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Most
enzymes make slightly staggered incisions, resulting
in "sticky ends", out of which one strand
protrudes.Incisions where the 5' end protrudes are known
as 5'overhangs or 5'sticke ends. An example would be
the enzyme Bam HI:
Bam
HI searches for the sequence GGATCC on each strand
(once again, GGATTC reads the same off of both strands
because the sequence is palindromic). When the sequence
is located, the enzyme BamHI digests the phosphodiester
backbone in two specific places - between the pair
of G nucleotides on each strand.
That
leaves us with a four nucleotide single stranded 5'
end on each side after separation.
5'-GGATCC-3'
Bam HI 5'-G -3' + 5'- GATCC-3'
3'-CCTAGG-5' ----> 3'-CCTAG -5' 3'- G-5'
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