Life in Dr Jim’s lab (part 1)

by Jim Caryl

AS promised, I have finally found some time to start documenting some of the things we’re doing in my lab.

However, I’m starting small. Very small.

I’m going to tell you about some of the toys tools we use in the lab; no, not hammers and nails, and not even the fancy equipment you’ve seen on CSI*, rather, some of the simple and time saving technologies that make our lives easier.

So, we’re going to have some fun with superparamagnetic beads. That’s a mouthful! Superparaganetic beads are basically beads that are attracted to magnets, but which don’t become magnetic as a result +.

dynabeads

Caitlin (200) Nature Methods 2: 71 - 77

Our magnetic beads are tiny. In fact, each one is just 100 nm (nanometers), which is about 1/10,000th of a millimetre on a ruler (smaller than those in the image to the left, which are microparticles). These beads have a number of uses, but their main use is to bind to something you want to purify, and drag it out of a mixture of hundreds of other things that you don’t want. This mixture could be a biological sample, like blood, urine or liquefied poo; it could be a sample of contaminated food, or it could be an environmental sample, such as soil or seawater. In each case, there may be one thing you want to extract, a particular protein, a piece of DNA, or even a whole cell (human or harmful bacteria), but how do you get at it?

All you need is some basic knowledge of what the thing you’re after might like to bind to, some sort of molecular glue. Some proteins bind to other proteins, or DNA. For example, antibodies are used in your body to bind specifically to different types of foreign materials in your blood, a different antibody for each foreign material; they then alert your immune system. If you coat each bead with a particular antibody, say one that binds to a particular harmful bacterial cell like Salmonella, then you can add your beads to a mushed up sample of biological material, and use magnets to drag the beads (and the cells attached to the beads) away from the rest of the mush. You can then wash your beads a few times in a fresh solution and start your experiments.

Here is a video of some beads in action – though my sample is a salt solution, rather than poo!


My soundtrack (when it activates!) reminds me of my favourite film, ‘Sideways’.

Uses of magnetic beads:

  • Finding binding partners of your molecule of interest.
  • Deliberately pulling out a known molecule of interest from a mixed salad of other chemicals.
  • Pulling whole cells (human or harmful bacteria) out of a biological sample.
  • Having fun with magnetic beads.

* Whom, I should add, have managed to get DNA sequences out of a centrifuge – a piece of kit for spinning things to the bottom of a tube – in the time it takes to say, ‘Well, it seems to be our guy’s blood on the a paint sample matching a 1979 B-Body Dodge Charger’, which is clearly ridiculous**)

** Dodge didn’t make a B-Body Charger in 1979.

+ Remember your school physics, where you scraped an iron nail against a strong magnet, and the nail then becomes magnetic? If you went a step further, as I did, you would take you now magnetised nail into the woods with you, and when you got lost, you would find a clear and stagnant pool, upon which you would set your nail, atop a leaf, and float it on the water. The nail should then align itself North-South. Unfortunately, I could never remember which end of the nail point North, so it was a little fun, but pointless. The point being, your beads won’t just start floating towards any iron that happens to be near by.

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