Substrate specificity of new methyl-directed DNA endonuclease GlaI

In a recent work we have studied the dependence of GlaI activity on the quantity and location of 5-methylcytosines in the enzyme recognition sequence 5'-GCGC-3'/3'-CGCG-5'. A significant DNA cleavage has been observed for oligonucleotide duplexes, which include either three or four 5-methylcytosines. In this work we have studied dependence of the GlaI activity on quantity and location of methylated cytosines, as well as on composition of the recognition sequence.The list of good substrates for GlaI includes a fully methylated site 5'-CGCG-3'/3'-GCGC-5', sites with three cytosines of a general structure 5'-PuMGM-3'/3'-PyGMG-5', and one recognition sequence with two methylated cytosines 5'-AMGT-3'/3'-TGMA-5', where M is 5-methylcytosine.GlaI intermediate substrates include sites with three methylated cytosines of a general structure 5'-GMPuM-3'/3'-MGPyG-5', as well as a site with two methylcytosines 5'-GMGT-3'/3'-CGMA-5'.The site 5'-GMGC-3'/3'-CGMG-5' may be considered a low activity substrate.Most bacterial site-specific DNA endonucleases are restriction endonucleases. Restriction endonucleases (restriction enzymes) and DNA-methyltransferases (methylases) of the same specificity form the so-called restriction-modification (R-M) system. It is supposed that restriction endonucleases (restriction enzymes) protect the cell against penetration of foreign DNA (for example phage DNA), whereas methylases protect the host DNA against cleavage from their own restriction enzyme. Methylases protect DNA by modifying the recognition sequence. Even the name "restriction endonuclease" originated from experimentally observed phenomenon – restriction of bacterial phage propagation in microorganisms [1]. Recently we have discovered site-specific endonucleases, which exist in bacterial cells without corresponding methylases and hydrolyze only cytosine-methylated DNA [2-5]. Based on the current classification [6,7] these enzymes may be placed into IIM group of site-specific endonucleases