If a suspension of materials containing different densities are allowed to sit, gravity will separate them, with the materials of the highest density sinking to the bottom and the lower densities floating on top. This is the reason why air floats above water and why cells in a blood sample will sink towards the bottom of the tube. In laboratories, we cannot afford to wait around for gravity to take its course, so we use centrifuges. Centrifuges are devices which use high rotational speeds to increase the rate at which materials settle out according to density.

In molecular biology, centrifuges are used for a variety of purposes – spinning down small volumes of liquids which may have collected on the sides of a vessel, separating and washing cells and forcing liquids through separation columns as in gel purification. At high enough rotational speeds (ultracentrifugation), we can even separate cell components and organelles, or even macromolecules based on their size.

Eppendorf tubeThe most commonly used bench centrifuges are used to separate small volumes (~1.5mL). These are also called microcentrifuges or microfuges. Centrifuges need to use specialized vessels, called centrifuge tubes. Sometimes they are given the names of the most prominent manufacturers of these vessels – you may often hear microfuge tubes called “Eppendorfs” after the manufacturer, although not all microfuge tubes are made by this company.

When using any centrifuge, the most important concept to keep in mind is that of balance. The tubes are spun at extremely high velocities (up to 13,000rpm for a simple microfuge), so any irregularity in mass between tubes can set up instability in the system. At low speeds, this can cause wobbling and a loud noise, while at high speeds, it can cause catastrophic failure with serious impacts on safety. In both cases, irreparable damage can be caused to the centrifuge.

In a bench centrifuge, tubes are placed into a solid rotor – the centrifuges we will be using have spaces for 24 x 1.5mL microfuge tubes.

Microcentrifuge rotor

When placing the tubes into the rotor, keep the following points in mind:

  • Make sure that tubes are placed into the rotor opposite each other. You can ensure this by imagining a line passing between the two tubes. If the line passes through the centre of the rotor, the centrifuge is balanced

Loading a microcentrifuge

  • Even if the tubes are in the correct position in the rotor, they need to be of equal mass (i.e. they need to contain the same volume of liquid). If your tubes have unequal volumes (or you have an odd number of tubes), make sure that you include a balance tube containing the correct volume of liquid

Balancing a microcentrifuge

  • Make sure that the lid is attached to the rotor before you spin