Question

The bacterium Thermus thermophilus was first isolated from hot springs in Japan, living in an environment with an average temperature of 68 degree C (154 degree F). This temperature would kill you, but these organisms are adapted to it. One of the adaptations to this lifestyle includes DNA that is 70% G-C base pairs, one of the more extreme departures from the average 50%. The chromosome is about 2.13 times 10^6 bp in length, quite normal for a bacterial species. The restriction enzyme, Haell, recognizes the degenerate sequence, 5'-XGCGC'Y-3', in which X can be any purine and Y can be any pyrimidine and the^v represents the site of strand cleavage. If you were to digest T. thermophiles DNA with Haell, what would be the average size of the fragments, and how many fragments would you expect to get?

Answer 1

Ans. DNA consists of 4 types of bases (A, C, T, G). A base at each position has the same probability of (1/4) at all positions- that is, probability of finding a “A” in [AAGCTT] at position 1 (first nucleotide) is (1/4); the same is also true for position 2 ; or any other base at any position. It is because the identity of a base at one position does not affect the identity of another base at different position.

So, the probability of finding 1 (any one) base out of total 4 type of base = 1/4.

The probability of finding a restriction site in a DNA molecule = (¼)ⁿ,

where n is the number of nucleotides in the restriction site.

Now,

#1. The probability of finding HaeII (n =6) restriction site = (1/4)⁶ = 1/ 4096 i.e. there is 1 restriction site every 4096 base pairs for dsDNA molecule.

Therefore, average size of fragments = 4096 base pairs

#2. No. of restriction fragments = Chromosome size / size of restriction fragment

                                                = (2.13 x 10⁶ bp) / 4096 bp

                                                = 520