlphaInotech gel documentation system. .. Bacteriophage λ DNA (N -methyladenine-free lambda DNA, New England Biolabs) was biotinylated by ligation to a 3’-biotinylated 12-mer oligonucleotide (cosA : 5’-GGGCGGCGACCT-3’ or cosB : 5’-AGGTCGCCGCCC-3’, Operon Technologies) that is complementary to one of the cohesive ends of λ DNA ; except for the thermal reannealing and control experiments, where cosA was used, all other experiments used the cosB oligonucleotide.

    Incubation:

    Article Title: A Novel Nonnucleoside Inhibitor Specifically Targets Cytomegalovirus DNA Maturation via the UL89 and UL56 Gene Products
    Article Snippet: Blocks were incubated twice for 24 h at 50°C in 1 ml of ESP buffer (0.5 M EDTA [pH 9.5], 1% sodium lauryl sarcosine, 0.1% proteinase K), washed three times for 2 h in 15 ml of TE buffer (0.1 M Tris-Cl [pH 8], 1 mM EDTA), and stored at 4°C until use. .. Lambda phage DNA concatemers (New England Biolabs, Frankfurt am Main, Germany) were used as molecular size standards.

    Article Title: SIRT6 exhibits nucleosome-dependent deacetylase activity
    Article Snippet: Pure chicken histone octamers (Abcam cat-ab45275) were subjected to the standard salt dialysis protocol, as described ( ). .. Briefly, 12 µg of pure chicken octamers and 15 µg of sonicated phage lambda DNA (NEB) were incubated for 30 min in a 2 M dialysis buffer (2 M NaCl, 20 mM Tris–HCl, pH = 7.2) in 700 µl of reaction volume. .. The mixture was dialyzed against descending concentrations of NaCl (1.2 M, 1 M, 0.8 M and 0.6 M) for 2 h each at 4 C. Finally, the complexes were dialyzed overnight in 10 mM Tris, pH = 7.2, without NaCl.

    Article Title: Optical mapping of the Mycobacterium avium subspecies paratuberculosis genome
    Article Snippet: The agarose inserts were melted by incubation at 65°C for 6 minutes and digested at 42°C for 2 hours in a β-agarase solution (2 units of β-agarase in 100 μl TE). .. Lambda phage DNA (NEB, Ipswich, MA) was added to the sample at 25 pg/μl to serve as an internal sizing standard.

    Bradford Assay:

    Article Title: RecA protein promotes the regression of stalled replication forks in vitro
    Article Snippet: The concentration of each protein was determined by absorbance at 280 nm by using their extinction coefficients: ɛ280 = 2.23 × 104 M−1 cm−1 for RecA , ɛ280 = 5.6 × 103 M−1 cm−1 for RecR , ɛ280 = 3.87 × 104 M−1 cm−1 for RecF , and ɛ280 = 2.83 × 104 M−1 cm−1 for SSB , with the exception of RecO protein, for which the concentration was measured by Bradford assay by using BSA as a standard. .. Restriction enzymes, λ DNA- Bst EII digest marker, and T4 DNA ligase were purchased from New England Biolabs, Tris buffer from Fisher Scientific, and ATP, dATP, phosphocreatine, and creatine phosphokinase (lot no. 78H 7824) from Sigma.

    Transformation Assay:

    Article Title: Genomic and proteomic characterization of SuMu, a Mu-like bacteriophage infecting Haemophilus parasuis
    Article Snippet: The size of the amplified DNA was compared to amplified Lambda kit control DNA, Lambda DNA (New England Biolabs (NEB), Ipswich, MA), and Hin d III-digested Lambda DNA (NEB). .. The amplified DNA was resolved by electrophoresis on a 0.8% agarose gel and DNA fragments between 2–23 kb were eluted from the gel using a Qiaquick kit (Qiagen).

    Inhibition:

    Article Title: Follicular Conjunctivitis due to Chlamydia felis—Case Report, Review of the Literature and Improved Molecular Diagnostics
    Article Snippet: DNA was prepared from 200 µl transport medium using the High Pure PCR Preparation Kit (Roche Diagnostics, Mannheim, Germany). .. Prior to DNA preparation, 150,000 copies of bacteriophage Lambda DNA (New England Biolabs, Frankfurt, Germany) were added to the sample for internal inhibition control. .. Real-time PCR for specific detection of C. trachomatis cryptic plasmid was performed as described by Jaton et al. ( ).

    Derivative Assay:

    Article Title: DNA Translocation through Hydrophilic Nanopore in Hexagonal Boron Nitride
    Article Snippet: A pair of Ag/AgCl electrodes supplied a bias voltage V to drive ions through the nanopore and the ionic current was monitored in real-time. is a cartoon picture of such device, and presents a typical I-V curve of a 4 nm nanopore in saline solution, through which a resistance of 45 MΩ is derived by a linear fit. .. When negative charged double-strand DNA molecules (λ-DNA from New England Biolabs) were added to one side of the chip, a series of spikes were observed in conductance traces , arisen from single DNA molecule translocation through the nanopore.

    Hybridization:

    Article Title: A Novel Nonnucleoside Inhibitor Specifically Targets Cytomegalovirus DNA Maturation via the UL89 and UL56 Gene Products
    Article Snippet: Lambda phage DNA concatemers (New England Biolabs, Frankfurt am Main, Germany) were used as molecular size standards. .. Electrophoretic separation was performed on a CHEF-DRII system (Bio-Rad, Munich, Germany) at a constant voltage of 200 V for 22 h at 14°C in 0.5× Tris-borate-EDTA buffer (pH 8.2) with pulse times increasing linearly from 5 to 70 s. Subsequently, DNA was immobilized on nylon membranes and probed with Hin dIII-digested genomic HCMV DNA entirely labeled with digoxigenin (DIG).

    Flow Cytometry:

    Article Title: DNA Translocation through Hydrophilic Nanopore in Hexagonal Boron Nitride
    Article Snippet: To conduct the DNA translocation experiments, the flow cell, PDMS gaskets and the fabricated h-BN nanopore chips were firstly treated with UVO on both the front and the back side for 15 minutes each and then assembled as fast as possible (typically within 2 minutes). .. When negative charged double-strand DNA molecules (λ-DNA from New England Biolabs) were added to one side of the chip, a series of spikes were observed in conductance traces , arisen from single DNA molecule translocation through the nanopore.

    Article Title: A Microneedle Functionalized with Polyethyleneimine and Nanotubes for Highly Sensitive, Label-Free Quantification of DNA
    Article Snippet: In order to check sensitivity of the functionalized microneedle, λ-DNA (48.5 kbp, 31.5 kDa, New England Biolabs, Ipswich, MA, USA) was used as a model analyte. .. For the concentration, an AC field (5 MHz, 20 Vpeak-to-peak ) was applied for 1 min while the functionalized microneedle was immersed in a 10 μL solution containing λ-DNA at different concentrations.

    Southern Blot:

    Article Title: A Novel Nonnucleoside Inhibitor Specifically Targets Cytomegalovirus DNA Maturation via the UL89 and UL56 Gene Products
    Article Snippet: Paragraph title: Pulsed-field gel electrophoresis and Southern blot analyses. ... Lambda phage DNA concatemers (New England Biolabs, Frankfurt am Main, Germany) were used as molecular size standards.

    Ligation:

    Article Title: Single-Molecule Methods for Nucleotide Excision Repair: Building a System to Watch Repair in Real Time
    Article Snippet: Heat block or thermocycler Standard agarose gel electrophoresis equipment .. 10× NEBuffer 2.1 (NEB) 50 m M EDTA Restriction enzyme ( Xho I, NEB) T4 DNA ligase (NEB) 2× Quick Ligation Reaction Buffer (NEB) Dry ice λ-DNA and λ-DNA Hin dIII digest fragments (NEB) .. Linearize ligated plasmids by incubating them with twice the number of units of Xho I (20 U/µL, NEB) as the amount of DNA in micrograms at 37°C for 2 h. Adjust the final concentration of NEBuffer 2.1 (NEB) to 1 × with 10 × stock if necessary.

    Article Title: DNA Unwinding Heterogeneity by RecBCD Results from Static Molecules Able to Equilibrate
    Article Snippet: The two mutant enzymes, RecBCDK177Q (RecBCD* ) and RecBK29Q CD (RecB* CD), were purified as described . .. Bacteriophage λ DNA (N -methyladenine-free lambda DNA, New England Biolabs) was biotinylated by ligation to a 3’-biotinylated 12-mer oligonucleotide (cosA : 5’-GGGCGGCGACCT-3’ or cosB : 5’-AGGTCGCCGCCC-3’, Operon Technologies) that is complementary to one of the cohesive ends of λ DNA ; except for the thermal reannealing and control experiments, where cosA was used, all other experiments used the cosB oligonucleotide. .. The pUC19 plasmid DNA was purified by cesium chloride gradient centrifugation.

    Article Title: TRF1 and TRF2 use different mechanisms to find telomeric DNA but share a novel mechanism to search for protein partners at telomeres
    Article Snippet: λ DNA was purchased from New England BioLabs. .. For Tel10 plasmid, digestions were carried out using XbaI (100 U) in Buffer 4.

    Transferring:

    Article Title: Self-associating block copolymer networks for microchip electrophoresis provide enhanced DNA separation via "inchworm" chain dynamics
    Article Snippet: For single-molecule videomicroscopy studies, linearized λ-phage DNA (48.5 kbp, N3011S, New England Biolabs, Ipswich, MA) was fluorescently stained with YOYO-1 (Molecular Probes / Invitrogen, San Diego CA) replacing TOTO. .. For single-molecule videomicroscopy studies, linearized λ-phage DNA (48.5 kbp, N3011S, New England Biolabs, Ipswich, MA) was fluorescently stained with YOYO-1 (Molecular Probes / Invitrogen, San Diego CA) replacing TOTO.

    Article Title: Kinetics and thermodynamics of salt-dependent T7 gene 2.5 protein binding to single- and double-stranded DNA
    Article Snippet: Captured Phage-λ DNA molecules, ∼48 500 base pairs (New England Biolabs, Ipswich, MA), were biotin-labeled on each 3′ terminus and were repurified by extraction with phenol and chloroform and ethanol precipitation. .. Captured Phage-λ DNA molecules, ∼48 500 base pairs (New England Biolabs, Ipswich, MA), were biotin-labeled on each 3′ terminus and were repurified by extraction with phenol and chloroform and ethanol precipitation.

    Article Title: A Microneedle Functionalized with Polyethyleneimine and Nanotubes for Highly Sensitive, Label-Free Quantification of DNA
    Article Snippet: In order to check sensitivity of the functionalized microneedle, λ-DNA (48.5 kbp, 31.5 kDa, New England Biolabs, Ipswich, MA, USA) was used as a model analyte. .. In order to check sensitivity of the functionalized microneedle, λ-DNA (48.5 kbp, 31.5 kDa, New England Biolabs, Ipswich, MA, USA) was used as a model analyte.

    Infection:

    Article Title: A Novel Nonnucleoside Inhibitor Specifically Targets Cytomegalovirus DNA Maturation via the UL89 and UL56 Gene Products
    Article Snippet: HELF were infected with HCMV AD169 at an MOI of 1 and cultivated in the presence of either BAY 38-4766 at 0.5, 1, 5, or 25 μM or BDCRB at 25 μM. .. Lambda phage DNA concatemers (New England Biolabs, Frankfurt am Main, Germany) were used as molecular size standards.

    Translocation Assay:

    Article Title: DNA Translocation through Hydrophilic Nanopore in Hexagonal Boron Nitride
    Article Snippet: A pair of Ag/AgCl electrodes supplied a bias voltage V to drive ions through the nanopore and the ionic current was monitored in real-time. is a cartoon picture of such device, and presents a typical I-V curve of a 4 nm nanopore in saline solution, through which a resistance of 45 MΩ is derived by a linear fit. .. When negative charged double-strand DNA molecules (λ-DNA from New England Biolabs) were added to one side of the chip, a series of spikes were observed in conductance traces , arisen from single DNA molecule translocation through the nanopore. .. The driving voltage is 100–250 mV and a 30 kHz 4-pole Bessel filter was employed during data acquisition and the sampling rate was 250 kHz.

    other:

    Article Title: Quantification of Trace-Level DNA by Real-Time Whole Genome Amplification
    Article Snippet: Concentrations of CTD, E. coli DNA, and lambda phage DNA were determined by measuring UV absorbance at 260 nm.

    Imaging:

    Article Title: Self-associating block copolymer networks for microchip electrophoresis provide enhanced DNA separation via "inchworm" chain dynamics
    Article Snippet: For single-molecule videomicroscopy studies, linearized λ-phage DNA (48.5 kbp, N3011S, New England Biolabs, Ipswich, MA) was fluorescently stained with YOYO-1 (Molecular Probes / Invitrogen, San Diego CA) replacing TOTO. .. Pipette tips were cut wider with a razor blade to avoid shearing and breaking the DNA.

    Article Title: TRF1 and TRF2 use different mechanisms to find telomeric DNA but share a novel mechanism to search for protein partners at telomeres
    Article Snippet: λ DNA was purchased from New England BioLabs. .. Other DNA substrates used in this study are shown in B and Supplementary Figure S1 . pSXneo(T2AG3) plasmid DNA containing 270 TTAGGG repeats was a gift from Dr Peter Lansdorp (University of British Columbia) ( ). pGTK4 plasmid-derived Tel10 plasmid is 5994-bp long and contains 10 TTAGGG repeats and was prepared as described previously ( ).

    Article Title: Cisplatin induces loop structures and condensation of single DNA molecules
    Article Snippet: Cisplatin was purchased from Sigma-Aldrich (USA), Pt(dach)Cl2 was obtained from the Institute of Precious Metal in Kunming of China. λ DNA for magnetic tweezers experiment was from New England Biolabs. .. Cisplatin was purchased from Sigma-Aldrich (USA), Pt(dach)Cl2 was obtained from the Institute of Precious Metal in Kunming of China. λ DNA for magnetic tweezers experiment was from New England Biolabs.

    Droplet Countercurrent Chromatography:

    Article Title: BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies
    Article Snippet: 1-4-dithio-DL-threitol (DTT), N -hydroxysuccinimide (NHS), N ,N ′-dicyclohexylcarbodiimide (DCC), 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC), 1-methyl-imidazole, BTA and 4-fluoro-7-nitrobenzofurazan (NBD-F) were purchased from Fluka. m -Maleimidobenzoyl-N -hydroxysulfosuccinimide ester (sulfo-MBS) was purchased from Pierce. .. Taq polymerase was supplied from Promega, Terminal Transferase, BbvI and bacteriophage lambda DNA were from New England Biolabs.

    Sequencing:

    Article Title: Genomic and proteomic characterization of SuMu, a Mu-like bacteriophage infecting Haemophilus parasuis
    Article Snippet: The size of the amplified DNA was compared to amplified Lambda kit control DNA, Lambda DNA (New England Biolabs (NEB), Ipswich, MA), and Hin d III-digested Lambda DNA (NEB). .. The size of the amplified DNA was compared to amplified Lambda kit control DNA, Lambda DNA (New England Biolabs (NEB), Ipswich, MA), and Hin d III-digested Lambda DNA (NEB).

    Sonication:

    Article Title: SIRT6 exhibits nucleosome-dependent deacetylase activity
    Article Snippet: Pure chicken histone octamers (Abcam cat-ab45275) were subjected to the standard salt dialysis protocol, as described ( ). .. Briefly, 12 µg of pure chicken octamers and 15 µg of sonicated phage lambda DNA (NEB) were incubated for 30 min in a 2 M dialysis buffer (2 M NaCl, 20 mM Tris–HCl, pH = 7.2) in 700 µl of reaction volume. .. The mixture was dialyzed against descending concentrations of NaCl (1.2 M, 1 M, 0.8 M and 0.6 M) for 2 h each at 4 C. Finally, the complexes were dialyzed overnight in 10 mM Tris, pH = 7.2, without NaCl.

    Pulsed-Field Gel:

    Article Title: A Novel Nonnucleoside Inhibitor Specifically Targets Cytomegalovirus DNA Maturation via the UL89 and UL56 Gene Products
    Article Snippet: Paragraph title: Pulsed-field gel electrophoresis and Southern blot analyses. ... Lambda phage DNA concatemers (New England Biolabs, Frankfurt am Main, Germany) were used as molecular size standards.

    DNA Sequencing:

    Article Title: Genomic and proteomic characterization of SuMu, a Mu-like bacteriophage infecting Haemophilus parasuis
    Article Snippet: Paragraph title: Cloning, DNA sequencing, and data analysis ... The size of the amplified DNA was compared to amplified Lambda kit control DNA, Lambda DNA (New England Biolabs (NEB), Ipswich, MA), and Hin d III-digested Lambda DNA (NEB).

    Fluorescence:

    Article Title: Real-time single-molecule imaging reveals a direct interaction between UvrC and UvrB on DNA tightropes
    Article Snippet: Approximately 10% of complexes showed dual color labeling ( Supplementary Figure S2 ); thus, although we cannot rule out that Qdot conjugation interferes with oligomerization, the majority of the complexes consisted of singly labeled presumably monomeric UvrC. .. All single-molecule fluorescence experiments used undamaged bacteriophage λ-DNA (New England Bio Labs). .. For atomic force microscopy (AFM) imaging, a 458-bp linear DNA substrate was made by TaqI digestion of pUC18 followed by separation over a 1% agarose gel and purification using the Illustra GFX™ PCR DNA and Gel Band Purification Kit (GE Healthcare).

    Article Title: TRF1 and TRF2 use different mechanisms to find telomeric DNA but share a novel mechanism to search for protein partners at telomeres
    Article Snippet: λ DNA was purchased from New England BioLabs. .. For Tel10 plasmid, digestions were carried out using XbaI (100 U) in Buffer 4.

    Methylation:

    Article Title: CD45RA Distinguishes CD4+CD25+CD127−/low TSDR Demethylated Regulatory T Cell Subpopulations With Differential Stability and Susceptibility to Tacrolimus-Mediated Inhibition of Suppression
    Article Snippet: A minimum of 60-ng bisulfite-treated (EpiTect; Qiagen) genomic DNA was used in a real-time polymerase chain reaction (PCR) to quantify the Foxp3 TSDR. .. Real-time PCR was performed in a final reaction volume of 20 μL containing 10-μL FastStart universal probe master (Roche Diagnostics, Mannheim, Germany), 50-ng/μL lamda DNA (New England Biolabs, Frankfurt, Germany), 5-pmol/μL methylation or nonmethylation-specific probe, 30-pmol/μL methylation or nonmethylation-specific primers, and 60-ng bisulfite-treated DNA or a respective amount of plasmid standard. .. The samples were analyzed in triplicates on an ABI 7500 cycler and reported as % T cells with demethylated TSDR region.

    Mutagenesis:

    Article Title: DNA Unwinding Heterogeneity by RecBCD Results from Static Molecules Able to Equilibrate
    Article Snippet: The two mutant enzymes, RecBCDK177Q (RecBCD* ) and RecBK29Q CD (RecB* CD), were purified as described . .. Bacteriophage λ DNA (N -methyladenine-free lambda DNA, New England Biolabs) was biotinylated by ligation to a 3’-biotinylated 12-mer oligonucleotide (cosA : 5’-GGGCGGCGACCT-3’ or cosB : 5’-AGGTCGCCGCCC-3’, Operon Technologies) that is complementary to one of the cohesive ends of λ DNA ; except for the thermal reannealing and control experiments, where cosA was used, all other experiments used the cosB oligonucleotide.

    Isolation:

    Article Title: Genomic and proteomic characterization of SuMu, a Mu-like bacteriophage infecting Haemophilus parasuis
    Article Snippet: The size of the amplified DNA was compared to amplified Lambda kit control DNA, Lambda DNA (New England Biolabs (NEB), Ipswich, MA), and Hin d III-digested Lambda DNA (NEB). .. The gel-extracted bacteriophage fragments were cloned into pCR2.1 TOPO XL (Invitrogen) and transformed into chemically competent E. coli bacteriophage-resistant cells (One Shot Mach1-T1R ) (Invitrogen) using manufacture-recommended conditions (Invitrogen).

    Article Title: CD45RA Distinguishes CD4+CD25+CD127−/low TSDR Demethylated Regulatory T Cell Subpopulations With Differential Stability and Susceptibility to Tacrolimus-Mediated Inhibition of Suppression
    Article Snippet: Regulatory T cell–specific demethylation region DNA methylation analysis was performed as previously described using genomic DNA isolated from freshly sorted or expanded Treg cells using the QIAamp DNA Mini Kit (QIAGEN, Hilden, Germany). .. Real-time PCR was performed in a final reaction volume of 20 μL containing 10-μL FastStart universal probe master (Roche Diagnostics, Mannheim, Germany), 50-ng/μL lamda DNA (New England Biolabs, Frankfurt, Germany), 5-pmol/μL methylation or nonmethylation-specific probe, 30-pmol/μL methylation or nonmethylation-specific primers, and 60-ng bisulfite-treated DNA or a respective amount of plasmid standard.

    Article Title: Follicular Conjunctivitis due to Chlamydia felis—Case Report, Review of the Literature and Improved Molecular Diagnostics
    Article Snippet: Paragraph title: Isolation of DNA ... Prior to DNA preparation, 150,000 copies of bacteriophage Lambda DNA (New England Biolabs, Frankfurt, Germany) were added to the sample for internal inhibition control.

    Microscopy:

    Article Title: Self-associating block copolymer networks for microchip electrophoresis provide enhanced DNA separation via "inchworm" chain dynamics
    Article Snippet: 1.4, 0.133 mm working distance apochromatic oil-immersion microscope objective. .. For single-molecule videomicroscopy studies, linearized λ-phage DNA (48.5 kbp, N3011S, New England Biolabs, Ipswich, MA) was fluorescently stained with YOYO-1 (Molecular Probes / Invitrogen, San Diego CA) replacing TOTO.

    Article Title: Kinetics and thermodynamics of salt-dependent T7 gene 2.5 protein binding to single- and double-stranded DNA
    Article Snippet: Briefly, an optical trap is formed by focusing two counter-propagating diode lasers, each with ∼200 mW of near-infrared laser power (JDS Uniphase, San Jose, CA) to a diameter of ∼1 μm using 60×, 1.0 numerical aperture water immersion microscope objectives (Nikon, Tokyo, Japan). .. Captured Phage-λ DNA molecules, ∼48 500 base pairs (New England Biolabs, Ipswich, MA), were biotin-labeled on each 3′ terminus and were repurified by extraction with phenol and chloroform and ethanol precipitation.

    Purification:

    Article Title: RecA protein promotes the regression of stalled replication forks in vitro
    Article Snippet: E. coli RecA , RecO , RecR , RecF , and single-strand DNA-binding protein ( ) proteins were purified as described. .. Restriction enzymes, λ DNA- Bst EII digest marker, and T4 DNA ligase were purchased from New England Biolabs, Tris buffer from Fisher Scientific, and ATP, dATP, phosphocreatine, and creatine phosphokinase (lot no. 78H 7824) from Sigma.

    Article Title: DNA Unwinding Heterogeneity by RecBCD Results from Static Molecules Able to Equilibrate
    Article Snippet: The two mutant enzymes, RecBCDK177Q (RecBCD* ) and RecBK29Q CD (RecB* CD), were purified as described . .. Bacteriophage λ DNA (N -methyladenine-free lambda DNA, New England Biolabs) was biotinylated by ligation to a 3’-biotinylated 12-mer oligonucleotide (cosA : 5’-GGGCGGCGACCT-3’ or cosB : 5’-AGGTCGCCGCCC-3’, Operon Technologies) that is complementary to one of the cohesive ends of λ DNA ; except for the thermal reannealing and control experiments, where cosA was used, all other experiments used the cosB oligonucleotide.

    Polymerase Chain Reaction:

    Article Title: CD45RA Distinguishes CD4+CD25+CD127−/low TSDR Demethylated Regulatory T Cell Subpopulations With Differential Stability and Susceptibility to Tacrolimus-Mediated Inhibition of Suppression
    Article Snippet: A minimum of 60-ng bisulfite-treated (EpiTect; Qiagen) genomic DNA was used in a real-time polymerase chain reaction (PCR) to quantify the Foxp3 TSDR. .. Real-time PCR was performed in a final reaction volume of 20 μL containing 10-μL FastStart universal probe master (Roche Diagnostics, Mannheim, Germany), 50-ng/μL lamda DNA (New England Biolabs, Frankfurt, Germany), 5-pmol/μL methylation or nonmethylation-specific probe, 30-pmol/μL methylation or nonmethylation-specific primers, and 60-ng bisulfite-treated DNA or a respective amount of plasmid standard.

    Article Title: Follicular Conjunctivitis due to Chlamydia felis—Case Report, Review of the Literature and Improved Molecular Diagnostics
    Article Snippet: DNA was prepared from 200 µl transport medium using the High Pure PCR Preparation Kit (Roche Diagnostics, Mannheim, Germany). .. Prior to DNA preparation, 150,000 copies of bacteriophage Lambda DNA (New England Biolabs, Frankfurt, Germany) were added to the sample for internal inhibition control.

    Labeling:

    Article Title: BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies
    Article Snippet: Cyanine Cy 5.0 labeled aminopropargyl dideoxynucleotides (ddNTP-Cy 5.0) were prepared according to reported methods ( ). .. Taq polymerase was supplied from Promega, Terminal Transferase, BbvI and bacteriophage lambda DNA were from New England Biolabs.

    Staining:

    Article Title: Self-associating block copolymer networks for microchip electrophoresis provide enhanced DNA separation via "inchworm" chain dynamics
    Article Snippet: Videos were adjusted for brightness and contrast using Adobe Premier 6.5™ and individual frames were exported to Adobe Photoshop 7.0™ for background subtraction and image smoothing. .. For single-molecule videomicroscopy studies, linearized λ-phage DNA (48.5 kbp, N3011S, New England Biolabs, Ipswich, MA) was fluorescently stained with YOYO-1 (Molecular Probes / Invitrogen, San Diego CA) replacing TOTO. .. Catalase, Glucose Oxidase (Fisher Scientific, Pittsburgh, PA) and β-mercaptoethanol (Sigma-Aldrich, St. Louis, MO) are added into the solution to reduce the amount of detrimental oxygen and free-radical interactions with DNA when exposed to air and light.

    Article Title: DNA Unwinding Heterogeneity by RecBCD Results from Static Molecules Able to Equilibrate
    Article Snippet: To check purity, protein was analyzed using a 12% denaturing polyacrylamide gel (1:29 bis:acrylamide in TBE buffer (89 mM Tris base, 2 mM EDTA, 89 mM boric acid), containing 10% SDS) stained with Coomassie blue dye. .. Bacteriophage λ DNA (N -methyladenine-free lambda DNA, New England Biolabs) was biotinylated by ligation to a 3’-biotinylated 12-mer oligonucleotide (cosA : 5’-GGGCGGCGACCT-3’ or cosB : 5’-AGGTCGCCGCCC-3’, Operon Technologies) that is complementary to one of the cohesive ends of λ DNA ; except for the thermal reannealing and control experiments, where cosA was used, all other experiments used the cosB oligonucleotide.

    Article Title: Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome
    Article Snippet: The gel was then stained with ethidium bromide and photographed with a Gel Doc apparatus (Bio-Rad, Hercules, California). .. The size of the insert in each BAC clone was determined by comparison with PFGE size standard markers (Lambda Ladder PFG Markers New England Biolabs, Ipswich, MA, USA).

    Chloramphenicol Acetyltransferase Assay:

    Article Title: SIRT6 exhibits nucleosome-dependent deacetylase activity
    Article Snippet: Pure chicken histone octamers (Abcam cat-ab45275) were subjected to the standard salt dialysis protocol, as described ( ). .. Briefly, 12 µg of pure chicken octamers and 15 µg of sonicated phage lambda DNA (NEB) were incubated for 30 min in a 2 M dialysis buffer (2 M NaCl, 20 mM Tris–HCl, pH = 7.2) in 700 µl of reaction volume.

    Chromatin Immunoprecipitation:

    Article Title: DNA Translocation through Hydrophilic Nanopore in Hexagonal Boron Nitride
    Article Snippet: A pair of Ag/AgCl electrodes supplied a bias voltage V to drive ions through the nanopore and the ionic current was monitored in real-time. is a cartoon picture of such device, and presents a typical I-V curve of a 4 nm nanopore in saline solution, through which a resistance of 45 MΩ is derived by a linear fit. .. When negative charged double-strand DNA molecules (λ-DNA from New England Biolabs) were added to one side of the chip, a series of spikes were observed in conductance traces , arisen from single DNA molecule translocation through the nanopore. .. The driving voltage is 100–250 mV and a 30 kHz 4-pole Bessel filter was employed during data acquisition and the sampling rate was 250 kHz.

    SDS Page:

    Article Title: SIRT6 exhibits nucleosome-dependent deacetylase activity
    Article Snippet: Briefly, 12 µg of pure chicken octamers and 15 µg of sonicated phage lambda DNA (NEB) were incubated for 30 min in a 2 M dialysis buffer (2 M NaCl, 20 mM Tris–HCl, pH = 7.2) in 700 µl of reaction volume. .. Briefly, 12 µg of pure chicken octamers and 15 µg of sonicated phage lambda DNA (NEB) were incubated for 30 min in a 2 M dialysis buffer (2 M NaCl, 20 mM Tris–HCl, pH = 7.2) in 700 µl of reaction volume.

    Plasmid Preparation:

    Article Title: Genomic and proteomic characterization of SuMu, a Mu-like bacteriophage infecting Haemophilus parasuis
    Article Snippet: The size of the amplified DNA was compared to amplified Lambda kit control DNA, Lambda DNA (New England Biolabs (NEB), Ipswich, MA), and Hin d III-digested Lambda DNA (NEB). .. The gel-extracted bacteriophage fragments were cloned into pCR2.1 TOPO XL (Invitrogen) and transformed into chemically competent E. coli bacteriophage-resistant cells (One Shot Mach1-T1R ) (Invitrogen) using manufacture-recommended conditions (Invitrogen).

    Article Title: TRF1 and TRF2 use different mechanisms to find telomeric DNA but share a novel mechanism to search for protein partners at telomeres
    Article Snippet: λ DNA was purchased from New England BioLabs. .. λ DNA was purchased from New England BioLabs.

    Article Title: CD45RA Distinguishes CD4+CD25+CD127−/low TSDR Demethylated Regulatory T Cell Subpopulations With Differential Stability and Susceptibility to Tacrolimus-Mediated Inhibition of Suppression
    Article Snippet: A minimum of 60-ng bisulfite-treated (EpiTect; Qiagen) genomic DNA was used in a real-time polymerase chain reaction (PCR) to quantify the Foxp3 TSDR. .. Real-time PCR was performed in a final reaction volume of 20 μL containing 10-μL FastStart universal probe master (Roche Diagnostics, Mannheim, Germany), 50-ng/μL lamda DNA (New England Biolabs, Frankfurt, Germany), 5-pmol/μL methylation or nonmethylation-specific probe, 30-pmol/μL methylation or nonmethylation-specific primers, and 60-ng bisulfite-treated DNA or a respective amount of plasmid standard. .. The samples were analyzed in triplicates on an ABI 7500 cycler and reported as % T cells with demethylated TSDR region.

    Software:

    Article Title: Self-associating block copolymer networks for microchip electrophoresis provide enhanced DNA separation via "inchworm" chain dynamics
    Article Snippet: Videos and images are directly captured onto a computer (Dell, 3 GHz processor, 1 Gigabyte of memory) via camera link technology to a PIXCI control board (EPIX INC., Buffalo Grove, IL) and the capture is controlled through XCAP-STD (EPIX INC, Buffalo Grove, IL) software. .. For single-molecule videomicroscopy studies, linearized λ-phage DNA (48.5 kbp, N3011S, New England Biolabs, Ipswich, MA) was fluorescently stained with YOYO-1 (Molecular Probes / Invitrogen, San Diego CA) replacing TOTO.

    Real-time Polymerase Chain Reaction:

    Article Title: CD45RA Distinguishes CD4+CD25+CD127−/low TSDR Demethylated Regulatory T Cell Subpopulations With Differential Stability and Susceptibility to Tacrolimus-Mediated Inhibition of Suppression
    Article Snippet: A minimum of 60-ng bisulfite-treated (EpiTect; Qiagen) genomic DNA was used in a real-time polymerase chain reaction (PCR) to quantify the Foxp3 TSDR. .. Real-time PCR was performed in a final reaction volume of 20 μL containing 10-μL FastStart universal probe master (Roche Diagnostics, Mannheim, Germany), 50-ng/μL lamda DNA (New England Biolabs, Frankfurt, Germany), 5-pmol/μL methylation or nonmethylation-specific probe, 30-pmol/μL methylation or nonmethylation-specific primers, and 60-ng bisulfite-treated DNA or a respective amount of plasmid standard. .. The samples were analyzed in triplicates on an ABI 7500 cycler and reported as % T cells with demethylated TSDR region.

    Agarose Gel Electrophoresis:

    Article Title: A Novel Nonnucleoside Inhibitor Specifically Targets Cytomegalovirus DNA Maturation via the UL89 and UL56 Gene Products
    Article Snippet: Lambda phage DNA concatemers (New England Biolabs, Frankfurt am Main, Germany) were used as molecular size standards. .. Lambda phage DNA concatemers (New England Biolabs, Frankfurt am Main, Germany) were used as molecular size standards.

    Article Title: Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome
    Article Snippet: Digested BAC DNA was fractionated by PFGE (CHEF-DRIII, Biorad, USA) in a 0.5% agarose gel in 0.5 × TBE buffer (0.09 M Tris-borate, 0.09 M boric acid, 0.002 M EDTA), with a 1-40 s linear ramp, 6 V/cm, 14°C and a 13 h run time. .. The size of the insert in each BAC clone was determined by comparison with PFGE size standard markers (Lambda Ladder PFG Markers New England Biolabs, Ipswich, MA, USA).

    Ethanol Precipitation:

    Article Title: Kinetics and thermodynamics of salt-dependent T7 gene 2.5 protein binding to single- and double-stranded DNA
    Article Snippet: Two 5-μm streptavidin-coated polystyrene beads (Bangs Laboratories, Fishers, IN) were trapped in the optical tweezers and on the end of a glass micropipette (World Precision Instrument, Sarasota, FL). .. Captured Phage-λ DNA molecules, ∼48 500 base pairs (New England Biolabs, Ipswich, MA), were biotin-labeled on each 3′ terminus and were repurified by extraction with phenol and chloroform and ethanol precipitation. .. The glass micropipette mounted on a feedback-compensated piezoelectric stage (Melles Griot, Carlsbad, CA) was moved causing the single DNA molecule captured between two beads to be stretched, resulting in a force-extension measurement, as described previously ( ).

    DNA Methylation Assay:

    Article Title: CD45RA Distinguishes CD4+CD25+CD127−/low TSDR Demethylated Regulatory T Cell Subpopulations With Differential Stability and Susceptibility to Tacrolimus-Mediated Inhibition of Suppression
    Article Snippet: Paragraph title: TSDR DNA Methylation Analysis ... Real-time PCR was performed in a final reaction volume of 20 μL containing 10-μL FastStart universal probe master (Roche Diagnostics, Mannheim, Germany), 50-ng/μL lamda DNA (New England Biolabs, Frankfurt, Germany), 5-pmol/μL methylation or nonmethylation-specific probe, 30-pmol/μL methylation or nonmethylation-specific primers, and 60-ng bisulfite-treated DNA or a respective amount of plasmid standard.

    Concentration Assay:

    Article Title: RecA protein promotes the regression of stalled replication forks in vitro
    Article Snippet: The concentration of each protein was determined by absorbance at 280 nm by using their extinction coefficients: ɛ280 = 2.23 × 104 M−1 cm−1 for RecA , ɛ280 = 5.6 × 103 M−1 cm−1 for RecR , ɛ280 = 3.87 × 104 M−1 cm−1 for RecF , and ɛ280 = 2.83 × 104 M−1 cm−1 for SSB , with the exception of RecO protein, for which the concentration was measured by Bradford assay by using BSA as a standard. .. Restriction enzymes, λ DNA- Bst EII digest marker, and T4 DNA ligase were purchased from New England Biolabs, Tris buffer from Fisher Scientific, and ATP, dATP, phosphocreatine, and creatine phosphokinase (lot no. 78H 7824) from Sigma.

    Article Title: DNA Unwinding Heterogeneity by RecBCD Results from Static Molecules Able to Equilibrate
    Article Snippet: Bacteriophage λ DNA (N -methyladenine-free lambda DNA, New England Biolabs) was biotinylated by ligation to a 3’-biotinylated 12-mer oligonucleotide (cosA : 5’-GGGCGGCGACCT-3’ or cosB : 5’-AGGTCGCCGCCC-3’, Operon Technologies) that is complementary to one of the cohesive ends of λ DNA ; except for the thermal reannealing and control experiments, where cosA was used, all other experiments used the cosB oligonucleotide. .. Bacteriophage λ DNA (N -methyladenine-free lambda DNA, New England Biolabs) was biotinylated by ligation to a 3’-biotinylated 12-mer oligonucleotide (cosA : 5’-GGGCGGCGACCT-3’ or cosB : 5’-AGGTCGCCGCCC-3’, Operon Technologies) that is complementary to one of the cohesive ends of λ DNA ; except for the thermal reannealing and control experiments, where cosA was used, all other experiments used the cosB oligonucleotide.

    Article Title: A Microneedle Functionalized with Polyethyleneimine and Nanotubes for Highly Sensitive, Label-Free Quantification of DNA
    Article Snippet: In order to check sensitivity of the functionalized microneedle, λ-DNA (48.5 kbp, 31.5 kDa, New England Biolabs, Ipswich, MA, USA) was used as a model analyte. .. In order to check sensitivity of the functionalized microneedle, λ-DNA (48.5 kbp, 31.5 kDa, New England Biolabs, Ipswich, MA, USA) was used as a model analyte.

    Alkaline Lysis:

    Article Title: Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome
    Article Snippet: BAC DNA was prepared by a standard alkaline lysis method [ ], from 3 ml of overnight culture in 2YT supplemented with 12.5 μg/ml chloramphenicol. .. The size of the insert in each BAC clone was determined by comparison with PFGE size standard markers (Lambda Ladder PFG Markers New England Biolabs, Ipswich, MA, USA).

    BAC Assay:

    Article Title: Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome
    Article Snippet: The gel was then stained with ethidium bromide and photographed with a Gel Doc apparatus (Bio-Rad, Hercules, California). .. The size of the insert in each BAC clone was determined by comparison with PFGE size standard markers (Lambda Ladder PFG Markers New England Biolabs, Ipswich, MA, USA). .. Universal chloroplast primers CCMP2 (F-GATCCCGGACGTAATCCTG/R-ATGGTACCGAGGGTTCGAAT) and udt 5 (F-TAAATCTGGAAATCTGGGAA/R-TTGATACATAGACTTGCCAA) were used to estimate the level of chloroplast contamination, in individual tests of 984 BAC clones [ , ].

    Marker:

    Article Title: RecA protein promotes the regression of stalled replication forks in vitro
    Article Snippet: The concentration of each protein was determined by absorbance at 280 nm by using their extinction coefficients: ɛ280 = 2.23 × 104 M−1 cm−1 for RecA , ɛ280 = 5.6 × 103 M−1 cm−1 for RecR , ɛ280 = 3.87 × 104 M−1 cm−1 for RecF , and ɛ280 = 2.83 × 104 M−1 cm−1 for SSB , with the exception of RecO protein, for which the concentration was measured by Bradford assay by using BSA as a standard. .. Restriction enzymes, λ DNA- Bst EII digest marker, and T4 DNA ligase were purchased from New England Biolabs, Tris buffer from Fisher Scientific, and ATP, dATP, phosphocreatine, and creatine phosphokinase (lot no. 78H 7824) from Sigma. .. ATPγS was purchased from Boehringer Mannheim, SeaPlaque GTG low-melting agarose from FMC, Sephacryl 300 resin from Amersham Pharmacia, and hydroxylapatite DNA grade Bio-Gel HTP from Bio-Rad.

    Lysis:

    Article Title: Optical mapping of the Mycobacterium avium subspecies paratuberculosis genome
    Article Snippet: The buffer was replaced with 5 ml secondary bacterial lysis buffer (0.25 mM EDTA, 1% N-lauroyl sarcosine and 1 mg/ml proteinase K) at 55°C for 48 hrs with a change of buffer after 24 hrs of incubation. .. Lambda phage DNA (NEB, Ipswich, MA) was added to the sample at 25 pg/μl to serve as an internal sizing standard.

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    New England Biolabs bacteriophage lambda dna
    Sustaining times of non-frozen <t>lambda</t> <t>DNA</t> samples under 25 and 35 pN tension. The x -axis represents the DNA sustaining time (min), and the y -axis represents the percentage of all DNA molecules tested in TE buffer with 4.6% Tween 80. Blue histograms denote samples from batch 1, and red histograms denote samples from batch 2 in a and b . a Of 100 molecules tested from batch 1 at a tensile force of 24.6 ± 1.9 pN, 6% lasted over 60 min. Of 45 molecules tested from batch 2 at a tensile force of 24.9 ± 1.0 pN, 9% lasted over 60 min. b Of 100 molecules tested from batch 1 at a tensile force of 34.9 ± 1.8 pN, only one lasted over 60 min. All 25 molecules tested from batch 2 at a tensile force of 34.7 ± 1.7 pN were broken within 60 min. c Differences in the percentages of broken DNA between the two batches of non-frozen DNA samples at a tensile force of 25 pN. d Differences in the percentages of broken DNA between the two batches of non-frozen DNA at a tensile force of 35 pN
    Bacteriophage Lambda Dna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 19 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Sustaining times of non-frozen lambda DNA samples under 25 and 35 pN tension. The x -axis represents the DNA sustaining time (min), and the y -axis represents the percentage of all DNA molecules tested in TE buffer with 4.6% Tween 80. Blue histograms denote samples from batch 1, and red histograms denote samples from batch 2 in a and b . a Of 100 molecules tested from batch 1 at a tensile force of 24.6 ± 1.9 pN, 6% lasted over 60 min. Of 45 molecules tested from batch 2 at a tensile force of 24.9 ± 1.0 pN, 9% lasted over 60 min. b Of 100 molecules tested from batch 1 at a tensile force of 34.9 ± 1.8 pN, only one lasted over 60 min. All 25 molecules tested from batch 2 at a tensile force of 34.7 ± 1.7 pN were broken within 60 min. c Differences in the percentages of broken DNA between the two batches of non-frozen DNA samples at a tensile force of 25 pN. d Differences in the percentages of broken DNA between the two batches of non-frozen DNA at a tensile force of 35 pN

    Journal: Journal of Biological Physics

    Article Title: Freezing shortens the lifetime of DNA molecules under tension

    doi: 10.1007/s10867-017-9466-3

    Figure Lengend Snippet: Sustaining times of non-frozen lambda DNA samples under 25 and 35 pN tension. The x -axis represents the DNA sustaining time (min), and the y -axis represents the percentage of all DNA molecules tested in TE buffer with 4.6% Tween 80. Blue histograms denote samples from batch 1, and red histograms denote samples from batch 2 in a and b . a Of 100 molecules tested from batch 1 at a tensile force of 24.6 ± 1.9 pN, 6% lasted over 60 min. Of 45 molecules tested from batch 2 at a tensile force of 24.9 ± 1.0 pN, 9% lasted over 60 min. b Of 100 molecules tested from batch 1 at a tensile force of 34.9 ± 1.8 pN, only one lasted over 60 min. All 25 molecules tested from batch 2 at a tensile force of 34.7 ± 1.7 pN were broken within 60 min. c Differences in the percentages of broken DNA between the two batches of non-frozen DNA samples at a tensile force of 25 pN. d Differences in the percentages of broken DNA between the two batches of non-frozen DNA at a tensile force of 35 pN

    Article Snippet: Bacteriophage lambda DNA samples were purchased from New England Biolabs (NEB, N3011S).

    Techniques: Lambda DNA Preparation

    Measurement of sustaining time. a Schematic presentation of a single DNA molecule subjected to a constant force in dual-beam optical tweezers. The figure also illustrates the dumbbell structure of streptavidin-coated polystyrene beads with biotinylated lambda DNA between them. Both traps were formed by a neodymium-doped yttrium orthovanadate (Nd:YVO4) laser (1064 nm, Spectra-Physics). One beam was controlled by an acoustic-optical deflector (AOD, IntraAction Corp) to apply tension, and the other served as a fixed trap. The displacement of the bead in the fixed trap was detected by a QPD (model SPOT-9DMI, UDT), and used to calculate the force applied to the DNA molecule. b Sample trace of a single lambda DNA molecule subjected to a constant force. The force was 5.3 ± 0.9 pN, and the sustaining time was 528 s

    Journal: Journal of Biological Physics

    Article Title: Freezing shortens the lifetime of DNA molecules under tension

    doi: 10.1007/s10867-017-9466-3

    Figure Lengend Snippet: Measurement of sustaining time. a Schematic presentation of a single DNA molecule subjected to a constant force in dual-beam optical tweezers. The figure also illustrates the dumbbell structure of streptavidin-coated polystyrene beads with biotinylated lambda DNA between them. Both traps were formed by a neodymium-doped yttrium orthovanadate (Nd:YVO4) laser (1064 nm, Spectra-Physics). One beam was controlled by an acoustic-optical deflector (AOD, IntraAction Corp) to apply tension, and the other served as a fixed trap. The displacement of the bead in the fixed trap was detected by a QPD (model SPOT-9DMI, UDT), and used to calculate the force applied to the DNA molecule. b Sample trace of a single lambda DNA molecule subjected to a constant force. The force was 5.3 ± 0.9 pN, and the sustaining time was 528 s

    Article Snippet: Bacteriophage lambda DNA samples were purchased from New England Biolabs (NEB, N3011S).

    Techniques: Lambda DNA Preparation

    Sustaining times of frozen and non-frozen lambda DNA samples under constant tension. The x -axis represents the DNA sustaining time (min), and the y -axis represents the percentage of all DNA molecules tested in TE buffer. Blue histograms represent frozen DNA samples, and red histograms represent non-frozen samples. a Histogram for frozen samples subjected to a tensile force of 5.0 ± 0.7 pN and non-frozen samples subjected to a force of 5.3 ± 1.1 pN. b Histogram for frozen samples subjected to a force of 15.3 ± 1.5 pN and non-frozen samples to a force of 15.1 ± 0.7 pN. c Differences in the percentage of broken DNA between frozen and non-frozen samples at 5 pN. d Differences in the percentage of broken DNA between frozen and non-frozen samples at 15 pN

    Journal: Journal of Biological Physics

    Article Title: Freezing shortens the lifetime of DNA molecules under tension

    doi: 10.1007/s10867-017-9466-3

    Figure Lengend Snippet: Sustaining times of frozen and non-frozen lambda DNA samples under constant tension. The x -axis represents the DNA sustaining time (min), and the y -axis represents the percentage of all DNA molecules tested in TE buffer. Blue histograms represent frozen DNA samples, and red histograms represent non-frozen samples. a Histogram for frozen samples subjected to a tensile force of 5.0 ± 0.7 pN and non-frozen samples subjected to a force of 5.3 ± 1.1 pN. b Histogram for frozen samples subjected to a force of 15.3 ± 1.5 pN and non-frozen samples to a force of 15.1 ± 0.7 pN. c Differences in the percentage of broken DNA between frozen and non-frozen samples at 5 pN. d Differences in the percentage of broken DNA between frozen and non-frozen samples at 15 pN

    Article Snippet: Bacteriophage lambda DNA samples were purchased from New England Biolabs (NEB, N3011S).

    Techniques: Lambda DNA Preparation

    RecBCD translocating through, and unwinding, an individual λ DNA molecule. (A) Kymograph showing a YOYO-1 stained λ dsDNA molecule being unwound by a RecBCD molecule bound to the free DNA end. The drawing to the left of the kymograph depicts

    Journal:

    Article Title: Watching Individual Proteins Acting on Single Molecules of DNA

    doi: 10.1016/S0076-6879(10)72007-3

    Figure Lengend Snippet: RecBCD translocating through, and unwinding, an individual λ DNA molecule. (A) Kymograph showing a YOYO-1 stained λ dsDNA molecule being unwound by a RecBCD molecule bound to the free DNA end. The drawing to the left of the kymograph depicts

    Article Snippet: Bacteriophage λ DNA (New England Biolabs, Ipswich, MA) is biotinylated by ligation to a 3′-biotinylated 12-mer oligonucleotide (5′-GGGCGGCG ACCT-3′ or 5′-AGGTCGCCGCCC-3′, Operon Technologies, Huntsville, AL) that is complementary to one of the cohesive ends of λ DNA ( ).

    Techniques: Staining

    Rad54 translocating on a single dsDNA molecule. (A) Schematic illustration of the optically trapped  λ  DNA–bead complex with a bound FITC–Rad54 complex. (B) Kymographs depicting upstream translocation (in the direction opposite

    Journal:

    Article Title: Watching Individual Proteins Acting on Single Molecules of DNA

    doi: 10.1016/S0076-6879(10)72007-3

    Figure Lengend Snippet: Rad54 translocating on a single dsDNA molecule. (A) Schematic illustration of the optically trapped λ DNA–bead complex with a bound FITC–Rad54 complex. (B) Kymographs depicting upstream translocation (in the direction opposite

    Article Snippet: Bacteriophage λ DNA (New England Biolabs, Ipswich, MA) is biotinylated by ligation to a 3′-biotinylated 12-mer oligonucleotide (5′-GGGCGGCG ACCT-3′ or 5′-AGGTCGCCGCCC-3′, Operon Technologies, Huntsville, AL) that is complementary to one of the cohesive ends of λ DNA ( ).

    Techniques: Translocation Assay

    Rad51 assembling onto, and dissociating from, a single dsDNA molecule. (A) Kymograph of Rad51 assembly on Cy3-end-labeled  λ  DNA. The schematic on the left side of kymograph depicts the optically trapped bead, initial position of Cy3-end-label

    Journal:

    Article Title: Watching Individual Proteins Acting on Single Molecules of DNA

    doi: 10.1016/S0076-6879(10)72007-3

    Figure Lengend Snippet: Rad51 assembling onto, and dissociating from, a single dsDNA molecule. (A) Kymograph of Rad51 assembly on Cy3-end-labeled λ DNA. The schematic on the left side of kymograph depicts the optically trapped bead, initial position of Cy3-end-label

    Article Snippet: Bacteriophage λ DNA (New England Biolabs, Ipswich, MA) is biotinylated by ligation to a 3′-biotinylated 12-mer oligonucleotide (5′-GGGCGGCG ACCT-3′ or 5′-AGGTCGCCGCCC-3′, Operon Technologies, Huntsville, AL) that is complementary to one of the cohesive ends of λ DNA ( ).

    Techniques: Labeling

    Visualization of RecA-promoted DNA pairing with an individual optically-trapped DNA-dumbbell, imaged by epifluorescence a , Four channel flowcell with a flow-free reservoir.  b , DNA-dumbbell assembly and RecA-pairing reaction: 1) trap two beads (yellow); 2) capture λ DNA molecule (green) on one bead; 3) capture free DNA end with second bead using steerable optical trap; 4) set center-to-center bead distance, and remove YOYO-1; 5) incubate DNA-dumbbell in reservoir with RecA nucleoprotein filaments (red); and 6) extend DNA to visualize products.  c , Images of pairing products with 430 and 1,762 nt nucleoprotein filaments.

    Journal: Nature

    Article Title: Single-Molecule Imaging of DNA Pairing by RecA Reveals a 3-Dimensional Homology Search

    doi: 10.1038/nature10782

    Figure Lengend Snippet: Visualization of RecA-promoted DNA pairing with an individual optically-trapped DNA-dumbbell, imaged by epifluorescence a , Four channel flowcell with a flow-free reservoir. b , DNA-dumbbell assembly and RecA-pairing reaction: 1) trap two beads (yellow); 2) capture λ DNA molecule (green) on one bead; 3) capture free DNA end with second bead using steerable optical trap; 4) set center-to-center bead distance, and remove YOYO-1; 5) incubate DNA-dumbbell in reservoir with RecA nucleoprotein filaments (red); and 6) extend DNA to visualize products. c , Images of pairing products with 430 and 1,762 nt nucleoprotein filaments.

    Article Snippet: Multiple biotin moieties were incorporated into both ends of Bacteriophage λ DNA (NEB) by an end-filling reaction.

    Techniques: Flow Cytometry

    DNA pairing by RecA, imaged using single-molecule TIRFM, suggests that the three-dimensional conformation of target dsDNA is important in the homology search a , DNA substrates.  b , DNA pairing between λ DNA (green) and RecA filament assembled on 430 nt ssDNA (red): i) ensemble reaction examined by TIRFM; ii-iv)  in situ  reactions, dsDNA attached prior to pairing: ii) doubly-attached extended DNA, iii) singly-attached DNA, and iv) doubly-attached DNA with ends in proximity. Homologously paired products were observed in iii and iv when DNA was relaxed by stopping flow, and then flow-extended for visualization. White bar = 2.4 μm.

    Journal: Nature

    Article Title: Single-Molecule Imaging of DNA Pairing by RecA Reveals a 3-Dimensional Homology Search

    doi: 10.1038/nature10782

    Figure Lengend Snippet: DNA pairing by RecA, imaged using single-molecule TIRFM, suggests that the three-dimensional conformation of target dsDNA is important in the homology search a , DNA substrates. b , DNA pairing between λ DNA (green) and RecA filament assembled on 430 nt ssDNA (red): i) ensemble reaction examined by TIRFM; ii-iv) in situ reactions, dsDNA attached prior to pairing: ii) doubly-attached extended DNA, iii) singly-attached DNA, and iv) doubly-attached DNA with ends in proximity. Homologously paired products were observed in iii and iv when DNA was relaxed by stopping flow, and then flow-extended for visualization. White bar = 2.4 μm.

    Article Snippet: Multiple biotin moieties were incorporated into both ends of Bacteriophage λ DNA (NEB) by an end-filling reaction.

    Techniques: In Situ, Flow Cytometry

    Recovery of nucleic acids and polyphosphate (polyP) using various purification methods. Known quantities of bacteriophage lambda DNA (DNA, striped bars), polyG (RNA, white bars), or long-chain polyP (black bars) were processed for nucleic acid purification using Qiaquick, DNeasy, or TRIzol kits, following the manufacturer’s instructions, or with phenol/chloroform extraction. Nucleic acid recovery was quantified using A 260 and polyP recovery by digestion with PPX1 and PiBlue assay. Results are plotted as percent of the input amount in each experiment. For all experiments except the Qiaquick kits, the three samples were: (A) DNA alone (5 µg lambda DNA); (B) RNA alone (5 µg polyG); (C) 5 µg polyP alone; (D) a mixture of 5 µg polyP plus 5 µg of DNA; or (E) 5 µg polyP plus 5 µg of RNA (E) . Experiments with the Qiaquick kit employed 2.5 µg of polyP and/or nucleic acid. Data are mean ± SEM ( n = 3).

    Journal: Frontiers in Medicine

    Article Title: Ability of Polyphosphate and Nucleic Acids to Trigger Blood Clotting: Some Observations and Caveats

    doi: 10.3389/fmed.2018.00107

    Figure Lengend Snippet: Recovery of nucleic acids and polyphosphate (polyP) using various purification methods. Known quantities of bacteriophage lambda DNA (DNA, striped bars), polyG (RNA, white bars), or long-chain polyP (black bars) were processed for nucleic acid purification using Qiaquick, DNeasy, or TRIzol kits, following the manufacturer’s instructions, or with phenol/chloroform extraction. Nucleic acid recovery was quantified using A 260 and polyP recovery by digestion with PPX1 and PiBlue assay. Results are plotted as percent of the input amount in each experiment. For all experiments except the Qiaquick kits, the three samples were: (A) DNA alone (5 µg lambda DNA); (B) RNA alone (5 µg polyG); (C) 5 µg polyP alone; (D) a mixture of 5 µg polyP plus 5 µg of DNA; or (E) 5 µg polyP plus 5 µg of RNA (E) . Experiments with the Qiaquick kit employed 2.5 µg of polyP and/or nucleic acid. Data are mean ± SEM ( n = 3).

    Article Snippet: Calf intestinal alkaline phosphatase (CIAP) was from Promega and bacteriophage lambda DNA, and DNA ladder were from New England Biolabs.

    Techniques: Purification, Lambda DNA Preparation, Nucleic Acid Purification

    Procoagulant activities of polyphosphate (polyP), DNA, and RNA. Panels display plasma clot times versus concentration, with horizontal dashed lines showing the mean clot time without activator (±SEM as horizontal dotted lines). Symbols represent the mean, and error bars the SE, of three separate experiments evaluating clot times versus concentration. (A) Clot times with short-chain polyP (74 mer, Δ); medium-chain polyP (385 mer, □); and long-chain polyP (1195 mer, ○). (B) Clot times with HEK 293 cell DNA isolated with phenol/chloroform (□, 3 distinct purifications); NET-derived DNA isolated with phenol/chloroform (■, 3 distinct purifications); or lambda DNA ( ). Note that for comparison purposes, the clotting data for HEK 293 DNA and NET DNA in this panel are replotted from those in Supplemental Figure S2 in Supplementary Material of Smith et al. ( 26 ). (C) Clot times with HEK 293 cell RNA (◆); baker’s yeast transfer RNA (○); or the RNA homopolymers, polyA ( ), polyC ( ), polyI ( ), or polyG ( ). PolyU was also tested, but had no procoagulant activity (data not shown).

    Journal: Frontiers in Medicine

    Article Title: Ability of Polyphosphate and Nucleic Acids to Trigger Blood Clotting: Some Observations and Caveats

    doi: 10.3389/fmed.2018.00107

    Figure Lengend Snippet: Procoagulant activities of polyphosphate (polyP), DNA, and RNA. Panels display plasma clot times versus concentration, with horizontal dashed lines showing the mean clot time without activator (±SEM as horizontal dotted lines). Symbols represent the mean, and error bars the SE, of three separate experiments evaluating clot times versus concentration. (A) Clot times with short-chain polyP (74 mer, Δ); medium-chain polyP (385 mer, □); and long-chain polyP (1195 mer, ○). (B) Clot times with HEK 293 cell DNA isolated with phenol/chloroform (□, 3 distinct purifications); NET-derived DNA isolated with phenol/chloroform (■, 3 distinct purifications); or lambda DNA ( ). Note that for comparison purposes, the clotting data for HEK 293 DNA and NET DNA in this panel are replotted from those in Supplemental Figure S2 in Supplementary Material of Smith et al. ( 26 ). (C) Clot times with HEK 293 cell RNA (◆); baker’s yeast transfer RNA (○); or the RNA homopolymers, polyA ( ), polyC ( ), polyI ( ), or polyG ( ). PolyU was also tested, but had no procoagulant activity (data not shown).

    Article Snippet: Calf intestinal alkaline phosphatase (CIAP) was from Promega and bacteriophage lambda DNA, and DNA ladder were from New England Biolabs.

    Techniques: Concentration Assay, Isolation, Derivative Assay, Lambda DNA Preparation, Coagulation, Activity Assay