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Dynabeads™ DNA DIRECT™ Universal Kit - FAQs

Dynabeads™ DNA DIRECT™ Universal Kit - FAQs

View additional product information for Dynabeads™ DNA DIRECT™ Universal Kit - FAQs (63006)

41 product FAQs found

I am seeing high PCR background when using the Dynabeads DNA DIRECT Kit. What could be the cause of this?

High PCR background could be caused by too high a concentration of template DNA, primers, Mg2+, or dNTPs. To fix this, reduce the amount of template DNA, primers, enzyme, and Mg2+ used, elute the DNA prior to PCR amplification, and/or try performing hot-start PCR. High background can also be caused by contamination. Ensure that the supernatant is completely removed at each washing step to avoid carryover.

I am getting inefficient elution of my DNA when using the Dynabeads DNA DIRECT Kit. Do you have any suggestions to improve this?

We recommend eluting the DNA in Resuspension Buffer, water, or low ionic strength buffer by incubation at 65 degrees C for > 5 mins. The complex must be fully resuspended before elution. The elution buffer can be pre-heated to 65 degrees C. After incubation, place tube in magnetic stand for 30 secs and transfer supernatant to a clean tube. To determine the elution efficiency, you can run some of the eluted DNA on an agarose gel. Alternatively, you can perform a PCR with the Dynabeads magnetic beads to determine if there is residual DNA remaining on the beads. Using more pre-heated elution buffer would be helpful to improve the elution efficiency.

I do not see any amplification when using your Dynabeads DNA DIRECT Kit for PCR. What should I do?

PCR may be inhibited by inhibitors, or an insufficient number of PCR cycles might have been used. For inhibitors, ensure that the washing buffer is brought to room temperature for use, and add the buffer more vigorously. You can also ensure that the supernatant is completely removed at each washing step, or introduce an additional washing step.

My Dynabeads magnetic beads are not pelleting well with the magnet. Do you have any suggestions for me?

Please review the following possibilities for why your Dynabeads magnetic beads are not pelleting:

- The solution is too viscous.
- The beads have formed aggregates because of protein-protein interaction.

Try these suggestions: - Increase separation time (leave tub on magnet for 2-5 minutes)
- Add DNase I to the lysate (~0.01 mg/mL)
- Increase the Tween 20 concentration to ~0.05% of the binding and/or washing buffer.
- Add up to 20 mM beta-merecaptoethanol to the binding and/or wash buffers.

Find additional tips, troubleshooting help, and resources within our Dynabeads Nucleic Acid Purification Support Center.

I have a long double-stranded DNA fragment I would like to isolate. What product do you recommend?

For biotin-labled DNA that is less than 1 kb, we recommend you use Dynabeads M270 Streptavidin and MyOne C1 magnetic beads. We recommend our Dynabeads KilobaseBINDER Kit, which is designed to immobilize long (>1 kb) double-stranded DNA molecules. The KilobaseBINDER reagent consists of M-280 Streptavidin-coupled Dynabeads magnetic beads along with a patented immobilization activator in the binding solution to bind to long, biotinylated DNA molecules for isolation. Please see the following link (https://www.thermofisher.com/us/en/home/life-science/dna-rna-purification-analysis/napamisc/capture-of-biotinylated-targets/immobilisation-of-long-biotinylated-dna-fragments.html) for more information in regards to long biotinylated DNA fragment isolation.

Find additional tips, troubleshooting help, and resources within our Dynabeads Nucleic Acid Purification Support Center.

Can I use Dynabeads magnetic beads to isolate single-stranded DNA templates?

Yes, Dynabeads magnetic beads can be used to isolate single-stranded DNA. Streptavidin Dynabeads magnetic beads can be used to target biotinylated DNA fragments, followed by denaturation of the double-stranded DNA and removal of the non-biotinylated strand. The streptavidin-coupled Dynabeads magnetic beads will not inhibit any enzymatic activity. This enables further handling and manipulation of the bead-bound DNA directly on the solid phase. Please see the following link (https://www.thermofisher.com/us/en/home/life-science/dna-rna-purification-analysis/napamisc/capture-of-biotinylated-targets/preparing-single-stranded-dna-templates.html) for more information in regards to single-stranded DNA capture.

Find additional tips, troubleshooting help, and resources within our Dynabeads Nucleic Acid Purification Support Center.

What is the magnetic susceptibility for Dynabeads magnetic beads?

Magnetic susceptibility is a measure of how quickly the beads will migrate to the magnet. This will depend on the iron content and the character of the iron oxide. The magnetic susceptibility given for the Dynabeads magnetic beads is the mass susceptibility, given either as cgs units/g or m^3/kg (the latter being an SI unit). For ferri- and ferromagnetic substances, the magnetic mass susceptibility is dependent upon the magnetic field strength (H), as the magnetization of such substances is not a linear function of H but approaches a saturation value with increasing field. For that reason, the magnetic mass susceptibility of the Dynabeads magnetic beads is determined by a standardized procedure under fixed conditions. The magnetic mass susceptibility given in our catalog is thus the SI unit. Conversion from Gaussian (cgs, emu) units into SI units for magnetic mass susceptibility is achieved by multiplying the Gaussian factor (emu/g or cgs/g) by 4 pi x 10^-3. The resulting unit is also called the rationalized magnetic mass susceptibility, which should be distinguished from the (SI) dimensionless magnetic susceptibility unit. In general, magnetic mass susceptibility is a measure of the force (Fz) influencing an object positioned in a nonhomogenous magnetic field. The magnetic mass susceptibility of the Dynabeads magnetic beads is measured by weighing a sample, and then subjecting the sample to a magnetic field of known strength. The weight (F1) is then measured, and compared to the weight of the sample when the magnetic field is turned off (F0). The susceptibility is then calculated as K x 10^-3 = [(F1-F0) x m x 0.335 x 10^6], where K is the mass susceptibility of the sample of mass m. The susceptibility is then converted to SI units.

Find additional tips, troubleshooting help, and resources within our Dynabeads Nucleic Acid Purification Support Center.

How can I determine coupling efficiency of Dynabeads magnetic beads?

There are different methods to check binding of ligands to the beads, including optical density (OD) measurement, fluorescent labeling, and radioactive labeling.

For OD measurement, you would measure the OD of the ligand before immobilization to the beads and compare it with the ligand concentration that is left in the supernatant after coating. This gives a crude measurement of how much protein has bound to the beads.

Protocol:

1.Set spectrophotometer to the right wavelength. As a blank, use the Coupling Buffer.
2.Measure the absorbance of the Pre-Coupling Solution. A further dilution may be necessary to read the absorbance, depending upon the amount of ligand added.
3.Measure the absorbance of the Post-Coupling Solution. A dilution may be necessary to read the absorbance.
4.Calculate the coupling efficiency, expressed as the % protein uptake, as follows. [(Pre-Coupling Solution x D) - (Post-Coupling Solution x D)] x 100/(Pre-Coupling Solution x D) where D = dilution factor.

For fluorescent labeling, we suggest negatively quantifying the amount of ligand bound by measuring ligand remaining in the coupling supernatant (compared to the original sample), rather than directly measuring the ligands on the beads. Add labeled ligand to the beads, and measure how much ligand is left in the supernatant (not bound to the beads). By comparing this with the total amount added in the first place, you can then calculate how much of the ligand that has been bound to the beads. Keep in mind that the Dynabeads magnetic beads are also autofluorescent, which is why direct measuring of fluorescence of the bead-bound ligands is not recommended, but rather this indirect approach. The label could be, for example, FITC/PE. Some researchers perform a direct approach with success (using a flow cytometer).

Radioactive labeling is the most sensitive method of the three, but it is also the most difficult one. It involves radioactively labeling a portion of the ligand. We use radiolabeled I-125 in tracer amounts and mix it with "cold" ligands in a known ratio before coupling. The absolute quantities for the ligand on the beads should be obtained by measuring the beads in a scintillation (gamma) counter and comparing the cpm with a standard.

Protocol:

1.Take out an appropriate amount of beads and wash the beads in 1 mL of binding buffer.
2.Pipette out desired amount of human IgG in a separate tube.
3.Mix the human IgG with I-125-labeled human IgG (30,000 - 100,000 cpm).
4.Dilute the mixture of human IgG and I-125-labeled human IgG to 100 mL in binding buffer.
5.Incubate for 30 minutes at room temperature and measure the cpm in a scintillation counter.
6.Wash the beads (with coating) four times, and measure cpm again.
The % binding is calculated by using the equation : (cpm after washing/cpm before washing)x100%.

Find additional tips, troubleshooting help, and resources within our Dynabeads Nucleic Acid Purification Support Center.

What sizes do you offer for the Dynabeads magnetic beads?

Dynabeads magnetic beads come in three sizes: 4.5 µm (M-450), 2.8 µm (M-270/M-280), and 1 µm (MyOne beads). The largest of the Dynabeads magnetic beads is ideal for big targets like cells. The 2.8 µm beads are recommended for proteomics and molecular applications. The smallest of the beads, 1 µm, are ideal for automated handling.

Find additional tips, troubleshooting help, and resources within our Dynabeads Nucleic Acid Purification Support Center.

Can Dynabeads magnetic beads be sonicated?

In general, short sonication is a good way to reduce aggregation of the beads and ensure optimal homogenous conditions at the time of ligand addition when coating the beads. When target is bound to the beads, more care is needed, as the binding might break. The streptavidin beads themselves should tolerate sonication. We have not tested sonication for long periods, but 5 minutes is fine. We do not have information about the streptavidin-biotin interaction being broken by such treatment.

Find additional tips, troubleshooting help, and resources within our Dynabeads Nucleic Acid Purification Support Center.

Can Dynabeads magnetic beads be sterilized?

If desired, the uncoated epoxy or tosylactivated beads can be sterilized by washing with 70% ethanol. Coated beads cannot be sterilized.

Find additional tips, troubleshooting help, and resources within our Dynabeads Nucleic Acid Purification Support Center.

What are Dynabeads magnetic beads?

Dynabeads magnetic beads are uniform, non-porous, superparamagnetic, monodispersed and highly cross-linked polystyrene microspheres consisting of an even dispersion of magnetic material throughout the bead. The magnetic material within the Dynabeads magnetic beads consists of a mixture of maghemite (gamma-Fe2O3) and magnetite (Fe3O4). The iron content (Fe) of the beads is 12% by weight in Dynabeads magnetic beads M-280 and 20% by weight in Dynabeads magnetic beads M-450. The Dynabeads magnetic beads are coated with a thin polystyrene shell which encases the magnetic material, and prevents any leakage from the beads or trapping of ligands in the bead interior. The shell also protects the target from exposure to iron while providing a defined surface area for the adsorption or coupling of various molecules.

Uniformity of bead size and shape provides consistent physical and chemical properties. These uniform physical characteristics lead to high-quality, reproducible results.

The Dynabeads magnetic beads are available in three different sizes: 4.5 µm (M-450 beads), 2.8 µm (M-270/M-280 beads) and 1 µm (MyOne beads).

Find additional tips, troubleshooting help, and resources within our Dynabeads Nucleic Acid Purification Support Center as well as our Protein Immunoprecipitation (IP), Co-Immunoprecipitation (Co-IP), and Pulldown Support Center.

Can Dynabeads DNA DIRECT Universal Kit be used for isolation of bacterial DNA directly from soil?

It might be possible to isolate bacterial DNA directly from soil but soil samples are difficult to work with, as there are a lot of PCR inhibitors present. Please check scientific literature for suggested protocols.

Why are LiCl and LiDS included in Dynabeads buffers?

Lithium chloride is included in Washing Buffer A to ensure that the mRNA remains annealed to the Oligo(dT)25 on the beads while everything else is washed away. The major advantage of using LiCl instead of other chloride salts is that LiCl does not efficiently precipitate DNA, proteins, or carbohydrates and therefore reduces the risk of contamination of the final mRNA preparation with DNA and inhibitors of cDNA synthesis, PCR etc.

LiDS is an ionic detergent, similar in function to SDS. LiDS is included in the lysis buffer is to aid in the lysis of the cells and to denature proteins, and in addition it is an effective RNase inhibitor. If you don't have LiDS in the lab, it is also possible to use SDS, but you may wish to add RNAse inhibitor as well.

What is the Dynabeads DNA DIRECT Universal kit?

Dynabeads DNA DIRECT Universal Kit (Cat. No. 63006) is designed for genomic DNA isolation. This kit will not be able to isolate small DNA fragments or plasmids, the smallest DNA isolated with this kit is about 17kb.

The Dynabeads DNA DIRECT Kit does not involve any "specific capture" of DNA, but rather adsorption of DNA onto the Dynabeads magnetic beads surface. Dynabeads DNA DIRECT Universal Kits contain a Lysis and Binding buffer that facilitate the precipitation of the DNA onto the beads surface - a combination of detergents and salt result in precipitation of DNA.

Can genomic DNA and mRNA be isolated from the same sample with Dynabeads magnetic beads?

Both genomic DNA and mRNA can be isolated from the same sample, but we recommend that you isolate the DNA first using the Dynabeads DNA DIRECT Universal Kit in order to avoid large DNA fragments binding to the Oligo(dT)25 beads during the mRNA isolation procedure.

After genomic DNA is isolated, you can use the Dynabeads mRNA DIRECT Kit or Dynabeads mRNA DIRECT Micro Kit to isolate the mRNA from the same lysate (just add the Dynabeads Oligo (dT)25 magnetic beads to the lysate, don't use the lysis/binding buffers in the kit, and follow the remainder of the protocol).

If the Dynabeads DNA Direct magnetic beads do become dried, will they still work?

Vials containing Dynabeads magnetic beads should be stored upright to ensure that the beads are covered with buffer. Drying of Dynabeads magnetic beads may reduce their efficiency. If Dynabeads magnetic beads do become dried, they should be resuspended by keeping the vial in motion on a roller for up to 12 hours. This should restore the functionality of the Dynabeads magnetic beads.

How should the Dynabeads DNA Direct kit be stored?

All components of the kit should be stored at 2 to 8 degrees C. Freezing of the kit is not recommended. All components of the kit needs to be brought to room temperature before use. Dynabeads magnetic beads and any precipitated detergent should be fully resuspended.

Can the Dynabeads DNA Direct Universal Kit be used to isolate plasmid DNA?

The kit is designed for the isolation of double-stranded DNA molecules larger than 17 kb. If you have a strain of bacteria with a high copy-number of plasmids, you will co-isolate some plasmid DNA together with the bacterial genomic DNA. The process of isolating DNA with this kit is based on unspecific adsorption of DNA to the surface of these specific beads upon lysis. Due to their low size, plasmids will be lost in the supernatant during washing steps. For specific capture of plasmid DNA, use a biotinylated oligo and Streptavidin-Coupled Dynabeads magnetic beads.

Are Dynabeads DNA Direct magnetic beads reusable?

Dynabeads DNA Direct magnetic beads are not reusable. It will never be possible to remove all traces of DNA from the magnetic beads. As with used tubes and pipette tips, traces of DNA on the beads will contaminate downstream PCR on a future sample.

Can the purity of the isolated DNA be measured by an OD reading?

To use optical density measurements to determine DNA purity, the DNA will first have to be eluted from the Dynabeads magnetic beads. Ensure that there are no Dynabeads magnetic beads left in the solution, as the beads will interfere with the spectrophotometrical readings.

How should DNA isolated with Dynabeads DNA Direct kit be stored?

The DNA/Dynabeads complex may be stored for up to one week at 4 degrees C. For longer periods, DNA should be eluted and stored at -20 to -70 degrees C.

Is it necessary to elute the DNA from Dynabeads magnetic beads prior to PCR?

No, the beads do not have inhibitory effects when recommended concentrations are applied. If the DNA is to be stored prior to PCR amplification, elution is recommended.

How should the DNA/Dynabeads complex be handled?

The complex will appear gelatinous. Removal of lysate should be performed carefully to avoid loss of the DNA/Dynabeads complex, and completely to remove all contaminants. To avoid withdrawing the complex into the pipette tip when aspirating the supernatant, a stepwise removal of the supernatant is recommended. Washing buffer should be pipetted into the test tube in a single, rapid pipetting action so that the complex is swirled around in the buffer. To avoid loss of material, it is important that the complex is not broken up until the addition of the Resuspension Buffer.

Why are the Dynabeads magnetic beads supplied in a lysis buffer?

Upon addition of the lysis buffer the cells will lyse and release the DNA, which will then bind instantly to the Dynabeads magnetic beads. The swirling created by the addition of the Dynabeads magnetic beads in the lysis buffer will mix the components sufficiently. Vortexing or mixing further is not recommended as this will damage the DNA/Dynabeads complex.

What is the length of the DNA isolated by Dynabeads DNA Direct kits?

The isolated DNA is maintained at chromosome length during the lysis and washing steps. During these steps, it is important to take care not to break up the DNA/Dynabeads complex. The amount of shear force applied during resuspension determines the final average fragment length. Normally, the average fragment length exceeds 20 kb.

Can Dynabeads DNA Direct protocols be automated?

The properties of Dynabeads magnetic beads are excellent for automated liquid handling. Their protocols can be adapted to all automatic liquid handling instruments equipped with magnets.

How many isolations does the Dynabeads DNA Direct Universal kit support?

Dynabeads DNA Direct Universal kit (Cat. No. 63006) supports 300 isolations directly from crude material such as cultured cells, clinical specimens, bacteria, mouse tails, and other solid tissues from various species.

How does the Dynabeads DNA Direct Universal protocol work?

Dynabeads magnetic beads supplied in a lysis/binding buffer are added to sample, and DNA released from the lysed cells are adsorbed onto the surface of the Dynabeads magnetic beads during a brief incubation. This is followed by magnetic separation of the intact DNA/Dynabeads complex, removal of the supernatant, and subsequent washing to remove any residual contaminants and potential PCR inhibitors. Finally, the complex is resuspended for direct use in downstream PCR reactions. Pure DNA is extracted in only 10 min. Tedious centrifugation and precipitation steps are eliminated in this protocol.

What should I do if the A260/A280 ratio of my purified RNA is very low (e.g., <1.8)?

Check that you have not over-diluted the sample. That is, the A260 value is within the linear range of the spectrophotometer that you are using. Most spectrophotometers are only linear in the range 0.1 to 2.0 absorbance units.

If your sample has an A260 reading of less than 0.1 units, decrease the dilution of the sample, or read the undiluted sample and re-measure the A260/A280 ratio.

If the sample still has a low A260/A280 ratio, your sample may be contaminated with protein.

Be sure to do extra washes the next time you run that sample.

What is the detection limit when using Dynabeads magnetic beads for immunoprecipitation (IP)?

Answering this question is not straightforward. It will depend on the detection method. When using HRP (horseradish peroxidase)-based detection system or radioactivity in combination with a good antibody, very little target is required. More target is required when using an AP (alkaline phosphatase)-based detection system. When a sensitive detection system is used, detection will most likely be in the nanogram range. In some cases, pictograms of target can be detected.

Find additional tips, troubleshooting help, and resources within our Protein Immunoprecipitation (IP), Co-Immunoprecipitation (Co-IP), and Pulldown Support Center.

What is the elution volume when using Dynabeads magnetic beads for immunoprecipitation (IP)?

Within practical limits, the elution volume can be scaled up or down to suit your experiment. However, volumes less than 10 µL become more difficult to work with. In addition, the amount of target is important. If you have a lot of beads with a lot of bound target in a small elution volume, your elution may not be very efficient. Typically, 15-100 µL of beads may be eluted in 30 µL. For efficient recovery of the antigen and/or binding partners, the elution volume should at minimum equal the volume of the beads.

Find additional tips, troubleshooting help, and resources within our Protein Immunoprecipitation (IP), Co-Immunoprecipitation (Co-IP), and Pulldown Support Center.

How can I quantify the amount of antibody bound to Dynabeads magnetic beads?

There are several methods to quantify the amount of antibody bound to the beads. The crudest method is to measure the concentration of antibody in the coupling reaction before and after antibody attachment. Either fluorescence measurements or absorbance at 280 nm can be used. Alternatively, you could measure the amount of antibody bound to the beads by fluorescence, chemiluminescence, or radiolabeling detection methods.

Find additional tips, troubleshooting help, and resources within our Dynabeads Nucleic Acid Purification Support Center as well as our Protein Immunoprecipitation (IP), Co-Immunoprecipitation (Co-IP), and Pulldown Support Center.

How long should I incubate my antibody with the lysates?

Incubation time will depend on the immunogenicity of the primary antibody and its binding affinity with the specific antigens. For a good primary antibody, 30-40 minutes incubation should work well. If you are working with a poor antibody or a very low-abundance protein, you could try to increase binding by incubating overnight. However, this also increases the chance of background protein binding.

Find additional tips, troubleshooting help, and resources within our Protein Immunoprecipitation (IP), Co-Immunoprecipitation (Co-IP), and Pulldown Support Center.

When should I covalently bind the antibody to the Dynabeads surface?

If the target protein has the same molecular weight as the heavy or light chain antibody, we would recommend covalently binding the antibody to the bead surface. This can be done by either crosslinking the antibody to the Dynabeads Protein A or G magnetic beads, or secondary coated beads, or by using one of the surface-activated Dynabeads magnetic beads.

Find additional tips, troubleshooting help, and resources within our Dynabeads Nucleic Acid Purification Support Center as well as our Protein Immunoprecipitation (IP), Co-Immunoprecipitation (Co-IP), and Pulldown Support Center.

What are the general advantages of using Dynabeads magnetic beads for protein isolation?

Using Dynabeads magnetic beads for protein isolation provides several advantages:

-Rapid binding kinetics: since the number of beads per volume for Dynabeads is approximately 1,000 times higher than for the same volume of a Sepharose slurry, the probability for Dynabeads magnetic beads to hit the target is far greater.

-Incubation time: due to the rapid binding kinetics, the protocol is usually very short.
-Low background: due to the rapid binding kinetics and the short incubation time, the background is also very low.
-Trapping of impurities: the beads offer no internal volume for binding or trapping of impurities.
-Low antibody consumption: this is because Dynabeads magnetic beads are nonporous, uniform superparamagnetic, monodispersed, highly crosslinked polystyrene microspheres consisting of an even dispersion of magnetic material throughout the bead. The beads are coated with a thin layer of a highly crosslinked polystyrene shell that encases the magnetic material and prevents any leakage from the beads or trapping of ligands in the bead interior. The outer layer also provides a defined surface area for the adsorption or coupling of various molecules such as antibodies. Uniformity of bead size and shape provide consistent physical and chemical properties. These uniform physical characteristics lead to high-quality, reproducible results.
-Reproducibility: due to easier practical handling, such as pipetting. No centrifugation steps or preclearing are required.

Find additional tips, troubleshooting help, and resources within ourProtein Immunoprecipitation (IP), Co-Immunoprecipitation (Co-IP), and Pulldown Support Center.

Are Dynabeads magnetic beads compatible with dithionite, DTT, and EDTA?

No. Not only is dithionite a reducing agent, but the strong affinity of the dithionite ion for bivalent and trivalent metal cations (M2+, M3+) allows it to enhance the solubility of iron, making it a chelating agent. As a result, the iron in the Dynabeads magnetic beads is reduced and pulled out when they are exposed to dithionite. The same is observed if Dynabeads magnetic beads are exposed to DTT and EDTA. With EDTA, we highly recommend checking the minimal amount of EDTA that your specific molecules would tolerate for binding to the Dynabeads, and if it will affect your specific application. For some applications, low concentrations of EDTA can be tolerated by Dynabeads. On the other hand, using 10 mM EDTA with heating affects the binding of biotin molecules to Dynabeads streptavidin.

Find additional tips, troubleshooting help, and resources within our Dynabeads Nucleic Acid Purification Support Center as well as our Protein Immunoprecipitation (IP), Co-Immunoprecipitation (Co-IP), and Pulldown Support Center.

Are Dynabeads magnetic beads compatible with Urea?

Yes, they are compatible with 6-8 M Urea when used during post-coupling steps.

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.

Are Dynabeads magnetic beads compatible with centrifugation?

Dynabeads magnetic beads, being magnetic in nature are really not designed to be centrifuged. That being said, the beads themselves are compact, as the pores in the polymer matrix are filled with magnetic material and coated with a final outer polymer shell that will further add to the rigidity of the beads. Hence, pressure should theoretically not be a problem for the beads themselves, but the force exerted by the beads on surrounding cells in the pellet may be detrimental to the cells.

Find additional tips, troubleshooting help, and resources within our Dynabeads Nucleic Acid Purification Support Center as well as our Protein Immunoprecipitation (IP), Co-Immunoprecipitation (Co-IP), and Pulldown Support Center.

What are the benefits of using magnetic beads in immunoprecipitation (IP) experiments?

Magnetic beads, unlike agarose beads, are solid and spherical, and antibody binding is limited to the surface of each bead. While magnetic beads do not have the advantage of a porous center to increase the binding capacity, they are significantly smaller than agarose beads (1 to 4 µm), which collectively gives them adequate surface area-to-volume ratios for optimum antibody binding.

High-power magnets are used to localize magnetic beads to the side of the incubation tube and out of the way to enable cell lysate aspiration without the risk of also aspirating immune complexes bound to the beads. Magnetic separation avoids centrifugation, which can break weak antibody-antigen binding and cause loss of target protein.

However, an issue with the use of magnetic beads is that bead size variations may prevent all beads from localizing to the magnet. Additionally, while immunoprecipitation using agarose beads only requires standard laboratory equipment, the use of magnetic beads for immunoprecipitation applications requires high-power magnetic equipment that can be cost-prohibitive. Read more about our Magnetic Immunoprecipitation Products (https://www.thermofisher.com/us/en/home/life-science/protein-biology/protein-assays-analysis/immunoprecipitation.html#products).

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.