Table of Contents
Recombinant DNA (rDNA) technology involves combining DNA fragments from two sources. The resulting DNA is called recombinant DNA. Naturally, DNA recombinants occur during crossing-over of homologous chromosomes. The context of recombinant DNA is the artificial or uncommon union of DNA fragments from two different sources of DNA. Some scientist also use the term chimeric DNA. The experimental manipulation to produce rDNA is what is called now as recombinant DNA technology.
Preparation of a rDNA involves a number of steps. These are DNA isolation, DNA splicing, DNA joining, and rDNA amplification. Before preparing the rDNA, it is important to identify the correct gene of interest depending on the target results. One of the main goals of rDNA technology is to develop species with characteristics or properties not normally found in them. For example, a bacterial species that does not naturally glow can be inserted with the gene from bioluminescent algae to produce a bacterial strain that is able to produce the same bioluminescent protein as the algae. The source of the desired DNA fragment will be called the donor while the DNA to be modified will be called the vector.
The first step in the preparation of the rDNA is to isolate both the vector and the donor DNA. For prokaryotic applications, the commonly used vector is the circular bacterial DNA plasmid. To be able to isolate the plasmid from the rest of the DNA genome, ultracentrifugation with addition of cesium chloride and ethidium bromide is done. The two DNA fragments selectively binds to the ethidium bromide producing a cesium chloride gradient after centrifugation. The plasmid DNA which sinks at the bottom can be collected for the next step.
The second step involves cutting the DNA fragment using restriction enzymes. Restriction enzymes are responsible for cutting the DNA of the bacteria, in the process, deactivating it. They cut at specific locations in the DNA strand which makes it possible to selectively obtain desired DNA fragment. They usually recognize specific DNA sequence where the cutting of DNA will occur. These sequences occur as palindromes, that is the two strands of the DNA have the same sequence but in opposite direction. The restriction enzyme recognizes this sequence and cut the fragments opening up the circular DNA. To be able to successfully produce the rDNA, the donor fragment should also be cut by the same restriction enzymes. This is to ensure that the sticky ends (points where the cut was made) are compatible with the sticky ends of the vector DNA.
The third step is the joining of the two DNA fragment. The two DNA fragments cut using same restriction enzyme will be mixed. Since the sticky ends of both fragments are complementary, the two DNA fragments can combine to form the rDNA. To further strengthen the joining, DNA ligase is used to create phosphodiester linkages between the two fragments.
The last step involves DNA amplification. When the rDNA obtained is entered to the bacterial cell by transformation, the plasmid vector will then be replicated via natural DNA replication processes. When they are replicated, the donor DNA is also replicated and multiple copies of it are produced. Continued cell division will lead to millions of cells containing the desired DNA fragment.
In the laboratory, large DNA fragments are hard to analyze because of the amount of nucleotide base contained in them. The use of restriction enzymes enable fragmentation of the DNA sequence to fragments of varying lengths or sizes. To be able to obtain the desired fragment, a separation technique must be employed. In molecular biology, these DNA fragments are separated by using Gel Electrophoresis. In this technique, mixture of DNA fragments are placed on top lanes of the gels. Electricity is then applied to separate the fragments in terms of size and charge. Smaller DNA fragments will naturally move faster than larger ones. After the separation, the DNA fragments can be visualized by adding fluorescent dyes that binds to DNA.
Bacterial transformation normally occur when bacteria uptakes DNA fragments from the environment. These DNA fragments enter the cell and can be integrated to the bacterial chromosome by nonreciprocal recombination. When recombination is successful, stable transformation will occur and the inserted DNA fragments may be expressed by the organism. Otherwise, the DNA fragment is degraded.
Molecular cloning follows basic steps in rDNA technology which are isolation, insertion and multiplication. The first step is isolation of the vector DNA. The next step is to use the correct restriction endonuclease to cut the DNA in a specific location. The foreign DNA is the inserted and connected using DNA ligase. Transformation will then occur to incorporate modified DNA to the bacterial species The species containing the modified gene will be amplified via natural cellular division and will exhibit different properties compared to natural species.
Host Vector System
To be able to produce multiple copies of a gene, the gene must be inserted to DNA segments which can spontaneously replicate. This DNA fragment that can replicate with the inserted DNA fragment is known as the vector or cloning vehicle. A good vector should have origin of replication, one or more genetic markers for selection, and a cloning site where foreign DNA can be inserted. Replication of the DNA can only be achieved inside a host which provides the enzymes and factors needed for replication. This is achieved by successful introduction of the vector into the host. Common hosts used are E. coli, yeast cell, mammalian tissue culture cells, and insect cells. Common vectors include plasmids, and bacterial and yeast artificial chromosomes.
Transforming Eukaryotic cells
Unlike in transformation of prokaryotic cells, transformation in eukaryotic cells is more challenging. A common technology employed is the use of a gene gun. The gene gun inserts DNA by bombarding electrically charged cells with gold or tungsten particles coated with DNA.
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Cas9 enables editing of DNA by having the Cas9 acting like a pair of molecular scissors to cut pieces of the DNA of the disease-causing organism, the organisms then later incorporate part of the invader’s DNA to its own genome so that it can recognize the invader in the future. In this technique, scientist creates a guide RNA sequences that matches the DNA they want to modify. This sequence is then added to cells together with a protein called Cas9. The Cas9 protein cuts the DNA and insert the Guide RNA in the DNA sequence. Enzymes then repair the cuts and leaves the modified DNA. This technique finds great application in fixing genetic defects. It was already used before to treat in Duchenne Muscular Dystrophy in Mice and Huntington’s Disease.
Polymerase Chain Reaction
Polymerase chain reaction (PCR) is a technique used to produce multiple replicates of DNA fragments. The process of DNA amplification is divided into three stages namely denaturing stage, annealing stage and extending stage. In the denaturing stage, the DNA molecule is heated up to 95ºC to separate the two strands. Primers then attach to each of the two strands in the annealing stage. Extending stage then proceeds by adding more nucleotides in the growing chain. The steps are then repeated to produce more copies of the DNA.
The correct answers can be found below the references.
1. What do you call enzymes that cut the DNA on specific palindromic sequence in the DNA strand?
- Restriction Enzyme
2. What do you call the technique used to separate DNA fragments in terms of its size an charge polarity?
- Gel electrophoresis
- CRISPR Cas9
- Gene gun
- Polymerase Chain Reaction