Restriction endonucleases recognition sequences. Table

TABLE I. Percentage of (G-iC) Content in and Within 10 Base Pairs of the Restriction Endonuclease Recognition Sequence... 

Table 11.5 lists many of the commonly used restriction endonucleases and their recognition sites. Because these sites all have twofold symmetry, only the sequence on one strand needs to be designated. 

Table 13.2 Recognition sequences of a selection of restriction endonucleases. The double-stranded DNA is cut at the positions arrowed...

Table A4.1 presents the origins and sequence recognition sites for the restriction endonucleases in the plasmid vector.

Thousands of restriction endonucleases have been discovered in different bacterial species, and more than 100 different DNA sequences are recognized by one or more of these enzymes. The recognition sequences are usually 4 to 6 bp long and palindromic (see Fig. 8-20). Table 9-2 lists sequences recognized by a few type II restriction endonucleases. In some cases, the interaction between a restriction endonuclease and its target sequence has been elucidated in exquisite molecular detail for example, Figure 9-2 shows the complex of the type II restriction endonuclease EcoRV and its target sequence. 

TABLE 9-2 Recognition Sequences for Some Type II Restriction Endonucleases... 

The cuts in the two strands are made at the points indicated by the arrows. This one endonuclease will cut almost any DNA into long pieces averaging about 5000 base pairs each. These pieces can in turn be cleaved by other restriction endonucleases to form smaller fragments. Since there are about 2400 of these enzymes known, with 188 different specificities,536 it is possible to cut any piece of DNA down to a size of 100-500 base pairs, ideal for sequencing.537 539 Each fragment has known sequences at the two ends. Some restriction enzymes cleave outside their specific recognition sequence (see Table 26-2). Some recognize 16-nucleotide palindromes and cut at rare sites. 

Figure 9.3. Restriction map produced by Webcutter. The partial restriction map shows the nucleotide sequence of human lysozyme gene submitted to Webcutter using options for all restriction endonucleases with recognition sites equal to or greater than six nucleotides long and cutting the sequence 2 6 times (at least 2 times and at most 6 times). The restriction profile (map) is returned if Map of restriction sites is selected for display. The tables by enzyme name and by base pair number can be also returned if displays for Table of sites, sorted alphabetically by enzyme name Table of sites, sorted sequentially by base pair number are chosen.

Table 2.6. Recognition sequences of some commonly used six-base-specific restriction endonucleases...

The recognition sites for restriction endonucleases arc specific palindromic sequences of DNA"" not more than 8 bp long. A number of these palindromes are listed in Table 6-2. A palindrome is a. sequence of letters that reads the same way forward and backward, for instance "A man. a plan, a canal Panama ." "DNA-land," "Did Hannah sec bees Hannah did." Restriction endonucleases cleave DNA at palindromic sites to yield several types of cuts ... 

TABLE 4.2 Selected example of type II restriction endonucleases and their cleavage sequences. The recognition sequences of type II restriction endonucleases are shown with the arrow (4-) indicating the cleavage site... 

The following is a section of the gene coding for bovine rhodopsin, along with a table listing several restriction endonucleases, their recognition sequences, and their hydrolysis sites ... 

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