Question

The genomic DNA of an organism has a base composition of 40% A-T base pairs and 60% G-C base pairs. If we digest a sample of this DNA with the 6-cutter enzyme Zra I (5'-GACGTC-3'), what will be the average fragment size?

Answer 1

The frequency by which a Class II restriction enzyme will cut DNA is mainly a function of the length of the sequence it is sensitive to. For instance:

BsuRI has a recognition sequence of 4 base-pairs.  There are 4 positions, and each position have 4 potential values, there are 4⁴ = 256 different possibilities for any given 4-base long strand. Therefore, theoretically (assuming completely random DNA), this enzyme will cut 1 in 256 4-base-pair long sites.

your enzyme ZraI RECOGNIZES 6 NUCLEOTIDES, so it will cut 4⁶ and this is 4096 times, this enzyme will cut 1 in 4096 nucleotides. so the average fragment size is 4096.