3: A real plasmid

OK, so let’s talk about plasmids. An average plasmid may be several thousand base pairs in length. So, with apologies, I will not actually be illustrating each base pair (bp) individually. Instead, I’ll just show you where base pair 0 is, and how many bp there are total.

The recognition site is also rather more complicated, so rather than write in all the bases, I’ll just show you with a line that is labeled A, for restriction enzyme site A.

Here’s an example:


If we use restriction enzyme A on this plasmid, how many pieces should we get?


How big will the shorter two pieces be?


How big will the longest piece be?


In the following applet, you can watch a virtual gel being run — just hit the start button, and make sure to stop it before it runs too long! Also, notice the “ladder” lane, which is composed of several fragments of known length. The ladder acts like a ruler, allowing you to measure the size of the unknown fragments.


  • Why does A have 2 bands?
  • Why are B bands closer together than A bands?
  • Why does A+B have 4 bands?
  • Why does top A band hardly move?