The ability to produce recombinant DNA molecules has not only revolutionized the study of genetics, but has laid the foundation for much of the biotechnology industry. The result is a molecule of recombinant DNA (rDNA). The union can be made permanent by another enzyme, a DNA ligase, that forms covalent bonds along the backbone of each strand. Mixed together, these molecules can join with each other by the base pairing between their sticky ends. Any other source of DNA treated with the same enzyme will produce such molecules. These are called "sticky ends" because they are able to form base pairs with any DNA molecule that contains the complementary sticky end. The ends of the cut have an overhanging piece of single-stranded DNA. However, many restriction enzymes cut in an offset fashion. HaeIII and AluI cut straight across the double helix producing "blunt" ends.
These fragments can be separated from one another and the sequence of each determined. Thus treatment of this DNA with the enzyme produces 11 fragments, each with a precise length and nucleotide sequence. This particular sequence occurs at 11 places in the circular DNA molecule of the virus φX174. The cut is made between the adjacent G and C. For example, the bacterium Hemophilus aegypticus produces an enzyme named HaeIII that cuts DNA wherever it encounters the sequenceģ'CCGG5' Figure 5.7.2: Restriction Enzymes Figure 5.7.1: Restriction DigestĪ restriction enzyme recognizes and cuts DNA only at a particular sequence of nucleotides. The rarer the site it recognizes, the smaller the number of pieces produced by a given restriction endonuclease.
The tools for this are the restriction endonucleases. What is needed is a way to cleave the DNA molecule at a few precisely-located sites so that a small set of homogeneous fragments are produced. This produces a heterogeneous collection of fragments of varying sizes. Many DNA-digesting enzymes (like those in your pancreatic fluid) can do this, but most of them are no use for sequence work because they cut each molecule randomly. To be able to sequence DNA, it is first necessary to cut it into smaller fragments. Because they cut within the molecule, they are often called restriction endonucleases. Restriction enzymes are DNA-cutting enzymes found in bacteria (and harvested from them for use).
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