DNA Modification and DNA Restriction
Besides DNA replication apparatus, other enzyme systems (methylases) are found in cells that may modify DNA through methylation of adenine or cytosine in a very specific manner. There are also restriction enzymes in a cell that can distinguish between its own DNA and any foreign invading DNA, so that the foreign DNA is attacked and degraded. These enzymes fall in two general classes, (i) Type II enzymes (e.g. EcoRI) have separate enzymes for methylase and restriction activities; the target sites for type II restriction enzymes (e.g. EcoRI, a dimer) are palindromes of 4-6 bp. Most of these enzymes cleave DNA at an unmethylated site; some of them create staggered cuts, while others create blunt ends (see Genetic Engineering and Biotechnology 1.  Recombinant DNA and PCR (Cloning and Amplification of DNA)). A methylase (usually a monomer as in EcoRIsystem) adds one methyl group at a time and dissociates. Another round of binding and methylation is needed for addition of another methyl group. The uses of some of these restriction enzymes are discussed in Genetic Engineering and Biotechnology 1.  Recombinant DNA and PCR (Cloning and Amplification of DNA), since they are extensively used in recombinant DNA technology, (ii) Type I and Type III enzymes are bi-functional, having both methylase and restriction activities; a type I enzyme (e.g. EcoK, EcoB)has three subunits R, M and S (R for restriction; M for methylation and S for specific target site), but type III (e.g. EcoPl, EcoP15)has only two subunits (R for restriction and MS for methylation and recognition). The properties of these three types of enzymes are summarized in Table 26.6 and a few important restriction enzymes are listed in Table 39.1.