association of the class II restriction endonuclease and its specific recognition sequence on the nucleic acid. Across this class of proteins there is considerable variation in the number of nucleotides in the recognition sequence and the pattern of cleavage (Table 1). Recognition sites with four nucleotides (tetramers), 5 nucle- otides (pentamers), and 6 nucleotides (hexamers) are all found in class II enzymes. Many of the recognition sites are palindromes; that is, they exhibit twofold rota- tional or dyad symmetry.Palindromes can best be defined by considering the direction of the two DNA strands in the double helix (Fig. 1). The complementary strands are antiparallel. Their phosphodiester bridges run in opposite directions. On each strand adjacent nucleotides are bonded with phosphodiester bridges on the IS’ carbon of one deox- yribose and S’ carbon of the second. Therefore one can talk about 5' to 3 direction or a 3’ to 5' direction. By convention, the recognition sites for class II restriction endonucleases are written 5' to S'.For a restriction endonuclease site to have twofold rotational symmetry, i.e., to be a palindrome, the nucleotide sequence in the endonuclease recognition site must be identical when it is read in the 5' to 3' direction of each complementary DNA strand (Rodriguez and Tait, 1983). The hexamer recognition site for HcoRI is a good example, 5'-GAATTC -3’ (Roberts, 1988). When one reads the complementary strand in the S to iS' direction, it is S' -CZ’Z’AAG-5', but when read 5’ to 6', it is identical to its complementary sequence (Fig. 1). Asymmetric endonuclease recog- nition sequences also occur, such as Mnll, 5' -CCTC-3', in which the complemen- tary strands do not have the same recognition sequence when read 5' to S' (Smith, 1979; Roberts, 1988). A yet further complication in a description of the sequences of endonuclease restriction sites is degeneracy. Many recognition sequences have sites that can be filled by two or more nucleotides (Roberts, 1988). For instance, the pentameric, symmetric sequence for Asul, 5' -GGNCC-3’, can have any of the four bases at its central nucleotide. Notice that this “degenerate” nucleotide is the axis of symmetry for this odd numbered site (Smith, 1979). The DNA sequences on either side of the central nucleotide are identical when each complementary strand is read in the 5’ to S' orientation.
正在翻譯中..
