Six Misunderstandings in the Magnetic Bead Method of Nucleic Acid Extraction

The use of biological magnetic beads to extract nucleic acid is a novel method of nucleic acid extraction. Compared with the traditional chloroform, isoamyl alcohol extraction method and spin column kit method, this method is still understood by many people. There are also some misunderstandings in the process of purification of nucleic acids by the pearl method.

Misunderstanding 1. The more magnetic beads, the better the extraction effect

Some people think that when the extraction effect is not good, increase the amount of magnetic beads. They think that adding a little more magnetic beads can attract more nucleic acids. In fact, this idea is not advisable.
The main feature of magnetic beads is that they can be dispersed in a liquid or separated from a liquid phase in a solid state under the action of an external magnetic field. For any reagent system, the ratio of magnetic beads to liquid should have a certain value, exceeding a certain ratio Excessive magnetic beads will lose their dispersion characteristics because they cannot be uniformly dispersed in the liquid, and the efficiency of contact between the nucleic acid magnetic beads and the liquid cannot be fully increased during the washing process.
Excessive magnetic beads will also adsorb more impurities, which has a great influence on the effect of impurity removal. Even sometimes, too many magnetic beads will adsorb protease, lysozyme and other functional components that play a major role in the liquid system, resulting in low efficiency of the entire kit. In many cases, when the extraction effect is not good, reducing the amount of magnetic beads used is the best way to improve the extraction effect.
Normally, the amount of reference magnetic beads given by the magnetic bead method kit is slightly excessive. Therefore, it is not often necessary to increase the amount of magnetic beads to improve the adsorption efficiency. However, if it is determined that the amount of magnetic beads is insufficient, the extraction effect is not good. Well, it is possible to improve the extraction effect by increasing the amount of magnetic beads within a certain range.

Misunderstanding 2. The more reagents used, the better the extraction effect

However, for the magnetic bead method, each increase in the volume of a part of the liquid reduces the probability of more magnetic bead collisions, and reducing the probability of magnetic bead collisions will result in a significant drop in the adsorption rate. Therefore, in many cases, although adding lysis solution and washing solution can indeed enhance lysis and enhance washing, the core of magnetic bead extraction is the efficiency of magnetic bead adsorption of nucleic acids. The efficiency of magnetic bead collision cannot be guaranteed, but the efficiency of nucleic acid extraction cannot be guaranteed. Yes, so simply increasing the amount of reagents used to improve the extraction effect may not be completely effective.

Misunderstanding 3. The more washing times, the better the extraction effect

When there are too many impurities in the extracted nucleic acid, the user will consider washing several times to obtain a purer nucleic acid. Increasing the number of washes is indeed conducive to the purification of nucleic acids, but considering that each wash will lose a certain amount of nucleic acid and increase the possibility of nucleic acid fragmentation and hydrolysis, it is generally appropriate to control the number of washes at 2 to 4 times.

Misunderstanding 4. The more samples are used, the better the extraction effect

When the sample is not fresh enough or the nucleic acid content itself is low, the nucleic acid extraction effect is often not good, and many teachers will use multiple samples to increase the amount of nucleic acid extraction.
However, simply increasing the sample sampling volume may sometimes introduce too many impurities, exceeding the lysing capacity of the lysate, and also reduce the extraction efficiency. Therefore, it is not recommended to simply increase the sample sampling volume to achieve the purpose of increasing the extraction volume.
If the extraction volume is indeed too low due to insufficient sample volume, it is recommended to go through the enrichment or concentration step before starting the extraction. Or increasing the completeness of lysis and exposing more nucleic acids is also a solution.

Misunderstanding 5. If a certain kind of magnetic bead is good, it should be effective in all tests

There are many types of magnetic beads, different particle size, different dispersion, different magnetic response time, different coating base matrix, different outer modified functional group, different coating density, different functional group arm length, which will lead to magnetic beads Features vary greatly.
Therefore, the experiments and systems that different magnetic beads adapt to are also different. Just like the reagents for nucleic acid extraction, the formulas are not exactly the same, and the properties of the magnetic beads that are also used for nucleic acid extraction are not exactly the same.
Some magnetic beads show higher adsorption efficiency in the extraction of constant nucleic acid, and some magnetic beads are more suitable for the extraction of trace nucleic acid. Some magnetic beads are suitable for more acidic reagent systems, and some magnetic beads are suitable for more alkaline reagent systems. Some magnetic beads have good magnetic responsiveness but fast settling speed, which is more suitable for magnetic rod type automatic extractor; some magnetic beads have slow settling speed but long magnetic response time, and are more suitable for pipette type automatic extractor.
There is rarely a kind of magnetic beads that can be applied to all experimental situations. Except for the fixed kit, in most cases, the magnetic beads and the reagent system need to be adjusted for a certain period of time.

Misunderstanding 6. It is not good to compare with a certain kit, that is, the magnetic beads are not good

In the process of screening magnetic beads, many customers simply replace the magnetic beads with the same amount under the mature reagent system to compare the effects of magnetic beads.
In this way, it is easy to conclude that certain magnetic beads are not effective, but in fact, because different magnetic beads are suitable for different systems and dosages, they often need to be adjusted to obtain better extraction results.