Diffusion in 10% PAGE gels is pretty minimal, so I would go ahead and do western blotting or whatever you intended to do. The real question is why are you running your gels overnight?  We do thousands of protein gels and our mini-gels run in 1-1.5 hours (140-150 V), which are fine for most every application.  If you must run larger gels, they  run in about 3-4 hours. 

Hi Gregory, Thank you for your answer! Yes it is a bigger gel but I am running it on very small current (30 - 50 mA; about 50 V). That is the reason I am running it overnight. 

Two thoughts:

1. Sure, go ahead and image your gel, or whatever, but my guess is that your buffer level dropped, cutting off the current, and that's why your gel stopped (you can figure that out if you noted the buffer level). When that happens, the level often drops unevenly, and the gel stops unevenly, and your lanes will be uneven. If that's the case you will not have a pretty gel and you might not be able to get much info from it. If the dye front is uneven, that's a hint the gel won't look good.

2. I agree with Gregory that you should be running your gels during the day (not what he said, but if you need to run them a long time, you need to check them from time to time). OR, especially since running a gel at low voltage often means you don't want much heat produced, fill the inner and upper tanks to the top to minimize the chance that a small leak will stop the gel (or did the power fail?). On minigels you can fill the outer tank a lot higher than you thing - the BioRad gel boxes have a 'failsafe' to prevent inner/outer buffer mixing and the level is so high that a small leak can't drop the buffer level enough to stop the gel. Whatever your larger gel system is might have a similar failsafe.

Hi Lori, the gel stopped not because of insufficient buffer level, but because the power supply was set on timer. The buffer level is more than sufficient and the dye front does not look uneven, nor the bands in the pre-stained ladder look distorted. I just hope the Western will work. Next time when I run the gels, I will try running it on higher voltage so that the protocol will be shorter. 

Nonetheless, thank you for your answer Lori!

To Gregory and Lori, will such high voltage (140-150 V) heat up the instrument setting overall? Will it be good for the samples?

Voltages are not the problem.  The protein is already denatured in SDS.  150V for a mini gel is not enough to heat it up because there is not enough current running through due to high resistance.  Heating is more a problem when doing a wet transfer to PVD membranes because of high currents, which is why wet transfers are done in the cold with an ice pack.

Ohh ok. That was very helpful! So what do you think would be the best current/voltage for a bigger gel (1.5 mm) for the wet transfer and how long? Can I put it in the cold room? I wish to do it quick enough so that I can block the membrane and then incubate with primary overnight. 

Go ahead and do western blotting or whatever you intended to do, your gel will be O.K. but you have to ensure about the cooling system when you run overnight gel.

Oh, OK, got it. Ignore most of what I said :-)

Thank you for your answers Mirza and Tarik!

It seems an interesting question for me.   Polyacrylamide gel elelctrophoresis (PAGE) is only applicable to hydrophilic nucleic acid (DNA and RNA) analysis.   Proteins usually absorb to PAG, and I have added non-ionic detergent (please see file; IEF for hydrophobic protein).

By the way, if electrophoresis is stopped, then proteins will aggregate onto the hydrophobic PAG.

Therefore, I would like to recommend the more reliable HPLC-Soap-SEC method instead of non-reliable SDS-PAGE method (please see file; SEC column 300 A silica).. 

if we have insufficient buffer, is it safe to pause the run and add more buffer and then continue the run..??