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Innuprep dna mini kit

Manufactured by Analytik Jena
Sourced in Germany

The InnuPREP DNA Mini Kit is a laboratory product designed for the fast and efficient extraction and purification of DNA from various sample materials. It utilizes a reliable spin column-based technology to isolate DNA with high purity and yield.

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26 protocols using innuprep dna mini kit

1

Genomic DNA Isolation and PCR Amplification

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Genomic DNA was isolated with the innuPREP DNA Mini Kit (Analytik Jena, Jena, Germany). PCRs were run under standard conditions (Hasselmann and Beye 2004 (link)) using Phusion High-Fidelity DNA Polymerase (Thermo Scientific) and oligonucleotide primers (forward primer: GATTCGTAATAATTCCTGTGC; reverse primer: CTTCCGCTACTCTTACTTTGAC; Custom DNA Oligos, Eurofins). For the Sanger sequencing (Mix2Seq Kit, Eurofins) amplicons were cloned into pGEM-T Easy Vector (Promega, Madison, WI).
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2

Genomic DNA Extraction and Sequencing

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First, genomic DNA was isolated from 1 × 106 cells using the MyTaq Extract-PCR Kit (Bioline GmbH, Luckenwalde, Germany) or innuPREP DNA Mini Kit (Analytik Jena, Jena, Germany) following the manufacturer’s recommendations. Next, a 403 bp DNA fragment within the lsr gene that contains the LSR-specific gRNA binding site was amplified by PCR with oligonucleotides 5′-GTC​CAA​CCC​CTA​CCA​CGT​GGT​G-3′ and 5′- GCT​TTC​AGA​TGG​GGA​CTC​CAG​G-3′ and by using genomic DNA as template (Hemmasi et al., 2015 (link)). Eventually, the PCR product was purified with the my-Budget Double Pure Kit (BioBudget Technologies GmbH, Krefeld, Germany) and subjected to DNA sequencing (Eurofins Genomics Europe Sequencing GmbH, Konstanz, Germany). Indels in the sequenced DNA fragments were identified by performing sequence alignments with the lsr reference sequence.
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3

Genomic Sequencing of SUMO4 in ALS

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DNA was isolated from fibroblasts of patient TALS004-01 and the non-ALS controls using the innuPREP DNA Mini Kit (Analytik Jena, Jena, Germany). The coding sequence and parts of the flanking untranslated regions of SUMO4 were amplified and sequenced using a conventional chain termination protocol. Sequence data were analyzed using the SeqPilot software v4.3.1 (JSI Medical Systems GmbH, Ettenheim, Germany).
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4

Genomic DNA Extraction from FFPE Samples

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Genomic DNA was isolated from formalin-fixed paraffin-embedded samples, according to innuPREP DNA Mini Kit (Analytik Jena AG, Jena, Germany) protocol, following manufacturer’s instructions. For neoplasia-free control group, DNA was obtained from peripheral blood white cells using the extraction kit Mini Spin (Biometrix, Curitiba, PR, Brazil), according to manufacturer’s instructions. All DNA samples were quantified in NanoDrop 2000® (NanoDrop Technologies, Wilmington, DE, USA).
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5

Microbiological Examination of Extraintestinal Tissues

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Microbiological examination was performed as described previously [36 (link)]. Briefly, swabs taken from extraintestinal tissues at necropsy were cultured on Columbia colistin-nalidixic acid (CNA) agar (Oxoid GmbH, Wesel, Germany) for 24 h at 37 °C under microaerophilic conditions. Colonies of an EC-typical morphology (small, grey, mucoid colonies with slight alpha-haemolysis) were subcultured and identified as EC via oxidase and catalase testing, Gram staining, and, in case of doubt, by 16S rRNA partial gene sequencing (Microsynth AG, Lindau, Germany [37 (link)–39 (link)]). DNA was isolated from swabs taken from the jejunum, ileum, and caecum (InnuPrep DNA Mini Kit, Analytik Jena AG, Jena, Germany), and EC-specific real-time PCR was performed exactly as published previously [36 (link)].
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6

DNA Extraction from Homogenized Eggs

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For molecular analysis, all eggs from each wooden spatula were homogenized using one ceramic bead (2.8 mm Precellys Ceramic Beads, VWR, Darmstadt, Germany) and a TissueLyser II (Qiagen, Hilden, Germany) as described previously [38 (link)]. DNA of the samples from 2021 was extracted by the University of Veterinary Medicine, Vienna using the innuPREP DNA Mini Kit (Analytik Jena, Jena, Germany) according to the manufacturer’s instructions. In 2022, molecular analyses were performed by the Austrian Agency for Health and Food Safety, which is why the protocol was changed and adapted to the available equipment at that laboratory. DNA isolation of the samples from 2022 was carried out with the BioExtract SuperBall Kit (Biosellal, Dardilly, France) on a KingFisher Flex96 robot (Thermo Fisher Scientific, Waltham, USA) following an in-house protocol.
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7

Quantification of Mitochondrial DNA Copy Number

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Mito copy No., which serves as a relative measure of mitochondrial DNA copies per cell, was evaluated in RAW 264.7 cells after 4 days of stimulation: DNA was extracted using the innuPREP DNA Mini Kit (Analytik Jena, Germany) according to the manufacturer’s protocol. In short, cells were lysed in lysis solution containing Proteinase K and DNA was extracted by a DNA binding column. DNA concentration of the eluate was measured using the NanoDrop® ND-1000 spectrophotometer. 10 ng DNA was transferred in a qPCR reaction with 60 °C annealing/extension temperature for 40 cycles. Primer pairs specific for murine nuclear DNA (nDNA: B2M fw ATGGGAAGCCGAACATACTG, B2M rev CAGTCTCAGTGGGGGTGAAT, NC_000068.7) and mitochondrial DNA (mtDNA: fw CTAGAAACCCCGAAACCAAA, rev CCAGCTATCACCAAGCTCGT, NC_005089.1) were extracted from [34 (link)] and used for amplification of specific DNA products with 2 × qPCRBIO SyGreen Mix Hi-ROX. Specificity of products was controlled by water sample and melting curves. Mito copy No. was calculated according to formula: mtDNA per cell (nDNA) = 2 × 2∆Cq, ∆Cq = (nDNA Cq – mtDNA Cq).
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8

Quantifying Mitochondrial DNA Dynamics

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A total of 7 × 104 cells were seeded in 1 mL of complete medium in 48 well-plate. On day 4, total genomic DNA was isolated with the innuPREP DNA Mini Kit (Analytik Jena, Jena, Germany). Subsequently, qPCR was run with 2 ng/μL of DNA to amplify and relatively quantify the amount of nuclear and mitochondrial DNA. The mitochondrial copy number in variously stimulated cells was determined by comparing the nuclear DNA amount with the amount of mitochondrial DNA in the cells.
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9

Humanized Mouse ABCB1 Locus Sequencing

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Genomic DNA of a hABCB1 mouse was purified using an innuPREP DNA Mini Kit (AnalytikJena AG, Germany). The humanized genomic locus was amplified in 25 µL reactions using TaKaRa LA TaqDNA Polymerase (TaKaRa Bio USA Inc.) according to manufacturer recommendations using 0.4 µM of each primer and an annealing temperature of 60 °C, resulting to single-banded PCR products. After amplification, the remaining primers and dNTPs were digested. The amplified fragments were sequenced using the Sanger process utilizing a primer walking strategy. For the sequencing of exons 3 and 4, PCR reactions were run with 12.5 ng template DNA in a total volume of 12.5 µL. PCR reactions including 0.3 µM of each PCR primer, 200 µM dNTPs, 1.5 mM MgCl2 and 0.02 U/µL KAPA2G Robust polymerase. 35 cycles were run for each PCR with an initial denaturation step of 180 s at 95 °C followed by 35 cycles with a denaturation step for 20 s at 95 °C, an annealing step at 61 °C for 20 s, an elongation step for 100 s at 72 °C and a final elongation step at 72 ° for 45 s. Excess dNTPs and primers were removed from PCR reactions and Sanger sequencing was performed. All primers used are listed in Supplementary Table 1. Amplification, primer design, and sequencing were realized by Microsynth AG (Switzerland).
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10

Gut Microbiome DNA Extraction

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DNA from colon content was extracted using the NucleoSpin® Soil kit (MACHEREY-NAGEL GmbH & Co. KG, Düren, Germany) according to the manufacturer's recommendations, adding a mechanical lysis process in a Mill Benchtop Mixer MM 2000 (Retsch GmbH, Haan, Germany). DNA from cecum and ileum tissues was isolated using the innuPREP DNA Mini Kit (Analytik Jena AG, Jena, Germany) following the instructions of the manufacturer after disruption of the tissue with liquid nitrogen in a mortar. Quality and quantity of isolated DNA was measured spectrophotometrically in a NanoDrop 2000c (Thermo Scientific, Waltham, USA).
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