DNA Ladders and Strain-Matching Techniques

DNA Ladders

DNA is a sequence of living cells, which are very delicate and need special care. Everything that occurs in living cells, including reproduction, is controlled by DNA. The job of DNA is to control and guide our complex and important body systems. A DNA ladder is a protein scaffold made up of amino acids linked together. It has recently become clear that DNA is a powerful biological tool, with implications ranging from controlling gene expression, to regulating cell physiology, to developing resistance to disease. The discovery of DNA’s role in natural selection came about when scientists used DNA to screen thousands of bacteria for its ability to adapt to temperature and conditions. The bacteria were found to display remarkably high levels of adaptation, and this led to an entirely new area of biology. By determining which bacteria were most able to adapt, the researchers were then able to use them to screen millions of other strains and select those that exhibited the greatest level of fitness.

One of the uses of DNA is to introduce or delete DNA into cells. This is done by two methods: non-permissive and transcriptional. Non-permissive DNA insertion and deletion procedures introduce DNA into a living cell, but does not allow for the generation of the material needed to build a copy of the DNA molecule. Transcriptional DNA synthesis, on the other hand, makes use of DNA to directly generate copies of the DNA needed for a cell.

Types of DNA Ladders

How do DNA ladders work? There are two basic types of DNA ladder: fluorescent and non-fluorescing. In a fluorescent DNA ladder, DNA molecules are deposited onto a glass slide, where they can be viewed with the aid of a microscope. They are then introduced into a host cell by electrophoresis and then used to generate a sequence of base pairs (a pair of adjacent DNA molecules). Because fluorescent DNA bases make use of light in order to generate their effect, this method is used commonly in biochemistry experiments. The next type of DNA ladder is non-fluorescing, which makes use of ultraviolet light to generate a sequence of base pairs, but again, uses fluorescent molecules in order to generate the visibility.

Use of DNA ladders In Molecular Biology 

At their most fundamental level, ladders are used to introduce sequences of DNA into a host cell so that it can divide and reproduce. The actual DNA used will depend on the particular experiment, but commonly, DNA strands are introduced into the host cell with restriction enzymes. Restriction enzymes are pieces of DNA that have been chemically changed into a form that allows them to seek out and grab specific DNA fragments. When these restriction enzymes attach to the DNA fragments they are seeking, they stop the DNA from being moved out of the plasmid.

There are several different methods for introducing DNA into a host cell, but two of the most common are known as gel electrophoresis and fluorescence in situ hybridization.

Gel Electrophoresis

With gel electrophoresis, a fluid containing a variety of DNA designs is injected into the cells. As the DNA is introduced, specific pairs of DNA are randomly split off of the design. These pieces then bind to a specific probe where they are detected by a detector (Wisecarver). This method is commonly used in conjunction with molecular weight markers.

Situ Hybridization

Another popular ways to introduce DNA into a cell is through the method known as optical in situ hybridization (Wisecarver). Using this technique, DNA strands of a particular sequence are injected into the desired locations. Then, chemicals are applied to the DNA fragments. These chemicals, which are different from those used to mix the DNA with the desired DNA templates, allow the DNA to be bound to the chemicals. Once the DNA is present in the desired location on the silica plate, it can be detected. The silica detector then measures the amount of bound DNA fragments against a previously designed template.


The third popular method of DNA binding is called immunoassay. This method requires the use of fluorescently labeled beads. These beads are then mixed with a variety of different DNA templates, some of which contain molecular weights. When these DNA templates bind to the fluorescently labeled beads, the bound DNA fragments are detected by a sensor array. The sensor measures the intensity of the bind and the degree of sequence identity. This method is commonly used in crime and murder investigations and in DNA profiling.

Wisecarver. (n.d.). Techniques Used To Test Native DNA. CE UPDATE —MOLECULAR BIOLOGY II, 1997.


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