Running gels!

I've got two gels running while I type. Both will help me decide if the MAP7 DNA preps we have are suitable for my tweezers experiments. Both gels contain high and low concentrations of two different MAP7 DNA preps, along with a size standard consisting of intact phage lambda DNA (48.5kb) and a HindIII digest of the same DNA.

The first gel is a conventional agarose gel - the voltage is created by a pair of simple wire electrodes, one running across each end of the gel box. To increase the resolution (i.e. separation) of DNA fragments bigger than 15-20kb, the gel has a lower concentration of agarose than is usually used (0.6% rather then 0.8-1.0%). This makes it more fragile, so I'll need to handle it very carefully tomorrow when I'm photographing it. I'm also using a much lower voltage, which will also help spread out the big fragments and squeeze together the little ones I don't need to resolve.

The second gel is a "CHEF" pulsed field gel. This uses pulsing electric fields in different directions (120 degrees to each other) to jiggle the DNA fragments back and forth as they move through the gel. This forward-left then forward-right pushing has little effect on the separation of small fragments (less than about 20kb) but it greatly improves the separation of the big fragments. The new apparatus (belonging to the new lab next door) is much more sophisticated than the old one that's collecting dust on our top shelf, and I had to call technical support to learn how to dumb it down enough that I could control what it was doing.

In admiring this new apparatus we developed a new rule of thumb relating the cost of a piece of scientific equipment to the number of buttons it has. This one has more than 50 buttons, and cost about $40,000; our old one had about 7 buttons and cost $4500. This only applies to equipment that doesn't come with its own computer. The real-time PCR machine we share with other labs cost $70,000; it gets away with having only a single button because it's controlled by very complicated software.