Oligodeoxynucleotides protecting groups

Phosphorus protection. The protecting group is stable to acid and is removed by fragmentation using aqueous NH4OH. It is introduced by the phosphoramidite approach and is useful for internucleotidic bonds in oligodeoxynucleotide synthesis. 

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). 

Andrus A, Beaucage SL. 2-Mercaptobenzothiazole An improved reagent for the removal of methylphosphate protecting groups from oligodeoxynucleotide phosphotriesters. Tetrahedron Lett 29 5479-5482, 1988. 

Sekine developed 8-thioxodeoxyadenosine residues in place of the proto-nated deoxycytidines to synthesise triplex forming oligodeoxynucleotides. The phosphoramidite precursor was prepared from 2-deoxyadenosine, which upon bromination, thionylation and subsequent protecting group manipulations was converted to the 6-7V-carbamoyl-8-thiooxodeoxyadenosine 3 -phosphoramidite (33). This phosphoramidite was used for DNA... 

The QCM was also used to monitor the electrochemical removal of protecting groups (hydroquinones) from the hydro-quinone monoester of thioacetic acid and the 12,12 -dithiobis-(dodecanoic acid hy-droquinone monoester) SAMs to form carboxylic acid-terminated SAMs for immobilizing the oligodeoxynucleotides [23]. 

Jones, R A., Fritz, H J., and Khorana, H G. (1978) Studies on polynucleotides 147 Use of the lipophilic rerr-butyldiphenylsilyl protecting group in synthesis and rapid separation of polynucleotides. Biochemistry 17, 1268-1278 Mishra, R. K. and Misra, K. (1988) Protecting groups as purification tool in large-scale synthesis of small oligodeoxynucleotides Indian J, Chem Sect. B, 27B, 817-820. 

Release the oligodeoxynucleotide from the support and remove the base and phosphate protection groups by treatment with 3% (v/v) ammonia for 3 h at 65 C. Remove ammonia by evaporation to dryness in vacuo. Dissolve the residue in ethanol/water (1 1) and evaporate the solvent to dryness in vacuo-, repeat this procedure. 

The high quantum efficiency and respectable protection and deprotection yields obtained for the methyl-substituted 2-(o-nitrophenyl)ethoxycarbonyl photoprotecting group prompted Pirrung et al. to use this protecting group for the solid-phase synthesis of oligodeoxynucleotides. 

It has been demonstrated that it is possible to insert paramagnetic probes into nucleic acids in a site- and type-specific manner. To this end, the 2,2,6,6-tet-ramethyl-l-piperidinyloxy free radical-labelled phosphoramidites of 2-amino-2 -deoxyadenosine, 2 -deoxyadenosine, 2 -deoxycytosine and 5-methyl-2 -deoxycytosine have been prepared and used for the automatic synthesis of mono-labeled oligodeoxynucleotides which proved active by EPR. The phosphoramidites carry a nitroxide spin-label directly linked to the exocyclic amino group. Starting from appropriately protected 2 -deoxyguanosine or 2 -deoxyinosine, the precursors to (66a) and (66b) were obtained by nucleophilic... 

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