Question

Eco RI restriction endonuclease requires a 6 bp sequence for recognition and cleavage. In a 10kb DNA fragment how many probable cleavage sites are present for this enzyme?

• A. Zero
• B. One
• C. Two
• D. Four
  

Answer 1

The correct option is C Two

Mathematically, the number of restriction sites for a particular endonuclease can be calculated for a given length of DNA by assuming that all four nucleotides are randomly present in equal proportion.
There are four different bases, so probability of finding a particular base at one position will be $\frac{1}{4}$ and frequency of cutting will be $4^n$, where n is number of base pairs in the recognition sequence. Eco RI recognizes the 6 bp sequence. Hence, there are $4^6$ = 4096 different cleavage site possibilities for given 6 bp recognition sequence.
So, EcoRI will cut once in 4096 base pairs along a DNA. In 10,000 bp DNA fragment, Eco RI will have $\frac{10000}{4096}$ = 2 cleavage sites.