plasmid dna isolation - (Nov/18/2009 )

I tried to extract Fosmid dna using the Epicentre FosmidMax purification kit. When I ran the gel there was no band. But when i checked the concentration in spectrophotometer it showed a concentration of 550 ng per microliter. what cud be the reason. can nyone help.

since a fosmid is quite big (ca 40kb), you should allow the gel to run enough. have you seen something still stuck in the well? if you see nothing, it could be genomic DNA/RNA contamination (or your fosmid got degraded). You may try to perform a simple alkaline lysis protocol (w/o kits), we could isolate sequencing-proof BACs with this.