double stranded dna dsdna  (New England Biolabs)


Bioz Verified Symbol New England Biolabs is a verified supplier
Bioz Manufacturer Symbol New England Biolabs manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 93

    Structured Review

    New England Biolabs double stranded dna dsdna
    CRISPR adaptation to HHPV-2 infection. ( A ) Depiction of the single CRISPR structure and the preceding cas operon carried by the H. hispanica ATCC 33960 genome. Primers used to examine CRISPR expansion (in panel B) are shown as black arrows and listed in Supplementary Table S2 . ( B ) PCR assay to detect CRISPR expansion at the leader end (L1–L2), the inner part (I1–I2) or the distal end (D1–D2). <t>DNA</t> sampled from infected (+) or uninfected (−) cells was used as PCR templates. Lane M, <t>dsDNA</t> size marker. ( C ) The sequence logo showing the conserved PAM of TTC. The 20 nt upstream of each protospacer observed during HHPV-2 infection were collected and analyzed with WebLogo ( http://weblogo.berkeley.edu/logo.cgi ).
    Double Stranded Dna Dsdna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/double stranded dna dsdna/product/New England Biolabs
    Average 93 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    double stranded dna dsdna - by Bioz Stars, 2020-04
    93/100 stars

    Images

    1) Product Images from "Adaptation of the Haloarcula hispanica CRISPR-Cas system to a purified virus strictly requires a priming process"

    Article Title: Adaptation of the Haloarcula hispanica CRISPR-Cas system to a purified virus strictly requires a priming process

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkt1154

    CRISPR adaptation to HHPV-2 infection. ( A ) Depiction of the single CRISPR structure and the preceding cas operon carried by the H. hispanica ATCC 33960 genome. Primers used to examine CRISPR expansion (in panel B) are shown as black arrows and listed in Supplementary Table S2 . ( B ) PCR assay to detect CRISPR expansion at the leader end (L1–L2), the inner part (I1–I2) or the distal end (D1–D2). DNA sampled from infected (+) or uninfected (−) cells was used as PCR templates. Lane M, dsDNA size marker. ( C ) The sequence logo showing the conserved PAM of TTC. The 20 nt upstream of each protospacer observed during HHPV-2 infection were collected and analyzed with WebLogo ( http://weblogo.berkeley.edu/logo.cgi ).
    Figure Legend Snippet: CRISPR adaptation to HHPV-2 infection. ( A ) Depiction of the single CRISPR structure and the preceding cas operon carried by the H. hispanica ATCC 33960 genome. Primers used to examine CRISPR expansion (in panel B) are shown as black arrows and listed in Supplementary Table S2 . ( B ) PCR assay to detect CRISPR expansion at the leader end (L1–L2), the inner part (I1–I2) or the distal end (D1–D2). DNA sampled from infected (+) or uninfected (−) cells was used as PCR templates. Lane M, dsDNA size marker. ( C ) The sequence logo showing the conserved PAM of TTC. The 20 nt upstream of each protospacer observed during HHPV-2 infection were collected and analyzed with WebLogo ( http://weblogo.berkeley.edu/logo.cgi ).

    Techniques Used: CRISPR, Infection, Polymerase Chain Reaction, Marker, Sequencing

    Adaptation to HHPV-2 infection under different cas genetic backgrounds. ( A ) Cas requirement for adaptation. For each cas mutant, DNA was sampled from cells transformed with an empty plasmid (−) or the plasmid carrying the deleted cas gene(s) (+). The plasmid-carried cas gene(s) was/were under the control of the cas operon promoter. ( B ) Requirements for the nuclease and helicase activities of Cas3. Alanine replacement was performed for the putative key residues in the HD nuclease domain (H20A, H55A, D56A and D229A) and the DExD/H helicase domain (K315A, D439A and E440A). Another two conserved residues (His6 and Lys113) were also mutated. The empty plasmid (−) and the plasmid carrying a wild-type Cas3 (Cas3 WT ) were used, respectively, as negative and positive controls. Lane Ms, dsDNA size markers.
    Figure Legend Snippet: Adaptation to HHPV-2 infection under different cas genetic backgrounds. ( A ) Cas requirement for adaptation. For each cas mutant, DNA was sampled from cells transformed with an empty plasmid (−) or the plasmid carrying the deleted cas gene(s) (+). The plasmid-carried cas gene(s) was/were under the control of the cas operon promoter. ( B ) Requirements for the nuclease and helicase activities of Cas3. Alanine replacement was performed for the putative key residues in the HD nuclease domain (H20A, H55A, D56A and D229A) and the DExD/H helicase domain (K315A, D439A and E440A). Another two conserved residues (His6 and Lys113) were also mutated. The empty plasmid (−) and the plasmid carrying a wild-type Cas3 (Cas3 WT ) were used, respectively, as negative and positive controls. Lane Ms, dsDNA size markers.

    Techniques Used: Infection, Mutagenesis, Transformation Assay, Plasmid Preparation, Mass Spectrometry

    2) Product Images from "The β-isoform of BCCIP promotes ADP release from the RAD51 presynaptic filament and enhances homologous DNA pairing"

    Article Title: The β-isoform of BCCIP promotes ADP release from the RAD51 presynaptic filament and enhances homologous DNA pairing

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkw877

    BCCIPβ binds DNA. ( A ) BCCIPβ (0.24 μM, 0.47 μM, 0.96 μM, 1.8 μM, 2.8 μM and 4.7 μM; lanes 2–7, respectively) incubated with ϕX174 (+) ssDNA (ss; 30 μM nucleotides). ( B ) BCCIPβ (0.24 μM, 0.47 μM, 0.96 μM, 1.8 μM, 2.8 μM and 4.7 μM; lanes 2–7, respectively) was incubated with ϕX174 RF (I) dsDNA (ds; 30 μM base pairs). The reaction products were separated on a 1.0% agarose gel, and were stained with ethidium bromide. Lane 1 contained no protein, and lane 8 was deproteinized with SDS and Proteinase K (S/P) prior to loading.
    Figure Legend Snippet: BCCIPβ binds DNA. ( A ) BCCIPβ (0.24 μM, 0.47 μM, 0.96 μM, 1.8 μM, 2.8 μM and 4.7 μM; lanes 2–7, respectively) incubated with ϕX174 (+) ssDNA (ss; 30 μM nucleotides). ( B ) BCCIPβ (0.24 μM, 0.47 μM, 0.96 μM, 1.8 μM, 2.8 μM and 4.7 μM; lanes 2–7, respectively) was incubated with ϕX174 RF (I) dsDNA (ds; 30 μM base pairs). The reaction products were separated on a 1.0% agarose gel, and were stained with ethidium bromide. Lane 1 contained no protein, and lane 8 was deproteinized with SDS and Proteinase K (S/P) prior to loading.

    Techniques Used: Incubation, Agarose Gel Electrophoresis, Staining

    3) Product Images from "Perturbation of base excision repair sensitizes breast cancer cells to APOBEC3 deaminase-mediated mutations"

    Article Title: Perturbation of base excision repair sensitizes breast cancer cells to APOBEC3 deaminase-mediated mutations

    Journal: eLife

    doi: 10.7554/eLife.51605

    Purification and activity of NEIL2. ( A ) Purified NEIL2-His 6 (50 ng) from E. coli was subjected to NuPAGE and stained with Coomassie blue. ( B ) Activity of purified NEIL2-His 6 on 5’-[ 32 P]-labeled oligonucleotides (51 nt) containing: hydroxyuracil (OHU), OHU/G, U, or U/G. ssDNA, single-stranded DNA; dsDNA, double-stranded DNA. S, substrate; P, product. ( C ) Validation of UDG-generated AP sites from 5’-[ 32 P]-labeled single-stranded and double-stranded oligonucleotides (35 nt) by treatment with NaOH. AP sites are lysed by alkali treatment. ( D ) NEIL2 cleaves Fluorescein (Fluor)-labeled U-containing single strand oligonucleotide (39 nt) in the presence of UDG. S, substrate; P, product.
    Figure Legend Snippet: Purification and activity of NEIL2. ( A ) Purified NEIL2-His 6 (50 ng) from E. coli was subjected to NuPAGE and stained with Coomassie blue. ( B ) Activity of purified NEIL2-His 6 on 5’-[ 32 P]-labeled oligonucleotides (51 nt) containing: hydroxyuracil (OHU), OHU/G, U, or U/G. ssDNA, single-stranded DNA; dsDNA, double-stranded DNA. S, substrate; P, product. ( C ) Validation of UDG-generated AP sites from 5’-[ 32 P]-labeled single-stranded and double-stranded oligonucleotides (35 nt) by treatment with NaOH. AP sites are lysed by alkali treatment. ( D ) NEIL2 cleaves Fluorescein (Fluor)-labeled U-containing single strand oligonucleotide (39 nt) in the presence of UDG. S, substrate; P, product.

    Techniques Used: Purification, Activity Assay, Staining, Labeling, Generated

    Related Articles

    Centrifugation:

    Article Title: Adaptation of the Haloarcula hispanica CRISPR-Cas system to a purified virus strictly requires a priming process
    Article Snippet: Nucleic acids in the aqueous phase were precipitated by adding 1/10 volume of 3 M sodium acetate (pH 4.8) and 2 volumes of ethanol, followed by incubation at −20°C for 20 min and centrifugation at 4°C for 10 min. .. The single-stranded DNA (ssDNA) (ФX174ss) and double-stranded DNA (dsDNA) (ФX174ds) from phiX174 phage (purchased from New England Biolabs) were used as controls.

    Amplification:

    Article Title: The β-isoform of BCCIP promotes ADP release from the RAD51 presynaptic filament and enhances homologous DNA pairing
    Article Snippet: The amplified product was inserted into the bacterial expression plasmid pET11c (Novagen), and sequenced to ensure no undesired mutations occurred. .. All oligonucleotides were purchased from Integrated DNA Technologies. pBluescript was purified from E. coli using a Giga Kit (Qiagen). ϕX174 (+) virion ssDNA and ϕX174 replicative form I double-stranded DNA (dsDNA) were purchased from New England BioLabs—ϕX174 dsDNA was linearized with ApaLI (New England BioLabs).

    Article Title: Disruption of the Opal Stop Codon Attenuates Chikungunya Virus-Induced Arthritis and Pathology
    Article Snippet: The Caribbean isolate of CHIKV used in this study was amplified once on C6/36 cells. .. Double-stranded DNA (dsDNA) was then produced by use of NEBNext mRNA second-strand synthesis module (New England Biolabs), and dsDNA was purified using a PureLink PCR microkit (Thermo, Fisher Scientific) according to standard procedures.

    Incubation:

    Article Title: Adaptation of the Haloarcula hispanica CRISPR-Cas system to a purified virus strictly requires a priming process
    Article Snippet: The precipitate was dissolved by distilled water, if necessary, with incubation at 37°C. .. The single-stranded DNA (ssDNA) (ФX174ss) and double-stranded DNA (dsDNA) (ФX174ds) from phiX174 phage (purchased from New England Biolabs) were used as controls.

    Article Title: A Novel C5a-neutralizing Mirror-image (l-)Aptamer Prevents Organ Failure and Improves Survival in Experimental Sepsis
    Article Snippet: Double-stranded DNA (dsDNA) was generated by single-step fill-in reaction using Vent (exo-) polymerase (New England BioLabs, Frankfurt am Main, Germany) and the forward primer followed by RNA transcription with T7 RNA polymerase (Stratagene, Waldbronn, Germany) to yield the RNA library: GGAGCUCAGACCGUACACCUGUGC-N34 -GCACAGGCUGCAGUGUCGGUUCCAG. .. In the first round of in vitro selection, 4 nmol RNA library (= 2.4 × 1015 individual molecules) 5′-labeled with [−32 P]-ATP by T4 polynucleotide kinase (Invitrogen, Karlsruhe, Germany) were incubated with equimolar bio-d -mC5a in selection buffer (20 mmol/l Tris, pH 7.4; 150 mmol/l NaCl; 5 mmol/l KCl; 1 mmol/l MgCl2 ; 1 mmol/l CaCl2 ; 0.1% Tween 20; 50 µg/ml bovine serum albumin (BSA); 10 µg/ml unspecific l -RNA; 4 U/ml RNaseOut, Invitrogen) at 37 °C for 16 hours.

    Article Title: Single-molecule correlated chemical probing reveals large-scale structural communication in the ribosome and the mechanism of the antibiotic spectinomycin in living cells
    Article Snippet: After incubation at 25 °C for 2 min, 1 μL of SuperScript II (Invitrogen, Carlsbad, CA) was added, and samples were incubated according to a stepped primer extension protocol: 25 °C for 10 min followed by 42 °C for 90 min, and then 10 cycles of 2 min at 50 °C and 2 min at 42 °C. .. Purified RNA was eluted from the beads in 68 μL nuclease-free water and converted to double-stranded DNA (dsDNA) using a second-strand synthesis enzyme mix (NEB, Ipswitch, MA).

    Article Title: Perturbation of base excision repair sensitizes breast cancer cells to APOBEC3 deaminase-mediated mutations
    Article Snippet: Reactions were incubated at 37°C for 30 min. After PCI extraction and ethanol precipitation, samples were treated with equal volume of 2× Novex TBE-Urea Sample Buffer (Invitrogen). .. For double-stranded DNA (dsDNA), 1 pmol 32 P-labeled dsDNA (35 nt) was mixed on ice with UDG (1 U/μl, 1 μl), various concentrations of purified NEIL2 or APE1 (indicated in figures and legends), and 1× NEBuffer 4 in 20 μl reactions.

    Activity Assay:

    Article Title: Perturbation of base excision repair sensitizes breast cancer cells to APOBEC3 deaminase-mediated mutations
    Article Snippet: Paragraph title: NEIL2 and APE1 glycosylase/lyase activity assay ... For double-stranded DNA (dsDNA), 1 pmol 32 P-labeled dsDNA (35 nt) was mixed on ice with UDG (1 U/μl, 1 μl), various concentrations of purified NEIL2 or APE1 (indicated in figures and legends), and 1× NEBuffer 4 in 20 μl reactions.

    Expressing:

    Article Title: The β-isoform of BCCIP promotes ADP release from the RAD51 presynaptic filament and enhances homologous DNA pairing
    Article Snippet: The amplified product was inserted into the bacterial expression plasmid pET11c (Novagen), and sequenced to ensure no undesired mutations occurred. .. All oligonucleotides were purchased from Integrated DNA Technologies. pBluescript was purified from E. coli using a Giga Kit (Qiagen). ϕX174 (+) virion ssDNA and ϕX174 replicative form I double-stranded DNA (dsDNA) were purchased from New England BioLabs—ϕX174 dsDNA was linearized with ApaLI (New England BioLabs).

    Translocation Assay:

    Article Title: Origins and Consequences of Velocity Fluctuations during DNA Passage through a Nanopore
    Article Snippet: Double-stranded DNA (dsDNA) of length 5.3 kilobases (kb) was prepared from a ϕ×174RF1 plasmid (obtained from New England Biolabs, Ipswich, MA) by cutting the plasmid with Ssp I restriction enzyme and purifying by gel electrophoresis. .. Single-molecule DNA-nanopore translocation events were observed as transient ionic current blockades.

    Gel Purification:

    Article Title: Quantitative amplification of single-stranded DNA (QAOS) demonstrates that cdc13-1 mutants generate ssDNA in a telomere to centromere direction
    Article Snippet: For global QAOS the target ssDNA was pHR85-31 cut with Sal I, heated at 95°C for 5 min and then chilled on ice and the double-stranded DNA (dsDNA) was λ DNA purchased from New England Biolabs (NEB No301-3s). .. Sonication was used to prepare low molecular weight samples of pHR85-31 and λ. DNA was sonicated until the average length was 400–500 bp, purified on Amersham GFX gel purification columns and concentration determined by absorbance at 260 nM.

    Generated:

    Article Title: A Novel C5a-neutralizing Mirror-image (l-)Aptamer Prevents Organ Failure and Improves Survival in Experimental Sepsis
    Article Snippet: .. Double-stranded DNA (dsDNA) was generated by single-step fill-in reaction using Vent (exo-) polymerase (New England BioLabs, Frankfurt am Main, Germany) and the forward primer followed by RNA transcription with T7 RNA polymerase (Stratagene, Waldbronn, Germany) to yield the RNA library: GGAGCUCAGACCGUACACCUGUGC-N34 -GCACAGGCUGCAGUGUCGGUUCCAG. .. In the first round of in vitro selection, 4 nmol RNA library (= 2.4 × 1015 individual molecules) 5′-labeled with [−32 P]-ATP by T4 polynucleotide kinase (Invitrogen, Karlsruhe, Germany) were incubated with equimolar bio-d -mC5a in selection buffer (20 mmol/l Tris, pH 7.4; 150 mmol/l NaCl; 5 mmol/l KCl; 1 mmol/l MgCl2 ; 1 mmol/l CaCl2 ; 0.1% Tween 20; 50 µg/ml bovine serum albumin (BSA); 10 µg/ml unspecific l -RNA; 4 U/ml RNaseOut, Invitrogen) at 37 °C for 16 hours.

    Sequencing:

    Article Title: Adaptation of the Haloarcula hispanica CRISPR-Cas system to a purified virus strictly requires a priming process
    Article Snippet: Paragraph title: Viral genome extraction, analysis and sequencing ... The single-stranded DNA (ssDNA) (ФX174ss) and double-stranded DNA (dsDNA) (ФX174ds) from phiX174 phage (purchased from New England Biolabs) were used as controls.

    Article Title: A Novel C5a-neutralizing Mirror-image (l-)Aptamer Prevents Organ Failure and Improves Survival in Experimental Sepsis
    Article Snippet: The oligonucleotide sequence of NOX-D20 is GCGAUG(dU)GGUGGU(dG)(dA)AGGGUUGUUGGG(dU)G(dU)CGACGCA(dC)GC. .. Double-stranded DNA (dsDNA) was generated by single-step fill-in reaction using Vent (exo-) polymerase (New England BioLabs, Frankfurt am Main, Germany) and the forward primer followed by RNA transcription with T7 RNA polymerase (Stratagene, Waldbronn, Germany) to yield the RNA library: GGAGCUCAGACCGUACACCUGUGC-N34 -GCACAGGCUGCAGUGUCGGUUCCAG.

    Article Title: Disruption of the Opal Stop Codon Attenuates Chikungunya Virus-Induced Arthritis and Pathology
    Article Snippet: Paragraph title: Sequencing of a CHIKV isolate. ... Double-stranded DNA (dsDNA) was then produced by use of NEBNext mRNA second-strand synthesis module (New England Biolabs), and dsDNA was purified using a PureLink PCR microkit (Thermo, Fisher Scientific) according to standard procedures.

    Article Title: High Prevalence of Hepatitis E Virus in Swedish Moose – A Phylogenetic Characterization and Comparison of the Virus from Different Regions
    Article Snippet: .. For RNA extraction from liver, the Qiagen RNEasy Mini kit was used according to the manufacturer’s instructions and cDNA synthesis was performed as described previously [ ]. cDNA from liver selected for MiSeq sequencing was converted to double-stranded DNA (dsDNA) by adding 0.5μl Klenow Fragment DNA polymerase (3’→5’exonuclase-negative; New England Biolabs, USA) in for 1 hour at 37°C, followed by 10 min inactivation at 75°C. .. HEV RNA detection by qPCR and PCR typing assay Detection of HEV RNA in the moose samples was performed with a one step TaqMan qPCR assay targeting the ORF2/3 overlapping region using the Qiagen One step RT-PCR kit.

    Sonication:

    Article Title: Quantitative amplification of single-stranded DNA (QAOS) demonstrates that cdc13-1 mutants generate ssDNA in a telomere to centromere direction
    Article Snippet: For global QAOS the target ssDNA was pHR85-31 cut with Sal I, heated at 95°C for 5 min and then chilled on ice and the double-stranded DNA (dsDNA) was λ DNA purchased from New England Biolabs (NEB No301-3s). .. Sonication was used to prepare low molecular weight samples of pHR85-31 and λ. DNA was sonicated until the average length was 400–500 bp, purified on Amersham GFX gel purification columns and concentration determined by absorbance at 260 nM.

    Injection:

    Article Title: Origins and Consequences of Velocity Fluctuations during DNA Passage through a Nanopore
    Article Snippet: Double-stranded DNA (dsDNA) of length 5.3 kilobases (kb) was prepared from a ϕ×174RF1 plasmid (obtained from New England Biolabs, Ipswich, MA) by cutting the plasmid with Ssp I restriction enzyme and purifying by gel electrophoresis. .. A 1:1 mixture of the purified 5.3-kb and 10-kb fragments was prepared at ∼1 nM each and injected into the cis reservoir.

    Binding Assay:

    Article Title: A Novel C5a-neutralizing Mirror-image (l-)Aptamer Prevents Organ Failure and Improves Survival in Experimental Sepsis
    Article Snippet: An RNA library was generated from a synthetic single-stranded DNA library with 34 random positions and flanking primer binding sites for the forward primer carrying a T7-promotor (5′-TCTAATACGACTCACTATAGGAGCTCAGACCGTACACC-3′) and the reverse primer (5′-CTGGAACCGACACTGCAGCC-3′). .. Double-stranded DNA (dsDNA) was generated by single-step fill-in reaction using Vent (exo-) polymerase (New England BioLabs, Frankfurt am Main, Germany) and the forward primer followed by RNA transcription with T7 RNA polymerase (Stratagene, Waldbronn, Germany) to yield the RNA library: GGAGCUCAGACCGUACACCUGUGC-N34 -GCACAGGCUGCAGUGUCGGUUCCAG.

    Molecular Weight:

    Article Title: Quantitative amplification of single-stranded DNA (QAOS) demonstrates that cdc13-1 mutants generate ssDNA in a telomere to centromere direction
    Article Snippet: For global QAOS the target ssDNA was pHR85-31 cut with Sal I, heated at 95°C for 5 min and then chilled on ice and the double-stranded DNA (dsDNA) was λ DNA purchased from New England Biolabs (NEB No301-3s). .. Sonication was used to prepare low molecular weight samples of pHR85-31 and λ. DNA was sonicated until the average length was 400–500 bp, purified on Amersham GFX gel purification columns and concentration determined by absorbance at 260 nM.

    Nucleic Acid Electrophoresis:

    Article Title: Origins and Consequences of Velocity Fluctuations during DNA Passage through a Nanopore
    Article Snippet: .. Double-stranded DNA (dsDNA) of length 5.3 kilobases (kb) was prepared from a ϕ×174RF1 plasmid (obtained from New England Biolabs, Ipswich, MA) by cutting the plasmid with Ssp I restriction enzyme and purifying by gel electrophoresis. .. A quantity of 10 kb dsDNA was purchased from New England Biolabs and purified by gel electrophoresis to yield no detectable contaminants.

    Isolation:

    Article Title: Disruption of the Opal Stop Codon Attenuates Chikungunya Virus-Induced Arthritis and Pathology
    Article Snippet: RNA was isolated from purified virus preparations by TRIzol extraction (Ambion). .. Double-stranded DNA (dsDNA) was then produced by use of NEBNext mRNA second-strand synthesis module (New England Biolabs), and dsDNA was purified using a PureLink PCR microkit (Thermo, Fisher Scientific) according to standard procedures.

    Article Title: High Prevalence of Hepatitis E Virus in Swedish Moose – A Phylogenetic Characterization and Comparison of the Virus from Different Regions
    Article Snippet: Paragraph title: RNA isolation and cDNA synthesis ... For RNA extraction from liver, the Qiagen RNEasy Mini kit was used according to the manufacturer’s instructions and cDNA synthesis was performed as described previously [ ]. cDNA from liver selected for MiSeq sequencing was converted to double-stranded DNA (dsDNA) by adding 0.5μl Klenow Fragment DNA polymerase (3’→5’exonuclase-negative; New England Biolabs, USA) in for 1 hour at 37°C, followed by 10 min inactivation at 75°C.

    Purification:

    Article Title: The β-isoform of BCCIP promotes ADP release from the RAD51 presynaptic filament and enhances homologous DNA pairing
    Article Snippet: .. All oligonucleotides were purchased from Integrated DNA Technologies. pBluescript was purified from E. coli using a Giga Kit (Qiagen). ϕX174 (+) virion ssDNA and ϕX174 replicative form I double-stranded DNA (dsDNA) were purchased from New England BioLabs—ϕX174 dsDNA was linearized with ApaLI (New England BioLabs). .. Cell growth, expression and purification of BCCIPβ The BCCIPβ-(HIS)6 pET11c expression plasmid was transformed into the E. coli strain BL21(DE3).

    Article Title: Single-molecule correlated chemical probing reveals large-scale structural communication in the ribosome and the mechanism of the antibiotic spectinomycin in living cells
    Article Snippet: .. Purified RNA was eluted from the beads in 68 μL nuclease-free water and converted to double-stranded DNA (dsDNA) using a second-strand synthesis enzyme mix (NEB, Ipswitch, MA). .. Following second-strand synthesis, dsDNA was purified (AmpureXP beads, 0.7:1 bead to sample ratio; Beckman Coulter, Indianapolis, IN).

    Article Title: Origins and Consequences of Velocity Fluctuations during DNA Passage through a Nanopore
    Article Snippet: Double-stranded DNA (dsDNA) of length 5.3 kilobases (kb) was prepared from a ϕ×174RF1 plasmid (obtained from New England Biolabs, Ipswich, MA) by cutting the plasmid with Ssp I restriction enzyme and purifying by gel electrophoresis. .. A quantity of 10 kb dsDNA was purchased from New England Biolabs and purified by gel electrophoresis to yield no detectable contaminants.

    Article Title: Disruption of the Opal Stop Codon Attenuates Chikungunya Virus-Induced Arthritis and Pathology
    Article Snippet: .. Double-stranded DNA (dsDNA) was then produced by use of NEBNext mRNA second-strand synthesis module (New England Biolabs), and dsDNA was purified using a PureLink PCR microkit (Thermo, Fisher Scientific) according to standard procedures. .. Libraries were created using a Nextera XT DNA library preparation kit and sequenced on a MiSeq desktop sequencer using MiSeq reagent kit v2 (300 cycles) (Illumina).

    Article Title: Perturbation of base excision repair sensitizes breast cancer cells to APOBEC3 deaminase-mediated mutations
    Article Snippet: .. For double-stranded DNA (dsDNA), 1 pmol 32 P-labeled dsDNA (35 nt) was mixed on ice with UDG (1 U/μl, 1 μl), various concentrations of purified NEIL2 or APE1 (indicated in figures and legends), and 1× NEBuffer 4 in 20 μl reactions. ..

    Polymerase Chain Reaction:

    Article Title: The β-isoform of BCCIP promotes ADP release from the RAD51 presynaptic filament and enhances homologous DNA pairing
    Article Snippet: A (HIS)6 tag was added to the 3′ end of BCCIPβ via PCR using the forward primer 5′-GGGAATCCCATATGGCGTCCAGGTCTAAGCGGCGTG and reverse primer 5′-CCCATATGGAATTCTTAATGATGATGATGATGATGAGGACCACCGACAGATAGATATTCTTTCAGTTTATCCATG. .. All oligonucleotides were purchased from Integrated DNA Technologies. pBluescript was purified from E. coli using a Giga Kit (Qiagen). ϕX174 (+) virion ssDNA and ϕX174 replicative form I double-stranded DNA (dsDNA) were purchased from New England BioLabs—ϕX174 dsDNA was linearized with ApaLI (New England BioLabs).

    Article Title: Disruption of the Opal Stop Codon Attenuates Chikungunya Virus-Induced Arthritis and Pathology
    Article Snippet: .. Double-stranded DNA (dsDNA) was then produced by use of NEBNext mRNA second-strand synthesis module (New England Biolabs), and dsDNA was purified using a PureLink PCR microkit (Thermo, Fisher Scientific) according to standard procedures. .. Libraries were created using a Nextera XT DNA library preparation kit and sequenced on a MiSeq desktop sequencer using MiSeq reagent kit v2 (300 cycles) (Illumina).

    Polyacrylamide Gel Electrophoresis:

    Article Title: Perturbation of base excision repair sensitizes breast cancer cells to APOBEC3 deaminase-mediated mutations
    Article Snippet: For competition assays between NEIL2 and APE1, cleaved products were separated using 20% 8M Urea PAGE. .. For double-stranded DNA (dsDNA), 1 pmol 32 P-labeled dsDNA (35 nt) was mixed on ice with UDG (1 U/μl, 1 μl), various concentrations of purified NEIL2 or APE1 (indicated in figures and legends), and 1× NEBuffer 4 in 20 μl reactions.

    Plasmid Preparation:

    Article Title: The β-isoform of BCCIP promotes ADP release from the RAD51 presynaptic filament and enhances homologous DNA pairing
    Article Snippet: The amplified product was inserted into the bacterial expression plasmid pET11c (Novagen), and sequenced to ensure no undesired mutations occurred. .. All oligonucleotides were purchased from Integrated DNA Technologies. pBluescript was purified from E. coli using a Giga Kit (Qiagen). ϕX174 (+) virion ssDNA and ϕX174 replicative form I double-stranded DNA (dsDNA) were purchased from New England BioLabs—ϕX174 dsDNA was linearized with ApaLI (New England BioLabs).

    Article Title: Origins and Consequences of Velocity Fluctuations during DNA Passage through a Nanopore
    Article Snippet: .. Double-stranded DNA (dsDNA) of length 5.3 kilobases (kb) was prepared from a ϕ×174RF1 plasmid (obtained from New England Biolabs, Ipswich, MA) by cutting the plasmid with Ssp I restriction enzyme and purifying by gel electrophoresis. .. A quantity of 10 kb dsDNA was purchased from New England Biolabs and purified by gel electrophoresis to yield no detectable contaminants.

    Article Title: Quantitative amplification of single-stranded DNA (QAOS) demonstrates that cdc13-1 mutants generate ssDNA in a telomere to centromere direction
    Article Snippet: Thus, at 1:4000 ( Eco RI) or 1:2000 ( Sal I) dilutions the plasmid was at a similar concentration to a 5.7 kb gene in the 13 469 kb yeast genome (1:2350). .. For global QAOS the target ssDNA was pHR85-31 cut with Sal I, heated at 95°C for 5 min and then chilled on ice and the double-stranded DNA (dsDNA) was λ DNA purchased from New England Biolabs (NEB No301-3s).

    RNA Extraction:

    Article Title: High Prevalence of Hepatitis E Virus in Swedish Moose – A Phylogenetic Characterization and Comparison of the Virus from Different Regions
    Article Snippet: .. For RNA extraction from liver, the Qiagen RNEasy Mini kit was used according to the manufacturer’s instructions and cDNA synthesis was performed as described previously [ ]. cDNA from liver selected for MiSeq sequencing was converted to double-stranded DNA (dsDNA) by adding 0.5μl Klenow Fragment DNA polymerase (3’→5’exonuclase-negative; New England Biolabs, USA) in for 1 hour at 37°C, followed by 10 min inactivation at 75°C. .. HEV RNA detection by qPCR and PCR typing assay Detection of HEV RNA in the moose samples was performed with a one step TaqMan qPCR assay targeting the ORF2/3 overlapping region using the Qiagen One step RT-PCR kit.

    Patch Clamp:

    Article Title: Origins and Consequences of Velocity Fluctuations during DNA Passage through a Nanopore
    Article Snippet: The trans reservoir was biased at Vbias = +100 mV relative to the cis reservoir by an Axopatch 200B patch-clamp amplifier (Molecular Devices, Sunnyvale, CA) coupled to the two reservoirs by Ag/AgCl electrodes. .. Double-stranded DNA (dsDNA) of length 5.3 kilobases (kb) was prepared from a ϕ×174RF1 plasmid (obtained from New England Biolabs, Ipswich, MA) by cutting the plasmid with Ssp I restriction enzyme and purifying by gel electrophoresis.

    Ethanol Precipitation:

    Article Title: Perturbation of base excision repair sensitizes breast cancer cells to APOBEC3 deaminase-mediated mutations
    Article Snippet: Reactions were incubated at 37°C for 30 min. After PCI extraction and ethanol precipitation, samples were treated with equal volume of 2× Novex TBE-Urea Sample Buffer (Invitrogen). .. For double-stranded DNA (dsDNA), 1 pmol 32 P-labeled dsDNA (35 nt) was mixed on ice with UDG (1 U/μl, 1 μl), various concentrations of purified NEIL2 or APE1 (indicated in figures and legends), and 1× NEBuffer 4 in 20 μl reactions.

    Spectrophotometry:

    Article Title: Adaptation of the Haloarcula hispanica CRISPR-Cas system to a purified virus strictly requires a priming process
    Article Snippet: The single-stranded DNA (ssDNA) (ФX174ss) and double-stranded DNA (dsDNA) (ФX174ds) from phiX174 phage (purchased from New England Biolabs) were used as controls. .. The nucleic acid concentrations were determined using a Nanodrop 1000 spectrophotometer (Thermo Fisher Scientific) and 1 μg was used for each reaction.

    Produced:

    Article Title: Disruption of the Opal Stop Codon Attenuates Chikungunya Virus-Induced Arthritis and Pathology
    Article Snippet: .. Double-stranded DNA (dsDNA) was then produced by use of NEBNext mRNA second-strand synthesis module (New England Biolabs), and dsDNA was purified using a PureLink PCR microkit (Thermo, Fisher Scientific) according to standard procedures. .. Libraries were created using a Nextera XT DNA library preparation kit and sequenced on a MiSeq desktop sequencer using MiSeq reagent kit v2 (300 cycles) (Illumina).

    Concentration Assay:

    Article Title: Quantitative amplification of single-stranded DNA (QAOS) demonstrates that cdc13-1 mutants generate ssDNA in a telomere to centromere direction
    Article Snippet: Thus, at 1:4000 ( Eco RI) or 1:2000 ( Sal I) dilutions the plasmid was at a similar concentration to a 5.7 kb gene in the 13 469 kb yeast genome (1:2350). .. For global QAOS the target ssDNA was pHR85-31 cut with Sal I, heated at 95°C for 5 min and then chilled on ice and the double-stranded DNA (dsDNA) was λ DNA purchased from New England Biolabs (NEB No301-3s).

    Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • N/A
    OneTaq Quick Load DNA Polymerase 500 units
      Buy from Supplier

    93
    New England Biolabs double stranded dna dsdna
    CRISPR adaptation to HHPV-2 infection. ( A ) Depiction of the single CRISPR structure and the preceding cas operon carried by the H. hispanica ATCC 33960 genome. Primers used to examine CRISPR expansion (in panel B) are shown as black arrows and listed in Supplementary Table S2 . ( B ) PCR assay to detect CRISPR expansion at the leader end (L1–L2), the inner part (I1–I2) or the distal end (D1–D2). <t>DNA</t> sampled from infected (+) or uninfected (−) cells was used as PCR templates. Lane M, <t>dsDNA</t> size marker. ( C ) The sequence logo showing the conserved PAM of TTC. The 20 nt upstream of each protospacer observed during HHPV-2 infection were collected and analyzed with WebLogo ( http://weblogo.berkeley.edu/logo.cgi ).
    Double Stranded Dna Dsdna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/double stranded dna dsdna/product/New England Biolabs
    Average 93 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    double stranded dna dsdna - by Bioz Stars, 2020-04
    93/100 stars
      Buy from Supplier

    87
    New England Biolabs m13mp18 dna sequencing standard m13mp18 dsdna
    Molecular events and ionic current trace for a 2D read of a 7.25 kb M13 phage <t>dsDNA</t> molecule. (a) Schematic for the steps in <t>DNA</t> translocation through the nanopore. (i) Open channel; (ii) dsDNA with a ligated lead adaptor (blue), with a molecular motor bound to it (orange), and a hairpin adaptor (red), is captured by the nanopore. DNA translocation through the nanopore begins through the effect of an applied voltage across the membrane and the action of a molecular motor; (iii) Translocation of the lead adaptor (blue); (iv) Translocation of the template strand (gold); (v) Translocation of the hairpin adaptor (red); (vi) Translocation of the complement strand (dark blue); (vii) Translocation of the trailing adaptor (brown); (viii) Return to open channel. (b) Raw current trace for the passage of the M13 dsDNA construct through the nanopore. Regions of the ionic current trace corresponding to steps i-viii are labeled. (c) Expanded time and current scale for raw current traces corresponding to steps i–viii. Each adaptor generates a unique current signal used to aid base calling.
    M13mp18 Dna Sequencing Standard M13mp18 Dsdna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 87/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/m13mp18 dna sequencing standard m13mp18 dsdna/product/New England Biolabs
    Average 87 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    m13mp18 dna sequencing standard m13mp18 dsdna - by Bioz Stars, 2020-04
    87/100 stars
      Buy from Supplier

    92
    New England Biolabs rna dependent dna recombinational repair rad52 dependent rna bridging reactions
    <t>RAD52</t> promotes <t>RNA-dependent</t> <t>DNA</t> recombination. a Schematic of assay (left). Non-denaturing gels showing RAD52 RNA−DNA recombination (RNA-bridging of homologous DNA) in the presence of the indicated substrates (right). b Schematic of assay (left). Non-denaturing gel showing RNase H digestion of a RAD52-mediated RNA−DNA recombination intermediate (RNA−DNA recombinant bridge) (right). c Graph showing a time course of RNA–DNA recombination (bridging) compared to DNA−DNA recombination (bridging) of left and right flanking ssDNA without RPA and in the presence and absence of RAD52. Data shown as average ± SD, n = 3. d Schematic of assay (left). Non-denaturing gel showing RAD52 RNA−DNA recombination in the presence of the indicated RPA-coated substrates (right). e Graph showing a time course of RNA−DNA recombination (bridging) compared to DNA−DNA recombination (bridging) of left and right flanking RPA-bound ssDNA in the presence and absence of RAD52. Data shown as average ± SD, n = 3. f Schematic of assay (left). Non-denaturing gel showing RAD51 RNA−DNA recombination (bridging) in the presence of RPA pre-coated substrates (right). g Schematic of assay (left). Non-denaturing gel showing RAD52 RNA−DNA recombination (bridging) of the indicated pssDNA substrates (right). h Schematic of assay (left). Non-denaturing gel showing RAD52 RNA−DNA recombination (bridging) of the indicated RPA-coated pssDNA substrates (right). * = 32 P label. % bridging indicated
    Rna Dependent Dna Recombinational Repair Rad52 Dependent Rna Bridging Reactions, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 92/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rna dependent dna recombinational repair rad52 dependent rna bridging reactions/product/New England Biolabs
    Average 92 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    rna dependent dna recombinational repair rad52 dependent rna bridging reactions - by Bioz Stars, 2020-04
    92/100 stars
      Buy from Supplier

    Image Search Results


    CRISPR adaptation to HHPV-2 infection. ( A ) Depiction of the single CRISPR structure and the preceding cas operon carried by the H. hispanica ATCC 33960 genome. Primers used to examine CRISPR expansion (in panel B) are shown as black arrows and listed in Supplementary Table S2 . ( B ) PCR assay to detect CRISPR expansion at the leader end (L1–L2), the inner part (I1–I2) or the distal end (D1–D2). DNA sampled from infected (+) or uninfected (−) cells was used as PCR templates. Lane M, dsDNA size marker. ( C ) The sequence logo showing the conserved PAM of TTC. The 20 nt upstream of each protospacer observed during HHPV-2 infection were collected and analyzed with WebLogo ( http://weblogo.berkeley.edu/logo.cgi ).

    Journal: Nucleic Acids Research

    Article Title: Adaptation of the Haloarcula hispanica CRISPR-Cas system to a purified virus strictly requires a priming process

    doi: 10.1093/nar/gkt1154

    Figure Lengend Snippet: CRISPR adaptation to HHPV-2 infection. ( A ) Depiction of the single CRISPR structure and the preceding cas operon carried by the H. hispanica ATCC 33960 genome. Primers used to examine CRISPR expansion (in panel B) are shown as black arrows and listed in Supplementary Table S2 . ( B ) PCR assay to detect CRISPR expansion at the leader end (L1–L2), the inner part (I1–I2) or the distal end (D1–D2). DNA sampled from infected (+) or uninfected (−) cells was used as PCR templates. Lane M, dsDNA size marker. ( C ) The sequence logo showing the conserved PAM of TTC. The 20 nt upstream of each protospacer observed during HHPV-2 infection were collected and analyzed with WebLogo ( http://weblogo.berkeley.edu/logo.cgi ).

    Article Snippet: The single-stranded DNA (ssDNA) (ФX174ss) and double-stranded DNA (dsDNA) (ФX174ds) from phiX174 phage (purchased from New England Biolabs) were used as controls.

    Techniques: CRISPR, Infection, Polymerase Chain Reaction, Marker, Sequencing

    Adaptation to HHPV-2 infection under different cas genetic backgrounds. ( A ) Cas requirement for adaptation. For each cas mutant, DNA was sampled from cells transformed with an empty plasmid (−) or the plasmid carrying the deleted cas gene(s) (+). The plasmid-carried cas gene(s) was/were under the control of the cas operon promoter. ( B ) Requirements for the nuclease and helicase activities of Cas3. Alanine replacement was performed for the putative key residues in the HD nuclease domain (H20A, H55A, D56A and D229A) and the DExD/H helicase domain (K315A, D439A and E440A). Another two conserved residues (His6 and Lys113) were also mutated. The empty plasmid (−) and the plasmid carrying a wild-type Cas3 (Cas3 WT ) were used, respectively, as negative and positive controls. Lane Ms, dsDNA size markers.

    Journal: Nucleic Acids Research

    Article Title: Adaptation of the Haloarcula hispanica CRISPR-Cas system to a purified virus strictly requires a priming process

    doi: 10.1093/nar/gkt1154

    Figure Lengend Snippet: Adaptation to HHPV-2 infection under different cas genetic backgrounds. ( A ) Cas requirement for adaptation. For each cas mutant, DNA was sampled from cells transformed with an empty plasmid (−) or the plasmid carrying the deleted cas gene(s) (+). The plasmid-carried cas gene(s) was/were under the control of the cas operon promoter. ( B ) Requirements for the nuclease and helicase activities of Cas3. Alanine replacement was performed for the putative key residues in the HD nuclease domain (H20A, H55A, D56A and D229A) and the DExD/H helicase domain (K315A, D439A and E440A). Another two conserved residues (His6 and Lys113) were also mutated. The empty plasmid (−) and the plasmid carrying a wild-type Cas3 (Cas3 WT ) were used, respectively, as negative and positive controls. Lane Ms, dsDNA size markers.

    Article Snippet: The single-stranded DNA (ssDNA) (ФX174ss) and double-stranded DNA (dsDNA) (ФX174ds) from phiX174 phage (purchased from New England Biolabs) were used as controls.

    Techniques: Infection, Mutagenesis, Transformation Assay, Plasmid Preparation, Mass Spectrometry

    BCCIPβ binds DNA. ( A ) BCCIPβ (0.24 μM, 0.47 μM, 0.96 μM, 1.8 μM, 2.8 μM and 4.7 μM; lanes 2–7, respectively) incubated with ϕX174 (+) ssDNA (ss; 30 μM nucleotides). ( B ) BCCIPβ (0.24 μM, 0.47 μM, 0.96 μM, 1.8 μM, 2.8 μM and 4.7 μM; lanes 2–7, respectively) was incubated with ϕX174 RF (I) dsDNA (ds; 30 μM base pairs). The reaction products were separated on a 1.0% agarose gel, and were stained with ethidium bromide. Lane 1 contained no protein, and lane 8 was deproteinized with SDS and Proteinase K (S/P) prior to loading.

    Journal: Nucleic Acids Research

    Article Title: The β-isoform of BCCIP promotes ADP release from the RAD51 presynaptic filament and enhances homologous DNA pairing

    doi: 10.1093/nar/gkw877

    Figure Lengend Snippet: BCCIPβ binds DNA. ( A ) BCCIPβ (0.24 μM, 0.47 μM, 0.96 μM, 1.8 μM, 2.8 μM and 4.7 μM; lanes 2–7, respectively) incubated with ϕX174 (+) ssDNA (ss; 30 μM nucleotides). ( B ) BCCIPβ (0.24 μM, 0.47 μM, 0.96 μM, 1.8 μM, 2.8 μM and 4.7 μM; lanes 2–7, respectively) was incubated with ϕX174 RF (I) dsDNA (ds; 30 μM base pairs). The reaction products were separated on a 1.0% agarose gel, and were stained with ethidium bromide. Lane 1 contained no protein, and lane 8 was deproteinized with SDS and Proteinase K (S/P) prior to loading.

    Article Snippet: All oligonucleotides were purchased from Integrated DNA Technologies. pBluescript was purified from E. coli using a Giga Kit (Qiagen). ϕX174 (+) virion ssDNA and ϕX174 replicative form I double-stranded DNA (dsDNA) were purchased from New England BioLabs—ϕX174 dsDNA was linearized with ApaLI (New England BioLabs).

    Techniques: Incubation, Agarose Gel Electrophoresis, Staining

    Molecular events and ionic current trace for a 2D read of a 7.25 kb M13 phage dsDNA molecule. (a) Schematic for the steps in DNA translocation through the nanopore. (i) Open channel; (ii) dsDNA with a ligated lead adaptor (blue), with a molecular motor bound to it (orange), and a hairpin adaptor (red), is captured by the nanopore. DNA translocation through the nanopore begins through the effect of an applied voltage across the membrane and the action of a molecular motor; (iii) Translocation of the lead adaptor (blue); (iv) Translocation of the template strand (gold); (v) Translocation of the hairpin adaptor (red); (vi) Translocation of the complement strand (dark blue); (vii) Translocation of the trailing adaptor (brown); (viii) Return to open channel. (b) Raw current trace for the passage of the M13 dsDNA construct through the nanopore. Regions of the ionic current trace corresponding to steps i-viii are labeled. (c) Expanded time and current scale for raw current traces corresponding to steps i–viii. Each adaptor generates a unique current signal used to aid base calling.

    Journal: Nature methods

    Article Title: Improved data analysis for the MinION nanopore sequencer

    doi: 10.1038/nmeth.3290

    Figure Lengend Snippet: Molecular events and ionic current trace for a 2D read of a 7.25 kb M13 phage dsDNA molecule. (a) Schematic for the steps in DNA translocation through the nanopore. (i) Open channel; (ii) dsDNA with a ligated lead adaptor (blue), with a molecular motor bound to it (orange), and a hairpin adaptor (red), is captured by the nanopore. DNA translocation through the nanopore begins through the effect of an applied voltage across the membrane and the action of a molecular motor; (iii) Translocation of the lead adaptor (blue); (iv) Translocation of the template strand (gold); (v) Translocation of the hairpin adaptor (red); (vi) Translocation of the complement strand (dark blue); (vii) Translocation of the trailing adaptor (brown); (viii) Return to open channel. (b) Raw current trace for the passage of the M13 dsDNA construct through the nanopore. Regions of the ionic current trace corresponding to steps i-viii are labeled. (c) Expanded time and current scale for raw current traces corresponding to steps i–viii. Each adaptor generates a unique current signal used to aid base calling.

    Article Snippet: M13mp18 DNA sequencing standard M13mp18 dsDNA was obtained from New England Biolabs (Cat No. N4018S).

    Techniques: Translocation Assay, Construct, Labeling

    RAD52 promotes RNA-dependent DNA recombination. a Schematic of assay (left). Non-denaturing gels showing RAD52 RNA−DNA recombination (RNA-bridging of homologous DNA) in the presence of the indicated substrates (right). b Schematic of assay (left). Non-denaturing gel showing RNase H digestion of a RAD52-mediated RNA−DNA recombination intermediate (RNA−DNA recombinant bridge) (right). c Graph showing a time course of RNA–DNA recombination (bridging) compared to DNA−DNA recombination (bridging) of left and right flanking ssDNA without RPA and in the presence and absence of RAD52. Data shown as average ± SD, n = 3. d Schematic of assay (left). Non-denaturing gel showing RAD52 RNA−DNA recombination in the presence of the indicated RPA-coated substrates (right). e Graph showing a time course of RNA−DNA recombination (bridging) compared to DNA−DNA recombination (bridging) of left and right flanking RPA-bound ssDNA in the presence and absence of RAD52. Data shown as average ± SD, n = 3. f Schematic of assay (left). Non-denaturing gel showing RAD51 RNA−DNA recombination (bridging) in the presence of RPA pre-coated substrates (right). g Schematic of assay (left). Non-denaturing gel showing RAD52 RNA−DNA recombination (bridging) of the indicated pssDNA substrates (right). h Schematic of assay (left). Non-denaturing gel showing RAD52 RNA−DNA recombination (bridging) of the indicated RPA-coated pssDNA substrates (right). * = 32 P label. % bridging indicated

    Journal: Nature Communications

    Article Title: How RNA transcripts coordinate DNA recombination and repair

    doi: 10.1038/s41467-018-03483-7

    Figure Lengend Snippet: RAD52 promotes RNA-dependent DNA recombination. a Schematic of assay (left). Non-denaturing gels showing RAD52 RNA−DNA recombination (RNA-bridging of homologous DNA) in the presence of the indicated substrates (right). b Schematic of assay (left). Non-denaturing gel showing RNase H digestion of a RAD52-mediated RNA−DNA recombination intermediate (RNA−DNA recombinant bridge) (right). c Graph showing a time course of RNA–DNA recombination (bridging) compared to DNA−DNA recombination (bridging) of left and right flanking ssDNA without RPA and in the presence and absence of RAD52. Data shown as average ± SD, n = 3. d Schematic of assay (left). Non-denaturing gel showing RAD52 RNA−DNA recombination in the presence of the indicated RPA-coated substrates (right). e Graph showing a time course of RNA−DNA recombination (bridging) compared to DNA−DNA recombination (bridging) of left and right flanking RPA-bound ssDNA in the presence and absence of RAD52. Data shown as average ± SD, n = 3. f Schematic of assay (left). Non-denaturing gel showing RAD51 RNA−DNA recombination (bridging) in the presence of RPA pre-coated substrates (right). g Schematic of assay (left). Non-denaturing gel showing RAD52 RNA−DNA recombination (bridging) of the indicated pssDNA substrates (right). h Schematic of assay (left). Non-denaturing gel showing RAD52 RNA−DNA recombination (bridging) of the indicated RPA-coated pssDNA substrates (right). * = 32 P label. % bridging indicated

    Article Snippet: RNA-dependent DNA recombinational repair RAD52-dependent RNA bridging reactions were performed in 20 μl of buffer A as described above (Fig. ), followed by ligation with 0.846 μm bacteriophage T4 DNA ligase (New England Biolabs) with 0.5 mm MgCl2 (Fig. ) for 2 h at 25 °C.

    Techniques: Recombinant, Recombinase Polymerase Amplification

    RAD52 promotes RNA-dependent recombinational repair of DSBs. a Schematic of assay (left). Non-denaturing gel showing a time course of RAD52-dependent RNA−DNA recombination (bridging) of blunt-ended DNA in the presence of RPA (middle). Plot showing time course of RAD52-dependent RNA−DNA recombination (bridging) of blunt-ended DNA in the presence of RPA (right). Data shown as average ± SEM, n = 3. b Schematic of assay (left). Non-denaturing gels showing RAD52-dependent RNA−DNA recombination (bridging) of blunt-ended DNA in the presence (left) and absence (right) of RPA. c Schematic of assays showing RAD52-dependent RNA−DNA recombination (bridging) of blunt-ended DNA employing either RAD52-dsDNA pre-incubation (right schematic) or RAD52-RNA (left schematic) pre-incubation steps, and performed either with and without RPA. Graph showing quantification of RAD52-dependent RNA−DNA recombination (bridging) of blunt-ended DNA utilizing the indicated pre-incubation steps and with and without RPA (right). Data shown as average ± SD, n = 3. d Schematic of assay (left). Denaturing gel showing RAD52-dependent RNA−DNA recombinational repair (bridging followed by ligation) of blunt-ended DNA in the presence of the indicated proteins and substrates (middle). Graph showing percent of RAD52-dependent RNA-mediated recombinational repair of blunt-ended DNA (% ligation) (right). Data shown as average ± SD, n = 3. ***, p = 0.0008 (unpaired Student’s t- test). * = 32 P label

    Journal: Nature Communications

    Article Title: How RNA transcripts coordinate DNA recombination and repair

    doi: 10.1038/s41467-018-03483-7

    Figure Lengend Snippet: RAD52 promotes RNA-dependent recombinational repair of DSBs. a Schematic of assay (left). Non-denaturing gel showing a time course of RAD52-dependent RNA−DNA recombination (bridging) of blunt-ended DNA in the presence of RPA (middle). Plot showing time course of RAD52-dependent RNA−DNA recombination (bridging) of blunt-ended DNA in the presence of RPA (right). Data shown as average ± SEM, n = 3. b Schematic of assay (left). Non-denaturing gels showing RAD52-dependent RNA−DNA recombination (bridging) of blunt-ended DNA in the presence (left) and absence (right) of RPA. c Schematic of assays showing RAD52-dependent RNA−DNA recombination (bridging) of blunt-ended DNA employing either RAD52-dsDNA pre-incubation (right schematic) or RAD52-RNA (left schematic) pre-incubation steps, and performed either with and without RPA. Graph showing quantification of RAD52-dependent RNA−DNA recombination (bridging) of blunt-ended DNA utilizing the indicated pre-incubation steps and with and without RPA (right). Data shown as average ± SD, n = 3. d Schematic of assay (left). Denaturing gel showing RAD52-dependent RNA−DNA recombinational repair (bridging followed by ligation) of blunt-ended DNA in the presence of the indicated proteins and substrates (middle). Graph showing percent of RAD52-dependent RNA-mediated recombinational repair of blunt-ended DNA (% ligation) (right). Data shown as average ± SD, n = 3. ***, p = 0.0008 (unpaired Student’s t- test). * = 32 P label

    Article Snippet: RNA-dependent DNA recombinational repair RAD52-dependent RNA bridging reactions were performed in 20 μl of buffer A as described above (Fig. ), followed by ligation with 0.846 μm bacteriophage T4 DNA ligase (New England Biolabs) with 0.5 mm MgCl2 (Fig. ) for 2 h at 25 °C.

    Techniques: Recombinase Polymerase Amplification, Incubation, Ligation, DNA Ligation

    RAD52 promotes RNA transcript-dependent DNA recombinational repair. a Schematic of assay (left). Denaturing gel showing RAD52-dependent RNA−DNA repair in the presence of left and right ssDNA flanks and the indicated proteins (right). b Schematic of assay (left). Denaturing gel showing RAD52-dependent RNA−DNA repair in the presence of RPA-coated left and right ssDNA flanks and indicated proteins (right). c Schematic of assay (left). Denaturing gel showing RAD52-mediated RNA transcript-dependent DNA repair in the presence of RPA-coated left and right ssDNA flanks and indicated proteins (middle). Graph showing percent of RNA transcript-dependent DNA recombinational repair (right). Data shown as average ± SD, n = 3. *, p = 0.016 (unpaired Student’s t -test). Sequencing chromatogram of RNA transcript-dependent DNA recombinational repair product (bottom). * = 32 P label

    Journal: Nature Communications

    Article Title: How RNA transcripts coordinate DNA recombination and repair

    doi: 10.1038/s41467-018-03483-7

    Figure Lengend Snippet: RAD52 promotes RNA transcript-dependent DNA recombinational repair. a Schematic of assay (left). Denaturing gel showing RAD52-dependent RNA−DNA repair in the presence of left and right ssDNA flanks and the indicated proteins (right). b Schematic of assay (left). Denaturing gel showing RAD52-dependent RNA−DNA repair in the presence of RPA-coated left and right ssDNA flanks and indicated proteins (right). c Schematic of assay (left). Denaturing gel showing RAD52-mediated RNA transcript-dependent DNA repair in the presence of RPA-coated left and right ssDNA flanks and indicated proteins (middle). Graph showing percent of RNA transcript-dependent DNA recombinational repair (right). Data shown as average ± SD, n = 3. *, p = 0.016 (unpaired Student’s t -test). Sequencing chromatogram of RNA transcript-dependent DNA recombinational repair product (bottom). * = 32 P label

    Article Snippet: RNA-dependent DNA recombinational repair RAD52-dependent RNA bridging reactions were performed in 20 μl of buffer A as described above (Fig. ), followed by ligation with 0.846 μm bacteriophage T4 DNA ligase (New England Biolabs) with 0.5 mm MgCl2 (Fig. ) for 2 h at 25 °C.

    Techniques: Recombinase Polymerase Amplification, Sequencing

    Models of RAD52-mediated RNA−DNA repair. a RNA-bridging DSB repair model. RAD52 utilizes RNA to tether both ends of a homologous DSB which forms a DNA synapse for ligation. RNA degradation by RNase H may also occur. b RNA-templated DSB repair model. RAD52 forms an RNA−DNA hybrid along the 3′ overhang of a DSB. The RNA is then used as a template for DNA repair synthesis by RT. The RNA is then degraded by RNase H and RAD52 promotes SSA of the opposing homologous ssDNA overhangs. Final processing of the DSB involves gap filling and ligation

    Journal: Nature Communications

    Article Title: How RNA transcripts coordinate DNA recombination and repair

    doi: 10.1038/s41467-018-03483-7

    Figure Lengend Snippet: Models of RAD52-mediated RNA−DNA repair. a RNA-bridging DSB repair model. RAD52 utilizes RNA to tether both ends of a homologous DSB which forms a DNA synapse for ligation. RNA degradation by RNase H may also occur. b RNA-templated DSB repair model. RAD52 forms an RNA−DNA hybrid along the 3′ overhang of a DSB. The RNA is then used as a template for DNA repair synthesis by RT. The RNA is then degraded by RNase H and RAD52 promotes SSA of the opposing homologous ssDNA overhangs. Final processing of the DSB involves gap filling and ligation

    Article Snippet: RNA-dependent DNA recombinational repair RAD52-dependent RNA bridging reactions were performed in 20 μl of buffer A as described above (Fig. ), followed by ligation with 0.846 μm bacteriophage T4 DNA ligase (New England Biolabs) with 0.5 mm MgCl2 (Fig. ) for 2 h at 25 °C.

    Techniques: Ligation

    RAD52 promotes RNA transcript-templated DNA recombination. a Schematic of assay (left). Denaturing gel showing reverse transcription of a RNA−DNA recombinant half-bridge in the presence of the indicated proteins and RNA (middle). Graph showing percent extension of a RNA−DNA recombinant half-bridge by RT in the presence and absence of RAD52 (right). Data shown as average ± SD, n = 4, ***, p

    Journal: Nature Communications

    Article Title: How RNA transcripts coordinate DNA recombination and repair

    doi: 10.1038/s41467-018-03483-7

    Figure Lengend Snippet: RAD52 promotes RNA transcript-templated DNA recombination. a Schematic of assay (left). Denaturing gel showing reverse transcription of a RNA−DNA recombinant half-bridge in the presence of the indicated proteins and RNA (middle). Graph showing percent extension of a RNA−DNA recombinant half-bridge by RT in the presence and absence of RAD52 (right). Data shown as average ± SD, n = 4, ***, p

    Article Snippet: RNA-dependent DNA recombinational repair RAD52-dependent RNA bridging reactions were performed in 20 μl of buffer A as described above (Fig. ), followed by ligation with 0.846 μm bacteriophage T4 DNA ligase (New England Biolabs) with 0.5 mm MgCl2 (Fig. ) for 2 h at 25 °C.

    Techniques: Recombinant