Immunoprecipitation (IP) is a cellular and molecular biology method used in laboratories to isolate or purify a specific antigen (or protein of interest) via a solid phase (agarose or Sepharose™ resin or magnetic particles). The IP method was first performed on small aliquots of agarose resin in microcentrifuge tubes. Use of magnetic beads is one method of isolating your protein of interest via IP. Dynabeads, DynaGreen, and Pierce magnetic beads for IP offer exceptional balance of capacity/yield, reproducibility, purity, and cost for smaller-scale isolation of specific proteins (e.g., IP) and protein complexes (co-IP).

What is immunoprecipitation?

Immunoprecipitation (IP) is a cellular and molecular biology method used in laboratories to isolate or purify a specific antigen (or protein of interest) via a solid phase (agarose or Sepharose™ resin or magnetic particles). The IP method was first performed on small aliquots of agarose resin in microcentrifuge tubes. The IP method has evolved to use superparamagnetic particles to specifically target proteins of interest.

View common IP myths and tips

How does immunoprecipitation work?

The Dynabeads magnetic beads IP procedure is simple, fast, requires no preclearing step, and results in high-target protein purity, yield, and consistent results. Both DynaGreen magnetic beads and Pierce magnetic beads can perform the same steps with slightly longer protocol times to complete. DynaGreen protocol finishes in <80min. Pierce protocol finishes in <120min.

Step 1: Binding of the antibody to the beads

Dynabeads, DynaGreen, and Pierce magnetic beads come pre-coated with protein A, protein G, anti-mouse IgG, or anti-rabbit IgG antibodies. Their rapid kinetics allow them to bind to the added antibody in about ten minutes (Figure 1). Biotinylated antibodies can also be used in combination with streptavidin-coupled Dynabeads and Pierce magnetic beads. After antibody incubation a wash step is performed to remove unbound antibodies.

Step 2: Add sample to the beads

The protein-containing sample is added to the beads-antibody mix and incubated for ten minutes to allow target protein binding. If the protein is of low abundance or low affinity, the incubation time can be increased to one hour or overnight. For most cases, a ten-minute incubation is sufficient.

Step 3: Wash the protein-bound beads

To help ensure high purity of the bound target protein, the beads should be washed 2 to 4 times with buffer on the magnet to remove all unbound proteins. This step in the isolation process helps ensure a high signal-to-noise ratio.

Step 4: Elute the protein

The protein can be eluted off the beads by using either a mild elution procedure or a denaturing elution procedure (Figure 2).

Chart demonstrating denaturing elution is best used during SDS-PAGE; mild elution is best used for protein characterization, immunization, enzyme studies, amino acid sequence determination, and crystallization; and no elution is needed when performing protein-protein interactions studies, enzyme studies, bioassays, and immunoassays
Figure 2. Types of elution buffers for immunoprecipitation with magnetic beads. Depending on your target protein and how they bind to the magnetic beads, there are three main types of elution buffers to unbind the target protein. Denaturing elution buffers are used for SDS-PAGE. Mild elution buffers are used for protein characterization, immunization, enzyme studies, amino acid sequence determination, and crystallization. Protein-protein interactions, enzyme studies, bioassays, and immunoassays may be performed without eluting your target protein from the magnetic beads.

Why are magnetic beads used in immunoprecipitation?

Magnetic beads for IP have become more common, especially compared to the traditional method of using agarose slurries or resin for protein isolation. This is because magnetic immunoprecipitation beads provide several advantages over the traditional method, such as:

  • Low background—Little to no non-specific binding and no preclearing required for high-purity protein yields
  • Highly reproducible—Uniform composition of the magnetic beads ensures the most consistent results
  • Highly sensitiveMost-cited method for sensitive applications, such as ChIP and IP for low- abundance proteins
  • Fast and easy—<40 min protocol with no centrifugation or preclearing steps
  • Antibody savings—All binding occurs on the smooth outer surface of the beads, which conserves precious antibodies compared to porous agarose beads; using beads for IP is a cost-efficient solution per sample
  • Automation compatible—Immunoprecipitation beads protocol can be automated on the Thermo Fisher Scientific KingFisher platform  

View common IP myths on agarose resins vs magnetic beads
Learn about co-immunoprecipitation

Immunoprecipitation beads selection guide

Antibody-binding magnetic beads for IP

 Protein A, G, A/GSecondary antibodies
(anti-mouse, anti-rabbit)
Recommended productsBeads only:Kits:Beads only:
Binding propertiesNon-covalent antibody binding
Antibody co-eluted off the beadsYes*
No (Pierce Crosslink Magnetic IP/Co-IP Kit)
Type of ligandDifferent ligands bind different species and antibody subclasses with different specificity
  • Anti-mouse binds mouse IgG1, IgG2a, IgG2b
  • Anti-rabbit binds all rabbit IgGs
Mass spec compatibleYes
  • DynaGreen Protein A/G
  • DynaGreen Protein A
  • DynaGreen CaptureSelect Anti-IgG-Fc (multispecies)
  • Pierce MS-Compatible Magnetic IP Kit, 
  • Pierce Protein A/G
Not validated
  • Dynabeads Protein A
  • Dynabeads Protein G 
No (Dynabeads M-280)
Non-specific bindingLow

* Crosslinking can be performed to avoid co-elution of the antibody, but this can decrease the yield of the target antigen.
† Learn which antibody-binding proteins are best for your IP antibody.

Dynabeads magnetic beads compared to Sepharose- and agarose-based solutions

Figure 3. Shorter protocol time and better target protein yields with Dynabeads magnetic beads. Equal amounts of sample material with respect to Ab content and cell lysate volume were used for all IP protocols according to the manufacturer’s protocol. For the Dynabeads-based method, all the antibodies on the bead surface are accessible for optimal, highly reproducible antigen binding.

Dynabeads magnetic beads compared to competitor magnetic beads

Figure 4. Electron microscopy of Dynabeads magnetic beads compared to competitor magnetic beads. (A) Dynabeads magnetic beads have a defined surface to carry out the necessary binding with no inner surface to trap any unwanted proteins. Dynabeads products are the most uniform, monodisperse superparamagnetic beads, manufactured with highly controlled product qualities to enable a high degree of reproducibility. (B–D) Magnetic particles from alternative suppliers have variable shapes and sizes that trap impurities, resulting in lower reproducibility and increased non-specific binding.

Dynabeads magnetic beads compared to competitor magnetic beads for IP

Figure 5. Dynabeads magnetic beads have exceptional immunoprecipitation performance with the combination of highest yield and lowest non-specific binding. (A) Silver staining of the protein membrane shows that Dynabeads magnetic beads have the most enriched binding at the antibody main band and very low non-specific binding with low signal/noise. (B) Western blot analysis of CD81 pulldown in Jurkat cells show that Dynabeads Protein G beads have the highest yield with a short ten-minute protein incubation.

Read tips on immunoprecipitation

Fusion tag-binding magnetic beads for IP

  • Consists of a peptide (EQKLISEEDL) derived from the human c-myc oncogene (p62 c-myc)
  • Immobilized anti-c-Myc antibodies are used to immunoprecipitate c-Myc-tagged recombinant proteins
  • Consists of a peptide (DYKDDDDK) which is recognized by an immobilized high-affinity rat monoclonal antibody (clone L5)
  • Primarily used for the isolation of protein complexes with multiple subunits because the mild purification process tends not to disrupt these interactions
  • Consists of a peptide (YPYDVPDYA) derived from the human influenza hemagglutinin (HA) protein
  • Immobilized anti-HA antibodies are used to immunoprecipitate HA-tagged recombinant proteins
  • Consists of a string of six to nine histidine residues
  • Primarily used for purification via immobilized metal affinity chromatography (IMAC)
  • Consists of glutathione S-transferase (GST), a complete 211 amino acid protein (26 kDa)
  • Primarily used for purification via glutathione agarose resin

Recommended products

His and GST are not true epitope tags, because they are not usually purified or detected via specific antibodies. By contrast, HA and c-Myc tags are true epitope tags, because their only means of purification or detection is via specific antibodies. Epitope tags are seldom used for bulk purification but are most often used for IP or co-IP. Nevertheless, all four of these tag systems can be used for either purification or pull-down applications.

View fusion tag-binding bead options for IP

Biotin-binding magnetic beads for IP

If you have a biotinylated antibody (or ligand) that recognizes your protein, use of streptavidin beads is recommended

Main advantages of magnetic beads for biotin-binding:

  • If you have a sample rich in soluble IgGs
  • If you have a recombinant antibody lacking Fc regions
  • If you need a bead compatible with mass spectrometry

View streptavidin bead options for IP

Surface-activated magnetic beads for IP

If your target protein or ligand needs to be covalently coupled, use surface-activated beads

Different ligands (antibodies, proteins, etc.) require different bead surface properties and immobilization chemistries. Choose surface-activated beads to control factors such as:

  • Hydrophobicity: choose hydrophilic of hydrophobic beads
  • Bead size: 1 µm, 2.8 µm, and 4.5 µm beads available
  • Surface chemistry: epoxy, amine, or tosylactivated

View surface-activated bead options for IP

Videos on immunoprecipitation

Immunoprecipitation with Dynabeads magnetic beads FAQs

Here are some frequently asked questions regarding the use of Dynabeads magnetic beads for immunoprecipitation.

A: Dynabeads Protein A and Dynabeads Protein G are 2.8-micron beads covalently coupled with Protein A and recombinant Protein G, respectively. Protein A and Protein G differ in their binding strength to immunoglobulins from different species and subclasses.

View the Dynabeads product selection guide for detailed information on Ig species and subclass specificity to Dynabeads

A: 1. Verify binding/specificity of your antibody to your antigen (e.g., by ELISA).

2. Check the binding of your antibodies to the beads. If the antibodies are not captured and bound to the beads, the immunoprecipitation experiment will not work.

3. If you have used the indirect method of immunoprecipitation, try the direct method. Conversely, if you have used the direct method, try the indirect method.

4. Check the amount of beads and sample volume. With reference to the capacity of different beads proposed in the package inserts, increase the amount of beads or the concentration of your antibody during coupling.

5. Increase the incubation time.

6. Try another antibody.

A: Yes, you can use the larger beads. Note: Smaller beads provide a larger surface area and therefore give higher yields of protein compared to the larger 4.5-micron beads.

Immunoprecipitation publications using Dynabeads magnetic beads

View publications on cell isolation using Dynabeads products
View publications on Dynabeads Streptavidin magnetic beads

Additional publications can be found in our Citations and References database. The database can be searched using a product catalog number or keyword. For example, searching with the term "10001D" will return a list of journal articles that cite the use of Dynabeads Protein A for Immunoprecipitation (Cat. No. 10001D) and searching with the term "dynabeads" will return a list of journal articles that cite the use of any Dynabeads product. Note that the Citations and References database on contains only the small subset of scientific journal articles that cite the use of our products. Many more can be found via targeted searches of the PubMed™ database and similar databases.

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