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Modern Genetic Analysis Chapter 10. Recombinant DNA Technology
Solved Problem

2. | The restriction enzyme HindIII cuts DNA at the sequence AAGCTT, and the restriction enzyme HpaII cuts DNA at the sequence CCGG. On average, how frequently will each enzyme cut double-stranded DNA? (In other words, what is the average spacing between restriction sites?) See answer

| Solution We need consider only one strand of DNA, because both sequences will be present on the opposite strand at the same site owing to the symmetry of the sequences. The frequency of the six-base-long HindIII sequence is (1/4)6 = 1/4096, because there are four possibilities at each of the six positions. Therefore, the average spacing between HindIII sites is approximately 4 kb. For HpaII, the frequency of the four-base-long sequence is (1/4)4, or 1/256. The average spacing between HpaII sites is approximately 0.25 kb. See question

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