BamHI recognizes 5'-GGATCC-3'
EcoRI recognizes 5'-GAATTC-3'
|Figure 8-2 Restriction enzymes may form (a) cohesive
or (b) blunt ends.
The resulting fragments of a restriction enzyme digestion can be visualized
by a procedure known as electrophoresis. Electrophoresis involves
the movement of charged molecules or ions through a semisolid
support medium under the influence of an electrical field. Agarose gels
are common media for the electrophoresis of DNA . The agarose gel, cast
as a thin slab in a mold with sample wells at one end, is submerged in a
buffer solution with the sample well side toward the negative pole (cathode). The samples are dispensed into the wells and a current from the
power supply is applied to the system. Since nucleic acids have a negative
charge at pH=8.0, they migrate within the gel matrix from the negative
to the positive pole (anode) at a rate dependent upon their size, shape,
and total charge. DNA molecules are invisible to the naked eye, but can
be seen in gels by staining them with a solution of a dye called ethidium
bromide, which intercalates between the stacked bases of the DNA molecule
The graphical representation of recognition sites for two or more restriction
endonucleases is known as a restriction map for that molecule.
Knowing the restriction maps for commonly used plasmids and bacteriophage
DNA genomes allows scientists to plan cloning stategies for isolating
and moving around pieces of DNA that contain genes of interest.