being obtained from different kinds of bacteria. Such enzymes are known as isoschizomers. The bases recognized by Type II enzymes are specific sequences within
a double strand of DNA, many of which have a palindromic structure with
double-rotation symmetry. Among Type II enzymes are those that cut the same site
on two strands of DNA to produce a flush end, and those for which the truncation
site is located between the two strands, resulting in a cohesive end where either the
5′ or 3′ end protrudes. In either case, the 3′ end has an OH group and the 5′ a
phosphate group, allowing for rejoining with DNA ligase.
Type III restriction enzymes possess endonuclease and methylase activity and
require Mg
2+ and ATP for DNA cutting. If ATP and s-adenosylmethionine are
present, DNA methylation also occurs. Moreover, while Type III restriction
enzymes recognize specific base sequences within the DNA molecule, they differ
from Type II and cutting the DNA at a location somewhat distant from that
sequence.
Fig. 2.21 Method of DNA cutting for the restriction enzymes Hind II and Eco RI
2.11 Restriction Endonuclease: Nomenclature, Types, and Characteristics
49