Restriction enzymes cut a DNA strand at specific places, resulting in multiple fragments. These can be separated into different sizes by pulse-field gel electrophoresis (PFGE) to generate a "fingerprint" for the DNA. DNA from related bacterial isolates may differ slightly due to genetic differences.
Questions:
(1) Has the number of bands changed?
(2) Has the migration of bands changed?
(3) Does the migration of bands indicate a greater or lesser number of bases?
Genetic Change
Change in PFGE Pattern
gain in a restriction site
additional cut results in 2 smaller fragments
1 band will be replaced by 2 bands with lower number of bases
loss of a restriction site
fewer cuts result in larger fragments
2 bands will be replaced by 1 band with a higher number of bases
insertion of DNA without change in restriction sites
greater number of bases in new restriction fragment
1 band migrates with a higher number of bases
deletion of DNA without change in restriction sites
lesser number of bases in new restriction fragment
1 band migrates with a lower number of bases
With a gain or loss of a restriction site, the number of bases(s) of the new band(s) should be the same as the number of bases of the original band, i.e. there is no new material.
The change in the estimated number of bases for the restriction fragment after an insertion or deletion can give an estimate of the size of the DNA strand change.
number of bases of the inserted or deleted DNA strand =
= ABS((number of bases of original restriction fragment) - (number of bases of new restriction fragment))
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