Oligo protecting groups

Kukula H,Veit S, Godt A (1999) Eur J Org Chem 277 Synthesis of monodisperse oligo-PEs using orthogonal protecting groups with different polarity for terminal acetylene units... 

In peptide synthesis the use of a suitable protection for the N-terminal amino group is required not only to prevent the formation of a complex mixture of oligo- and cyclo-peptides, but an additional demand on the functionality applied for this purpose is that it should prevent possible racemization of the activated amino acid. Racemization usually takes place via an intermediate oxazolone (7) that forms readily from A -acyl-protected amino acids (Scheme 2). This side reaction can be mostly suppressed by using a carbamate as an N-terminal-protecting group. Therefore, nearly all blocking functions currently applied in this field are of the urethane type. 

Sutherland and coworkers used ethyl carboxylate protecting groups when they reacted an oligo(ethyleneoxy)bis(carbamate) with a ditosylate or dihalide... 

Figure 2 Base protecting groups typically used for the synthesis of oligo-ribonucleotides.

Rao MV, Reese CB, Schehlmann V, Yu PS. Use of the l-(2-fluorophenyl)-4-methoxypiperidin-4-yl (Fpmp) protecting group in the solid-phase synthesis of oligo- and poly-ribonucleotides. J Chem Soc Perkin Trans I 43-55, 1993. 

Figure 2.5 Solid Phase DNA Synthesis Cycle (Contd.). Most frequently used base protecting groups are shown Bz Af-6 benzoyl (adenine), W-4 benzoyl (cytosine) N-2 isobutyroyl (guanine). All are base sensitive. DNA chain is built up from 3 to 5 on controlled-pore glass (CPG) bead solid support. Post global deprotection and resin removal, the desired product oligo-/polydeoxynucleotide is then separated initially by precipitation by means of an agent such as ethanol and purified finally by reversed phase liquid chromatography, or ion exchange chromatography as appropriate (see later in Chapter 2).

Chemical synthesis of oligo-Zpolysaccharides demands the use of orthogonal protecting groups capable of selective removal. Benzyl ether protecting groups have seen widespread use... 

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