Fast oligonucleotide deprotection

McBride LJ, Kierzek R, Beaucage SL, Caruthers, MH. Amidine protecting groups in oligonucleotide synthesis. J Am Chem Soc 108 2040-2048, 1986. Vinayak R, Anderson P, McColum C, Hampel A. Chemical synthesis of RNA using fast oligonucleotide deprotection chemistry. Nucleic Acids Res 20 1265-1269, 1992. 

Vu H, McColum C, Jacobson K, Theisen P, Vinayak R, Spiess E, Andras A. Fast oligonucleotide deprotection phosphoramidite chemistry for DNA synthesis. Tetrahedron Lett 31 7269-7272, 1990. 

The recent revolution in molecular biology has brought with it an increased demand for the efficient chemical synthesis of short DNA segments, called oligonucleotides. The problems of DNA synthesis are similar to those of protein synthesis (Section 26.10) but are more difficult because of the complexity of the nucleotide monomers. Each nucleotide has multiple reactive sites that must be selectively protected and deprotected at the proper times, and coupling of the four nucleotides must be carried out in the proper sequence. Automated DNA synthesizers are now available, however, that allow the fast and reliable synthesis of DNA segments up to 200 nucleotides in length. 

Recently, Leuck et al. [282] have described an acyl-type anchor for the fast and efficient preparation of 3 -aminoalkyl oligonucleotides based on the 2-hydroxy-methyl-6-nitrobenzoyl group (Figure 19.12). The linker is prepared from 6-nitroph-thalide by acylation of the respective aminoalcohol and attachment to LCAA-CPG through the benzylic hydroxyl via the succinyl group. Cleavage is achieved under conditions of basic hydrolysis by the intramolecular attack of the liberated hydroxyl onto the amide carbonyl with the expulsion of the amine. Complete detachment of the oligomer requires 2 h at 55 °C in concentrated ammonia or 30 min at 65 °C in 40% aqueous methylamine-concentrated aqueous ammonia (l lv/v), or can be accomplished at room temperature within 24 h in concentrated ammonia. The new anchor was shown to be superior to the phthalimido support [279] in terms of product yield and deprotection time. 

Reddy MP, Hanna NB, Farooqui F. Fast cleavage and deprotection of oligonucleotides. Tetrahedron Lett 35 4311-4314, 1994. 

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