Restriction enzymes table

Type II restriction enzymes (Table 1) require physiologic pH, usually divalent cations (primarily Mg ), and, most importandy, a DNA substrate with the... 

Restriction. The bacterial restriction modification system consists of DNA restriction endonuclease (Pingoud, 2004) and a matched modification enzyme (methylase, i.e. methyltransferase). The restriction endonucleases recognize specific sequences within dsDNA on which the hydrolysis takes place. Three types of restriction enzymes (Table 13.4) have been identified (Yuan, 1981). 

This polylinker contains restriction sites for BamHl, EeoRL, Pst, Sal, Smal, Sphl, and Xbal. Indicate the location of each restriction site in this sequence. (See Table 11.5 of restriction enzymes for their cleavage sites.)... 

Restriction enzymes are named after the bacterium from which they are isolated. For example, EcoRI is from Escherichia coli, and BamEII is from Bacillus amyloliquefaciens (Table 40-2). The first three letters in the restriction enzyme name consist of the first letter of the genus (E) and the first two letters of the species (co). These may be followed by a strain designation (R) and a roman numeral (I) to indicate the order of discov-ery (eg, EcoRI, EcoRIE). Each enzyme recognizes and cleaves a specific double-stranded DNA sequence that is 4—7 bp long. These DNA cuts result in blunt ends (eg,... 

The sequences of some recognition sites for some restriction enzymes are given in Table 3.3. 

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. 

Restriction enzymes that cleave DNA at a large number of specific sequences are available commercially. A few are listed in Table 26-2. Another group of restriction enzymes have similar recognition sequences... 

Several hundred restriction enzymes have been isolated and characterized. Nomenclature for the enzymes consists of a three-letter abbreviation representing the source (Eco — E. colt), a letter representing the strain (R), and a roman numeral designating the order of discovery. fcoRI is the first to be isolated from E. coli (strain R) and characterized. Table E15.1 lists several other restriction enzymes, their recognition sequence for cleavage, and optimum reaction conditions. 

The reaction conditions are specific for each restriction enzyme. The commercial supplier of the enzyme will provide an information sheet giving details of the reaction conditions. For a detailed listing of optimal conditions for many restriction enzymes, see Brooks (1987) or Table E15.1. 

Most of the enzymes that are absolutely essential for cloning were discussed in the previous chapter. The most important enzymes that have not been discussed yet are the restriction enzymes. Systematic cleavages of duplex DNA at specific sites requires restriction enzymes. Each species of bacteria harbors a unique restriction enzyme, and hundreds of restriction enzymes with different specificities have been isolated, giving researchers a great deal of choice as to how and where DNA is cut. Some of the most commonly used restriction enzymes and their recognition sites are indicated in table 27.1. Most of these enzymes recognize a sequence... 

To search for an appropriate restriction enzyme and its restriction profile, subject the query DNA to Webcutter at http //www.firstmarket.com/cutter/ cut2.html. Upload the sequence file (enter drive directoryseqfilename) or paste the sequence into the query box. Indicate your preferences with respect to the type of analysis, site display, and restriction enzymes to include in the analysis. After clicking the Analyze Sequence button, the restriction map (duplex sequence with restriction enzymes at the cleavage sites), as shown in Figure 9.3, is returned if Map of restriction sites is selected for display. You may also select Table of sites, sorted alphabetically by enzyme name for display which lists number of cuts, positions of sites, and recognition sequences. 

An alternative method involves the assembly of the library by cloning. To do this one must use restriction enzymes which do not cut frequently within V regions (see Table 18.6 for a list of enzymes based on VBASE [23]). 

For sequencing an entire plasmid or virus DNA one can simply begin by cleaving a sample of the DNA into fragments, preferably using a restriction enzyme which yields protruding 5 -ends for ease of labelling. Table 5.II. lists fifteen restriction enzymes which make... 

Cleavage sites for restriction enzymes occur randomly in the DNA. The frequency of a particular restriction site is dependent on the size of the DNA and the size of the recognition sequence. The probability of finding a particular four-base run in DNA is 1/256 (l/4>base-specific restriction sites in the 5243 base pair, circular genome of the simian virus SV40 is shown in Table 2.7. 

All restriction enzymes are named after the bacterium W here they originated. The Cutting sites (restriction sites are also named, and they bear the same name as the relevant enzyme. Table H.f shows several commonly used restriction enzymes, the structures of the target site that is hydrolyzed by the enzyme, and the organisms that originally produced the enzymes in nature (Bhagw at, 1992). 

Appendut B Dot Blots, Mol ular Cloning ind DNA Sequencing 949 TABLE B.l Restriction Enzymes and Target Cleavage Sites... 

---