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Quickextract dna extraction solution

Manufactured by Biosearch Technologies
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QuickExtract DNA Extraction Solution is a reagent used for the rapid and efficient extraction of DNA from a variety of sample types. It is designed to provide high-quality DNA suitable for downstream applications such as PCR amplification, sequencing, and other molecular biology techniques.

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Lab products found in correlation

Monarch pcr dna cleanup kit, by New England Biolabs (3 mentions) Dreamtaq, by Thermo Fisher Scientific (1 mentions) Primestar gxl dna polymerase, by Takara Bio (1 mentions) Dna clean concentrator 5 kit, by Zymo Research (1 mentions) Q5 high fidelity 2x master mix, by New England Biolabs (1 mentions) Gotaq green master mix, by Promega (1 mentions) Miseq system, by Illumina (1 mentions) Qubit dsdna hs assay kit, by Thermo Fisher Scientific (1 mentions) Monarch dna gel extraction kit, by New England Biolabs (1 mentions)

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QuickExtract (5 citations) QuickExtract (QE) DNA Extraction Solution (2 citations)

14 protocols using quickextract dna extraction solution

1

GAA Exon Amplification and Genotyping

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Genomic DNA was isolated using QuickExtract™ DNA Extraction Solution (Biosearch Technologies) as per the manufacturer’s protocol. GAA exons 2, 13 and 16 were amplified by PCR. The genotypes were confirmed through Sanger sequencing. Primers are listed in Table 2.
, & Sibbald B. (2001). Canada “behind eight ball” in fighting youth smoking. CMAJ: Canadian Medical Association Journal, 164(10), 1479.
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2

Extraction and Amplification of C. reinhardtii DNA

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C. reinhardtii genomic DNA was extracted from wild-type and mst3 mutant strains using QuickExtract DNA extraction solution (Biosearch Technologies). Cells grown on TAP plates were suspended in the solution and incubated at 65°C for 6 min and 98°C for 2 min. PCR reactions were performed using Q5 (BioLabs) and DreamTaq (Thermo Scientific) DNA polymerases following the manufacturer’s protocols. Primers are listed in Table S4. Annealing temperatures (between 55 and 71°C) were determined using the NEB Tm calculator (v.1.16.5). PCR cycle number was set to 31.
Dai J., Ma M., Niu Q., Eisert R.J., Wang X., Das P., Lechtreck K.F., Dutcher S.K., Zhang R, & Brown A. (2024). Mastigoneme structure reveals insights into the O-linked glycosylation code of native hydroxyproline-rich helices. Cell, 187(8), 1907-1921.e16.
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3

Genomic DNA Extraction and Sanger Sequencing

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HEK293T cells were transfected with plasmid DNA and DNA templates and harvested after 72 h for genomic DNA using the QuickExtract DNA Extraction Solution (Biosearch Technologies) following the manufacturer's protocol. The target genomic region was amplified using specific primers outside of the homology arms of the DNA template. PCR products were purified with Monarch PCR & DNA Cleanup Kit (New England BioLabs). 100 ng of purified product was sent for Sanger sequencing with target-specific primers (EtonBio or Genewiz).
Wang C., Cheng J.K., Zhang Q., Hughes N.W., Xia Q., Winslow M.M, & Cong L. (2021). Microbial single-strand annealing proteins enable CRISPR gene-editing tools with improved knock-in efficiencies and reduced off-target effects. Nucleic Acids Research, 49(6), e36.
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4

DNA Extraction and PCR Amplification

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The genomic DNA was extracted using the QuickExtract™ DNA extraction solution (Biosearch Technologies). The PCR assay was performed using the PrimeSTAR GXL DNA Polymerase (Clontech) and the primers (Table 2) under the following conditions: 98 °C for 5 s 60 °C for 15 s, 72 °C for 30 s for 35 cycles. The PCR products were purified, and the sequencing was performed at Stanford Protein and Nuclear Acid (PAN) facility.
Zhang M., Venkateshappa R., Li A., Fowler M.B., Telli M.L, & Wu J.C. (2023). Generation and characterization of induced pluripotent stem cells from breast cancer patients carrying ATM mutations. Stem cell research, 73, 103246.
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5

HEK293T Transfection DNA Extraction

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HEK293T cells were harvested 72 h after transfection. The genomic DNA was extracted using QuickExtract DNA extraction solution (Biosearch Technologies) following the manufacturer’s instructions. The target genomic region was amplified using specific primers that bound outside of the HAs of the donor template. The primers used for the Sanger and NGS analyses are listed in Supplementary Table 4. The PCR products were purified using a Monarch PCR & DNA cleanup kit (New England BioLabs). The purified product (80–100 ng) was sent for Sanger sequencing with target-specific primers (EtonBio or Genewiz). The Sanger trace was analysed using the SnapGene software.
Wang C., Qu Y., Cheng J.K., Hughes N.W., Zhang Q., Wang M, & Cong L. (2022). dCas9-based gene editing for cleavage-free genomic knock-in of long sequences. Nature Cell Biology, 24(2), 268-278.
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6

Sequencing and Variant Analysis of SLC17A5

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Genomic DNA was extracted from each cell line using QuickExtract DNA Extraction Solution (LGC Biosearch Technologies). SLC17A5 sequence analysis was conducted using previously established intronic primers that flank each side of the exon.7 (link) Minor modifications to the primer design of some exons are listed in the supplemental information (Table S1). PCR products were purified using the DNA Clean & Concentrator-5 kit (Zymo Research) before Sanger sequencing with both forward and reverse primers, resulting in complete coverage of the amplified regions (Eurofins Genomics). Analysis of the GM11850 cell line revealed two heterozygous changes in exon 2, and therefore a set of allele-specific oligos (C115: 5′- CAGTGTGCTGCTCTGCTC-3′ and T115: 5′- CAGTGTGCTGCTCTGCTT-3′) was designed to identify the relative allelic position between c.251delC and c.115C>T in SLC17A5.
Harb J.F., Christensen C.L., Kan S.H., Rha A.K., Andrade-Heckman P., Pollard L., Steet R., Huang J.Y, & Wang R.Y. (2023). Base editing corrects the common Salla disease SLC17A5 c.115C>T variant. Molecular Therapy. Nucleic Acids, 34, 102022.
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7

GAA Exon Amplification and Genotyping

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Genomic DNA was isolated using QuickExtract™ DNA Extraction Solution (Biosearch Technologies) as per the manufacturer’s protocol. GAA exons 2, 13 and 16 were amplified by PCR. The genotypes were confirmed through Sanger sequencing. Primers are listed in Table 2.
Christensen C., Heckman P., Rha A., Kan S.H., Harb J, & Wang R. (2023). Generation of two induced pluripotent stem cell lines (CHOCi002-A and CHOCi003-A) from Pompe disease patients with compound heterozygous mutations in the GAA gene. Stem cell research, 69, 103117.
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8

Genomic DNA Extraction and Analysis

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HEK293T cells were harvested 72 hours after transfection. The genomic DNA was extracted using the QuickExtract DNA Extraction Solution (Biosearch Technologies) following the manufacturer’s instruction. The target genomic region was amplified using specific primers outside of the homology arms of the donor template. The primers used for Sanger sequencing or NGS analysis are listed in the Supplementary Table 4. PCR products were purified with Monarch PCR & DNA Cleanup Kit (New England BioLabs). 80–100 ng of purified product was sent for Sanger sequencing with target-specific primers (EtonBio or Genewiz). The Sanger trace was analyzed using SnapGene software.
Wang C., Qu Y., Cheng J.K., Hughes N.W., Zhang Q., Wang M, & Cong L. (2022). dCas9-based gene editing for cleavage-free genomic knock-in of long sequences. Nature Cell Biology, 24(2), 268-278.
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9

Engineered CD8+ T cell editing

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CD8+ T cells were activated from n = 3 donors and underwent editing on day 0 and/or day 2 after Dynabead removal. TRAC editing involved Cas9 RNP and NY-ESO-1 TCR AAV, and B2M editing involved Cas9 RNP and 1928z CAR AAV. Cells were passaged every 2 days. Flow cytometry was conducted 6 days after the first edit. Cells were pelleted and resuspended in QuickExtract DNA extraction solution (Biosearch Technologies #SS000035-D2), incubated at 65 °C for 10 min and then 96 °C for 5 min, and stored at −20 °C until genomic DNA extraction.
Foss D.V., Muldoon J.J., Nguyen D.N., Carr D., Sahu S.U., Hunsinger J.M., Wyman S.K., Krishnappa N., Mendonsa R., Schanzer E.V., Shy B.R., Vykunta V.S., Allain V., Li Z., Marson A., Eyquem J, & Wilson R.C. (2023). Peptide-mediated delivery of CRISPR enzymes for the efficient editing of primary human lymphocytes. Nature Biomedical Engineering, 7(5), 647-660.
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10

CRISPR-Cas9 Mediated Cpox Intron 5 and TSS Deletion

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sgRNAs were designed by using CRISPick (Broad institute, MIT), cloned into pSpCas9(BB)-2A-Puro (PX459) V2.0 (pSpCas9(BB)-2A-Puro (PX459) V2.0 was a gift from Feng Zhang (Addgene plasmid # 62988; http://n2t.net/addgene:62988; RRID: Addgene_62988)) according to the protocol from Ran F., et. al(18 (link)). For Cpox intron 5 TFBS deletion, sgRNA plasmids were electroporated into MEL cells with BTXpress High Performance Electroporation Kit & Solution (BTXpress, catalog no. 89130–538). Cells were transferred immediately into DMEM medium with 20% FBS and cultured for one day, then treated with 4μg/ml puromycin for 12 hours, washed and cultured in puromycin-free DMEM with 10% FBS. Cpox TSS deletion was performed with same procedure except continuous cultured in medium with 2μg/ml puromycin to select permanent integrated cells. Selection of single colonies by serial dilution culture was performed in 96 well plates. Genotyping of single colonies was performed after extraction of DNA with QuickExtract DNA Extraction Solution (Biosearch Technologies, catalog no. 76081–766) and PCR amplification with Q5® High-Fidelity 2X Master Mix (NEB, catalog no. M0492S). PCR products were confirmed by Sanger sequencing (Genewiz)
Xie B, & Dean A. (2023). Noncoding function of super enhancer derived mRNA in modulating neighboring gene expression and TAD interaction. bioRxiv.
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