Solid-phase oligonucleotide synthesi

The protected nucleoside-3-phosphoramidite monomer units such as 671 are used in the solid-phase oligonucleotide synthesis. In the 60mer synthesis, 104 allylic protective groups are removed in almost 100% overall yield by the single Pd-catalyze reaction with formic acid and BuNH2[432], N,(9-protection of uridine derivatives was carried out under pha.se-transfer conditions[433]. 

SCHEME 34. synthesis of protected phosphoramidites suitable for solid-phase oligonucleotide synthesis. 

An anionic ligand effect in iron porphyrin complex-catalyzed competitive epoxidations of cis- and frawi-stilbenes by BU4NHSO5 has been studied in detail . Oxidation of the thiophosphite to the thiophosphate in solid phase oligonucleotide synthesis using BU4NHSO5 was also reported. ... 

F. Bardella, R. Eritja, E. Pedroso and E. Giralt, Gel-phase -31-NMR-a new analytical tool to evaluate solid-phase oligonucleotide synthesis, Bioorg. Med. Chem. Lett., 1993, 3, 2793-2796. 

Palladium-mediated (Sonogashira) coupling [332] of 5-iodouracil with alkynes can be performed under mild reaction conditions, and is compatible with the supports, linkers, and protective groups used in solid-phase oligonucleotide synthesis (Entries 12 and 13, Table 15.28). This coupling reaction has been used to prepare modified oligonucleotides on polystyrene and on CPG. The reaction of halopyrimidines with amines to yield aminopyrimidines is discussed in Section 10.1.2. 

Figure 16.12. Solid-phase oligonucleotide synthesis using phosphoramidites [83],...

A supported sulfide source has been demonstrated by Zhang et al.16 to synthesize oligonucleotide phosphorothioates (entry 12). Aminodithiazole-thione attached to a methacrylate-ethyleneglycol copolymer is used to efficiently convert a nucleotide phosphite to a phosphorothioate. The product nucleotide possesses protecting groups suitable for solid-phase oligonucleotide synthesis and thus is a valuable building block for nucleic acid therapeutics. 

An improved protocol for the efficient conversion of inosine into its 3 -phosphoramidite synthons for solid-phase oligonucleotide synthesis has been described. This procedure, which almost doubled the literature reported overall yields starting from inosine, was optimized for scale-up to multigram quantities. The portion-wise addition of DMT-Cl to a solution of inosine in DMSO and pyridine prevented multiple-site protections, which was also reported to occur in the presence of DMAP or triethylamine. Treatment with TBDMSCl in the presence of silver nitrate and pyridine in THF offered a mixture of the 2 - and 3 -substituted nucleosides from which the 5 -0-dimethoxytrityl-2 -0-tert-butyl-dimethylsilyl-protected inosine was crystallized in ethyl acetate. The mother liquor was enriched with the 2 -isomer by treatment with triethylamine in methanol. Standard conditions for phosphitylation were then applied to yield... 

The only exception was an attempt at the 5 -to-3 solid-phase oligonucleotide synthesis using nucleoside 3 -H-phosphonate monoesters, polymer-bound through a trityl-type linker, and oxidative coupling conditions (HgCl2) [123], The H-phosphonates were produced by phosphitylation of the polymer-bound N-unpro-tected nucleoside with phosphorus trichloride followed by hydrolysis by aqueous pyridine [61c]. However, despite some advanced features [124] the stepwise yields were comparable with those in the contemporary phosphodiester method-that is they were too low for the method to be truly competitive. 

However, the best results were obtained when the first nucleoside was attached via the succinyl linker onto the ethylenediamine-treated polydimethylacrylamide resin (Figure 19.4) [178,179] or Enzacryl Gel K-2 [177]. The polydimethylacrylamide support has been utilized by Gait et al. [180] in the automated solid phase oligonucleotide synthesis by the phosphotriester method on a peptide synthesizer. 

Many other polymers have been tried as supports for solid phase oligonucleotide synthesis. Even before the first use of polyacrylamide for oligonucleotide synthesis,... 

Linkers and Anchor Croups for Solid Phase Oligonucleotide Synthesis 545... 

Linkers and Anchor Groups for Solid Phase Oligonucleotide Synthesis 561... 

Pon RT, Usman N, Ogilvie KK. Derivatization of controlled pore glass beads for solid-phase oligonucleotide synthesis. Biotechniques 6 768-775. 

Damha MJ, Giannaris PA, Zabarylo S. An improved procedure for derivati-zation of controlled pore glass beads or solid-phase oligonucleotide synthesis. Nucleic Acids Res 18 3813-3821, 1990. 

Pon RT, Yu S. Hydroquinone-0,0 -diacetic acid as a more labile replacement for succinic acid linkers in solid-phase oligonucleotide synthesis. Tetrahedron Lett 38 3327-3330, 1997. 

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