Difference between Linker and Adaptor

Linkers and adaptors are oligonucleotides (short stretches of DNA or RNA molecules) that are useful in DNA ligation. In recombinant DNA technology, DNA sequences are cut for various techniques, and need ligation to join back the strands. The cleaved DNA often has blunt or sticky ends. Sticky ends are easy to ligate but DNA strands with blunt ends are hard to ligate. The linker and adaptor molecules then come into play.

The linker and adapter molecules have both blunt and sticky ends and internal restriction sites as well, which help in DNA ligation.

What is a Linker?

The linkers are short double-stranded sequences of DNA. Both the ends of a linker molecule are blunt in nature. They are chemically synthesized oligonucleotides.

It contains restriction sites for the identification of restriction enzymes. The restriction enzymes cleave the ligated linker and the DNA fragment to produce cohesive ends.

One drawback of linkers is that the DNA fragment sometimes already possesses the restriction sites for producing cohesive ends. This limits the use of linker molecules.

Example: Eco-RI linkers and Sal-I linkers

What is an Adaptor?

An adaptor molecule is a single or double-stranded, chemically synthesized oligonucleotide that is used for the ligation of DNA and RNA strands.

The adaptors can have both blunt ends or one sticky and one blunt end. The sticky end helps in easy ligation of the DNA fragments. The adaptors also have restriction sites that can be used to create new protruding terminuses by the action of restriction enzymes.

One disadvantage of adaptor molecules is that two sticky ends can join to form dimers. This can however be prevented by treating the molecules with alkaline phosphatases.

Uses of adaptor molecules include the addition of a sticky end to cDNA for easy ligation into the plasmids and similar vector ligations.




Linkers are chemically synthesized oligonucleotides that have two blunt ends.

Adaptors are chemically synthesized oligonucleotides with one blunt and one sticky end.


It is double-stranded.

It can be single-stranded or double-stranded.


No single-stranded tail is present.

A single-stranded tail is present at the sticky end.


The DNA fragment might already have a restriction site, limiting the use of linker molecules.

The adaptor molecules tend to join and make dimers.

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Frequently Asked Questions on Difference between Linker and Adaptor

What are adaptors in PCR?

Adaptors in PCR are used to amplify DNA fragments with arbitrary sequences; it also suppresses non-specific DNA interactions.

What is the difference between primers and adapters?

Primers are short molecules that are required for the initiation of DNA synthesis, whereas adaptors are molecules that are required for ligation purposes.

What are adaptors in DNA sequencing?

Sequence adaptors are short DNA sequences that help in fishing unknown DNA sequences during various techniques.

What are blunt and sticky ends?

Blunt ends are non-cohesive ends where both strands terminate with a base pair. On the other hand, sticky ends are cohesive ends that have non-paired nucleotides on one strand, creating an overhang.

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