Empty Plasmid taken by C2?

 In the previous post, I did mention about the amplification of the target MaSpCL gene using the extracted plasmid. However, apart from getting the target band, there were also a lot of other bands present in the sample. At first, I thought the bands were merely due to the effect of repetitive motif of the spidroin but after discussing with the SV, he said I should be better off double confirm the problem. So what I did was to run the extract on gel and found that apart from the plasmid with insert, there was also a small band at the bottom (not shown). Then, I treated the plasmid with restriction enzyme to linearize it and ran again. Surprisingly, the small band was still there. When compared to the empty plasmid, the small band was also obtained. Thus, I believed that it was the empty plasmid taken up by the cells and indeed, I read somewhere that a single cell can uptake more than one plasmid. To resolve this problem, I digested the plasmid in a couple of tubes and pooled them in a large well, cut it out and purified it.

The hole made on the gel is where the linearized plasmid band was cut out and you can see the small band at the bottom that was believed to be the empty plasmid.