Oligonucleotide linkers phosphorylation

Linkers for the Synthesis of Phosphorylated, Thiophosphorylated or Other Related Oligonucleotides... 

Fig. 8. Easily cleavable nucleoside linkages. Fig 1 A disulfide linkage that yields 3 -phosphorylated products (39) Figs. 2. and 3. Linkages containing a 2-(2-nitrophenyl)ethyl linker, which can be cleaved by DBU, for the synthesis of oligonucleotides with either free or phosphorylated 3 -ends (40) Fig. 4. The oxalyl-CPG linkage (41), which is the most easily hydrolyzable linkage avmlable.

Except for some special applications (see below), the conventional linker method of cloning is now largely superseded by a simpler and more efficient adapter method. In this improved method, two synthetic oligonucleotides are annealed to form a restriction site (e.g., EcoRI) in such a way that it has the necessary cohesive termini on one end, while the other end is blunt-ended and 5 -phosphorylated to allow ligation to the DNA (20,21). 

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