Some observations relating to the oximate ion promoted unblocking of oligonucleotide aryl esters.
The action of the N1, N1, N3, N3-tetramethylguanidinium salts of a number of oximes on 5'-O-methoxytetrahydropyranylthymidylyl-(3' leads to 5')-3'-O-methoxytetrahydropyranylthmidine aryl esters (7a-c) in dioxan-water (1:1 v/v) has been investigated. The O-chlorophenyl ester (7a) was unblocked by 4-nitrobenzaldoximate ion ca. 2.5 times as rapidly as the p-chlorophenyl ester (7b) and ca. 25 times as rapidly as the phenyl ester (7c). syn-2-Nitrobenzaldoxime (15a) is the unblocking agent of choice; its conjugate base reacts with 7a and 7b ca. 4 and 2.5 times, respectively, as rapidly as does the conjugate base of its 4-isomer (1). Internucleotide cleavage cannot be detected in the reaction between 2-nitrobenzaldoximate ion and 7a; its extent has been estimated to be no greater than 0.1%. Experiments with the corresponding fully-protected tetranucleoside triphosphate (14a) confirm the greater reactivity of 2- and 4-nitrobenzaldoximate ion and suggest that, if the molecular concentrations both of protected oligonucleotide and oximate ions are maintained, rates of unblocking may not decrease significantly with increasing oligonucleotide chain lengths.
D007202:Indicators and Reagents; D008722:Methods; D009841:Oligonucleotides / Q000138:chemical synthesis*; D010091:Oximes; D013936:Thymidine
D007202:Indicators and Reagents; D009841:Oligonucleotides; D010091:Oximes; D013936:Thymidine