Oligonucleotides phosphate protection groups

The lipophilicity of this phosphate protective group helps in the chromatographic purification of oligonucleotides. It is removed by the oximate method. ... 

This highly lipophilic group is cleaved with isoamyl nitrite in Pyr/AcOH. The use of a lipophilic 5 -phosphate protective group aids in reverse-phase HPLC purification of oligonucleotides. 

This past year has been highlighted by the development of novel phosphate protecting groups and their use in nucleotide and chiral nucleoside thiophos-phate chemistry. Concise methodologies have been described for cost effective syntheses of oligonucleotide building blocks. Finally, the collection of unnatural nucleotides reported to have been synthesised has been expanded significantly. 

A second method for synthesizing oligonucleotides with specific base sequences, using H-phosphonate monomers, has the advantage over the phosphoramidite method in that the monomers are easier to handle and phosphate protecting groups... 

The deprotection of crude oligodeoxynucleotides traditionally requires a basic treatment that allows the concomitant removal of the exocyclic acyl protecting groups, -elimination of the 2-cyanoethyl phosphate protecting group, and cleavage of the succinic ester bond that links the oligonucleotide to the solid support (Fig. 9). 

Wada T, Sekine M. TSE as a phosphate protecting group in oligonucleotide synthesis. Tetrahedron Lett 35 757-760, 1994. 

DNA synthesis employs silica as a support on which the growing oligonucleotide sequence is built up with the help of base, alcohol, and phosphite-phosphate protecting groups. 

The facile preparation of deoxyribonucleoside phosphoramidites from the selective activation of phosphorodiamidites by N.N-diiso-propylammonium tetrazolide (16) or 1/f-tetrazole (77) provides an excellent tool for the incorporation of new phosphate-protecting groups during oligonucleotide synthesis. Several phosphorodiamidites have recently been prepared, and a few of them are shown in Table 2. 

A number of standard synthetic reference books are available. A review article by Kossell and Seliger discusses protective groups used in oligonucleotide syntheses, including protection for the phosphate group, which is not included in this book, and a series of articles describe various aspects of protective group chemistry. 

The steps involved in automated oligonucleotide synthesis illustrate the current use of protective groups in phosphate chemistry (Scheme 1). Oligonucleotide synthesis involves the protection and deprotection of the 5 -OH, the amino groups on adenine, guanine, and cytosine, and -OH groups on phosphorus. 

The disadvantage of this method is that the dichloridites and monochloridites are sensitive to water and thus could not be used readily in automated oligonucleotide synthesis. This problem was overcome by Beaucage and Caruthers, who developed the phosphoramidite approach. In this method, derivatives of the form R 0P(NR2)2 react with one equivalent of an alcohol (catalyzed by species such as l//-tetrazole) to form diesters, R OP(OR")NR2, which usually are stable, easily handled solids. These phosphoroamidites are easily converted to phosphite triesters by reaction with a second alcohol (catalyzed by l//-tetrazole). Here, again, oxidation of the phosphite triester with aqueous iodine affords the phosphate triester. Over the years, numerous protective groups and amines have been examined for use in this approach. Much of the work has been reviewed. ... 

This group, used for 5 -phosphate protection, has hydrophobicity similar to that of the dimethoxytrityl group and thus was expected to assist in reverse-phase HPLC purification of product from failure sequences in oligonucleotide synthesis. The group is cleaved with Bu4N F in DMSO at 70°. ... 

This lipophilic group, developed for 5 -phosphate protection in oligonucleotide synthesis, is removed with 80% AcOH in 1 h. The related trityloxyethylamino group has been used in a similar capacity for phosphate protection and is also cleaved with 80% AcOH. ... 

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