Endonuclease and

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 ...

Genetic recombination arises by exchange of homologous segments of DNA between viral genomes, most often during the replication process. The enzymes involved in recombination are DNA polymerases, endonucleases, and ligases, which also play a role in DNA repair and synthesis processes. 

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.

DON T WASTE TIME ON ABSOLUTE TRIVIA UNLESS YOU HAVE THE TIME TO WASTE. It is possible to decide that something is just not worth remembering for example, cleavage specificities of proteases or restriction endonucleases, and protein molecular weights, are... 

Lu Y (2002) New transition-metal-dependent DNA-zymes as efficient endonucleases and as selective metal biosensors. Chem Eur J 8 4588-4596... 

The most recent advances on enzymatic inhibition are related to endonucleases and polymerases. A tris-malonic acid fullerene derivative can interfere with DNA restrictive enzymatic reactions, demonstrating a dose-dependent inhibition of these enzymes, with an IC50 in the micromolar range. The addition of ROS scavenger does not revert the enzymatic activity, indicating that the fullerene action should be exerted in a direct way (Yang et al., 2007d). 

Yang X, Chen Z, Meng X, Li B, Tan X (2007d) Inhibition of DNA restrictive endonucleases and Taq DNA polymerase by trimalonic acid Cm. Chin. Sci. Bull. 52 1802-1806. 

The vector is cut with the restriction endonuclease and mixed with the DNA restriction fragments to be cloned. As shown in Figure 1-6-3, once the vectors have combined with one of the restriction fragments, DNA ligase is used to form permanent PDE bonds between the fragment and the vector. This produces recombinant DNA. 

Bennett, R.A., Wilson, D.M., 3rd, Wong, D., and Demple, B. (1997) Interaction of human apurinic endonuclease and DNA polymerase beta in the base excision repair pathway. Proc. Natl. Acad. Sci. USA 94, 7166-7169. 

This enzyme (also known as DNA-(apurmic or apyrimid-inic site) lyase, AP endonuclease class I, E. coli endonuclease III, Phage-T4 UV endonuclease, and Micrococcus luteus UV endonuclease) catalyzes the cleavage of the phosphodiester bond in a lyase-type reaction, not hydro-... 

Fujimura M, Moiita-Fujimura Y, Narasimhan P, Copin J, Kawase M, Chan P (1999) Copper-zinc superoxide dismutase prevents the early decrease of apurinic/apyrimidinic endonuclease and subsequent DNA fragmentation after transient focal cerebral ischemia in mice. Stroke... 

FIGURE 3.13 Insertion of a foreign DNA sequence into a plasmid cloning vehicle, using restriction endonucleases and ligase. 

Drelich M, Wilhelm R, Mous J. Identification of amino acid residues critical for endonuclease and integration activities of HIV-1 IN protein in vitro. Virol 1992 188 459-468. 

Schatz O, Mous J, Le Grice SFJ. HIV-1 RT-associated ribonuclease H displays both endonuclease and 3 5 exonuclease activity. EMBO J 1990 9 1171-1176. 

Work that may prove of immense industrial significance is the isolation from Kluyveromyces lactis, by Dickson and Markin,394 of the gene for /3-D-galactosidase by use of recombinant-DNA techniques. The DNA from the yeast was partly digested with endonuclease, and the product was joined to a plasmid DNA by means of DNA ligase. The ligated DNA was then successfully used to transform a lactose-nega-... 

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. 

To complete the reaction, the process must be repeated at a second point within each of the two recombination sites (steps (3) and (4)). In some systems, both strands of each recombination site are cut concurrently and rejoined to new partners without the Holliday intermediate. The exchange is always reciprocal and precise, regenerating the recombination sites when the reaction is complete. We can view a recombinase as a site-specific endonuclease and ligase in one package. 

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