Viruses are basically little packages of DNA (or RNA) in a lipoprotein capsule. They lack any cell machinery for making their own protein or for replicating their own DNA. They reproduce themselves by invading the cells of living organisms where they seize the cell’s machinery (ribosomes, mitochondria, etc.) and the nutrients and other compounds the organisms have amassed for their own life processes. The virus DNA then directs the host cell’s machinery to replicate its DNA and package it into new viruses. This process goes on until the cell’s resources are exhausted and it dies. The new viruses are then released to attack more cells.

Though not perfect, evolution has blessed higher organisms with immune systems to combat viral invaders. However, bacteria which are prime candidates for many virus invaders have no immune systems. Their only weapons against viruses are special enzymes called restriction endonucleases.

Restriction endonucleases are essentially tiny molecular scissors produced by bacteria to chop up the DNA (or in some cases RNA) of invading viruses. These micro-scissors work by cutting through the foreign DNA wherever they find specific sequences of nucleotides called recognition sites. All restriction endonucleases cleave (cut) nucleotide chains in at least two places.

Some work by cutting directly across the chain creating fragments with blunt ends.

Others such as EcoR1 cut in an offset pattern creating segments with one or more unpaired bases at either end of the segment.

Restriction endonucleases that cut directly through the nucleotide chain can be useful for cutting large DNA chains into smaller sizes for analysis. However, it is the restriction endonucleases whose cuts leave offset ends that have been harnessed by scientist to perform critical roles in research and genetic engineering.

No matter what the source of the DNA, fragments cut by one of these restriction endonucleases can join with DNA from any other source that has been cut with the same restriction enzyme because they will have the same exposed complementary bases at their ends. These offset ends are called sticky ends.

Because there are many different viruses with a variety of nucleotide sequences, there is a subsequent variety of restriction endonucleases. There are over 3000 known restriction endonucleases with over 600 of those currently commercially available.