The restriction enzyme AcyI cuts duplex DNA at the sequence 5' GPuCGPyC 3'
3' CPyGCPuG 5'
Where Pu = either purine and Py = either pyrimidine.On average, what is the length of DNA fragments in base pairs created by this enzyme? (Assume that the four bases are found in equal frequencies in this DNA sample.)

Question

Quizplus · Accepted Answer

The restriction enzyme AcyI recognizes a specific sequence of 6 base pairs (bp) where Pu represents a purine (A or G) and Py represents a pyrimidine (C or T). Given that each position represented by Pu or Py can be occupied by 2 different bases and the other positions are fixed, the total number of possible sequences recognized by AcyI is 2^2 (for the two positions that can be either purine or pyrimidine). Since the DNA is double-stranded, we consider the sequence on both strands, but the recognition site is the same for both strands, so we don't multiply by 2 again for the strand count. The average fragment length is calculated as the total length of the DNA divided by the number of fragments, which is determined by the frequency of the recognition site. The total number of possible 6 bp sequences is 4^6 (since there are 4 possible bases for each of the 6 positions), leading to 4096 possible sequences. However, with a specific recognition sequence that can vary at two positions (PuPy), the calculation for the average fragment length involves dividing the total number of base pairs by the number of specific sequences recognized by the enzyme. Since there are 2 choices for Pu (A or G) and 2 choices for Py (C or T), for the two variable positions, there are 2^2 = 4 combinations. Thus, the DNA is cut into 1/4 of the total possible 6 bp sequences, leading to an average fragment length of 4^6 / 4 = 1024 base pairs.

The Restriction Enzyme AcyI Cuts Duplex DNA at the Sequence