You plan to identify the relative position of sequences recognized by the restri

Question

You plan to identify the relative position of sequences recognized by the restriction enzymes PstI and EcoRV on a circular plasmid.

The restriction sites are the following:

PstI: 5’-CTGCA^G-3’

EcoRV: 5’-GAT^ATC-3’

The sign ^ indicates the position of the cleaved phosphodiester bond.

1) In theory what is the expected frequency of restriction sites for PstI or EcoRV in a DNA sequence assuming that the distribution of nucleotide in the sequence is random?

You can express the frequency as 1 site per X nucleotides, X being the numerical value that you have to calculate.

Explanation / Answer

To find out the frequency of the restriction site we can find out the cleavage fragment size.

A fragment can be 256bases long. This can be calculate on the basis that the 4 bases can occur at any one of the 4 places.

So 44 = 256.

In the 256 base fragment of DNA, the chances that you will find the exact restriction site of either PstI or EcoRV is 1 in 256.

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