I'm having some problems confirming my plasmid after I perform a midi prep. Briefly, here is what I did:
I received spotted DNA, soaked in 300ul of TE, transformed bacteria with 2ul of my eluted DNA, then streaked on amp plates. I picked two colonies from the plate and grew them in 5ml of LB. The next morning, I performed a mini prep and restriction digest with enzymes 1 and 2. My band sizes looked as expected so I transferred 1ml of my 5ml culture into 200ml of LB. The next day, I performed a midi prep using Invitrogen's kit and did a restriction digest with enzymes 1 and 2 again. When I imaged the gel, however, I did not see any bands (marker came out fine). I tried another digest with enzymes 3 and 4, and ran the digested and undigested (should be supercoiled) on a gel. The picture showed that there were no bands in the digested DNA, and the supercoiled DNA showed a pattern similar to linearized DNA and was also above my marker (highest band 10kb). My plasmid should be ~9kb and I assume that the supercoiled would show up a little bit below that.
Can anyone tell me what could be a source of error? My mini prep bands were fine, but every time I perform the midi prep (done this once before with no result) and digest it, the plasmid shows no bands. I've used the same kits in conjunction with other plasmids on the same day with no problems.