Linkers and Adapters - Linkers are short stretches of double stranded DNA of length 8-14 bp and have recognition site for 3-8 RE. These linkers are ligated to blunt end DNA by ligase. Because of the high concentration of these small molecules present in the reaction, the ligation is every efficient when compared with blunt-end ligation of large molecules.

The cohesive ends are generated by digesting the DNA with appropriate RE that generates cohesive ends by cleaving in the linkers. The problem with linker is that the sites for the enzyme used to generate cohesive ends may be present in the target DNA fragment. This drawback limits the use of linkers for cloning.