Question

Eco RI and Rsa I restriction endonucleases require $6$ and $4$ bp sequences respectively for cleavage. In a $10kb$ DNA fragment how many probable cleavage sites are present for these enzymes

• A. $0$ Eco RI and $10$ Rsa I
• B. $1$ Eco RI and $29$ Rsa I
• C. $4$ Eco RI and $69$ Rsa I
• D. $2$ Eco RI and $39$ Rsa I

Answer 1

The correct option is D $2$ Eco RI and $39$ Rsa I

There are four different bases, so probability of finding a particular base at one position will be 1/4 and frequency of cutting will be 4${}^n$ where n is number of base pairs in recognition sequence. Eco RI recognizes the 6 bp sequence. Hence, there are 4${}^6$ = 4096 different cleavage site possibilities for given 6 bp sequence. Similarly, Rsa I recognizes 4 bp sequence. Hence, there are 4${}^4$ = 256 different cleavage site possibilities for given 4 bp sequence. So, EcoRI will cut 1 in 4096 6-base-pair long sites and Rsa I will cut 1 in 256 4-base-pair long sites. In 10,000 bp DNA fragment, Rsa I will have 10,000/256 = 39 cleavage sites and Eco RI will have 10,000/4096 = 2 cleavage sites.

Thus, the correct answer is option D.