Question

3. XhoII has the recognition site R/GATCY. BamHI has the recognition site G/GATCC. What fraction of BamHI sites will be cut by XhoII? What fraction of XhoII sites will be cut by BamHI? What fraction of XhoII cut DNA fragments will be ligatable into a BamHI cut vector?  

Answer 1

3.

[Also refer to the image attached below for detailed explanation]

Restriction site of XhoII :

Therefore the recognition sites of XhoII : A|GATCT, A|GATCC, G|GATCT, G|GATCC
( ' | ' indicates the site of cutting)

Restriction site of BamHI:

(G|GATCC)

Out of the four sites of XhoII, only one site (GGATCC) is identical to BamHI site. Hence the BamHI site can be cut by XhoII. But only one of the four XhoII sites can be cut by BamHI.

Therefore, the fraction of BamHI sites that will be cut by XhoII = 1  

And the fraction of XhoII sites that will be cut by BamHI = 1/4 = 0.25

Sticky ends formed after XhoII digestion:

----(A/G) GATC(T/C)-----

----(T/C)CTAG (A/G)-----

Sticky ends formed after BamHIdigestion:  

----G GATCC-------

----CCTAG G-------

The regions in bold represent the overhanging stretches that form complementarity and help in ligation.

As we can see, the overhangs are the same for BamHI and XhoII

Thus all XhoII cut DNA fragments will be ligatable into BamHI cut vectors

Therefore, fraction of XhoII cut DNA fragments will be ligatable into a BamHI cut vector = 1

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