Question

A plasmid containing the sequence 5??GTCGGATCCTTA?3?3??CAGCCTAGGAAT?5? is combined with BamHI. Write the unpaired bases of the 5??3? sticky end, and then write the unpaired bases of the 3??5? sticky end from left to right as you read them on your screen.

Express your answer as the sequence of the 5??3? sticky end followed by the sequence of the 3??5? sticky end separated by a comma (e.g., AGTGC,TCACG).

Answer 1

BamHI, from Bacillus amyloli, is a type II restriction endonuclease that recognizes and cleaves a six base pair short sequences (6 b.p.) of DNA. BamHI binds recognizes 5'-GGATCC-3' and cleaves the sequence after 5'-guanine on each strand, resulting in four base pair "sticky ends". In its unbound form, BamHI displays a central b sheet, which resides in between a helices.

Sequence shown is

5’- GTCGGATCCTTA-3’

3’- CAGCCTAGGAAT-5’

Bam H1 cleaves between G and G. Cleavage site is shown below as ^.

5’- GTCG^GATCCTTA-3’

3’- CAGCCTAG^GAAT-5’

Hence Stick ends are

5’ GTCG          GATCCTTA-3’

3’-CAGCCTAG        GAAT-5’

Unpaired Sticky ends from left to right: 5’ GATC-3’ and 3’-CTAG-5’

Answer: GATC, CTAG