Magnetizing biomolecules: an interview with Dr. Fred Whipple, AMSBIO

Interview conducted by April Cashin-Garbutt, BA Hons (Cantab)

insights from industryDr. Fred WhippleAMSBIO

When was magnetic bead technology first made possible and what are its main uses?

Nanoparticle technology was originally developed in the 1980s and 1990s. As the technology evolved, it soon became possible to produce uniform nanoscopic beads that are magnetic, and that also have a variety of specific surface chemistries. It was immediately evident that such beads could be used to great advantage for biochemical separations.

A slurry of nanoparticles presents a very large surface area to the surrounding liquid. That surface can be engineered to have chemical properties that favor the binding of specific biomolecules.

Further, if the particles are magnetic, they are easily immobilized as a pellet simply by placing a magnet next to the test tube. Thus, appropriately designed magnetic nanobeads offer a simple and elegant way to capture a desired biomolecule on beads, remove it from its original solution, and then redisssolve it in a “clean” elution buffer, away from undesired contaminants.

There are many sophisticated variations of the basic technique. These are widely used for purification of proteins, nucleic acids, and other biological molecules. Magnetic technology is also an essential component of nearly all modern DNA sequencing procedures, including both Sanger and “Next Generation” methods.

Please can you give a brief introduction to MagSi-Direct?

What MagSi-Direct brings to the table is the ability to combine magnetic bead technology with a second technique: affinity-based target capture.

In nature, most biological processes involve highly specific interactions between pairs of biomolecules. For example, cytokines bind to specific cell receptors, protein subunits bind together in very specific combinations, pharmaceuticals bind to specific targets, and so on.

If a researcher has a purified preparation of one member of a binding pair, it is often possible to use that molecule as “bait” to attract and “fish out” its binding partner from complex biological specimens (such as cell extracts, culture media, laboratory reaction mixtures, serum, plasma, other biofluids, etc.)

Affinity chromatography is a classic technique for this. One molecule (which the researcher has previously purified) serves as the “bait”. It is attached to the matrix of a chromatography column.

A specimen solution, which contains the partner molecule (the “prey”) is then passed through the column. The prey interacts specifically with the bait and is thus retained on the column until it is intentionally released by the researcher using an appropriate elution buffer.

With MagSi-Direct, one can perform essentially the same procedure, but using magnetic beads instead of chromatography columns. This makes the procedure much simpler and more flexible.

In addition unlike chromatography, MagSi-Direct makes it possible to perform affinity-capture experiments in automated high throughput laboratory environments.

With MagSi-Direct, the researcher simply binds the “bait” to the beads, places those beads in the biological specimen solution of choice, and uses magnetic technology to recapture those beads – together with whatever “prey” molecules they have interacted with.

In effect, MagSi-Direct converts any desired “bait” molecule into a powerful customized magnetic affinity reagent that is specific for the bait’s binding partners.

What types of biomolecule can be used with MagSi-Direct?

Almost any type of biomolecule may be used as bait. The chemistry of the MagSi-Direct system enables the formation of very strong, very stable coordinate bonds between the surface of the beads and any electron-donating chemical group present on the bait molecule. Such groups include carboxyl, amide, amine, hydroxyl, sulfhydryl, halogen, and other moieties.

Binding is random and nonspecific. As a result, within a population of beads, all orientations of the bait molecule will be present and available for interaction with partner molecules.

The list of possible bait molecule types is very long. It includes: cytokines, peptides, protein monomers, aptamers, antibodies, lectins, enzymes, blood components, glycans, pharmaceuticals, antibiotics, viral capsid proteins, etc.

The list possible targets (“prey”) is even longer. It includes all of the above, plus large protein complexes, intact viruses, bacteriophage, and even living cells.

How does MagSi-Direct compare to traditional antibody-based and biotin-based binding methods?

MagSi-Direct is much more flexible than traditional binding methods involving antibodies or biotin-streptavidin binding.

Unlike the latter techniques, MagSi direct does not require any cloning or modifications to the bait molecule. And it does not enforce a specific orientation on the bound molecule. All orientations of the bait molecule will be present in the pool of bait-bound beads.

MagSi-Direct is also much faster, simpler, and usually less expensive than the traditional methods

How long does binding take with MagSi-Direct?

The coupling reaction procedure takes about 2 hours, of which only a few minutes require operator intervention

Does magnetic separation technology require any harsh chemicals or conditions?

Neither the bait molecule nor the targeted “prey” are exposed to harsh chemicals or non-physiological conditions.

What are the main applications of MagSi-Direct?

The range of possible applications is very broad, and is limited only by the ingenuity of the researcher. Wherever two biomolecules interact stably via specific contact surfaces, MagSi-Direct can potentially be used to study the interaction, or to capture or purify one of the partners by using the other as bait.

A few examples include:

• Protein chemistry:  Purify delicate proteins or protein complexes easily
• Cell biology:  Use your own cell specific ligands to isolate cells of interest. Isolate or concentrate minority cell populations gently and efficiently
• Diagnostics:  Capture or purify ANY analyte that binds to a partner that you have in hand
• Flow Cytometry:  Remove interfering cell populations prior to flow analysis
• Drug development:  Design novel high throughput assays for screening interactions between candidate drug molecules and your biological target
• Stem cell biology:  Use your own cell specific ligands to isolate cells of interest

Where can readers find more information?

More information is available at: http://www.amsbio.com/MagSi-Direct.aspx

About Fred Whipple

Dr. Fred Whipple received his Ph.D. in Molecular Biology from Tufts Medical School in 1991. He spent seven years at Harvard Medical School performing research in genetics and molecular biology. He then joined the faculty of California State University, Fullerton, where he served for seven years teaching genetics and molecular biology, and performing research in the field of DNA damage and repair.

Since 2008, Dr. Whipple has been an independent consultant in molecular biology, focusing mainly on applications of magnetic beads, DNA sequencing, molecular pathology, and cancer biology.