BAC DNA purification
I am trying to purify BAC DNA (106 kb) using Qiagen large construct kit. I am able to elute 5 -10 μg DNA (measured by nanodrop) but when I run on agarose gel I see a a big chunk near the well (attached agarose gel pic). I contacted Qiagen technical help and they told it might be ecoli genomic DNA contamination. There is an exonuclease digestion step and I tried different exonuclease concentrations and incubation times but still I see the band near the well. Can anyone suggest me how to troubleshoot this problem and some other BAC DNA purification kit.