The predominant form of DNA produced should be supercoiled, which typically has faster mobility during agarose gel electrophoresis than a linear plasmid. In addition to these two forms, you might also observe:
- An open, single-stranded form at lower molecular weights than the supercoiled form. This is due to excessive alkaline lysis, leading to denaturing of the plasmid.
- A nicked or relaxed form, referred to as open circular, typically migrating higher than the linear form.
- Concatemers or plasmid multimers at even higher molecular weights.
The relative positions of these bands may differ in TAE vs. TBE buffers.
