A restriction enzyme is able to cut a segment of DNA several times. The number of times the DNA is cut (4n) depends on the length of the recognition site (n). A restriction enzyme cuts how many times? According to statistics, an enzyme makes an average of one cut per 4n base pairs, where n is the length of the recognition site. As a result, a DNA molecule's likelihood of containing one or more restriction sites increases with length. Where on the double-stranded DNA are restriction enzymes active? Restriction enzymes (RE) are endonucleases that recognize particular DNA sequences between four and eight base pairs in length and normally break the strands at a specified and constant point within or before the recognition site. You can get a much more accurate estimate if you take into account the probability of GC and AT pairs independently. If the GC content of the organism is (say) 70%, and the recognition site of the enzyme is GAATTC (EcoRI site), then the probability of its presence will be (.35)(.15)(.15)(.15)(.15)(.35) = , since the probability of G is half of the probability of GC, and the probability of A is half of the probability of AT. Instead of the naively calculated 4096 bp between sites on average, the 70% GC content version will have an expected distance of 1/ = 16,129 bp.
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