One of the great discoveries in molecular biology, which paved the way for the current golden age in biological research, was the discovery of restriction enzymes. For the nonbiologist, and to help set up the programming material that follows, here's a short overview.
are proteins that cut DNA at short, specific sequences; for
example, the popular restriction enzymes
EcoRI and HindIII are widely used in the lab. EcoRI cuts where it
GAATTC, between the
Actually, it cuts both complementary strands, leaving an overhang on each end.
These "sticky ends" of a few bases in single strands make it possible for the
fragments to re-form, making possible the insertion of
DNA into vectors for cloning and sequencing, for instance. HindIII
AAGCTT and cuts between the
As. Some restriction enzymes cut in the middle and
result in "blunt ends" with no overhang. About 1,000 restriction enzymes are
If you look at the reverse complement of the restriction enzyme EcoRI, you see it's
GAATTC, the same sequence. This is a
biological version of a palindrome, a word that reads the same in reverse. Many
restriction sites are palindromes.
Computing restriction maps is a common and practical bioinformatics calculation in the laboratory. Restriction maps are computed to plan experiments, to find the best way to cut DNA to insert a gene, to make a site-specific mutation, or for several other applications of recombinant ...