Creating the clone

The steps in cloning are as follows. DNA is extracted from the organism under study and is cut into small fragments of a size suitable for cloning. Most often this is achieved by cleaving the DNA with a restriction enzyme. Restriction enzymes are extracted from several different species and strains of bacteria, in which they act as defense mechanisms against viruses. They can be thought of as “molecular scissors,” cutting the DNA at specific target sequences. The most useful restriction enzymes make staggered cuts; that is, they leave a single-stranded overhang at the site of cleavage. These overhangs are very useful in cloning because the unpaired nucleotides will pair with other overhangs made using the same restriction enzyme. So, if the donor DNA and the vector DNA are both cut with the same enzyme, there is a strong possibility that the donor fragments and the cut vector will splice together because of the complementary overhangs. The resulting molecule is called recombinant DNA. It is recombinant in the sense that it is composed of DNA from two different sources. Thus, it is a type of DNA that would be impossible naturally and is an artifact created by DNA technology.

The next step in the cloning process is to cut the vector with the same restriction enzyme used to cut the donor DNA. Vectors have target sites for many different restriction enzymes, but the most convenient ones are those that occur only once in the vector molecule. This is because the restriction enzyme then merely opens up the vector ring, creating a space for the insertion of the donor DNA segment. Cut vector DNA and donor DNA are mixed in a test tube, and the complementary ends of both types of DNA unite randomly. Of course, several types of unions are possible: donor fragment to donor fragment, vector fragment to vector fragment, and, most important, vector fragment to donor fragment, which can be selected for. Recombinant DNA associations form spontaneously in the above manner, but these associations are not stable because, although the ends are paired, the sugar-phosphate backbone of the DNA has not been sealed. This is accomplished by the application of an enzyme called DNA ligase, which seals the two segments, forming a continuous and stable double helix.

The mixture should now contain a population of vectors each containing a different donor insert. This solution is mixed with live bacterial cells that have been specially treated to make their cells more permeable to DNA. Recombinant molecules enter living cells in a process called transformation. Usually, only a single recombinant molecule will enter any individual bacterial cell. Once inside, the recombinant DNA molecule replicates like any other plasmid DNA molecule, and many copies are subsequently produced. Furthermore, when the bacterial cell divides, all of the daughter cells receive the recombinant plasmid, which again replicates in each daughter cell.

The original mixture of transformed bacterial cells is spread out on the surface of a growth medium in a flat dish (Petri dish) so that the cells are separated from one another. These individual cells are invisible to the naked eye, but as each cell undergoes successive rounds of cell division, visible colonies form. Each colony is a cell clone, but it is also a DNA clone because the recombinant vector has now been amplified by replication during every round of cell division. Thus, the Petri dish, which may contain many hundreds of distinct colonies, represents a large number of clones of different DNA fragments. This collection of clones is called a DNA library. By considering the size of the donor genome and the average size of the inserts in the recombinant DNA molecule, a researcher can calculate the number of clones needed to encompass the entire donor genome, or, in other words, the number of clones needed to constitute a genomic library.

Another type of library is a cDNA library. Creation of a cDNA library begins with messenger ribonucleic acid (mRNA) instead of DNA. Messenger RNA carries encoded information from DNA to ribosomes for translation into protein. To create a cDNA library, these mRNA molecules are treated with the enzyme reverse transcriptase, which is used to make a DNA copy of an mRNA. The resulting DNA molecules are called complementary DNA (cDNA). A cDNA library represents a sampling of the transcribed genes, whereas a genomic library includes untranscribed regions.

Both genomic and cDNA libraries are made without regard to obtaining functional cloned donor fragments. Genomic clones do not necessarily contain full-length copies of genes. Furthermore, genomic DNA from eukaryotes (cells or organisms that have a nucleus) contains introns, which are regions of DNA that are not translated into protein and cannot be processed by bacterial cells. This means that even full-sized genes are not translated in their entirety. In addition, eukaryotic regulatory signals are different from those used by prokaryotes (cells or organisms lacking internal membranes—i.e., bacteria). However, it is possible to produce expression libraries by slicing cDNA inserts immediately adjacent to a bacterial promoter region on the vector; in these expression libraries, eukaryotic proteins are made in bacterial cells, which allows several important technological applications that are discussed below in DNA sequencing.

Several bacterial viruses have also been used as vectors. The most commonly used is the lambda phage. The central part of the lambda genome is not essential for the virus to replicate in Escherichia coli, so this can be excised using an appropriate restriction enzyme, and inserts from donor DNA can be spliced into the gap. In fact, when the phage repackages DNA into its protein capsule, it includes only DNA fragments the same length of the normal phage genome.

Vectors are chosen depending on the total amount of DNA that must be included in a library. Cosmids are engineered vectors that are hybrids of plasmid and phage lambda; however, they can carry larger inserts than either pUC plasmids (plasmids engineered to produce a very high number of DNA copies but that can accommodate only small inserts) or lambda phage alone. Bacterial artificial chromosomes (BACs) are vectors based on F-factor (fertility factor) plasmids of E. coli and can carry much larger amounts of DNA. Yeast artificial chromosomes (YACs) are vectors based on autonomously replicating plasmids of Saccharomyces cerevisiae (baker’s yeast). In yeast (a eukaryotic organism) a YAC behaves like a yeast chromosome and segregates properly into daughter cells. These vectors can carry the largest inserts of all and are used extensively in cloning large genomes such as the human genome.