I am completely lost on this issue. I have used the gel extraction kit hundreds of times and never seen this. I took my pcr product and ran it out on a 1% agarose gel. I then used the Qiagen kit. After adding buffer QG and dissolving my gel slices the mixture turned a deeper yellow (almost orange) color. When I added isopropanol and spun the column i noticed that the column had stained orange. When I ran my gel extraction product on a gel I got no band, and also my elution did not seem to freeze at -20 overnight.
I have tried passing buffer QG through my sample several times and washing with buffer PE several times as well. I also have added sodium acetate as suggested by the protocol.
Has anyone experienced something like this before?