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. 1981 Sep 25;9(18):4611–4626. doi: 10.1093/nar/9.18.4611

Some observations relating to the oximate ion promoted unblocking of oligonucleotide aryl esters.

C B Reese, L Zard
PMCID: PMC327462  PMID: 7301585

Abstract

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.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Arentzen R., Reese C. B. The phosphotriester approach to oligonucleotide synthesis: Preparation of oligo- and poly-thymidylic acids. J Chem Soc Perkin 1. 1977;4:445–460. doi: 10.1039/p19770000445. [DOI] [PubMed] [Google Scholar]
  2. Chattopadhyaya J. B., Reese C. B. Chemical synthesis of tridecanucleoside dodecaphosphate sequence of SV40 DNA. Nucleic Acids Res. 1980 May 10;8(9):2039–2053. doi: 10.1093/nar/8.9.2039. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Gait M. J., Singh M., Sheppard R. C., Edge M. D., Greene A. R., Heathcliffe G. R., Atkinson T. C., Newton C. R., Markham A. F. Rapid synthesis of oligodeoxyribonucleotides. IV. Improved solid phase synthesis of oligodeoxyribonucleotides through phosphotriester intermediates. Nucleic Acids Res. 1980 Mar 11;8(5):1081–1096. doi: 10.1093/nar/8.5.1081. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Gough G. R., Singleton C. K., Weith H. L., Gilham P. T. Protected deoxyribonucleoside-3' aryl phosphodiesters as key intermediates in polynucleotide synthesis. Construction of an icosanucleotide analogous to the sequence at the ends of Rous sarcoma virus 35S RNA. Nucleic Acids Res. 1979 Apr;6(4):1557–1570. doi: 10.1093/nar/6.4.1557. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Reese C. B., Saffhill R., Sulston J. E. 4-methoxytetrahydropyran-4-yl. A symmetrical alternative to the tetrahydropyranyl protecting group. Tetrahedron. 1970 Feb;26(4):1023–1030. doi: 10.1016/s0040-4020(01)98779-4. [DOI] [PubMed] [Google Scholar]

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