What would be the average fragment size which would be expec

What would be the average fragment size which would be expected following the digestion of genomic DNA with ApoI? Assume an equal distribution of A, G, C, and T.

Solution

ApoI, a novel type-II restriction endonuclease enzyme, has been isolated from Arthrobacter protophormiae.

ApoI recognizes the six base palindromic sequence 5\' RAATTY 3\' and cleaves after the first base pair (R), to create a four base 5\' extension.

PhiX174 DNA was completely digested with ApoI.The sizes of the resulting fragments were determined by agarose gel electrophoresis.

The sizes of the fragments observed experimentally were approximately 2680, 1325, 550, 320, 225 and 170 base pairs. The computer calculated number and sizes of the fragments that would be generated by cleavage at 5\' RAATTY 3\' site are 2690, 1290, 554, 326, 239, 185 and 102 base pairs, correlate well with the observed fragments.

ApoI will be an important tool for molecular biology because it is ideal for cloning, producing EcoRI compatible ends. Fragments produced by ApoI can be ligated to EcoRI fragments without the loss of the ApoI site.

Also, ApoI will be important in structural studies of restriction enzymes because of its relationship with EcoRI. Both enzymes recognize a sequence with an internal AATT palindrome.