Classification of type-II restriction endonucleases and cloning of non-identical cohesive-end fragments without self-polymerization using nonpalindromic oligodeoxyribonucleotide adapters.

Enzymatic partial filling-in of recessed 3'-end sequences, left after digestion of DNA by the restriction endonucleases (ENases) Sau3A and SalI, with the Klenow fragment of E. coli DNA polymerase I allows the forced ligation of the resulting fragments; this technology is already used for subcloning and for genomic bank construction. To simplify and generalize its utilization, class-II ENases have been arranged into 16 different families according to the composition of the 5'-protruding sequences present after cleavage. Moreover, this system was extended to allow the joining of noncompatible ends by the use of nonpalindromic complementary oligodeoxyribonucleotides (NPCOs) containing two nucleotides protruding at each 5' end. The use of these synthetic adapters maintains all the advantages of the initial gap-filling cloning technique: only one insert can be cloned per vector molecule and no self-ligation or -polymerization can occur with any of the DNA molecules involved. Only 22 such oligodeoxyribonucleotides are needed to generate the 60 NPCO pairs necessary to ligate to each other any member of twelve ENase families when the regeneration of ENase recognition sites is not required.