A rapid deprotection procedure for phosphotriester DNA synthesis

Abstract

An equimolar solution of aldoxime and tetramethylguanidine at 70 degrees C removes both the base and phosphate protection from oligonucleotides prepared by solid phase phosphate triester technology. The rate of cleavage from the succinyl linkage commonly used for solid phase synthesis is also increased. The method is simpler, faster and more easily automated than existing methods.

Chemical Synthesis of Oligodeoxyribonucleotides Using N-Unprotected H-Phosphonate Monomers and Carbonium and Phosphonium Condensing Reagents: O-Selective Phosphonylation and Condensation

“…In some cases, reagents of both the types react with the 6-O-position of the guanine and the 4-O-position of the uracil and thymine bases. [14][15][16][17][18][19][20][21][22] Therefore, in the current synthesis of DNA and RNA as well as their analogs, the nucleobases are generally blocked by base-labile protecting groups during chain elongation. 23 However, highly base-sensitive DNA analogs, which readily decompose under the standard basic conditions prescribed for removal of the protecting groups, could not be synthesized with such protection modes.…”

“…It is well known that a pentavalent phosphorus(V)-type phosphorylating reagent (type A) − and a trivalent phosphorus(III)-type phosphitylating reagent (type B) − will react with the exocyclic amino groups of nucleosides (Scheme ). In some cases, reagents of both the types react with the 6- O -position of the guanine and the 4- O -position of the uracil and thymine bases. − Therefore, in the current synthesis of DNA and RNA as well as their analogs, the nucleobases are generally blocked by base-labile protecting groups during chain elongation . However, highly base-sensitive DNA analogs, which readily decompose under the standard basic conditions prescribed for removal of the protecting groups, could not be synthesized with such protection modes.…”

Synthesis and characterization of oligodeoxynucleotides containing O6-methyl-, O6-ethyl-, and O6-isopropylguanine

“…However, the benzoyl group can also be removed by equimolar (£)-2-nitrobenzaldoxime (oxime) and TMG (Patel et al, 1984), and a solution of oxime and TMG in ammonia rapidly removed the benzoyl group. The i1/2 at 22 °C for the removal of the benzoyl group from AÉ-benzoyl-2'-deoxyadenosine by ammonia was 9.6 h, but in a solution of 0.06 M oxime/0.054 M TMG in aqueous ammonia the Z,/2 for removal of the benzoyl group was only 1.8 h (Table III).…”

Modification of guanine bases by nucleoside phosphoramidite reagents during the solid phase synthesis of oligonucleotides

“…For example, substituted side-products on guanine, thymine and uracil bases are known to occur when either arylsulphonyl condensing reagents (11)(12)(13) or phosphorylating reagents (14)(15)(16)(17)(18) are used. Although some of these modifications can be reversed by extended treatment with aldoximate reagents (11,19) at the end of the synthesis, the complete elimination of these side-products in long oligonucleotides is unproven.…”