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In the methods we have described, restriction enzymes separately cut both vector and foreign DNA. The two are then mixed in the presence of ligase. The many products that are created can be divided generally into three categories: vectors with foreign DNA, vectors without foreign DNA, and fragments. In a later section, we will discuss methods of nding a particular piece of foreign DNA in a vector. Here, we point out how vectors with inserts of any kind are selected.
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III. Molecular Genetics
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13. Genomics, Biotechnology, and Recombinant DNA
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The McGraw Hill Companies, 2001
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Treat with a restriction endonuclease EcoRII
Join
Foreign DNA Insert
Plasmid
Treat with ligase
Recombinant plasmid Figure 13.6 Formation of a recombinant plasmid. The same restriction endonuclease, in this case EcoRII, is used to cleave both host and foreign DNA. Some of the time, cleaved ends will come together to form a plasmid with an insert of the foreign DNA. Ligase seals the nicks. P. Berg was the rst scientist to clone a piece of foreign DNA when he inserted the genome of the SV40 virus into phage in 1973.
Tamarin: Principles of Genetics, Seventh Edition
III. Molecular Genetics
13. Genomics, Biotechnology, and Recombinant DNA
The McGraw Hill Companies, 2001
Genomic Tools
Part of plasmid
Cloned insert
Part of plasmid 5 CCCGCCGC TGGA
GGGCGGCGACCT
Package in heads
Linear DNA
Infect E. coli
Bacterial chromosome
Cosmid Circular DNA
E. coli
Figure 13.7 A cosmid is a plasmid with cos sites that can be transferred into bacteria within phage lambda heads, a very ef cient method of infection. The cos sites are single-stranded; they reanneal to a circle when inside the host. (The heavy lines of the linear DNA, bacterial chromosome, and cosmid are double-stranded DNA.)
Charon phages are selected simply by their ability to infect E. coli cells. As we mentioned, after manipulation, only DNA with a foreign insert is packaged because of the size requirement. Plasmids that contain foreign DNA can be selected through screening for antibiotic resistance. For example, a widely used cloning plasmid is named pBR322. (Plasmids are often named with the initials of their developers. The vector pBR322 was rst described in a paper published in 1977 by authors F. Bolivar and R. Rodriguez, hence pBR.) Plasmid pBR322 contains genes for tetracycline and ampicillin resistance and various restriction sites. There is, for example, a BamHI site in the tetracycline-resistance gene ( g. 13.8). After the ligating procedure, plasmids with and without foreign DNA will be present. E. coli cells are then exposed to this DNA mixture in the presence of calcium chloride; after taking up the DNA, the E. coli cells are plated on a medium without antibiotics. Replica-plating is done onto plates with one or both antibiotics. Colonies resistant to both antibiotics are composed of cells with plasmids having no inserts; those resistant only to ampicillin have a plasmid with an insert. Colonies resistant to neither antibiotic have cells with no plasmids.
Blunt-End Ligation
Restriction endonuclease treatment may not suf ce for cloning; an endonuclease may cut in the wrong place, say in the middle of a desired gene, or the foreign DNA may have been isolated by other methods, such as physical shearing. In these cases, several other methods of cloning can be used. The most common method of joining foreign and vehicle molecules that do not have sticky ends is called blunt-end ligation; the phage enzyme, T4 DNA ligase, can join blunt-ended DNA. Blunt ends can be generated when segments of DNA to be cloned are created by physically breaking the DNA or by using certain restriction endonucleases, such as HindII (see g. 13.2), that form blunt ends. Since the ligase is nonspeci c about which blunt ends it joins, many different, unwanted products result from its action. Restriction enzymes that produce sticky ends are preferred for cloning. A variation of blunt-end ligation uses linkers short, arti cially synthesized pieces of DNA containing a restriction endonuclease recognition site. When these linkers are attached to blunt pieces of DNA and then
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