May 29, 2019

Magbeads 101: A guide to choosing and using magnetic beads

By Andrew Gane, Product Strategy and Technology Manager, Genomics and Diagnostic Solutions, Cytiva

Magnetic beads (or superparamagnetic particles) are versatile little tools for easy and effective isolation of biomolecules. Use this guide to compare the different surface chemistries and find the type for your application.

What are magnetic beads?

Magnetic beads are made up of tiny (20 to 30 nm) particles of iron oxides, such as magnetite (Fe3O4), which give them superparamagnetic properties.

Superparamagnetic beads are different to more common ferromagnets in that they exhibit magnetic behavior only in the presence of an external magnetic field. This property is dependent on the small size of the particles in the beads, and enables the beads to be separated in suspension, along with anything they are bound to. Since they don’t attract each other outside of a magnetic field, they can be used without any concern about unwanted clumping.

There are many types of magnetic beads available. Different surface coatings and chemistries give each type of bead its own binding properties, which can be used for magnetic separation (isolation and purification) of nucleic acids, proteins, or other biomolecules in an easy, effective, and scalable way.

This ease-of-use makes them automation friendly and well suited for a range of applications, including sample preparation for next generation sequencing (NGS) and PCR, protein purification, molecular and immunodiagnostics, and even magnetic activated cell sorting (MACS), among many others. They also ease some of the challenges associated with extracting nucleic acids from different sample types.

What is magnetic separation?

Magnetic separation uses a magnetic field to separate micrometer-sized paramagnetic particles from a suspension. In molecular biology, magnetic beads provide a simple and reliable method of purifying various types of biomolecule, including genomic DNA, plasmids, mitochondrial DNA, RNA, and proteins.

For example, under optimized conditions, DNA selectively binds to an appropriately-coated bead surface, leaving contaminants in solution. You can then use this purified DNA directly in molecular biology applications.

A key advantage to using magnetic beads is that you can isolate nucleic acids and other biomolecules directly from a crude sample, and from a variety of different types of sample, with minimal processing. This sets magnetic beads apart from other methods of nucleic acid isolation, which might have different protocols for different types of sample, and involve more hands-on time.

How does magnetic bead DNA extraction work?

Magnetic beads have been around in one form or another for decades. Their potential in nucleic acid purification was recognized in the 1990’s, as demonstrated by the US patent: “DNA purification and isolation using magnetic particles”. The approach, largely unchanged since, relies on using magnetic beads with a coating that can bind nucleic acids reversibly by just adjusting buffer conditions (Fig 1).

Overview of magnetic bead-based DNA extraction using Sera-Mag beads

Fig 1. Overview of magnetic bead-based DNA extraction using Sera-Mag beads.

After binding DNA, an external magnetic field attracts the beads to the outer edge of the containing tube, immobilizing them. While the beads are immobilized, the bead-bound DNA is retained during the washing steps. Adding elution buffer, and removing the magnetic field then releases the DNA as a purified sample, ready for quantitation and analysis.

This approach removes the need for vacuum or centrifugation, which minimizes stress or shearing forces on the target molecules, requires fewer steps and reagents than other DNA extraction protocols, and is amenable to automation in 24, 96, and 384-well plates.

So, it’s no wonder that magnetic beads are gaining in popularity. Indeed, manufacturers have now developed numerous commercial nucleic acid isolation kits based on magnetic beads. They have options for various surface chemistries and a range of applications. The ligand-binding properties can range from being indiscriminate to sequence- or tag-specific, all of which can be a challenge to keep up with!

Table 1 gives an overview of the latest range of magnetic bead types, with their key properties and applications.

Table 1. Comparison of magnetic bead surface chemistries and applications

Type Properties Applications Variations
Carboxylate-modified magnetic beads
  • Can associate with nucleic acids for direct capture.
  • Surface suitable for conjugation through covalent bonding.
  • Can capture molecules containing amino groups.
Conjugation or direct binding applications:
  • Covalent attachment
  • Affinity purification and pull-down
  • Nucleic acid isolation and purification
  • NGS size selection
  • High-speed version available
    Amine-blocked magnetic beads
    • Surface suitable for conjugation through covalent bonding.
    • Non-surfactant, non-protein-blocked surface.
    • Low non-specific binding.
    Conjugation applications, similar to carboxylate-modified beads. High-speed version available
    Oligo(dT)-coated magnetic beads
    • Hybridizes with mRNA poly-A tails.
    • High colloidal stability.
    mRNA binding applications:
    • mRNA extraction and purification
    • RT-PCR
    • cDNA library construction
    • Subtractive hybridization
    • NGS (RNA sequencing)
    Streptavidin-coated magnetic beads
    • Binds biotinylated ligands such as proteins, nucleic acids, and peptides.
    • Covalently bound streptavidin coating.
    • Fast reaction kinetics.
    • Low non-specific binding.
    • High throughput and precision.
    Immunoassay and molecular biology applications:
    • Sample preparation and assay development for genomics and proteomics.
    High-speed version available
    Biotin binding ranges:
    • 2500 to 3500 pmol/mg
    • 3500 to 4500 pmol/mg
    4500 to 5500 pmol/mg
    Streptavidin-blocked magnetic beads
    • Binds biotinylated ligands such as proteins, nucleic acids, and peptides.
    • Non-surfactant, non-protein-blocked surface.
    • Lower non-specific binding than streptavidin-coated beads via additional blocking of non-specific binding sites.
    High-specificity biotin binding applications
    • Molecular and immunodiagnostics
    • NGS library preparation
    High-speed version available
    NeutrAvidin™-coated magnetic beads
    • Binds biotinylated ligands such as proteins, nucleic acids, and peptides.
    • Fast reaction kinetics.
    • Low non-specific binding.
    • High throughput and precision.
    Alternative to Streptavidin in immunoassay and molecular biology applications:
    • Sample preparation and assay development for genomics and proteomics.
    High-speed version available
    Biotin binding range:
    • 3500 to 4500 pmol/mg
    Protein A/G magnetic beads
    • Binds IgA and IgG proteins
    • Coating based on IgA/IgG fusion protein.
    • Broad binding capabilities.
    Antibody isolation applications:
    • Affinity purification and pull-down
    • Immunoprecipitation
    Silica-coated magnetic beads
    • Reversibly binds nucleic acids based on salt concentration.
    • Monodisperse particles with narrow size ranges of 400 µm or 700 µm.
    Applications with low sample amounts
    • Nucleic acid extraction for molecular diagnostics applications such as qPCR.
    • Broad range of ligand options.
    • Porous, providing greater surface area than other magnetic beads.
    Convenient alternative to sepharose columns, with protein purification applications including:
    • Affinity purification or capture
    • Immunoprecipitation

    Magnetic separation racks

    Magnetic separation racks provide a quick and easy method to purify specific proteins, nucleic acids, and other biomolecules. The target biomolecules are separated from biological samples using magnetic beads. A magnetic force is applied to the sample mixture, and the molecule of interest, which is attracted to the magnetic beads, is separated from the mixture. The magnetic separation technique has applications in DNA and mRNA purification, cell isolation, and protein purification. Cytiva’s Magnetic Separation Rack 15 mL is a 3D printed, magnetized tube rack with a strong, removable magnetic force and easy pipette access. It facilitates high capture, retention, and release of magnetic beads from various liquid sample media, allowing high-throughput parallel processing of up to six 15 mL samples.

    Custom bead conjugation

    Even with all these surface chemistry options, it’s impossible to cover every need and eventuality. That’s where custom conjugation comes in.

    Do you need to conjugate a custom ligand? Or need a custom particle size?

    At Cytiva, we make it possible to customize all our Sera-Mag magnetic beads . Our dedicated customization experts can help you every step of the way, from defining the product specifications to delivery completion.

    We provide custom conjugations of enzymes or antibodies , as well as a range of custom ligands that we can develop in parallel with your projects. We also offer lyophilization of the customized microspheres as part of our Lyo-Stable services , based on Ready-To-Go stabilization technology.

    Drawing on our R&D and manufacturing resources, and history of supplying magnetic beads to kit manufacturers, we will provide custom magnetic bead technology that is ready to use with little or no need for further modification. From completing complex conjugations, to performing your quality control tests before the beads leave our factory, we are equipped to meet your needs.

    At Cytiva, we provide a broad range of magnetic beads for molecular biology applications such as NGS and PCR. Read more about optimizing your research or clinical workflows in our other blogs. For support in any aspect of your workflow, contact our Scientific Support team or your local Cytiva representative.