Restriction endonuclease table

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 40-2. Selected restriction endonucleases and their sequence specificities ...

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.

The EcoRI endonuclease cleaves this hexanucleotide sequence on each strand between the G and the first A residue (reading 5 -to-30 this point of cleavage is marked by arrows in the sequences in Table 3.1. Notice that the points of cleavage are offset, or staggered, for EcoRI. Not all restriction endonucleases make staggered cuts in DNA some cleave the DNA without any offset, to produce blunt-ended cuts. 

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 26-7 Genetic map of cloning plasmids pBR322 and pUC18. Abbreviations ori, origin of replication Amp1, ampicillin resistance gene Tet1, tetracycline resistance gene. Other abbreviations are for sites cleaved by specific restriction endonucleases, a few of which are defined in Table 26-2. The nucleotide sequence numbers and directions of transcription are also indicated. Reproduced by permission of Amersham Pharmacia Biotech Inc.

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.

Type II restriction endonucleases recognize specific base sequences in double-stranded DNA, and cleave both strands of the duplex. More than 600 restriction endonucleases have been reported in the literature. Some 121 restriction endonucleases are listed in Current Protocols in Molecular Biology as commercially available ( 3). Table II, adapted from the 1988 Sigma Chemical Company Catalog, lists 35 of the endonucleases available from that source. Endonucleases are found in many bacteria where their function is to hydrolyze foreign DNA introduced by phage infection, conjugation or transformation. The first restriction endonucleases were discovered and isolated in 1968 (4,5). 

SPECIFICITY. Restriction endonucleases are highly specific in hydrolyzing doubled-stranded DNA. Not only do they recognize a specific sequence of four to six base pairs (up to 11 base pairs in case of Bgl I see Table II) but the base pairs must be patind/iomic in the two strands of DNA. The cleavage sites possess twofold rotational symmetry as shown in Scheme I for restriction endonuclease Aat II from AcdtobacXdA OUddtL (Table II A, T, G, C indicate deoxyribonucleotides in this paper). In this example, the T-C phosphodiester bond in each strand two residues distal to the symmetry axis is cleaved by restriction endonuclease Aat II. 

The specificities of some of the restriction endonucleases listed in Table II are included in Figure 3. The cleavage sites may be staggered or even. The high specificity of restriction... 

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

Table 2.7. Frequency of restriction endonuclease sites in SV40 virus DNA (5243 base pairs)...

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 10.3. Examples of Restriction Endonucleases and Their Recognition Sites... 

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