DNA ladder running faster than samples during agarose gel electrophoresis - (Dec/07/2011 )

Hello, I am using Invitrogen 1 kb plus DNA ladder as a marker for agarose gel electrophoresis. We buy the marker and mix it with loading dye to a final concentration of 1 ug in 5 ul. I load 5 ul per agarose gel. Sometimes this marker workes fine and sometimes it is not. What I mean is that , the bands in the ladder seem to be migrating faster than the other DNA samples being electrophoresed. As a result, for example, a DNA band in a test sample thats should be at 2.8 kb appears to be at 4 kb. At first I though all my samples are wrong, and then I realized that if I downshift all the bands a little, then I would get the results I expect. This has happened on and off over a long period of time, with a wide variety of DNA samples, buffers and gel percentages. What is even more weird than this is the fact that all the DNA ladder bands less than about 500 bp seem to be running normally i.e they are aligning perfectly with my test samples. It is the higher sizes that are not. Is there an explanation for this problem and how to avoid it?

Hmmm, I would trust the gel over supposed band sizes, especially if you are doing PCR! Waht percentage gel are you running for bands over 500bp, and under waht conditions - voltage, buffer etc?