The Restriction Enzyme Song

(to the tune of “Chim Chim Cher-ee”)
Copyright © 2012 Kevin Ahern


I'm obsessed with A-A-G-C-T-T

Because it’s the binding site of Hin-d-III

Cutting up DNA most readily

The ends are not blunt when they’re cut up you see


Five prime overhangs of A-G-C-T


Bacteria don’t have an immune system so

They must fight off phages or they will not grow

Protection by chopping is their strategy

And one of the cutters we call Hin-d-III


On binding to A-A-G-C-T-T

The site recognition site’s bent easily

Phosphodiester attacking meanwhile

Has water behaving as nucleophile


To stave off the phage for a little while


Why don’t these enzymes cut cell DNAs?

The answer’s provided by a methylase

Adding a methyl group on top of what

The sequence these enzymes would otherwise cut


So cells get protected in this simple way

From nuclease chewing of their DNA

The phage is not lucky in most every case

Unless methylases win the enzyme race


If that happens then, the cell gets erased


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