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Cleavage

How Does a Restriction Endonuclease Cut DNA?

Unfortunately, no one knows for sure. A mechanism hasn't been proven yet, but most likely it involves a phsophoryl transfer to water. A metal ion is also needed in order to stabilize the leaving group. Because restriction endonucleases have a conserved catalytic core, they probably all follow the same mechanism, with a few exceptions. Some restriction enzymes such as BfiI don't have a metal ion cofacter, and this will change the process. The enzyme makes one cut on each strand of the DNA. If it doesn't cut right in the middle of the restriction site ("blunt-cutter"), then it leaves single stranded DNA overhangs called sticky ends.

Restriction endonuclease NgoMIV holding onto DNA after cleavage.

Push to animate The enzyme cleaves between a guanine and a cytosine (both shown in red). The sequence is the same on the other strand, so the same bond is cleaved. Magnesium in the active site is shown in blue.

Push to view the conserved core.

HOME

INTRODUCTION

STRUCTURE

DNA BINDING

CLEAVAGE

REFERENCES