Isolation of DNA
Preparing The Sample
Nucleic acid is routinely isolated from human, fungal, bacterial, and viral sources in the clinical laboratory. The initial steps in nucleic acid isolation depends on the nature of the starting material.
Nucleated Cells in Suspension
Depending on the type of clinical sample that is sent for analysis, the specimen may have to be pretreated to make nucleated cells available from which the nucleic acid will be extracted. For instance, white blood cells (WBCs) must be isolated from blood or bone marrow specimens.
This is done by either differential density gradient centrifugation or differential lysis. For differential density gradient centrifugation, whole blood or bone marrow mixed with isotonic saline is overlaid with Ficoll.
Ficoll is a highly branched sucrose polymer that does not penetrate biological membranes. Upon centrifugation, the mononuclear WBCs (the desired cells for isolation of nucleic acid) settle into a layer in the Ficoll gradient that is below the less dense plasma components and above the polymorphonuclear cells and red blood cells (RBCs). The layer containing the mononuclear cells is removed from the tube and washed by at least two rounds of resuspension and centrifugation in saline before proceeding with the nucleic acid isolation procedure.
Another method used to isolate nucleated cells takes advantage of the differences in the osmotic fragility of RBCs and WBCs. Incubation of whole blood or bone marrow in hypotonic buffer or water will result in the lysis of the RBCs before the WBCs. The WBCs are then pelleted by centrifugation, leaving the empty RBC membranes (ghosts) and hemoglobin, respectively, in suspension and solution.
Tissue Samples
Fresh or frozen tissue samples must be dissociated before DNA isolation procedures can be started. Grinding the frozen tissue in liquid nitrogen, homogenizing the tissue, or simply mincing the tissue using a scalpel can disrupt whole tissue samples. Fixed embedded tissue has to be deparaffinized by soaking in xylene (a mixture of three isomers of dimethylbenzene). Less toxic xylene substitutes, such as Histosolve, Anatech Pro-Par, or ParaClear, are also often used for this purpose. After xylene treatment, the tissue is usually rehydrated by soaking it in decreasing concentrations of ethanol.
Microorganisms
Some bacteria and fungi have tough cell walls that must be broken to allow the release of nucleic acid. Several enzyme products, e.g., lyzozyme or zymolyase, that digest cell wall polymers are commercially available. Alternatively, cell walls can be broken mechanically by grinding or by vigorously mixing with glass beads. Gentler enzymatic methods are less likely to damage chromosomal DNA and thus are preferred for methods involving larger chromosomal targets as opposed to plasmid DNA.
Treatment with detergent (1% sodium dodecyl sulfate) and strong base (0.2 M NaOH) in the presence of Tris base, ethylenediaminetetraacetic acid (EDTA), and glucose can also break bacterial cell walls.
Boiling in 8% sucrose, 8% Triton X-100 detergent, Tris buffer, and EDTA after lysozyme treatment releases DNA that can be immediately precipitated with alcohol. DNA extracted with NaOH or boiling procedures is denatured (single-stranded) and may not be suitable for methods such as restriction enzyme analysis that require double-stranded DNA. The advantage of these types of
extraction is their speed and simplicity. Amplification methods will work with this type of DNA isolation.
Organic Isolation Methods
After release of DNA from the cell, further purification requires removal of contaminating proteins, lipids, carbohydrates, and cell debris. This is accomplished using a combination of high salt, low pH, and an organic mixture of phenol and chloroform. The combination readily dissolves hydrophobic contaminants such as lipids and lipoproteins, collects cell debris, and strips away most DNA associated proteins. Isolation of small amounts of DNA from challenging samples such as fungi
can be facilitated by pretreatment with cetyltrimethylammonium bromide, a cationic detergent that efficiently separates DNA from polysaccharide contamination. To avoid RNA contamination, RNAse, an enzyme that degrades RNA, can be added at this point. Alternatively, RNAse may also be added to the resuspended DNA at the end of the procedure.
When phenol and chloroform are added to the hydrophilic cleared cell lysate, a biphasic emulsion forms. Centrifugation will settle the hydrophobic layer on the bottom, with the hydrophilic layer on top. Lipids and other hydrophobic components will dissolve in the lower hydrophobic phase. DNA will dissolve in the upper aqueous phase. Amphiphilic components, which have both hydrophobic and hydrophilic properties as well as cell debris, will collect as a white precipitate at the interface between the two layers.
The upper phase containing the DNA is collected, and the DNA is then precipitated using ethanol or isopropanol in a high concentration of salt (ammonium,potassium or sodium acetate, or lithium or sodium chloride). The ethyl or isopropyl alcohol is added to the upper phase solution at 2:1 or 1:1 ratios, respectively, and the DNA forms a solid precipitate.
The DNA precipitate is collected by centrifugation. Excess salt is removed by rinsing the pellet in
70% ethanol, centrifuging and discarding the ethanol supernatant, and then dissolving the DNA pellet in rehydration buffer, usually 10 mM Tris, 1 mM EDTA (TE), or water.
General scheme of Organic DNA isolation |
Inorganic Isolation Methods
Safety concerns in the clinical laboratory make the use of caustic reagents such as phenol undesirable. Methods of DNA isolation that do not require phenol extraction have, therefore, been developed and are used in many laboratories. Initially, these methods did not provide the efficient
recovery of clean DNA achieved with phenol extraction; however, newer methods have proven to produce high-quality DNA preparations in good yields.
Inorganic DNA extraction is sometimes called “salting out”. It makes use of low pH and high salt conditions to selectively precipitate proteins, leaving the DNA in solution. The DNA can then be precipitated as described above using isopropanol pelleted and resuspended in TE buffer or water.
General scheme of Organic DNA isolation |
Solid-Phase Isolation
More rapid and comparably effective DNA extraction can be performed using solid matrices to bind and wash the DNA. Silica-based products were shown to effectively bind DNA in high salt conditions. Many variations on this procedure have been developed, including use of diatomaceous earth as a source of silica particles. More modern systems can be purchased with solid matrices in
the form of columns or beads. Columns come in various sizes, depending on the amount of DNA to be isolated. Columns used in the clinical laboratory are usually small “spin columns” that fit inside microcentrifuge tubes. These columns are commonly used to isolate viral and bacterial DNA from serum, plasma, or cerebrospinal fluid. They are also used routinely for isolation of cellular DNA in genetics and oncology. Preparation of samples for isolation of DNA on solid-phase media starts with cell lysis and release of nucleic acids, similar to organic and inorganic procedures. Specific buffers are used to lyse bacterial, fungal, or animal cells. Buffer systems designed for specific applications (e.g., bacterial cell lysis or human cell lysis) are commercially available.
For solid-phase separation, the cell lysate is applied to a column in high salt buffer, and the DNA in solution adsorbs to the solid matrix. After the immobilized DNA is washed with buffer, the DNA is eluted in a specific volume of water, TE, or other low salt buffer. The washing solutions and the eluant can be drawn through the column by gravity, vacuum, or centrifugal force. DNA absorbed
to magnetic beads is washed by suspension of the beads in buffer and collection of the beads using a magnet applied to the outside of the tube while the buffer is aspirated or poured off. The DNA IQ system (Promega) uses a magnetic resin that holds a specific amount of DNA (100 ng). When the DNA is eluted in 100µL, the DNA concentration is known, 1 ng/µL, and ready for analysis.
Solid-phase isolation is the methodology employed for several robotic DNA isolation systems such as Roche MagnaPure and Qiagen BioRobot, which use magnetized glass beads or membranes to bind DNA. These systems are finding increased use in clinical laboratories for automated isolation of DNA from blood, tissue, bone marrow, plasma, and other body fluids. A measured amount of sample, e.g., 200–400µL of whole blood or 10–50 mg of tissue, in sample tubes is placed into the instrument along with cartridges or racks of tubes containing the reagents used for isolation. Reagents are formulated in sets depending on the type and amount of starting material. The instrument is then programmed to lyse the cells and isolate and elute the DNA automatically.