Choosing the correct DNA extraction kit can save crucial time in optimizing and running the experiment. Factors to consider when selecting a kit include:
Sample Origin: Different kits are used to extract material from specific sources, including human tissue, blood, hair, rodent tissues, leaf tissue, bacteria, yeast, fungi, insects, faeces, body fluids, spores, soil, samples clinical (eg, biopsy specimens, fine needle aspirates), forensic specimens (eg, dried blood drops, buccal swabs), and fingerprints.
Preparation method: Sample preparations can be: fresh or previously frozen cell pellets, formalin-fixed or paraffin-embedded tissue sections, frozen tissue sections, ethanol-fixed cells, Oragene® preserved samples and samples from forensic sources. that can contain very little material
Intended use: the quality and purity of the DNA provided by the kit should be suitable for the intended subsequent application, which could be sequencing, fingerprinting, PCR, quantitative PCR (qPCR), Southern blotting, random amplification of polymorphic DNA (RAPD), applications of amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP), restriction endonuclease digestion or preparation of shotgun libraries.
Humic content: If the sample has humic content such as compost, sediment and manure, a kit/method should be used that removes humic substances as they can inhibit downstream applications such as PCR.
Sample quantity: The kit to use depends on the size of the sample being analyzed. For example, the number of cultured mammalian cells (105-107) and bacterial cells (106-1011), the weight of human tissue, plant tissue or soil, the volume of blood or even traces of DNA samples from the scene of the crime.
Yield: the desired or expected amount of DNA to be purified from the sample. This depends on the sample and subsequent applications.
Simplicity: the operation of the kit depends on the user experience and the desired degree of control over each stage of the sample processing.
Kits for animal cells and tissues and microbes
Kits that can be applied for the extraction of DNA from mammalian sources, as well as microorganisms, are described below.
1. DNA isolation for cells and tissues (Roche):
This kit can be used for the extraction of genomic DNA from tissues (up to 1 g), cultured cells (up to 107), bacterial cells (up to 1011) and yeast cells. It avoids the use of organic extracts, anion exchange columns, and chaotropic reagents, instead of isolating DNA by removing proteins, RNA, and cellular components. It extracts genomic DNA ranging in size from 50 to 150 kb.
2. Purelink Genomic DNA (Thermo Fisher):
This kit isolates DNA from a wide range of sample sizes from blood (eg, 100 ul to 1 ml), tissues, cells, bacteria, buccal swabs, blood spots, tissues FFPE and Oragene®- preserved samples. This gives the user flexibility, as one kit can be used to isolate DNA from many sample sources. It also includes a 96-well version that does not require special equipment and can be processed manually or with automated platforms. The chemistry of this kit is based on silica-membrane technology in which silica membranes with the ability to specifically bind DNA are packed in spin columns.
3. DNeasy Blood and Tissue (QIAGEN) –
This kit can be used to isolate total DNA (genomic, mitochondrial, and pathogen) from a variety of sample sources, including fresh or frozen, formalin-fixed, or paraffin-embedded animal cells and tissues, rodent tails, blood, bacteria, yeast, hair, insects, etc. Purified DNA is up to 50 kb in size and the kit efficiently recovers DNA fragments as small as 100 bp. This kit also uses silica-based technology. After cell lysis with lysis buffer, the DNA extraction procedure can be completed in about 20 minutes.
4.NucleoSpin Tissue XS (Macherey Nagel) –
This kit can be used for the isolation of genomic DNA from tissues (eg, mouse kidney, laser microdissection), cells (eg, bacteria, yeast and cultured cells ), clinical specimens (eg, Biopsy specimens, fine needle aspirates), and forensic specimens (eg, dried blood spots, buccal swabs, fingerprints). The main advantage is that this kit provides reliable and reproducible DNA recovery from as few as 10 cells prepared by LCM and also has the flexibility to be used for larger samples up to several milligrams of tissue or cell pellets.
This kit is also based on silica membrane-based technology. Related products include NucleoSpin® Tissue for larger samples, NucleoBond® AXG, which is based on anion-exchange chromatography, NucleoSpin® 8 Tissue, and the 96 Tissue Core kit that enables high-throughput processing and automation.
5. GeneJET Genomic DNA Purification –
This kit facilitates the rapid and efficient purification of high-quality genomic DNA from various mammalian cell cultures and tissue, whole blood, bacteria, and yeast samples. The kit uses silica-based membrane technology in the form of a convenient spin column and the procedure takes less than 20 minutes after cell lysis. Provides purified DNA greater than 30 kb in size that can be used directly in PCR, Southern blotting, and enzymatic reactions.
6. FastDNA SPIN (MP Biomedicals) –
This kit is designed for the isolation of genomic DNA from plants, animals, bacteria, yeast, algae, and fungi using a silica spin filter method. It can be used in conjunction with any FastPrep® instrument to lyse and subsequently isolate DNA up to 200 mg from almost any sample in less than 30 minutes. The FastPrep® instrument is a benchtop device that uses a patented vertical angular motion to homogenize samples by simultaneous multidirectional impaction with lysis matrix particles.
The instrument provides fast, efficient, and highly reproducible homogenization that outperforms traditional extraction methods, using enzymatic digestion, sonication, mixing, dancing, and vortexing. After lysis, the samples are centrifuged to pellet debris and the lysis matrix. The DNA is then purified from the supernatant with a silica-based GENECLEAN procedure using SPIN filters. The purified DNA is suitable for digestion, electrophoresis, PCR, and any other desired application.