Optimal use of restriction enzymes in the analysis of human DNA polymorphism

Numerous biological factors have an effect upon the probability of the presence of a theoretical restriction site at a given point, (1/4)n, in a DNA molecule, where n represents the number of base pairs composing the site. Indeed, it is a fact that the ratio (formula; see text) does not usually equal unity. In addition, the sequence of the nucleotides appears to change haphazardly, with certain dinucleotides present more often than others. When considering (formula; see text), it is observed that the influence of this first parameter is very important for sites with either four or six base pairs. The balance of the average frequency of each site according to the preponderance of certain dinucleotides and the G + C content has been the subject of an involved study which makes use of a certain number of restriction enzymes which are commercially available. The important frequency variations of different sites are due primarily to the presence of one or two GC doublets which go as far as reducing the frequency by a factor of 3.