Some restriction enzymes cut at specific and unambiguous sequences (e.g., NotI at GCGGCCGC). As such, the distance between two such sites in a large random DNA sequence is 4⁸, assuming a 50% G+C DNA content. However, the sequence recognized by XhoII is said to be ambiguous (Pu-GATC-Py, where Pu = any purine and Py any pyrimidine). What, therefore, is the expected distance between two XhoII sites in a large random sequence? A)4 × 4 × 4 × 4 B)1 × 4 × 4 × 4 × 4 × 1 C)2 × 4 × 4 × 4 × 4 × 2 D)4⁶ E)4² × 2²

Question

Quizplus · Accepted Answer

The XhoII recognition sequence is ambiguous, meaning that any purine (A or G) can be present in the first position, and any pyrimidine (C or T) can be present in the fourth position. Thus, there are 4 possible nucleotides for the first position, 4 for the second, 4 for the third (since it has to be A or T), and 4 for the fourth. Therefore, the expected distance between two XhoII sites in a large random DNA sequence is 2 × 4 × 4 × 4 × 4 × 2, which simplifies to 512 base pairs (bp).

Some Restriction Enzymes Cut at Specific and Unambiguous Sequences (E