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Endonucleases are used in biotechnology because they are able to be applied to a specific part of a DNA sequence and will cut the DNA only in these locations. Exonucleases on the other hand have the following issues:
1) An exonuclease will digest and entirely consume DNA/RNA. As opposed to cut a specific location of DNA, they will eat the entire strand if they are not stopped.
2) They will only begin digestion at the ends of the DNA/RNA molecule. Circular plasmid DNA will not be affected by an exonuclease, because there are no beginnings or ends to the DNA sequence.
3) More over, as mentioned in (2) they will only begin digestion at the ends of the DNA sequences, thus they are much less accurate in where they begin cutting the DNA/RNA.
Because of this lack of control of exonucleases, they are difficult to use and generally not used in biotechnological techniques.
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