Although magnetic extraction is not always the method to use for your situation, it has several distinct advantages that make it situationally effective as an extraction method over older methods like phenol extraction which requires repeated centrifugal processing after each chemical application and a lot more invested time. Magnetic extraction is faster because it relies on binding specific functional groups on the surface of coated magnetic beads and can be separated by use of a simple magnet (which may be combined with centrifuge use, as desired).
Magnetic Beads?
Specific sets of magnetic beads are commonly employed for extraction of DNA. Since each system, which includes a mechanical processor to save labor, comes with its own brand, you should use only beads designed for a given system. Bead size and coatings can change results if used in different devices, which diminishes the credibility of your research. Even specially made alternatives can increase experimental error and should be disclosed when reporting results if the extractor is not made to work with your specific beads.
Should I "Mix And Match" Systems In Research?
Systems using various beads can affect the results. Henderson et al. came to the conclusion that, of the nine bead types tested, Dynabeads® DNA DIRECT™ by Invitrogen™can only pick up DNA that has a geometrically twisted straining. This means that the magnetized beads only retained the larger bits of DNA. Further, it was stated that the DNA had to be free-floating (in a solution). This condition also rules it out for use under certain circumstances. This also means, however, that this product is a good way to separate out the high molecular weight DNA (the big pieces) from the low molecular weight DNA ("degraded," small, or broken pieces). The bottom line in all this is that it is always up to researchers to determine best use the characteristics of these products.
Why Use Magnets For DNA Extraction?
This new method can make things more complicated (logistically), but the majority of studies involving magnetic extraction method still use phenol as a control and comparison, but typically shown an improvement in speed and accuracy by reducing experimental error through automation. Further, the magnetic approach lends itself to reversible immobilization through that automated means which can improve the efficacy of research funds by increasing the DNA yield per run.
Coatings
Magnetic beads come in a variety of types where they may be coated with antibodies specifically designed for one type of protein, or they may be more generalized with coatings or amines, carboxyls, or other suitable groups. Once the chemical coating on the magnet has bound the chemical in question, the bead-bound chemicals can then be rapidly removed by means of a simple magnet.
Does Size Matter?
Size affects properties such as the amount of time that should be allowed for binding because of surface area which increases in smaller beads. Another advantage of the smaller bead is that it makes a better suspension since the particles are more fine and can be more easily dispersed. Micro-size beads are much larger (sometimes as much as 15000 times larger) than their nano-sized buddies (which cost a lot more).
Costs
The disadvantage of this process is that there is a considerable expense involved in the nano-beads since 5mL can run a over $400 at shops. Micro-sized beads can be considerably cheaper, at about one third the cost, though it makes the work move more slowly.
Centrifuge Tubes
Magnetic separators are available that hold the centrifuge tubes and allow mass of separation in many full centrifuge tubes all at once. Some of these hold mass capacities of up to 24 or more centrifuge tubes full of material at one time while others only hold two at a time. The magnet is typically centrally located in the multi tube versions and is either below or beneath the tubes. Putting these tubes in a centrifuge makes sense because of the high density of the beads which can aid in the magnetic separation process. More information is available on the web or through your local supplier.
Tags: centrifuge tubes, experimental error, extraction method, magnetic extraction, molecular weight, simple magnet