Unclear bands in bp marker of agarose gel - should i lower the voltage? (May/08/2006 )

Hi,

Attached is a picture of a recent gel that I ran. Left lane: 1kb NEB DNA marker. Middle lane: Digested vector and fragment. Right lane: 100bp NEB DNA marker.



Consistently I have noticed that my bands are not as clear / well defined as the ones that other people post on this site.

My lab runs gels at 120 volts, but someone told me this is a little high. SHould i try lowering it to 100?

THe other thing is, if i run the gel for more than about 30 mins the end of the gel melts, so I was thinking that perhaps this is the reason they run it at a faster speed.

What are the dimensions of your gels? 30 minutes to melting makes me suspect there's something wrong with your buffer. What buffer do you use? Are you melting your agarose in it? Are you sure your power supply is displaying volts and not amps?

I think there is a problem with your agarose. 120 volt is high enough to make it more complicate. my lab uses 100 and its work good but I dont think this is your problem.

standard is 5V/cm....if this is a small gel, you are probably running it too high

although I would also check your buffer composition...perhaps make a fresh batch and see if the problem improves. also, how many times do you re-use your buffer?

three possibilities :
*as said by other posters, voltage may be too high. Drives a heat of solution and a partial melting.
*you have a bad composition of your runnning buffer and/or not the same buffer in the gel vs the running buffer
*your agarose gel is not enough solidified.