Problems with having to run the gels for so long - (Sep/23/2012 )

Im having an issue with my electrophoresis. For some reason the DNA is not moving down the gels as fast as it should. Im having to run the gels for about 20 hours (instead of the normal 4-5 hours). Does anyone know what the reason is or could be?

What gel percentage and what DNA size? 4-5 hours is not normal, unless you have extra long fragments on a low voltage or something.
Your power source can be bad, your electrodes/tank can be bad. Try to change both. Does your gel heat during run even on low voltage? That could mean increased resistance through bad wiring/electrodes, gel or buffer. If the gel is running slow and is cool, and also bands are diffused, you may just not get enough current because of malfunctioning power source.
If you change both tank and power source and it's still slow, try to find problems in buffer and gel composition.
No more ideas for now.

I would also suggest making fresh buffer - try switching to SB (sodium borate) or LB (lithium borate) buffers, they run much neater and faster for many sizes of DNA.

I use 4.5% gel, I think, and run at 100 volts. Im doing a gene mapping study so i need to run the gels enough so that I can tell when the polymorphic markers separate

It used to get warm when it worked fine but now its always cool.

make new buffer and check whether the electrodes are fine. For that I would check the current (mA) to check whether the tank is not short circuiting.

Andreea

how do I check the electrodes, and what should the mA be around?

Check electrodes = you check whether you have bubbles in the buffer when you start the run; check whether they are not loose
mA should not be 1 mA. I am not familiar with your gel system to tell you exactly. But you shouldn't get too low current. Check and tell me how much you get. For your gel composition I would expect smth around 10 mA (but I might be wrong)

alejandro LSU on Mon Sep 24 20:51:44 2012 said:

Find a multimeter or something that can measure resistance - touch the probes to each end of the electrodes and/or leads and read the reisitance - if it approaches 0, then they are fine.

Short circuiting will lead to very high current.

Actually bob is right: short circuiting leads to high current. Anyhow.

Your current should not be 1 mA and not too much. Now, it would have been nice for you to know what the current should be from a nice run. Next time when you have a nice run, check the current and note it down. It might be handy to know it for next time when you have troubles.