Restriction enzyme ECO

Figure 7.8 Sequence-specific recognition sites in the major groove of DNA for three restriction enzymes—Eco RI, Bal I, and Sma I. The DNA sequences that are recognized by these enzymes ate represented by tbe color code defined in Figure 7.7.

Only a rather limited number of base pairs is needed to provide unique and discriminatory recognition sites in the major groove. This is illustrated in Figure 7.8, which gives the color codes for the hexanucleotide recognition sites of three different restriction enzymes—Eco Rl, Bal 1, and Sma 1. It is clear that these patterns are quite different, and each can be uniquely recognized by specific protein-DNA interactions. 

Rossi, S., Buera, M.R, Moreno, S., and Chirife, J. Stabilization of the restriction enzyme Eco R1 dried with trehalose and other selected glass-forming solutes, Biotechnol. Prog., 13, 609, 1992. 

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. 

Every restriction enzyme recognizes and cuts a specific DNA sequence which usually consists of four or six nucleotide pairs. For example, a restriction endonuclease Eco RI obtained from Escherichia coli cuts wherever it encounters the nucleotide sequence GAATTC, whereas Bal 1 from... 

Restriction endonucleases are named in accordance with the proposals of Smith and Nathans (1973). Their names consist of a three letter abbreviation for the host organism (e.g. Eco for E. coli, Hin for Haemophilus influenzae. Bam for Bacillus amyloliquefaciens) followed by a strain designation and a Roman numeral. Thus Haemophilus influenzae, strain Rd contains at least three distinct restriction endonucleases and these are called Hindi, Hindll and Hindlll respectively. Restriction enzymes are generally known and described in the catalogues of suppliers by this code. 

More than 100 restriction enzymes have been purified and characterized. Their names consist of a three-letter abbreviation for the host organism (e.g., Eco for Escherichia coli, ERn for Haemophilus influenzae, Hae for Haemophilus... 

Fig. 9.6. Plasmon ruler study of DNA cleavage by the Eco RV restriction enzyme. Upon cleavage, the light scattering spectrum and intensity change abruptly. The single particle trajectories can be used to observe the sequence of events prior to cutting, including bending of the DNA. Collaborative work with Prof. Jan Liphardt [19]...

Restriction enzymes recognize certain regions, or sequences, of the DNA. These are relatively short, and occur at multiple sites over the entire native genome. Some examples of restriction enzymes and their recognition sites are listed in Table 10.3. Cleavage of the double-stranded DNA occurs where the slashes (/) are shown in the recognition sequence. The names of the restriction enzymes are derived from the species from which they are isolated (e.g., Eco is E. coli) and contain further classification numbers. 

Lane 1 shows the mobility of nicked (N) and supercoiled (S) forms of SV40 DNA. Lanes 2-6 contain SV40 DNA cleaved with Bam HI, Eco RI, Bgl 1, Hpa II, and Kpn I, respectively. These controls demonstrate complete cleavage to the linear (L) form. Lanes 7-11 contain SV40 DNA [9.0 X M DNAiN) that was reacted with cis-DDP (1.8 X lO M) for 3 h at 25 C, spot dialyzed, and then cleaved with the restriction enzyme. The order is the same as in the control series. Lanes 12-16 contain SV40 DNA reacted similarly with trans-DDP followed by cleavage with restriction enzymes in the same order as controls. 

Restriction enzymes are named for the baoterium from which they were isolated (e.g., ECO is from Escherichia coli.). 

Figure 3.6 Heterologous (foreign) DNA (from either genomic DNA or a cDNA library) (see Section 3.2) is cut with two different restriction endonuclease enzymes (Eco Rl Xho I) producing a restriction digest.

The names are generally derived from the initials of the organism in which the particular enzyme was found, so for example all the restriction enzymes beginning Eco are derived from... 

Figure 1. Mutagenesis scheme for Rb. capsulatus RCs. Single letters indicate restriction enzyme recognition sites H, Hind III K, Kpn I B, Bam HI E, Eco Rl S, Sac I. See experimental section for a description of pU2924 and pU2925.

Figure 12.10 Some genes and restriction sites on the E. coli plasma pBR322. Eco RI, Pst I, and Sal I are restriction endonucleases and the sites cleaved by these enzymes.

---