Nucleoside phosphoramidites synthesis

The chemical synthesis of RNA has the distinct advantage of allowing for site-selective incorporation of modified nucleosides into the oligonucleotide chain. The early phosphodi-ester method developed by Khorana (30) was followed by the H-phosphonate and phosphoramidite approaches (31). Although the H-phosphonate approach has distinct advantages over phosphoramidite synthesis, it is not as widely used. Therefore, the focus of this section will be on the more commonly employed... 

Another type of convertible nucleoside phosphoramidite, a derivative of (5 S)-5 -C-(5-bromo-2-penten-l-yl)-2 -deoxyribosylfuranosyl thymidine (49), has been reported. The synthesis of this phosphoramidite was stereoselective and involved a Sakurai reaction between 5 -C-thymidine aldehyde and allyltrimethylsilane. Seela has reported the synthesis of the ribosyl-phosphoramidite derivatives of 7-bromo- and 7-iodo-8-aza-7-deazapurine-2,6-diamine (50a,b) from advanced synthetic precursors and of the bromo- and iodo-derivatives at the 5-position of uracyl phosphoramidite (51a,b). He further described the effect on base-pair stability due to their incorporation into oligonucleotide duplexes. ... 

Monaharan has developed a versatile synthetic route for the synthesis of 2 -0-[(N, iV-dimethylamino)-oxyethyl] modified purine and pyrimidine nucleoside phosphoramidites (63a-d) to be used as antisense oligonucleotide building blocks. In the syntheses of the purine-based analogues, the (iV, N-dimethylamino)-oxyethyl group was introduced via a 2 -allyloxy nucleoside intermediate, while the pyrimidine-based nucleosides were obtained from the TBDMS-protected 2,2 -anhydro-5-methyluridine via ring opening reaction in the presence of borane and ethylene glycol. The aminoxy derivatives were... 

A new method for the removal of the 5 -0-DMT group during the synthesis of ODNs on a microarray has been studied" which uses all the steps involved in phosphoramidite synthesis, but uses a photogenerated acid (PGA) rather than trichloroacetic acid to deprotect. The photolabile 3 -0- [2-(2-nitrophenyl)propoxy]carbonyl -protected 5 -phosphoramidites (5) have been prepared for the 5 ->3 light-directed synthesis of DNA on microarrays." Developments for the synthesis of high-density DNA probe arrays employ nucleoside monomers protected with 5 -(a-methyl-6-nitropiperonyloxycarbonyl) (MeN-POC) with proximity photolithography, which is currently capable of printing 10 m probe features at a density of 10 probes/cm. "... 

A selective method which involves the selective pivaloyloxymethyl protection of the N1 of pseudouridine followed by methylation at N3 was developed to prepare the 5-benzhydryloxybis(trimethylsilyloxy)silyl, bis(2-acetoxy-ethoxy)me-thyl- protected phosphoramidite derivative (139) of the nucleoside 3-methylpseu-douridine. The methylated pseudouridine phosphoramidite was successfully used in oligonucleotide synthesis for the NMR study of helix 69 of E. coli 23S rRNA. 2-Thiouridines incorporating 2 -modified nucleoside phosphoramidites... 

Vargeese C, Carter Yegge J, Krivjansky S, Settle A, Kropp E, Peterson K, Pieken W. Efficient activation of nucleoside phosphoramidites with 4,5-di-cyanomidazole during oligonucleotide synthesis. Nucleic Acids Res 26 1046-1050, 1998. 

Lyttle MH, Wright PB, Sinha ND, Bain JD, Chamberlin AR. New nucleoside phosphoramidites and coupling protocols for solid-phase RNA synthesis. J Org Chem 56 4608-4615, 1991. 

Pon RT, Damha MJ, Ogilvie KK. Modification of guanine bases by nucleoside phosphoramidite reagents during the solid-phase synthesis of oligonucleotides. Nucleic Acids Res 13 6447-6465, 1985. 

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