MAAD Scientist Technologies

Learn · Gel electrophoresis

The Gel Race

Six racers, five gels. The winner changes with the percentage. One racer runs backwards. Then everyone is boiled in SDS.

Best full screen: the text is small otherwise. Click the game first, then use the arrow keys to choose, Enter to confirm and Esc to leave. It needs a keyboard, and takes a few seconds to load. Open it in its own tab.

What you do

Before each heat you see the gel and the field, and you choose which racer you are. Then the gel runs.

The racers are proteins and peptides of different sizes. Some carry far more charge than others. Two of them, Ada and Bea, are exactly the same size, and Bea has half as many acidic residues again.

The first four heats are native gels, each a different percentage of acrylamide. In a native gel a racer’s engine is its own charge, and the gel is the traffic. The last heat is in SDS.

What you find out

  • Why the biggest racer on the track can win in a loose gel and trail in a tight one.
  • Why two proteins of the same size never swap places, whatever gel you pour.
  • Why one racer leaves the gel from the wrong end, and what that means for every native gel you run.
  • Where a photo finish comes from, and why a percent or two either way undoes it.
  • What SDS takes away, and what it leaves.
  • Why the size a gel reports is an estimate.

After each heat a small plot shows why it went the way it did. It is a Ferguson plot: one straight line per racer. Where a line starts is the engine. How steeply it falls is the size.

The equations

You can predict every heat before it runs. Each racer needs two numbers: its engine and its drag.

Net charge. Add up the charged groups at the pH of the gel, here 8.8. Each basic group (lysine, arginine, the amino end) contributes

+1 / (1 + 10pH − pKa)

and each acidic group (aspartate, glutamate, the carboxyl end) contributes

−1 / (1 + 10pKa − pH)

The sum is the net charge, z.

The engine. With no gel in the way, speed goes as charge over size. For a racer of mass M in kDa:

μ0 = −z / M2/3

The minus sign is there because the far end of the gel is positive, so negative racers run forwards. In SDS the detergent sets the charge in proportion to mass, and μ0 is the same for everyone.

The drag. A bigger molecule is held back more by each extra percent of gel. With radius R in nanometres:

R = 0.066 × (M in Da)1/3

KR = 0.012 × (R + 0.5)2

The line. At a gel percentage T:

log10(speed) = log10(μ0) − KR × T

That is the straight line on the plot. Charge sets where it starts. Size sets how steeply it falls.

The photo finish. Two racers, a and b, draw level where their lines cross:

T = (log10 μ0,a − log10 μ0,b) / (KR,a − KR,b)

For Pip and Bea that is (log10 0.44 − log10 1.89) / (0.025 − 0.071), which is 14%. For Ada and Bea the bottom of the fraction is zero. They are the same size, so their lines are parallel and no gel brings them level.

The shape of each equation comes from the literature. The constants 0.066, 0.5 and 0.012 are the game’s own, chosen to give sensible drag for proteins between 3 and 66 kDa. For a real protein you measure the line: run it in four or five gels of different percentages and plot the logarithm of how far it went.

Where the science comes from

The rules are the classic ones: speed falls off with gel percentage along a straight line on a log scale, more steeply for bigger molecules, and SDS coats proteins in proportion to their mass. One racer has the charged residues of hen egg lysozyme. The others are invented, and every distance on the track is the game’s own model.