DNA extraction is required for a variety of molecular biology applications. Figure 1 lists the basic steps involved in all DNA extraction methods. Many commercial kits are available to isolate DNA from a variety of biological materials [1, 2]. The sensitivity of polymerase chain reaction (PCR) detection has been shown to be different for various DNA kits [3]. Therefore, selecting the best methodology for your application is crucial.

Figure 1. Basic steps involved in all DNA extraction methods.

Choosing the correct DNA extraction kit can save crucial time on optimization and execution of the experiment. Factors to be considered for selecting a kit include:

1. Sample origin: Different kits are used to extract material from specific sources, including human tissues, blood, hair, rodent tissues, leaf tissue, bacteria, yeast, fungi, insect, stool, body fluids, spores, soil, clinical samples (e.g., biopsy samples, fine needle aspirates), forensic samples (e.g., dried blood spots, buccal swabs), and fingerprints [1, 2].
2. Preparation method: Sample preparations can be: fresh or previously frozen cell pellets, paraffin-embedded or formalin-fixed tissue sections, frozen tissue sections, ethanol-fixed cells, Oragene®-preserved samples, and samples from forensic sources which might contain very limited material
3. Intended use: The quality and purity of the DNA provided by the kit should be suitable for the intended downstream application, which could be sequencing, fingerprinting, PCR, quantitative PCR (qPCR), Southern blotting, random amplification of polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), and restriction fragment length polymorphism (RFLP) applications, restriction endonuclease digestion, or the preparation of shotgun libraries.
4. Humic content: If the sample has humic content such as compost, sediment and manure, a kit/method that removes humic substances should be used, as they can inhibit downstream applications like PCR.
5. Sample quantity: The kit to be used depends on the size of the sample being analysed. 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 trace DNA samples from a crime scene.
6. Yield: the desired or expected amount of DNA to be purified from the sample. This is dependent upon the sample as well as the downstream applications
7. Simplicity: The kit operation depends on the experience of the user, and the degree of control desired over each stage of the sample processing.

The basic criteria that any method of DNA isolation from any sample type should meet include: (1) efficient extraction of DNA from the sample , (2) production of a sufficient amount of DNA for use in downstream processes, (3) successful removal of contaminants, (4) isolation of high quality and high purity DNA.

Ultraviolet absorbance can be used to assess the purity of the extracted DNA. For a pure DNA sample, the ratio of absorbance at 260 nm and absorbance at 280 nm (A260/A280) is 1.8. A ratio of < 1.8 indicates the sample is contaminated with protein or an organic solvent such as phenol, often used during extraction processes. The quantification of double-stranded DNA can also be assessed by the Qubit assay, which relies on the principle of DNA-selective fluorescent dyes although it may underestimate in DNA extracted after RNA extraction with Trizol [4]. DNA quality can be assessed by visualization on agarose gels.

Different extraction methods result in different yields and purity of DNA. Some of the extraction methods have been systematically evaluated for specific applications such as soil and sediment samples [5], human microbiome [6], and fecal samples [7-9].

In this conventional, widely used method, cells are lysed and cell debris is usually removed by centrifugation. Then, proteins are denatured/digested using a protease, and precipitated with organic solvents such as phenol, or 1:1 mixture of phenol and chloroform. The protein precipitate is removed following separation by centrifugation. Purified DNA is usually recovered by precipitation using ethanol or isopropanol. At some point in the process, RNAs are degraded through incubation with RNase. In the presence of monovalent cations such as Na⁺, and at -20°C, absolute ethanol efficiently precipitates polymeric nucleic acids and leaves behind short-chain and monomeric nucleic acid components, including the ribonucleotides from RNase treatment in solution. This method uses hazardous organic solvents, is relatively time-consuming, and residual phenol or chloroform may affect downstream applications such as PCR. An example of a commercially available kit that relies on this chemistry is the Easy-DNA® Kit from Thermo Fisher.

Silica-based technologies are widely employed in current kits. DNA adsorbs specifically to silica membranes/beads/particles in the presence of certain salts and at a defined pH [10]. The cellular contaminants are removed by wash steps. DNA is eluted in a low salt buffer or elution buffer. Chaotropic salts are included in the kit buffers to aid in protein denaturation and extraction of DNA. This method can be incorporated in spin columns and microchips, is cost-effective, has a simpler and faster procedure than the organic extraction, and is suitable for automation [10]. Kits based on this method include Purelink Genomic DNA extraction kit from Thermo Fisher and DNeasy Blood and Tissue Kit from QIAGEN.

Magnetic separation is based on DNA reversibly binding to a magnetic solid surface/bead/particles that have been coated with a DNA binding antibody, or a functional group that interacts specifically with DNA [11]. After DNA binding, beads are separated from other contaminating cellular components, washed, and the purified DNA is eluted using ethanol extraction [12]. This method is rapid, simple to perform and can be automated. However, it can be more costly than other methodologies. Examples of commercially available kits include the Agencourt DNAdvance Kit from Beckman Coulter) and Magnetic Beads Genomic DNA Extraction Kit from Geneaid.

DNA extraction by anion exchange chromatography is based on the specific interaction between negatively charged phosphates of the nucleic acid and positively charged surface molecules on the substrate. DNA binds specifically to the substrate in the presence of low salt, contaminants are removed by wash steps using a low or medium salt buffer, and purified DNA is eluted using a high salt buffer [13]. This technology is most commonly employed in plasmid isolation kits such as PureLink® HiPure Plasmid DNA Purification Kits from Thermo Fisher, QIAGEN plasmid mini/midi kits and Genomic-tip, and NucleoBond® PC kits from Macherey Nagel.

Other methods of DNA extraction include salting out [14], cesium chloride density gradients [15], and chelex 100 resin [16, 17]. DNA isolation methods are often modified and optimized for different cell types or sample sources. For example, cetyltrimethylammonium bromide (CTAB) and guanidium thiocyanate (GITC) are often included in protocols for DNA extraction from plant materials, and are discussed in more detail in "DNA extraction from plant tissue and cells".

Table 1 lists kits broadly used for DNA extraction and purification, based on source materials.

Bacterial cells are cultured in liquid media until they reach a maximum density of 2-3x10⁹ cells/ml, and then harvested. The collected cells are lysed, often done chemically, using reagents such as lysozyme, EDTA, lysozyme and EDTA and other detergents, etc. Cellular components are then removed using one of the above listed technologies, for example organic extraction or silica-based technologies. The final step involves DNA precipitation to obtain pure DNA at a high concentration. This procedure can be applied to a wide variety of microbes and other unicellular organisms such as yeast.

Commercially available kits differ in a variety of ways, including the components of the lysis buffer, the method used to separate DNA, the type of membrane used, the wash buffer used and the method of DNA recovery. Such modifications are outlined below and in Table 2.

1. GenElute™ Bacterial Genomic DNA (MilliporeSigma): This kit is applicable for both Gram-negative and Gram-positive bacteria, and isolates DNA that is suitable for restriction endonuclease digestions, PCR, and Southern blots. The kit employs a silica-based system with centrifugation,, and can isolate DNA up to 50 kb in length. In this kit, cells are lysed enzymatically in a chaotropic salt-containing solution, and DNA is specifically adsorbed on the silica membrane. Other components in the cell lysate and contaminants are then removed by washing. Lastly, DNA is eluted in a suitable buffer.
2. QIASymphony Virus/Bacteria (QIAGEN): These kits are used in combination with the QIASymphony SP, an automation platform, and can purify DNA from viruses, retroviruses, Gram-negative and Gram-positive bacteria. The kit and platformy provide automated and simultaneous purification of viral nucleic acids from sera, plasma, or cerebrospinal fluid (CSF), or both viral nucleic acids and bacterial DNA from samples including swabs, aspirates, sputum, bronchoalveolar lavage (BAL), and urine and urogenital swabs. These kits are based on magnetic-particle technology, and purify nucleic acids to be used directly in downstream applications including PCR amplification and enzymatic reactions.
   This kit is particularly useful for analysing large numbers of samples efficiently and reproducibly. A study assessing the effectiveness of different DNA extraction kits at purifying DNA from fecal samples found this kit to be highly effective, giving the highest diversity score, highest quality, and highest yield of DNA from human fecal samples, as compared to other widely used kits [7].
3. Quick-DNA Fecal/Soil Microbe Miniprep (Zymo Research): Host as well as bacterial and protist DNA (up to 25 μg/prep) can be efficiently extracted from ≤ 150 mg sample of mammalian feces using this kit. Samples are efficiently lysed by bead beating with ultra-high density BashingBeads™. Fast-Spin column technology is then used to isolate the DNA which is subsequently filtered to remove humic acids/polyphenols that can inhibit PCR or other downstream procedures. The eluted DNA is ready to use for molecular-based applications including PCR, arrays, genotyping, and methylation detection.
   This kit has also been shown to give a higher diversity score and higher quality and yield of DNA from human fecal samples as compared to other widely used kits, but performs similarly to QIASymphony Virus/Bacteria Kits [7].
4. DNeasy PowerSoil (QIAGEN / Mo Bio): This kit can be used to isolate microbial genomic DNA from all soil types and environmental samples, as well as fecal, stool and biosolid samples. It provides a patented humic substance/brown color removal procedure that eliminates PCR inhibitors from even the most difficult soil types, and produces high-quality DNA that can be used for downstream applications such as PCR, qPCR and next-generation sequencing. This kit has been employed for DNA extraction for assessing human gut microbiota composition by 16S rRNA sequencing [8].
5. DNeasy PowerMax Soil (QIAGEN): This kit extractsDNA from large quantities of any soil or environmental sample, with high or low microbial load. It can isolate DNA from Gram-positive and Gram-negative bacteria, fungi, algae, and actinomycetes, and with humic content including compost, sediment and manure. It is based on PowerSoil® DNA Isolation Kit, and also utilizes a novel, patented Inhibitor Removal Technology® to remove PCR inhibiting compounds, including humic substances.
6. DNeasy UltraClean Microbial DNA (QIAGEN): This kit enablesfthe isolation of high-quality genomic DNA, up to 50 kb or larger, from 1.8 ml of microbial culture of many types of microorganisms including yeast, fungi, Gram-negative and Gram-positive bacteria and bacterial spores. The principal of this kit is to lyse the microorganisms by a combination of heat, detergents, and mechanical force against specialized beads. The released DNA is then bound to a silica spin filter, washed, and the DNA recovered in certified DNA-free Tris buffer. This kit has been used for analyzing fecal microbiomes [9] and anaerobic bacterial cultures [18].
7. QIAprep Spin Miniprep (QIAGEN): This kit provides a fast, simple, and cost-effective plasmid miniprep method for routine molecular biology laboratory applications. It utilizes silica-membrane technology, and the procedure is based on alkaline lysis of bacterial cells, followed by adsorption of DNA onto silica in the presence of high salt. Purified plasmid DNA is eluted in a small volume of Tris buffer or water, and is ready for use in downstream processes without the need for phenol extraction and ethanol precipitation. Related products include the QIAGEN Plasmid Midi and QIAGEN Plasmid Maxi, which are adapted to allow users to obtain a greater yield of DNA from larger samples.

The basic steps involved in extracting DNA from animal cells and tissues is the same as discussed for microbes. However, kits need to incorporate modifications to take into account the special features of animal cells. Culturing and preparing of animal cells is often very different from that of microbial cells. Animal cells do not have a cell wall like microbial cells, and consequently, are easier to lyse. Thus, they can be lysed using only detergents. However, when cells are part of intact animal tissue, the tissue needs to first be mechanically homogenized or treated with enzymes for lysis. Cell lysis is followed by the isolation and purification of DNA from other cellular components.

Many kits do not use the conventional organic extraction method requiring phenol/chloroform extraction and ethanol precipitation. This can be useful, as it minimizes damage to DNA by organic solvents. For example AccuPrep Genomic DNA Extraction (Bioneer) employ columns packed with glass fibers to extract the DNA. QIAamp DNA mini (QIAGEN) uses silica-membrane containing columns, which are able to retain DNA under specific pH and salt conditions. Agencourt DNAdvance (Beckman Coulter) is an example of a kit employing magnetic separation.

Kits available for DNA extraction and purification from mammalian cells and tissue are discussed below. An overview of these kits has been included in Table 3.

1. AccuPrep Genomic DNA Extraction Kit (Bioneer): This kit can be used to extract DNA from mammalian blood, tissues, and cultured cells. An average of 6 ug of DNA from 200 ul of whole human blood and up to 20 ug from 5x10⁶lymphocytes, 25-50 mg mammalian tissue, or 10⁴-10⁸ cultured cells can be extracted. This kit does not use the conventional method for DNA isolation, and does not require phenol/chloroform extraction or ethanol precipitation. The tissue must first be homogenized using a mortar and pestle before being processed and transferred to the column. This kit uses glass fibers within a column which are capable of binding specifically to the DNA in the presence of chaotropic salt. After washing away contaminants, DNA is eluted in a low salt solution.
2. Arcturus® PicoPure® DNA Extraction (Thermo Fisher): These kits are specialised for DNA extraction from a very small amount of cells. It complements the IR laser-enabled laser capture microdissection (LCM) technique, for example [25], which is ideal for microdissection of single cells or small numbers of cells. This kit also allows users to extract and amplify DNA in the same tube, minimizing sample loss.
3. InnuPrep DNA mini (Analytik Jena): This kit isolates genomic DNA from tissue samples (up to 50 mg), rodent tails (0.5-1 cm), paraffin-embedded tissue samples, and eukaryotic cells (5x10⁶ cells). The kit is based on a patented Dual Chemistry (DC) technology, which combines a stringent Lysis Buffer with a novel Binding Buffer to help minimize the time required to purify DNA, along with spin filter columns. After the initial lysis step using the lysis buffer, the extraction takes less than 8 minutes. Related products include the InnuPREP DNA Micro Kit for small samples, and the InnuPREP DNA/RNA Mini Kit for parallel extraction of both DNA and RNA
4. QIAamp DNA mini (QIAGEN): This kit extracts genomic, mitochondrial, bacterial, parasite, or viral DNA from human tissues, swabs (buccal, eye, nasal, pharyngeal, and others), CSF, blood, body fluids, and washed cells from urine. The tissue is lysed enzymatically, and DNA is purified through binding to a column membrane, followed by washing to remove contaminants. This kit is especially useful for bacterial community structure analysis of the human microbiome. The use of QIAamp DNA mini kit along with employing bead beating and/or mutanolysin for cell lysis has been shown to give a better representation of microbial diversity in the sample as compared to methods without both of them (e.g., DNeasy Tissue kit, QIAamp stool kit) [6]. Related products include QIAamp PowerFecal DNA [26, 27], QIAamp DNA blood mini [28], QIAamp DNA stool mini [29], and QIAmp DNA Blood Midi [30] and Maxi [31]. Each of these kits are specialised for different sample sources.
5. Gentra Puregene Blood (QIAGEN): This kit is ideal for the isolation of high molecular weight genomic DNA from whole blood, bone marrow, buffy coat and body fluid. Cells are lysed with an anionic detergent in the presence of a DNA stabilizer. The DNA stabilizer inhibits the activity of intracellular and environmental DNases. RNA is degraded by an RNA digesting enzyme. Other contaminants are removed by salt precipitation. Finally, the genomic DNA is recovered by ethanol precipitation and dissolved in TE buffer (1 mM EDTA, 10 mM Tris-HCI pH 7.5). Related products include the Gentra Puregene Tissue Kit [32, 33] and Gentra Puregene Cell Kit [28] for tissues and cell culture samples, respectively.
6. AllPrep DNA/RNA Mini (QIAGEN):This kit allows simultaneous purification of both genomic DNA and total RNA from a single cell or tissue sample, using the AllPrep DNA spin column, and an RNeasy Mini spin column, respectively. It can be used with up to 10⁷ cells or 30 mg tissue. The AllPrep DNA/RNA Micro Kit is a related product that can be used for smaller starting samples.
7. Agencourt DNAdvance (Beckman Coulter): This kit is a high throughput genomic DNA (gDNA) isolation reagent kit for DNA extraction from fresh or frozen mammalian tissue samples. It uses Agencourt's patented SPRI® paramagnetic bead technology to isolate genomic DNA. This procedure is performed in a 96-well format and is suitable for automation.

The basic steps used for DNA isolation require adaptations to make them suitable for the different characteristics of the plant cells and tissue. Chemicals or enzymes used to lyse microbial and mammalian cells may not be equally effective on plant cells. For example, lysozyme is often included in kits to lyse bacterial cells but has no effect on plant cells due to the presence of the cell wall. Furthermore, the biochemical content of plant cells is very different from microorganisms and animal cells. Many plant species have a high content of polysaccharides and polyphenols which are not removed by phenol extraction (unlike microbes). Therefore, different methods and reagents need to be included in commercially available kits to address the special features of plant cells.

One method is to utilize a detergent called cetyltrimethylammonium bromide (CTAB) which forms an insoluble complex with nucleic acid and selectively precipitates DNA, leaving behind carbohydrates, proteins and other contaminating components. The DNA-containing precipitate can be decomplexed by dissolving it in NaCl. CTAB can be included in any step of the extraction process. To remove polyphenols higher concentration of CTAB with polyvinylpyrrolidone (PVP) or polyvinylpolypyrrolidone (PVPP) can be employed [44].

Another method is to use guanidium thiocyanate (GITC), which assists DNA purification from plant materials in two ways. Firstly, it denatures and dissolves proteins, disintegrates cellular structures, and dissociates nucleoproteins from the nucleic acid. Due to this property, GITC can be used to release DNA from almost any type of tissue [45] Secondly, DNA binds strongly to silica particles in the presence of GITC. This property can be utilized to separate DNA from the denatured proteins and other biochemical or cellular components. Commonly, silica particles are packed in chromatography columns and a DNA extract treated with GITC is applied. DNA binds selectively to the column and can be eluted in the last step after washing away the cellular contaminants.

In some DNA extraction procedures, ascorbic acid, diethyldithiocarbamic acid and 2-mercaptoethanol might be included to protect DNA against oxidation and degradation. RNA can be removed by using RNase. The quality of the DNA isolated is largely dependent on the physiological condition of the plant material, rather than the kit protocol.

Kits available for DNA extraction from plant material are discussed below. An overview of these kits is included in Table 4.

1. NucleoSpin 8 Plant and NucleoSpin 96 Plant II (Clontech): These kits can be used for isolation of genomic DNA from plant cells and tissues. The isolated DNA is suitable for PCR, Southern blotting, or any kind of enzymatic reaction. These kits also offer time-saving parallel isolation of genomic DNA in a flexible 8-well strip format and a 96-well plate high-throughput format. After homogenization of plant material, the kit protocol uses a CTAB-containing lysis buffer, which ensures the lysis of the plant material. As an alternative, SDS-containing lysis buffer is also provided. After removal of polysaccharides, contaminants, and residual cellular debris in the subsequent steps, the lysate containing mainly DNA is applied to the silica membrane for further purification. Finally, DNA is eluted in an elution buffer or distilled water. RNase is also included in the kit for efficient removal of RNA from the DNA sample.
2. DNeasy 96 Plant (QIAGEN): This kit can be used to isolate up to 15 ug total cellular DNA from plant tissue, including plant cells, plant tissues and fungi. The DNeasy Plant Mini Kit can process up to 100 mg of tissue, and the DNeasy Plant Maxi Kit can process up to 1 g of tissue. Briefly, the plant material is homogenized, and then incubated in lysis buffer containing RNase. After lysis, proteins and polysaccharides are salt precipitated. Cell debris and precipitates are removed using the QIAshredder column. The sample is then applied to a silica membrane packed in spin columns, and after a few wash steps, DNA is eluted in a low-salt buffer or water. These kits are available in a convenient 96-well plate format and provide highly reproducible yields of total cellular DNA [46-48].
3. Nucleon PhytoPure Genomic DNA Extraction (GE Healthcare): This kit can be used to isolate DNA from fresh, frozen or freeze-dried plant samples, and can also be used for fungal samples. This kit utilizes a unique method, with a Nucleon PhytoPure proprietary resin that specifically binds to polysaccharides. The Nucleon Phytopure DNA extraction system has a relatively simple protocol that does not require phenol or CTAB. Briefly, the cell wall is disrupted and the cells are lysed with a reagent containing potassium SDS. SDS is used here for its ability to form complexes with proteins and polysaccharides. Subsequently, chloroform is added along with the specially modified Nucleon PhytoPureproprietary resin, which covalently binds polysaccharides. Finally, high-quality DNA is purified using cold isopropanol and 70% ethanol.

Kits that can be applied for DNA extraction from mammalian sources, as well as microorganisms are covered below. An overview of these kits is included in Table 5.

1. DNA Isolation for cells and tissues (Roche): This kit can be used for genomic DNA extraction 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 extractions, anion exchange columns, and chaotropic reagents, instead isolating DNA through removing protein, 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 large range of sample sizes from blood (e.g., 100 ul to 1 ml), tissues, cells, bacteria, buccal swabs, blood spots, FFPE tissues, 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 needs no special equipment and can be processed manually or with automated platforms. This kit’s chemistry is based on silica membrane technology where silica membranes with the ability to bind specifically to 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 tissues and cells, 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 a silica-based technology. After cell lysis using lysis buffer, the DNA extraction procedure can be completed in around 20 minutes.
4. NucleoSpin® Tissue XS (Macherey Nagel): This kit can be used for isolation of genomic DNA from tissues (e.g., mouse kidney, laser microdissection), cells (e.g., bacteria, yeast, and cultured cells), clinical samples (e.g., biopsy samples, fine needle aspirates) and from forensic samples (e.g., 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 of up to several milligrams of tissue or cell pellets. This kit also relies on silica membrane-based technology. Related products include NucleoSpin® Tissue for larger samples, NucleoBond® AXG, which relies on anion-exchange chromatography, the NucleoSpin® 8 Tissue and96 Tissue Core kit which allows for high throughput processing and automation.
5. GeneJET Genomic DNA Purification: This kit facilitates rapid and efficient purification of high-quality genomic DNA from various mammalian cell culture and tissue samples, whole blood, bacteria and yeast. The kit utilizes silica-based membrane technology in the form of a convenient spin column and the procedure takes less than 20 minutes following cell lysis. It 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 isolation of genomic DNA from plants, animals, bacteria, yeast, algae, and fungi using a silica spin filter method. It can be used along with any FastPrep® Instrument to lyse and subsequently isolate DNA from up to 200 mg of almost any sample in less than 30 minutes. The FastPrep® Instrument is a benchtop device which uses a patented vertical angular motion to homogenize samples by multidirectional, simultaneous impaction with lysing matrix particles. The instrument provides a quick, efficient and highly reproducible homogenization that surpasses traditional extraction methods, using enzymatic digestion, sonication, blending, douncing and vortex. Following lysis, samples are centrifuged to pellet debris and lysing matrix. 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.

Kits that can be applied for DNA extraction from most sources including mammalian, microbial and plant sources are covered below. An overview of these kits is included in Table 6.

1. ArchivePure DNA purification (5Prime): This kit is used for purifying genomic, mitochondrial or viral DNA from whole blood and bone marrow, cultured cells, animal and plant tissues, Gram-negative and Gram-positive bacteria, and yeast. It has a liquid-phase, genomic DNA purification system, and uses non-toxic detergents and salts. 95% of purified DNA is greater than 50kb in length, and is usually around 100-200 kb.
2. FastDNA (MP Biomedicals): This kit extracts genomic DNA from plant and animal tissues, cultured cells, bacteria, yeast, fungi, algae, viruses, and insects. It utilizes optimized Lysing Matrix tubes and a silica-based GeneClean® procedure for purifying DNA.
3. DNAzol® Reagent (Thermo Fisher): This reagent can be used to isolate genomic DNA from solid and liquid samples of animal, plant, yeast, and bacterial origin. It is designed for use with tissues, cells, or blood. It is a complete and ready-to-use reagent, providing versatility and efficiency.
4. Easy-DNA® gDNA Purification (Thermo Fisher): This kit can be used for isolation of high-molecular-weight genomic DNA from many types of cells and tissues including mammalian tissue, blood, hair follicles, mouse tails, plant leaves, yeast, and E. coli. It is based on a modification of the organic extraction method. It utilizes chloroform to remove contaminants and ethanol to precipitate and recover the isolated DNA.
5. Wizard® Genomic DNA Purification (Promega): This simple kit can be used for DNA isolation from whole blood, white blood cells, tissue culture cells, animal tissue, plant tissue, yeast and Gram-positive and Gram-negative bacteria. Briefly, cells are lysed, then cellular proteins are removed by salting-out, and RNA is removed using RNase. Finally, the DNA is precipitated using isopropanol.
6. DNA Isolation (BioBasic): these kits include animal tissue & fungi genomic DNA extraction prep kit, Bacteria genomic DNA prep kit, Blood genomic DNA prep kit, Plant genomic DNA prep kit, Yeast genomic DNA extraction prep Kit. BioBasic kits can be used for DNA isolation from blood, plant tissue, mammalian cells and tissue, bacteria and fungi [59]. Biobasic aim to offer the same simplicity and reliability as other kits, but at a significantly reduced cost.

Kits are also available to isolate genomic DNA specifically from whole blood. These kits include the following:

1. DNA Isolation for mammalian blood (Roche): This kit can be used for genomic DNA extraction from 1-10 ml whole blood (e.g., from human, mouse, rat). It can also be used for the isolation of DNA from buffy coat and lymphocyte samples. The average yield obtained using this kit is approximately 350 ug/10 ml, ranging from 200-700 ug for healthy human blood (average, 5x10⁶ leukocytes/ml). It provides DNA suitable for PCR, long PCR, sequencing, and Southern blots. The benefits of this kit include the short time taken for the entire procedure (less than 1.5 hours). Also, the A260/A280 ratio for isolated DNA samples is typically 1.7-1.9 [53, 66].
2. InnuPREP Blood DNA Mini (AJ Innuscreen): This kit can directly isolate genomic DNA from whole blood samples of up to 300 ul. It provides high yields of up to 12 ug depending on the sample. The advantages of this kit are that it produces extremely high-quality gDNA, is easy to use, and is also certified for in vitro-diagnostics use (CE-IVD). Related products include the InnuPREP Blood DNA Master Kit, the InnuPREP Blood DNA MIDI Kit and the InnuPREP Blood DNA MIDI Direct Kit for larger samples.

1. Wizard® PCR Preps DNA Purification System (Promega): This kit is used for purifying double-stranded PCR-amplified DNA. PCR products are effectively purified from contaminants, including amplification primers and primer-dimers. It provides greater than 95% recovery, which can be obtained when applying between 50 ng and 16 ug of a 500 bp PCR product to 1 ml of resin. Typical yields of 70-90% for 500 bp fragments can be expected with purification from low-melting-temperature agarose. The benefits of this kit are that it is a quick and simple, 15-minute direct purification method, and is relatively cost-effective [43, 67].
2. QIAquick PCR Purification (QIAGEN): This kit can directly purify double- or single-stranded PCR products (100 bp-10 kb) from amplification reactions and DNA cleanup from other enzymatic reactions with yield up to 10 ug and 90-95% recovery. The QIAquick system combines the convenience of spin-column technology with the selective binding properties of a uniquely designed silica membrane. DNA adsorbs to the silica membrane in the presence of high concentrations of salt with contaminants passing through the column. Impurities are efficiently washed away, and pure DNA is eluted with Tris buffer or water. Purified DNA can be used to perform restriction, labeling, hybridization, PCR, ligation and transformation, radioactive and fluorescent sequencing, in vitro transcription, or microinjection. The main advantage of this kit is rapid DNA cleanup [68, 69]. Related products include the QIAquick Nucleotide Removal Kit and QIAquick Gel Extraction Kit.
3. MinElute PCR Purification (QIAGEN): This kit is specially designed for fast and easy isolation of smaller DNA fragments (70 bp - 4 kb) from PCR reactions, agarose gels, or enzymatic reactions with an elution volume of only 10 µl. The MinElute PCR Purification Kit contains a silica membrane assembly for binding of DNA in high-salt buffer and elution with low-salt buffer or water. It removes primers, nucleotides, enzymes, mineral oil, salts, and other impurities from DNA sample. An optional pH indicator allows easy determination of the optimal pH for DNA binding to the spin column. The procedure can be fully automated on the QIAcube. The purified and highly concentrated DNA obtained is suitable for direct use in applications such as ligation and transformation, in vitro transcription, radioactive and fluorescent sequencing, amplification, restriction enzyme digestion, microinjection, labeling and hybridization.
4. GenElute™ PCR Clean-Up (MilliporeSigma): The kit is designed for rapid purification of PCR amplification products (100 bp to 10 kb) from other components in the reactions including excess primers, nucleotides, DNA polymerase, oil and salts. DNA is bound on a silica membrane within the spin column. The bound DNA is then washed and the clean, concentrated DNA is eluted in the desired buffer. Each column can purify up to 100 µl or 10 µg of PCR amplified DNA and recover up to 95% of PCR products between 100 bp and 10 kb. The kit removes ≥ 99% of the primers and most primer-dimers (<40 bp). Purified DNA is suitable for enzymatic reactions, sequencing, cloning and microarray analysis.
5. PureLink® PCR Purification (Thermo Fisher): This kit provides rapid and efficient removal of short primers, dNTPs, enzymes, short-tailed PCR products, and salts from PCR products. This kit is based on the selective binding of dsDNA to silica-based membrane in the presence of chaotropic salts, removal of impurities by thorough washing with Wash Buffer and elution of purified DNA in a low salt elution buffer. The kits are supplied with two proprietary buffers: 1) Binding Buffer for purifying 100 bp - 12 kb dsDNA PCR fragments, and 2) Binding Buffer High-Cutoff (HC) for removing primer dimers or short spurious PCR products (<300 bp). The purified PCR product is suitable for automated fluorescent DNA sequencing, restriction enzyme digestion, and cloning.
6. GeneJet PCR Purification (Thermo Scientific): This kit utilizes a proprietary silica-based membrane technology in the form of a convenient spin column for purification of DNA fragments from 25 bp to 20 kb with high recovery rates up to 100%. It effectively removes primers, dNTPs, unincorporated labeled nucleotides, enzymes, and salts from PCR and other reaction mixtures. Each GeneJET purification column has a total binding capacity of up to 25 µg of DNA, and the entire procedure takes 5 minutes. The purified DNA can be used in common downstream applications, such as sequencing, restriction digestion, labeling, ligation, cloning, in vitro transcription, blotting or in situ hybridization.

1. MinElute Gel Extraction (QIAGEN): This kit can be used for extraction of DNA fragments (70 bp-4 kb) from standard or low-melt agarose gels with 80% recovery. All enzymes are removed, independent of size and secondary structure. This kit combines the convenience of spin-column technology with the selective binding properties of a uniquely designed silica membrane. DNA adsorbs to the silica membrane in the presence of high concentrations of salt while contaminants pass through the column. Impurities are efficiently washed away, and the pure DNA is eluted with Tris buffer or water. Purified DNA can be used to perform ligation and transformation, radioactive and fluorescent sequencing, restriction enzyme digestion, labeling, hybridization, PCR, in vitro transcription, or microinjection. The main advantage of this kit is the ability to give high end-concentrations of purified DNA fragments (10 ul elution volume) [20, 81, 82]. Related products include the MinElute Reaction Cleanup Kit and MinElute PCR Purification Kit [20, 60, 83, 84].
2. Zymoclean^TM Gel DNA Recovery (Zymo Research): This kit provides for rapid purification of high-quality DNA from TAE/TBE-buffered agarose gels. It is based upon Fast-Spin technology. For DNA 50 bp to 10 kb, the recovery is 70-90%. For DNA 11 kb to 23 kb, the recovery is 50-70%. Purified DNA is suitable for DNA ligation reactions, sequencing, DNA labeling reactions, PCR, etc. The main advantage of this kit is the capability to yield ≥6 µl high-quality, purified DNA in 15 minutes [85, 86].

Kits are also available 1) to prepare DNA samples for application such as next-generation sequencing and preparation of expression libraries, 2) to purify double-stranded PCR-amplified DNA and 3) to create a library of fragments from a DNA sample. Some examples are as follows:

1. NEBNext® DNA Library Prep Reagent Set for Illumina® (New England Biolabs): This kits consists of enzymes and buffers that are used for sample preparation for next-generation sequencing, and for preparation of expression libraries. The components of the kit are Lot Controlled, both individually and as a set of reagents. The reagents go through additional quality controls, and are functionally validated to provide maximum yield. The main advantages of this kit include: its availability in sets, master mixes and modules; stringent quality controls; and functionally validation. Moreover, it prepares samples for next-generation sequencing, expression library construction, high-density hybridization arrays (SPRS2 and SPMMS2) and genomic subtraction hybridization methods (SPRS2 and SPMMS2) [61, 87, 88].
2. Wizard® PCR Preps DNA Purification System (Promega): This kit is used for purifying double-stranded PCR-amplified DNA. PCR products are effectively purified from contaminants, including primer-dimers and amplification primers. It provides greater than 95% recovery, which can be obtained when applying between 50 ng and 16 ug of a 500 bp PCR product to 1 ml of resin. Typical yields of 70-90% for 500bp fragments can be expected with purification from low-melting-temperature agarose. The benefits of this kit are that it is a 15 minute direct purification method, it is a quick and simple process, and is relatively less expensive [86].
3. QIAquick PCR Purification (QIAGEN): This kit can directly purify double- or single-stranded PCR products (100 bp-10 kb) from amplification reactions and DNA cleanup from other enzymatic reactions with yield up to 10 ug and 90-95% recovery. The QIAquick system combines the convenience of spin-column technology with the selective binding properties of a uniquely designed silica membrane. DNA adsorbs to the silica membrane in the presence of high concentrations of salt with contaminants passing through the column. Impurities are efficiently washed away, and DNA is eluted with Tris buffer or water. Purified DNA can be used to perform restriction, labeling, hybridization, PCR, ligation and transformation, radioactive and fluorescent sequencing, in vitro transcription, or microinjection. The main advantage of this kit is rapid DNA cleanup [69]. Related products include the QIAquick Nucleotide Removal Kit and QIAquick Gel Extraction Kit.
4. GS FLX Titanium Rapid Library Preparation (Roche): This kit consists of reagents for the creation of a library of fragments from a DNA sample to be sequenced, such as genomic DNA from an organism of interest. The procedure requires 500 ng of input DNA, which must be double-stranded, has an A₂₆₀/A₂₈₀ ratio of about 1.8 and a concentration of at least 5 ng/ul. The output library will consist of a set of single-stranded DNA fragments representing the entire sample sequence. Each fragment is flanked by suitable amplification and sequencing DNA adaptors, then purified and quantified. The main advantages are that this technology is suitable for sequencing genomes of any size, and that the process can be performed by a single person in a suitably equipped laboratory [89].

Kits from many suppliers have been used to extract or purify DNA from various sources among the formal publications Labome has surveyed.

Anzalone AV et al extracted genomic DNA from HEK293T, K562, U2OS and HeLa cells with Agencourt DNAdvance Kit from Beckman Coulter [94]. Laflamme C et al extracted genomic DNA from HEK-293 and U2OS cells for PCR to verify gene KO with QuickExtract DNA extraction solution from Epicentre Biotechnologies [96]. Van der Kant R et al used Epicentre QuickExtract kit to isolate DNA from iPSC to verify the genome editing of APP gene [116]. Ciccone R et al extracted genomic DNA from mouse tails with TRI-reagent from MilliporeSigma and phenol:chloroform:isoamyl alcohol for PCR to study neuronal hyperactivity [101]. QIAGEN DNeasy Blood and Tissue extraction kit is a very common choice. It has been used to extract mouse papillomavirus type 1 DNA from mouse skin biopsies for PCR detection [40] ; canine genomic DNA for exome sequencing from canine transmissible venereal tumor tissues and gonad, skin, liver tissues [111] ; genomic DNA from iPSC clones [117] ; genomic DNA from worms [118] ; zebrafish genomic DNA for PCR [119] ; genomic DNA from rhesus macaque rectal and jejunal biopsy samples for SIV proviral load measurement [120]. Wang L et al purified HSV-1 genomic DNA with ChargeSwitch DNA Preparation Kit from Thermo Fisher for in vitro binding with RAW264.7 cell nuclear extract [91]. de Goffau MC et al isolated DNA from placenta for metagenomic sequencing with QIAGEN QIAamp DNA mini kit from QIAGEN and Fast DNA Spin kit from MP Biomedical (116540600) [37]. Garrett-Bakelman FE et al extracted DNA and RNA from NASA twin astronaut blood RLT+ lysates using QIAGEN’s Allprep kit (Cat #80204) and extracted DNA from blood cell pellets using Lucigen MasterPure (Cat #MCD85201) [39]. Dominy SS et al extracted DNA from human postmortem cortex brain tissues for the PCR analysis of Porphyromonas gingivalis 16S rRNA and hmuY genes [121]. Gifford CA et al extracted DNA from the formalin-fixed paraffin embedded block using Thermo Fisher RecoverAll Total Nucleic Acid Isolation Kit for FFPE [122].

Ling Q et al extracted total genomic DNA from Arabidopsis thaliana plant inflorescence tissue with an EZNA plant DNA kit from Omega Bio-tek [123].

QIAGEN DNeasy Plant Mini Kit was used to investigate the strain of Phytophthora infestans responsible for the Irish potato famine [124].

Baez-Ortega A et al extracted canine genomic DNA for exome sequencing from blood samples with QIAGEN DNeasy Blood and Tissue extraction kit [111]. Gifford CA et al extracted DNA from venous blood using the QIAGEN DNA Mini kit [122].

N Attar et al extracted yeast DNA with phenolchloroform and isopropanol precipitation, followed by MNase and RNase A treatments, and purification with the Wizard SV PCR kit from Promega [114]. Sánchez-Busó L et al extracted genomic DNA from 419 gonococcal isolates from across the globe with the Promega Wizard DNA purification kit to conduct a genome-based phylogeographical analysis of Neisseria gonorrhoeae [65]. Rosshart SP et al isolated microbial DNA from mouse cecal and fecal samples with QIAGEN MagAttract PowerMicrobiome DNA/RNA kit and from mouse vaginal and skin preparations with QIAGEN AllPrep PowerViral DNA/RNA kit [93]. Maini Rekdal V et al extracted genomic DNA with DNeasy UltraClean Microbial kit (QIAGEN, catalog #: 12224-50) from anaerobic bacterial cultures [18].

Maini Rekdal V et al purified PCR products from gels with GE healthcare GFX PCR DNA and Gel Band Purification Kit (catalog# 28-9034-70) [18]. QIAGEN QIAquick Gel Extraction Kit was used to investigate the protective effect an ApoE3 mutation [68], cell migration [125], the development of Tornado circular RNA aptamer expression system [69]. Its QIAquick PCR Purification Kit was used to the development of Tornado circular RNA aptamer expression system [69].

de Goffau MC et al used Wizard SV Gel and PCR Clean-Up System to extract PCR products from gels for Illumina MiSeq sequencing [37]. Boettcher S et al concentrated PCR products with a QIAquick PCR Purification Kit from QIAGEN (#28104) and extracted DNA from gels with a QIAquick Gel Extraction Kit from QIAGEN (#28704) followed by AMPure XP beads from Beckman Coulter (#A63880) for ORF purification in TP53 MITE-seq screen [30].

Anzalone AV et al used Plasmid Plus Midiprep kits from QIAGEN or PureYield plasmid miniprep kits from Promega with endotoxin removal steps [94]. Zhao N et al prepared plasmids from bacterial hosts with NucleoBond Xtra Midi EF kit from Macherey-Nagel [115]. Butler AA et al obtained endotoxin-free plasmids using Macherey-Nagel endotoxin-free plasmid DNA purification kit for mouse brain infusion [126].

CA Douglas et al evaluated DNeasy PowerLyzer PowerSoil DNA Isolation, Sigma-Aldrich GenElute Bacterial Genomic DNA Kit, QIAamp DNA Stool Mini Kit, QIAamp DNA Stool Mini Kit with bead beating and the phenol-chloroform-based method in breast milk DNA extraction to study its microbiome and yielded very different microbiome composition and spurious contaminant inclusion [127]. Francis R et al extracted DNA from amoebas with an EZ1® DNA Tissue Kit from QIAGEN for the direct quantitation of amoebal DNA content with the Qubit dsDNA HS Assay Kit from Thermo Fisher [128]. Kaya-Okur HS et al used Ampure XP beads from Beckman Coulter to extract DNA after the tagmentation step during their CUT&Tag experiments [129]. Dominy SS et al extracted DNA from human cerebrospinal fluids and matching saliva samples with QIAGEN Puregene Core Kit A for the qPCR analysis of Porphyromonas gingivalis hmuY gene [121].