When a transposon inserted into the target DNA, identical duplicated sequences are generated on both the sides of it, these sequences are called target site duplication.

The transposable elements are made up of the three different components, the gene body that encodes for the transposase protein, The terminal repeats and the target site duplication.

The terminal repeats are present on both ends of the transposon which helps in recognition of transposase protein.

However, the clear function of target site duplication is still unknown for scientists. It is believed that the TSDs might be involved in the process of evolution.

In the present article, we will discuss the mechanism of how the target site duplication occurred into the target DNA.

Let us start the topic,

As we discussed above and in the earlier articles, structurally the transposons contain three distinct components gene body, terminal repeat and target site duplication.

The entire process of the transposition depends on the role of transposase protein that has excision and insertion activity.

It catalyses the reaction by excising a transposon from one position and inserting it to another location in the genome.

Although, the mechanism of excision is different in both transposon as well as at the target site.

The target site is a DNA sequence at which our transport will going to insert. 

The two types of transposons viz DNA and retrotransposons perform transposition through the replicative or non-replicative mechanism.

In the replicative mechanism the copy of a transposon left behind into the original position while in the non-replicative transposition, instead of a copy, a gap occurred at the original position.

Read more on replicative and non-replicative transposition:

  1. Replicative Transposition of DNA transposons and Retrotransposons
  2. Non-Replicative (Cut and Paste) Mechanism of Transposition

Interestingly in both the type of the transposition process, the transposase performs excision in a similar fashion.

The transposase creates double stranded excision on the terminal repeats and single-stranded excision on the target DNA.

The process of single-stranded excision is a reason for the creation of target site duplication.

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 Let us stepwise understand the mechanism,

In the first step, each transposase proteins binds to the terminal ends of the transposon. The terminal repeats might be direct, inverse or in the same direction.

Depending upon the nature of the terminal repeats, the transposase recognizes it.

In the next step, the protein complex stretches both ends of it inward and creates a circular loop-like structure, then after it cuts both the ends of the transposon.

Here, the protein cuts the double-stranded DNA directly and removes it from that position.

In the next step, the complex moves towards the target site. The insertion site or the target site is randomly selected. Scientists do not have any significant data about whether the transposition is specific or random.

However, the data suggest that the insertion site are generally AT-rich regions.

After identifying and situating on the target site, the transposase starts the second round of excision.

Here, each transposase cuts each single DNA strand. See the figure below,

The process of target site duplication

Instead of cutting at the same position, the excision occurred on two different locations which create a sticky end like DNA structures. 5 to 9 nucleotide long target site duplication is commonly observed.

In the next step, the transposase protein inserts the transposon between both the sticky ends.

The gap remains unfilled and the transposase protein released.

The transposase can only fill gaps in 3′ to 5′ direction, therefore, the target site duplication gap cannot be filled by the enzyme.

DNA repair mechanism of the host cells now actively involves in the process of gap filling. The polymerase attached at the 3’ end of the gap use it as a primer and by adding nucleotides, it fills the gap on both sides.

Now in the final step, the ligase enzyme joins the transposon with the newly synthesized DNA.

Now, carefully examine the figure below, I will explain to you how the duplication occurred.


The process of target site duplication

In the figure, you can see that the sticky ends are complementary to each other therefore when polymerase finish the gap filling process, the base pairs present on both the sides become similar.

When the transposon migrates from this position to another position, it catches the target site duplication with them to another location.

This extra piece of DNA inserted into a new location can create new mutation and hence new allele.

If this new variation is helpful for the organism to survive, it will remain into the genome for a longer period of time.

That is how transposon creates new variation in our genome and favours evolution.

Eukaryotic transposons are mostly retrotransposon while prokaryotes contain DNA transposons.

For more detail on the transposons please refer our previous articles:

Transposons: A Jumping Entity and a Foe with Benefits

  • Overview, history, different types of transposons, LINEs-SINEs, retrotransposons, DNA transposons 

Transposase, Transposons and Antibiotic Resistance in Bacteria

  • Bacterial transposons, IS elements, composite transposons, Mu phage, transposon and antibiotic resistance

Transposons in eukaryotes

  • The general structure, transposon in Drosophila (P element, retrotransposon), TY elements in Yeast, transposon in Maize (Ac/Dc elements, spm/dspm elements), human transposons

Role of transposons in evolution

  • How transposon involved in the process of evolution

Replicative Transposition of DNA transposons and Retrotransposons

Non-Replicative (Cut and Paste) Mechanism of Transposition

Sleeping Beauty Transposon System: The Future of Gene Therapy

Some of the Quick FAQs:

What are the terminal repeats? 

The terminal repeats are the short inverted or direct sequences present on both ends of transposon. Terminal repeats are recognized by transposase protein for transposition.

What is a “copy and paste” mechanism of transposition? 

It is a replicative mode of transposition in which the transposon inserted in a new location by leaving a copy of it at the original (native position).

What is a “cut and paste” mechanism of transposition?

Cut and paste is a non-replicative/ conservative mode of transposition in which transposon migrates uni-direction, create a gap at the native position.

What is composite transposon?

Composite transposons are bacterial transposon, made up of two Insertional sequences (IS) elements.

What is the consequence of transposition? 

In creates mutation or new variation in nature.

What is the target site duplication? 

A target site duplication is the identical sequences present on both end ends of the transposon, originated due to the insertion of a transposon.

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Target site duplication is a very important process for creating variations, however, not all the target site DNA can migrate to another location.

Yet, no clear mechanism is postulated that explains how much amount of host DNA will be transferred by the TE. Also, On what basis the transposase protein recognizes the target DNA is still not clear.

We are far behind in the transposon research. We do not have enough knowledge regarding how to use TEs for targeted gene transfer and gene expression.

I hope these topics will help you to understand the basic mechanism behind the process of transposition.

Our series on the transposable elements are now completed, in the next articles I will provide you with some external resources related to transposon.