dna purification kit  (Zymo Research)


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    Name:
    Quick DNA Viral Kit
    Description:
    The Quick DNA Viral Kits provide for the rapid isolation of high quality viral DNA from a wide range of biological sources A uniquely designed buffer is included for the efficient denaturation of viral particles in whole blood fresh and stored plasma serum tissue ascites cultured cells and from liquid samples DNA can be eluted with elution buffer or water and is suitable for subsequent PCR nucleotide blotting and restriction endonuclease digestion procedures
    Catalog Number:
    d3016
    Product Aliases:
    ZR Viral DNA Kit
    Price:
    None
    Applications:
    Viral DNA Purification
    Size:
    50 units
    Category:
    Life Science Reagents and Media
    Buy from Supplier


    Structured Review

    Zymo Research dna purification kit
    Quick DNA Viral Kit
    The Quick DNA Viral Kits provide for the rapid isolation of high quality viral DNA from a wide range of biological sources A uniquely designed buffer is included for the efficient denaturation of viral particles in whole blood fresh and stored plasma serum tissue ascites cultured cells and from liquid samples DNA can be eluted with elution buffer or water and is suitable for subsequent PCR nucleotide blotting and restriction endonuclease digestion procedures
    https://www.bioz.com/result/dna purification kit/product/Zymo Research
    Average 99 stars, based on 140 article reviews
    Price from $9.99 to $1999.99
    dna purification kit - by Bioz Stars, 2020-10
    99/100 stars

    Images

    1) Product Images from "Efficient Homology-directed Repair with Circular ssDNA Donors"

    Article Title: Efficient Homology-directed Repair with Circular ssDNA Donors

    Journal: bioRxiv

    doi: 10.1101/864199

    Preparation of different ssDNA templates. (A) Donor DNA is cloned into phagemid vectors containing an f1 bacteriophage origin of replication and an antibiotic resistance marker. The plasmid is transformed into E. coli cells and superinfected with a helper phage. Depending on the orientation of the f1 origin, one particular strand is packaged into phage particles and extruded into the media from which phage particles are precipitated and cssDNA is purified. ( B) PCR product encoding donor DNA is generated using a 5’ primer containing a T7 promoter within the tail. The product is then used as a template for in vitro transcription to generate RNA. This RNA in turn is used as a template for reverse transcription using a reverse transcriptase such as TGIRT to generate linear ssDNA (T-lssDNA). ( C) A PCR primer is biotinylated at the 5’ end. The resulting biotinylated PCR product is then immobilized on streptavidin magnetic beads. The immobilized PCR product is then subjected to alkaline denaturation to separate the biotinylated strand from the non-biotinylated strand. The eluted non-biotinylated DNA strand is then recovered for use as an lssDNA (B-lssDNA). (D) S1 nuclease digestion of DNA templates. To determine whether the templates generated are entirely single stranded, dsDNA products (Plasmid and PCR templates) and ssDNA templates (cssDNA,T-lssDNA and B-lssDNA) were digested with S1 nuclease. Undigested product (“Undig.”) was loaded alongside digested products (“Dig.”)
    Figure Legend Snippet: Preparation of different ssDNA templates. (A) Donor DNA is cloned into phagemid vectors containing an f1 bacteriophage origin of replication and an antibiotic resistance marker. The plasmid is transformed into E. coli cells and superinfected with a helper phage. Depending on the orientation of the f1 origin, one particular strand is packaged into phage particles and extruded into the media from which phage particles are precipitated and cssDNA is purified. ( B) PCR product encoding donor DNA is generated using a 5’ primer containing a T7 promoter within the tail. The product is then used as a template for in vitro transcription to generate RNA. This RNA in turn is used as a template for reverse transcription using a reverse transcriptase such as TGIRT to generate linear ssDNA (T-lssDNA). ( C) A PCR primer is biotinylated at the 5’ end. The resulting biotinylated PCR product is then immobilized on streptavidin magnetic beads. The immobilized PCR product is then subjected to alkaline denaturation to separate the biotinylated strand from the non-biotinylated strand. The eluted non-biotinylated DNA strand is then recovered for use as an lssDNA (B-lssDNA). (D) S1 nuclease digestion of DNA templates. To determine whether the templates generated are entirely single stranded, dsDNA products (Plasmid and PCR templates) and ssDNA templates (cssDNA,T-lssDNA and B-lssDNA) were digested with S1 nuclease. Undigested product (“Undig.”) was loaded alongside digested products (“Dig.”)

    Techniques Used: Clone Assay, Marker, Plasmid Preparation, Transformation Assay, Purification, Polymerase Chain Reaction, Generated, In Vitro, Magnetic Beads

    2) Product Images from "Detection of Low-Abundance KRAS Mutations in Colorectal Cancer Using Microfluidic Capillary Electrophoresis-Based Restriction Fragment Length Polymorphism Method with Optimized Assay Conditions"

    Article Title: Detection of Low-Abundance KRAS Mutations in Colorectal Cancer Using Microfluidic Capillary Electrophoresis-Based Restriction Fragment Length Polymorphism Method with Optimized Assay Conditions

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0054510

    Schematic view of microfluidic capillary electrophoresis-based restriction fragment length polymorphism (µCE-based RFLP) platform. (a) Mismatched primer PCR. A KRAS gene fragment containing codon 12 was amplified from gDNA with mismatched primer, by which a base substitution was introduced to the amplicon and a Mva I restriction endonuclease recognition site was created for wild-type codon 12. (b) Mva I digestion. The amplicon from wild-type template could be cleaved into two fragments, the amplicon from mutant template could not be digested due to the loss of recognition site, and the amplicon from heterozygous template was halfly digested. (c) µCE. The digested amplicon was loaded into microfluidic chip and separated by CE according to the fragment length. The wild type template resolved into two peaks, the mutant template only showed one peak, and the heterozygous template resolved into three peaks. gDNA, genomic DNA. SR: sample reservoir; BR: buffer reservoir; SW: sample waste reservoir; BW: buffer waste reservoir. →, the direction of fluid flow during sample loading and separation modes.
    Figure Legend Snippet: Schematic view of microfluidic capillary electrophoresis-based restriction fragment length polymorphism (µCE-based RFLP) platform. (a) Mismatched primer PCR. A KRAS gene fragment containing codon 12 was amplified from gDNA with mismatched primer, by which a base substitution was introduced to the amplicon and a Mva I restriction endonuclease recognition site was created for wild-type codon 12. (b) Mva I digestion. The amplicon from wild-type template could be cleaved into two fragments, the amplicon from mutant template could not be digested due to the loss of recognition site, and the amplicon from heterozygous template was halfly digested. (c) µCE. The digested amplicon was loaded into microfluidic chip and separated by CE according to the fragment length. The wild type template resolved into two peaks, the mutant template only showed one peak, and the heterozygous template resolved into three peaks. gDNA, genomic DNA. SR: sample reservoir; BR: buffer reservoir; SW: sample waste reservoir; BW: buffer waste reservoir. →, the direction of fluid flow during sample loading and separation modes.

    Techniques Used: Electrophoresis, Polymerase Chain Reaction, Amplification, Mutagenesis, Chromatin Immunoprecipitation, Flow Cytometry

    3) Product Images from "Technical and Regulatory Considerations for Taking Liquid Biopsy to the Clinic: Validation of the JAX PlasmaMonitorTM Assay"

    Article Title: Technical and Regulatory Considerations for Taking Liquid Biopsy to the Clinic: Validation of the JAX PlasmaMonitorTM Assay

    Journal: Biomarker Insights

    doi: 10.1177/1177271919826545

    PlasmaMonitor™ pre-analytical and technical considerations. (A) Comparison of four commercial cfDNA extraction kits for yield; (B) quantification and qualification of the extracted cfDNA using a custom Human Genomic DNA QC Assay; (C) comparison data demonstrating that using our custom quality approach provides more robust quantification data in comparison with the standard Qubit assay; (D) pre-analytical validation steps including sensitivity and limit of detection (LOD), inter-assay reproducibility, intra-assay reproducibility, and specificity and accuracy; (E) post-sequencing validation steps including sensitivity and LOD, inter-assay reproducibility, intra-assay reproducibility, and specificity and accuracy.
    Figure Legend Snippet: PlasmaMonitor™ pre-analytical and technical considerations. (A) Comparison of four commercial cfDNA extraction kits for yield; (B) quantification and qualification of the extracted cfDNA using a custom Human Genomic DNA QC Assay; (C) comparison data demonstrating that using our custom quality approach provides more robust quantification data in comparison with the standard Qubit assay; (D) pre-analytical validation steps including sensitivity and limit of detection (LOD), inter-assay reproducibility, intra-assay reproducibility, and specificity and accuracy; (E) post-sequencing validation steps including sensitivity and LOD, inter-assay reproducibility, intra-assay reproducibility, and specificity and accuracy.

    Techniques Used: Inter Assay, Intra Assay, Sequencing

    4) Product Images from "The role of the DNA damage response in zebrafish and cellular models of Diamond Blackfan anemia"

    Article Title: The role of the DNA damage response in zebrafish and cellular models of Diamond Blackfan anemia

    Journal: Disease Models & Mechanisms

    doi: 10.1242/dmm.015495

    Rescue of RP-deficient zebrafish with exogenous nucleosides. (A) At 48 hpf, Rpl11 mutants incorporated more [ 3 H] deoxycytidine into DNA than their wild-type siblings ( P
    Figure Legend Snippet: Rescue of RP-deficient zebrafish with exogenous nucleosides. (A) At 48 hpf, Rpl11 mutants incorporated more [ 3 H] deoxycytidine into DNA than their wild-type siblings ( P

    Techniques Used:

    RP-deficient zebrafish show activation of the DNA damage checkpoint pathway. (A) Phosphorylation of residue Ser139 of histone H2A.X was induced in embryos that had been injected with an Rps19-specific morpholino (MO). Western blotting was performed at 24 hpf. Staining of tubulin was used for a loading control. Molecular masses are shown on the right. Wt, wild type. (B) Phosphorylation of residue Ser345 in Chk1 kinase was increased in Rps19-deficient embryos (MO). Western blotting was performed at 24 hpf. (C) Embryos that had been injected with an Rps19 morpholino had increased levels of p53; the treatment of morphants with 3 nM of Chk1 inhibitor PF477736 (PF), 10 nM of the ATR and ATM inhibitor CGK733 (GCK), or 3 nM of the ATM inhibitor KU60019 (KU) reduced p53 levels. Western blotting was performed at 24 hpf. (D) Treatment of Rpl11 mutants with inhibitors of the ATR-ATM-Chk1 pathway resulted in downregulation of the p53 targets p21 and puma . Gene expression was analyzed by using RT-qPCR. The fold change of gene expression was calculated relative to expression in wild-type siblings. Means±s.d. are shown. (E) Embryos that had been injected with a morpholino against Rps19 (Rps19 MO) had few red blood cells at 3.5 days post-fertilization. The treatment of Rps19 morphants with PF477736 partially rescued this hematopoietic defect.
    Figure Legend Snippet: RP-deficient zebrafish show activation of the DNA damage checkpoint pathway. (A) Phosphorylation of residue Ser139 of histone H2A.X was induced in embryos that had been injected with an Rps19-specific morpholino (MO). Western blotting was performed at 24 hpf. Staining of tubulin was used for a loading control. Molecular masses are shown on the right. Wt, wild type. (B) Phosphorylation of residue Ser345 in Chk1 kinase was increased in Rps19-deficient embryos (MO). Western blotting was performed at 24 hpf. (C) Embryos that had been injected with an Rps19 morpholino had increased levels of p53; the treatment of morphants with 3 nM of Chk1 inhibitor PF477736 (PF), 10 nM of the ATR and ATM inhibitor CGK733 (GCK), or 3 nM of the ATM inhibitor KU60019 (KU) reduced p53 levels. Western blotting was performed at 24 hpf. (D) Treatment of Rpl11 mutants with inhibitors of the ATR-ATM-Chk1 pathway resulted in downregulation of the p53 targets p21 and puma . Gene expression was analyzed by using RT-qPCR. The fold change of gene expression was calculated relative to expression in wild-type siblings. Means±s.d. are shown. (E) Embryos that had been injected with a morpholino against Rps19 (Rps19 MO) had few red blood cells at 3.5 days post-fertilization. The treatment of Rps19 morphants with PF477736 partially rescued this hematopoietic defect.

    Techniques Used: Activation Assay, Injection, Western Blot, Staining, Expressing, Quantitative RT-PCR

    Related Articles

    DNA Extraction:

    Article Title: Fructophilic Lactobacillus kunkeei and Lactobacillus brevis isolated from fresh flowers, bees and bee-hives.
    Article Snippet: .. Two-hundred-and-thirty-six isolates were collected from fresh flowers, bees and bee-hives. .. Two-hundred-and-thirty-six isolates were collected from fresh flowers, bees and bee-hives.

    Article Title: New Primers for Discovering Fungal Diversity Using Nuclear Large Ribosomal DNA
    Article Snippet: .. Total genomic DNA was extracted from 25 mg of each sub-sample of peat moss from each horizon using a Zymo DNA isolation kit (Zymo Research Corporation) to obtain genomic DNA free of PCR-inhibitory phenolic compounds. .. Genomic DNA was quantified and tested for extraction quality using a nanodrop (Nanodrop 2000, Thermo Scientific) ( ).

    Isolation:

    Article Title: Fructophilic Lactobacillus kunkeei and Lactobacillus brevis isolated from fresh flowers, bees and bee-hives.
    Article Snippet: .. Two-hundred-and-thirty-six isolates were collected from fresh flowers, bees and bee-hives. .. Two-hundred-and-thirty-six isolates were collected from fresh flowers, bees and bee-hives.

    Article Title: Technical and Regulatory Considerations for Taking Liquid Biopsy to the Clinic: Validation of the JAX PlasmaMonitorTM Assay
    Article Snippet: .. We evaluated four commercial cfDNA extraction kits across 35 samples; QIAamp circulating nucleic acid kit (Qiagen), NucleoSpin Plasma XS (Macherey-Nagel), ZR Serum DNA kit (ZYMO Research), and the NEXTPrep-Mag cfDNA isolation kit (Bioo Scientific) ( ). .. Based on the yield, scalability, turnaround time for processing, and cost effectiveness, we opted for the NEXTPrep-Mag cfDNA isolation kit.

    Purification:

    Article Title: Detection of Low-Abundance KRAS Mutations in Colorectal Cancer Using Microfluidic Capillary Electrophoresis-Based Restriction Fragment Length Polymorphism Method with Optimized Assay Conditions
    Article Snippet: .. The PCR was performed with preheating at 95°C for 5 min, followed by 35 cycles at 94°C for 40 seconds, 55°C for 40 seconds, 72°C for 1 min, and a final extension at 72°C for 7 min. All amplicons of the KRAS gene were purified using a DNA purification kit (Zymo, Inc. ) and directly sequenced using both forward and reverse primers on an ABI 377 sequencer. .. Clone Sequencing Clone sequencing was performed for the PETs that showed mutation peak profiles in the µCE electropherograms that were not detectable by direct sequencing.

    Article Title: Efficient Homology-directed Repair with Circular ssDNA Donors
    Article Snippet: .. Subsequently, PCR product was purified using the Zymo DNA purification kit and sent for analysis by Sanger sequencing along with primers listed in Supplementary Table S4. ..

    Polymerase Chain Reaction:

    Article Title: Detection of Low-Abundance KRAS Mutations in Colorectal Cancer Using Microfluidic Capillary Electrophoresis-Based Restriction Fragment Length Polymorphism Method with Optimized Assay Conditions
    Article Snippet: .. The PCR was performed with preheating at 95°C for 5 min, followed by 35 cycles at 94°C for 40 seconds, 55°C for 40 seconds, 72°C for 1 min, and a final extension at 72°C for 7 min. All amplicons of the KRAS gene were purified using a DNA purification kit (Zymo, Inc. ) and directly sequenced using both forward and reverse primers on an ABI 377 sequencer. .. Clone Sequencing Clone sequencing was performed for the PETs that showed mutation peak profiles in the µCE electropherograms that were not detectable by direct sequencing.

    Article Title: New Primers for Discovering Fungal Diversity Using Nuclear Large Ribosomal DNA
    Article Snippet: .. Total genomic DNA was extracted from 25 mg of each sub-sample of peat moss from each horizon using a Zymo DNA isolation kit (Zymo Research Corporation) to obtain genomic DNA free of PCR-inhibitory phenolic compounds. .. Genomic DNA was quantified and tested for extraction quality using a nanodrop (Nanodrop 2000, Thermo Scientific) ( ).

    Article Title: Efficient Homology-directed Repair with Circular ssDNA Donors
    Article Snippet: .. Subsequently, PCR product was purified using the Zymo DNA purification kit and sent for analysis by Sanger sequencing along with primers listed in Supplementary Table S4. ..

    Incubation:

    Article Title: Bacteriophage biodistribution and infectivity from honeybee to bee larvae using a T7 phage model
    Article Snippet: .. Zymo Quick-DNA™ Viral Kit was used for DNA purification, with some modifications relatively to the manufacturer instructions: a 3 hours period of incubation with the supplied Lysis Buffer and the elution in 15 µL of the supplied Storage Buffer. .. In order to quantify the IAC concentration present in the purified DNA, a standard curve was obtained (CqIAC = −3.781 × Log [IAC] (ng.µL−1 ) + 8.369 (Cq = quantification cycle)) using several concentrations of the LacZ amplicon (5.5, 0.55, 0.11, 0.055 ng.µL−1 ).

    DNA Purification:

    Article Title: The role of the DNA damage response in zebrafish and cellular models of Diamond Blackfan anemia
    Article Snippet: .. At 48 hpf, genomic DNA was prepared from 25 embryos using DNA purification kit (Zymo Research, Irvine, CA). ..

    Article Title: Detection of Low-Abundance KRAS Mutations in Colorectal Cancer Using Microfluidic Capillary Electrophoresis-Based Restriction Fragment Length Polymorphism Method with Optimized Assay Conditions
    Article Snippet: .. The PCR was performed with preheating at 95°C for 5 min, followed by 35 cycles at 94°C for 40 seconds, 55°C for 40 seconds, 72°C for 1 min, and a final extension at 72°C for 7 min. All amplicons of the KRAS gene were purified using a DNA purification kit (Zymo, Inc. ) and directly sequenced using both forward and reverse primers on an ABI 377 sequencer. .. Clone Sequencing Clone sequencing was performed for the PETs that showed mutation peak profiles in the µCE electropherograms that were not detectable by direct sequencing.

    Article Title: Bacteriophage biodistribution and infectivity from honeybee to bee larvae using a T7 phage model
    Article Snippet: .. Zymo Quick-DNA™ Viral Kit was used for DNA purification, with some modifications relatively to the manufacturer instructions: a 3 hours period of incubation with the supplied Lysis Buffer and the elution in 15 µL of the supplied Storage Buffer. .. In order to quantify the IAC concentration present in the purified DNA, a standard curve was obtained (CqIAC = −3.781 × Log [IAC] (ng.µL−1 ) + 8.369 (Cq = quantification cycle)) using several concentrations of the LacZ amplicon (5.5, 0.55, 0.11, 0.055 ng.µL−1 ).

    Article Title: Efficient Homology-directed Repair with Circular ssDNA Donors
    Article Snippet: .. Subsequently, PCR product was purified using the Zymo DNA purification kit and sent for analysis by Sanger sequencing along with primers listed in Supplementary Table S4. ..

    Sequencing:

    Article Title: Efficient Homology-directed Repair with Circular ssDNA Donors
    Article Snippet: .. Subsequently, PCR product was purified using the Zymo DNA purification kit and sent for analysis by Sanger sequencing along with primers listed in Supplementary Table S4. ..

    Lysis:

    Article Title: Bacteriophage biodistribution and infectivity from honeybee to bee larvae using a T7 phage model
    Article Snippet: .. Zymo Quick-DNA™ Viral Kit was used for DNA purification, with some modifications relatively to the manufacturer instructions: a 3 hours period of incubation with the supplied Lysis Buffer and the elution in 15 µL of the supplied Storage Buffer. .. In order to quantify the IAC concentration present in the purified DNA, a standard curve was obtained (CqIAC = −3.781 × Log [IAC] (ng.µL−1 ) + 8.369 (Cq = quantification cycle)) using several concentrations of the LacZ amplicon (5.5, 0.55, 0.11, 0.055 ng.µL−1 ).

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  • 99
    Zymo Research dna purification kit
    Preparation of different ssDNA templates. (A) Donor <t>DNA</t> is cloned into phagemid vectors containing an f1 bacteriophage origin of replication and an antibiotic resistance marker. The plasmid is transformed into E. coli cells and superinfected with a helper phage. Depending on the orientation of the f1 origin, one particular strand is packaged into phage particles and extruded into the media from which phage particles are precipitated and cssDNA is purified. ( B) <t>PCR</t> product encoding donor DNA is generated using a 5’ primer containing a T7 promoter within the tail. The product is then used as a template for in vitro transcription to generate RNA. This RNA in turn is used as a template for reverse transcription using a reverse transcriptase such as TGIRT to generate linear ssDNA (T-lssDNA). ( C) A PCR primer is biotinylated at the 5’ end. The resulting biotinylated PCR product is then immobilized on streptavidin magnetic beads. The immobilized PCR product is then subjected to alkaline denaturation to separate the biotinylated strand from the non-biotinylated strand. The eluted non-biotinylated DNA strand is then recovered for use as an lssDNA (B-lssDNA). (D) S1 nuclease digestion of DNA templates. To determine whether the templates generated are entirely single stranded, dsDNA products (Plasmid and PCR templates) and ssDNA templates (cssDNA,T-lssDNA and B-lssDNA) were digested with S1 nuclease. Undigested product (“Undig.”) was loaded alongside digested products (“Dig.”)
    Dna Purification Kit, supplied by Zymo Research, used in various techniques. Bioz Stars score: 99/100, based on 38 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dna purification kit/product/Zymo Research
    Average 99 stars, based on 38 article reviews
    Price from $9.99 to $1999.99
    dna purification kit - by Bioz Stars, 2020-10
    99/100 stars
      Buy from Supplier

    Image Search Results


    Preparation of different ssDNA templates. (A) Donor DNA is cloned into phagemid vectors containing an f1 bacteriophage origin of replication and an antibiotic resistance marker. The plasmid is transformed into E. coli cells and superinfected with a helper phage. Depending on the orientation of the f1 origin, one particular strand is packaged into phage particles and extruded into the media from which phage particles are precipitated and cssDNA is purified. ( B) PCR product encoding donor DNA is generated using a 5’ primer containing a T7 promoter within the tail. The product is then used as a template for in vitro transcription to generate RNA. This RNA in turn is used as a template for reverse transcription using a reverse transcriptase such as TGIRT to generate linear ssDNA (T-lssDNA). ( C) A PCR primer is biotinylated at the 5’ end. The resulting biotinylated PCR product is then immobilized on streptavidin magnetic beads. The immobilized PCR product is then subjected to alkaline denaturation to separate the biotinylated strand from the non-biotinylated strand. The eluted non-biotinylated DNA strand is then recovered for use as an lssDNA (B-lssDNA). (D) S1 nuclease digestion of DNA templates. To determine whether the templates generated are entirely single stranded, dsDNA products (Plasmid and PCR templates) and ssDNA templates (cssDNA,T-lssDNA and B-lssDNA) were digested with S1 nuclease. Undigested product (“Undig.”) was loaded alongside digested products (“Dig.”)

    Journal: bioRxiv

    Article Title: Efficient Homology-directed Repair with Circular ssDNA Donors

    doi: 10.1101/864199

    Figure Lengend Snippet: Preparation of different ssDNA templates. (A) Donor DNA is cloned into phagemid vectors containing an f1 bacteriophage origin of replication and an antibiotic resistance marker. The plasmid is transformed into E. coli cells and superinfected with a helper phage. Depending on the orientation of the f1 origin, one particular strand is packaged into phage particles and extruded into the media from which phage particles are precipitated and cssDNA is purified. ( B) PCR product encoding donor DNA is generated using a 5’ primer containing a T7 promoter within the tail. The product is then used as a template for in vitro transcription to generate RNA. This RNA in turn is used as a template for reverse transcription using a reverse transcriptase such as TGIRT to generate linear ssDNA (T-lssDNA). ( C) A PCR primer is biotinylated at the 5’ end. The resulting biotinylated PCR product is then immobilized on streptavidin magnetic beads. The immobilized PCR product is then subjected to alkaline denaturation to separate the biotinylated strand from the non-biotinylated strand. The eluted non-biotinylated DNA strand is then recovered for use as an lssDNA (B-lssDNA). (D) S1 nuclease digestion of DNA templates. To determine whether the templates generated are entirely single stranded, dsDNA products (Plasmid and PCR templates) and ssDNA templates (cssDNA,T-lssDNA and B-lssDNA) were digested with S1 nuclease. Undigested product (“Undig.”) was loaded alongside digested products (“Dig.”)

    Article Snippet: Subsequently, PCR product was purified using the Zymo DNA purification kit and sent for analysis by Sanger sequencing along with primers listed in Supplementary Table S4.

    Techniques: Clone Assay, Marker, Plasmid Preparation, Transformation Assay, Purification, Polymerase Chain Reaction, Generated, In Vitro, Magnetic Beads

    Schematic view of microfluidic capillary electrophoresis-based restriction fragment length polymorphism (µCE-based RFLP) platform. (a) Mismatched primer PCR. A KRAS gene fragment containing codon 12 was amplified from gDNA with mismatched primer, by which a base substitution was introduced to the amplicon and a Mva I restriction endonuclease recognition site was created for wild-type codon 12. (b) Mva I digestion. The amplicon from wild-type template could be cleaved into two fragments, the amplicon from mutant template could not be digested due to the loss of recognition site, and the amplicon from heterozygous template was halfly digested. (c) µCE. The digested amplicon was loaded into microfluidic chip and separated by CE according to the fragment length. The wild type template resolved into two peaks, the mutant template only showed one peak, and the heterozygous template resolved into three peaks. gDNA, genomic DNA. SR: sample reservoir; BR: buffer reservoir; SW: sample waste reservoir; BW: buffer waste reservoir. →, the direction of fluid flow during sample loading and separation modes.

    Journal: PLoS ONE

    Article Title: Detection of Low-Abundance KRAS Mutations in Colorectal Cancer Using Microfluidic Capillary Electrophoresis-Based Restriction Fragment Length Polymorphism Method with Optimized Assay Conditions

    doi: 10.1371/journal.pone.0054510

    Figure Lengend Snippet: Schematic view of microfluidic capillary electrophoresis-based restriction fragment length polymorphism (µCE-based RFLP) platform. (a) Mismatched primer PCR. A KRAS gene fragment containing codon 12 was amplified from gDNA with mismatched primer, by which a base substitution was introduced to the amplicon and a Mva I restriction endonuclease recognition site was created for wild-type codon 12. (b) Mva I digestion. The amplicon from wild-type template could be cleaved into two fragments, the amplicon from mutant template could not be digested due to the loss of recognition site, and the amplicon from heterozygous template was halfly digested. (c) µCE. The digested amplicon was loaded into microfluidic chip and separated by CE according to the fragment length. The wild type template resolved into two peaks, the mutant template only showed one peak, and the heterozygous template resolved into three peaks. gDNA, genomic DNA. SR: sample reservoir; BR: buffer reservoir; SW: sample waste reservoir; BW: buffer waste reservoir. →, the direction of fluid flow during sample loading and separation modes.

    Article Snippet: The PCR was performed with preheating at 95°C for 5 min, followed by 35 cycles at 94°C for 40 seconds, 55°C for 40 seconds, 72°C for 1 min, and a final extension at 72°C for 7 min. All amplicons of the KRAS gene were purified using a DNA purification kit (Zymo, Inc. ) and directly sequenced using both forward and reverse primers on an ABI 377 sequencer.

    Techniques: Electrophoresis, Polymerase Chain Reaction, Amplification, Mutagenesis, Chromatin Immunoprecipitation, Flow Cytometry

    PlasmaMonitor™ pre-analytical and technical considerations. (A) Comparison of four commercial cfDNA extraction kits for yield; (B) quantification and qualification of the extracted cfDNA using a custom Human Genomic DNA QC Assay; (C) comparison data demonstrating that using our custom quality approach provides more robust quantification data in comparison with the standard Qubit assay; (D) pre-analytical validation steps including sensitivity and limit of detection (LOD), inter-assay reproducibility, intra-assay reproducibility, and specificity and accuracy; (E) post-sequencing validation steps including sensitivity and LOD, inter-assay reproducibility, intra-assay reproducibility, and specificity and accuracy.

    Journal: Biomarker Insights

    Article Title: Technical and Regulatory Considerations for Taking Liquid Biopsy to the Clinic: Validation of the JAX PlasmaMonitorTM Assay

    doi: 10.1177/1177271919826545

    Figure Lengend Snippet: PlasmaMonitor™ pre-analytical and technical considerations. (A) Comparison of four commercial cfDNA extraction kits for yield; (B) quantification and qualification of the extracted cfDNA using a custom Human Genomic DNA QC Assay; (C) comparison data demonstrating that using our custom quality approach provides more robust quantification data in comparison with the standard Qubit assay; (D) pre-analytical validation steps including sensitivity and limit of detection (LOD), inter-assay reproducibility, intra-assay reproducibility, and specificity and accuracy; (E) post-sequencing validation steps including sensitivity and LOD, inter-assay reproducibility, intra-assay reproducibility, and specificity and accuracy.

    Article Snippet: We evaluated four commercial cfDNA extraction kits across 35 samples; QIAamp circulating nucleic acid kit (Qiagen), NucleoSpin Plasma XS (Macherey-Nagel), ZR Serum DNA kit (ZYMO Research), and the NEXTPrep-Mag cfDNA isolation kit (Bioo Scientific) ( ).

    Techniques: Inter Assay, Intra Assay, Sequencing

    Rescue of RP-deficient zebrafish with exogenous nucleosides. (A) At 48 hpf, Rpl11 mutants incorporated more [ 3 H] deoxycytidine into DNA than their wild-type siblings ( P

    Journal: Disease Models & Mechanisms

    Article Title: The role of the DNA damage response in zebrafish and cellular models of Diamond Blackfan anemia

    doi: 10.1242/dmm.015495

    Figure Lengend Snippet: Rescue of RP-deficient zebrafish with exogenous nucleosides. (A) At 48 hpf, Rpl11 mutants incorporated more [ 3 H] deoxycytidine into DNA than their wild-type siblings ( P

    Article Snippet: At 48 hpf, genomic DNA was prepared from 25 embryos using DNA purification kit (Zymo Research, Irvine, CA).

    Techniques:

    RP-deficient zebrafish show activation of the DNA damage checkpoint pathway. (A) Phosphorylation of residue Ser139 of histone H2A.X was induced in embryos that had been injected with an Rps19-specific morpholino (MO). Western blotting was performed at 24 hpf. Staining of tubulin was used for a loading control. Molecular masses are shown on the right. Wt, wild type. (B) Phosphorylation of residue Ser345 in Chk1 kinase was increased in Rps19-deficient embryos (MO). Western blotting was performed at 24 hpf. (C) Embryos that had been injected with an Rps19 morpholino had increased levels of p53; the treatment of morphants with 3 nM of Chk1 inhibitor PF477736 (PF), 10 nM of the ATR and ATM inhibitor CGK733 (GCK), or 3 nM of the ATM inhibitor KU60019 (KU) reduced p53 levels. Western blotting was performed at 24 hpf. (D) Treatment of Rpl11 mutants with inhibitors of the ATR-ATM-Chk1 pathway resulted in downregulation of the p53 targets p21 and puma . Gene expression was analyzed by using RT-qPCR. The fold change of gene expression was calculated relative to expression in wild-type siblings. Means±s.d. are shown. (E) Embryos that had been injected with a morpholino against Rps19 (Rps19 MO) had few red blood cells at 3.5 days post-fertilization. The treatment of Rps19 morphants with PF477736 partially rescued this hematopoietic defect.

    Journal: Disease Models & Mechanisms

    Article Title: The role of the DNA damage response in zebrafish and cellular models of Diamond Blackfan anemia

    doi: 10.1242/dmm.015495

    Figure Lengend Snippet: RP-deficient zebrafish show activation of the DNA damage checkpoint pathway. (A) Phosphorylation of residue Ser139 of histone H2A.X was induced in embryos that had been injected with an Rps19-specific morpholino (MO). Western blotting was performed at 24 hpf. Staining of tubulin was used for a loading control. Molecular masses are shown on the right. Wt, wild type. (B) Phosphorylation of residue Ser345 in Chk1 kinase was increased in Rps19-deficient embryos (MO). Western blotting was performed at 24 hpf. (C) Embryos that had been injected with an Rps19 morpholino had increased levels of p53; the treatment of morphants with 3 nM of Chk1 inhibitor PF477736 (PF), 10 nM of the ATR and ATM inhibitor CGK733 (GCK), or 3 nM of the ATM inhibitor KU60019 (KU) reduced p53 levels. Western blotting was performed at 24 hpf. (D) Treatment of Rpl11 mutants with inhibitors of the ATR-ATM-Chk1 pathway resulted in downregulation of the p53 targets p21 and puma . Gene expression was analyzed by using RT-qPCR. The fold change of gene expression was calculated relative to expression in wild-type siblings. Means±s.d. are shown. (E) Embryos that had been injected with a morpholino against Rps19 (Rps19 MO) had few red blood cells at 3.5 days post-fertilization. The treatment of Rps19 morphants with PF477736 partially rescued this hematopoietic defect.

    Article Snippet: At 48 hpf, genomic DNA was prepared from 25 embryos using DNA purification kit (Zymo Research, Irvine, CA).

    Techniques: Activation Assay, Injection, Western Blot, Staining, Expressing, Quantitative RT-PCR