Figure 1. Schematic diagram of the structure of magnetic beads

02 Principle

Commercial magnetic bead systems include magnetic beads, polyethylene glycol (PEG), salt ions, etc. The main factors affecting DNA recovery are PEG, DNA size and concentration, incubation time, etc. Among them, PEG is the decisive factor. High concentrations of PEG and NaCl cause DNA to shed its hydration layer, compress into a spherical shape, and expose the negatively charged phosphate groups. Through the formation of an "electric bridge" by Na+ with the carboxyl groups on the surface of the magnetic beads, DNA is adsorbed onto the magnetic beads. After the removal of PEG and NaCl, the hydration effect breaks the ionic bonds, and the DNA is purified. DNAs of different lengths can be selectively precipitated according to the changes in PEG and salt concentrations.

figure2. Schematic diagram of the principle of DNA adsorption by magnetic beads.

Applications

Magnetic beads are highly regarded in high-throughput sequencing due to their characteristics of high throughput and suitability for automation. They are widely used for the extraction, purification, and sorting of DNA in the construction of Next Generation Sequencing (NGS) libraries.

01 Nucleic acid extraction

In the magnetic bead extraction method, cell lysis buffer, acting as a protein denaturant, can lyse cells and release nucleic acids. Magnetic beads are positively charged and tend to adsorb negatively charged nucleic acids. After binding, impurities are removed through washing and magnetic field capture. Finally, the nucleic acids are dissociated with an elution buffer. The purified DNA/RNA can be used for tests such as PCR. This method is widely applied in the diagnostic industry and supports high-throughput and automated nucleic acid extraction.

figure3. Schematic diagram of the magnetic bead nucleic acid extraction process.

02 DNA purification

The purpose of DNA purification is to remove non-target fragments. Magnetic beads preferentially adsorb large fragments. By controlling the proportion of magnetic beads, DNA of specific sizes can be selectively adsorbed, and small fragments in the supernatant can be discarded. Finally, the target DNA is eluted and recovered. It is often used to remove small fragments such as adapter dimers/primer dimers, or for sample enrichment.

figure 4. Schematic diagram of the DNA purification process.

During the DNA purification process using magnetic beads, there will be some sample loss. The recovery efficiency can be calculated by the formula: Recovery Efficiency = (Mass of DNA after purification / Mass of Input DNA) × 100%. The data shows that the batch stability of Yeasen DNA magnetic beads is good, and the recovery efficiency is comparable to that of XP magnetic beads, making it a cost-effective alternative product.

Table 1. Calculation of Magnetic Bead Recovery Efficiency

【NOTE】：The test data of magnetic beads were sourced from a certain biotechnology company in Shanghai. In the table, A represents AMPure XP magnetic beads; B, C, and D are three different batches of Yeasen magnetic beads respectively.

03 DNA Double Size Selection

Next-generation sequencing (NGS) requires NGS libraries to reach a specific length. Fragment screening is used to select target fragments from fragmented DNA. Taking advantage of the characteristic that magnetic beads preferentially adsorb large fragments, after the first round of adsorption of large fragments, the magnetic beads are discarded and the supernatant is retained, with the target fragments remaining in the supernatant. In the second round, the magnetic beads adsorb the target fragments, and after discarding the supernatant, the target fragments are eluted and recovered.

Figure 5. DNA double size selection process overview

To evaluate the sorting accuracy, the fragment sizes sorted under different proportions of magnetic bead input are usually detected by the Agilent 2100 instrument.

Under a specific proportion of magnetic beads, the fragment distributions of different samples should be concentrated in the same position. The ideal sorting effect is a single narrow and rounded peak at the top. Due to differences in buffers among different manufacturers, the distributions will vary under a specific proportion of magnetic beads. Before use, it is necessary to refer to the instruction manual to confirm the sorting proportion of the target fragments. The data shows that under the same sorting proportion, the sorting effects of Yeasen magnetic beads and imported XP magnetic beads are highly consistent.

Table 2. Typical Recovery

【note】：The test data of magnetic beads were sourced from a certain biotechnology company in Shanghai. In the table, A represents AMPure XP magnetic beads, while B, C and D are three different batches of Yeasen magnetic beads respectively.

Product Information

Hieff NGS^TM DNA Selection Beads are based on the SPRI principle and combined with an optimized buffer system, being suitable for DNA fragment sorting and purification in next-generation sequencing libraries. This product is compatible with library construction kits of various brands, and its fragment recovery efficiency and library size distribution are similar to those of XP magnetic beads. It is worth noting that the price of Yeasen magnetic beads can be as low as 3 yuan per library, which is three times lower than that of the imported XP magnetic beads!

Table 3. Recommendations for Hieff NGS^TM Series Magnetic Bead Products