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Beginning Perl for Bioinformatics by James Tisdall

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Restriction Maps and Restriction Enzymes

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.

Background

Restriction enzymes 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 finds GAATTC, between the G and A. 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 cuts at 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 known.

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 ...

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