Biotechnology : Principles and Processes
Tools of Recombinant DNA Technology
Cloning Vectors
You know that plasmids and bacteriophages have the ability to replicate within bacterial cells independent of the control of chromosomal DNA
Bacteriophages because of their high number per cell, have very high copy numbers of their genome within the bacterial cells
Some plasmids may have only one or two copies per cell whereas others may have 15-100 copies per cell
Their numbers can go even higher
If we are able to link an alien piece of DNA with bacteriophage or plasmid DNA, we can multiply its numbers equal to the copy number of the plasmid or bacteriophage
Vectors used at present, are engineered in such a way that they help easy linking of foreign DNA and selection of recombinants from non-recombinants
The following are the features that are required to facilitate cloning into a vector
(i) Origin of replication (ori) : This is a sequence from where replication starts and any piece of DNA when linked to this sequence can be made to replicate within the host cells
This sequence is also responsible for controlling the copy number of the linked DNA
So, if one wants to recover many copies of the target DNA it should be cloned in a vector whose origin support high copy number
(ii) Selectable marker : In addition to ‘ori’, the vector requires a selectable marker, which helps in identifying and eliminating nontransformants and selectively ermitting the growth of the transformants
Transformation is a procedure through which a piece of DNA is introduced in a host bacterium (you will study the process in subsequent section)
Normally, the genes encoding resistance to antibiotics such as ampicillin, chloramphenicol, tetracycline or kanamycin, etc., are considered useful selectable markers for E. coli
The normal E. coli cells do not carry resistance against any of these antibiotics
(iii) Cloning sites: In order to link the alien DNA, the vector needs to have very few, preferably single, recognition sites for the commonly used restriction enzymes
The ligation of alien DNA is carried out at a restriction site present in one of the two antibiotic resistance genes
For example, you can ligate a foreign DNA at the BamH I site of tetracycline resistance gene in the vector pBR322
The recombinant plasmids will lose tetracycline resistance due to insertion of foreign DNA but can still be selected out from non-recombinant ones by plating the transformants on tetracycline containing medium
The transformants growing on ampicillin containing medium are then transferred on a medium containing tetracycline
The recombinants will grow in ampicillin containing medium but not on that containing tetracycline
But, non- recombinants will grow on the medium containing both the antibiotics
In this case, one antibiotic resistance gene helps in selecting the transformants, whereas the other antibiotic resistance gene gets ‘inactivated due to insertion’ of alien DNA, and helps in selection of recombinants
Selection of recombinants due to inactivation of antibiotics is a cumbersome procedure because it requires simultaneous plating on two plates having different antibiotics
Therefore, alternative selectable markers have been developed which differentiate recombinants from non-recombinants on the basis of their ability to produce colour in the presence of a chromogenic substrate
In this, a recombinant DNA is inserted within the coding sequence of an enzyme, β-galactosidase
This results into inactivation of the gene for synthesis of this enzyme, which is referred to as insertional inactivation
The presence of a chromogenic substrate gives blue coloured colonies if the plasmid in the bacteria does not have an insert
Presence of insert results into insertional inactivation of the β-galactosidase gene and the colonies do not produce any colour, these are identified as recombinant colonies
(iv) Vectors for cloning genes in plants and animals : You may be surprised to know that we have learnt the lesson of transferring genes into plants and animals from bacteria and viruses which have known this for ages - how to deliver genes to transform eukaryotic cells and force them to do what the bacteria or viruses want
For example, Agrobacterium tumifaciens, a pathogen of several dicot plants is able to deliver a piece of DNA known as ‘ T-DNA’ to transform normal plant cells into a tumor and direct these tumor cells to produce the chemicals required by the pathogen
Similarly, retroviruses in animals have the ability to transform normal cells into cancerous cells
A better understanding of the art of delivering genes by pathogens in their eukaryotic hosts has generated knowledge to transform these tools of pathogens into useful vectors for delivering genes of interest to humans
The tumor inducing (Ti) plasmid of Agrobacterium tumifaciens has now been modified into a cloning vector which is no more pathogenic to the plants but is still able to use the mechanisms to deliver genes of our interest into a variety of plants
Similarly, retroviruses have also been disarmed and are now used to deliver desirable genes into animal cells
So, once a gene or a DNA fragment has been ligated into a suitable vector it is transferred into a bacterial, plant or animal host (where it multiplies)
Competent Host (For Transformation with Recombinant DNA)
Since DNA is a hydrophilic molecule, it cannot pass through cell membranes
Why? In order to force bacteria to take up the plasmid, the bacterial cells must first be made ‘competent’ to take up DNA
This is done by treating them with a specific concentration of a divalent cation, such as calcium, which increases the efficiency with which DNA enters the bacterium through pores in its cell wall
Recombinant DNA can then be forced into such cells by incubating the cells with recombinant DNA on ice, followed by placing them briefly at $42^oC$ (heat shock), and then putting them back on ice
This enables the bacteria to take up the recombinant DNA
This is not the only way to introduce alien DNA into host cells
In a method known as micro-injection, recombinant DNA is directly injected into the nucleus of an animal cell
In another method, suitable for plants, cells are bombarded with high velocity micro-particles of gold or tungsten coated with DNA in a method known as biolistics or gene gun
And the last method uses ‘disarmed pathogen’ vectors, which when allowed to infect the cell, transfer the recombinant DNA into the host