Endonucleases with substrate-sequence specificities, such as restriction enzymes, usually cleave small, defined nucleic acid molecules used in enzyme assays at one or only a few sites. The methods in common use for analysis of endonucleases are based on the Poisson distribution. A critical, but usually unstated, assumption of this distribution, however, is that there is a large number of possible reactive sites on each substrate molecule. Thus use of the Poisson distribution may introduce large errors into analysis of such assays. Here we develop a series of appropriate expressions for use in analyzing endonucleases with substrate-sequence specificities.
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