MathBench > Visualization

Chopping up plasmids

A real plasmid

OK, so let’s talk 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:

plasmid

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

 

How big will the shorter 2 pieces be?

(To make this problem interactive, turn on javascript!)

I think I have the answer: 700 base pairs and 3000 base pairs

 

How big will the longest piece be?

(To make this problem interactive, turn on javascript!)

I think I have the answer: 4300 base pairs (NOT 2800 read the hints!)

 

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.

Answers