Prevention of guanine modification and chain cleavage during the solid phase synthesis of oligonucleotides using phosphoramidite derivatives

Abstract

Phosphoramidite reagents can phosphitylate guanine bases at the O⁶-position during solid phase synthesis and serious chain cleavage occurs if the base phosphitylation is not eliminated before the iodine/water oxidation step. This can be accomplished by i) blocking the O⁶-position with a 2-cyanoethyl protecting group for deoxyribonucleotides or with a p-nitrophenylethyl group for ribonucleotides, ii) regenerating the guanine base with water or acetate ions, or iii) using N-methylanilinium trifluoroacetate (TAMA) as the phosphoramidite activator. The effectiveness of these methods was demonstrated by both ³¹P NMR studies and by the synthesis of d(Gp)₂₃G, (Gp)₁₄G, and d-(Gp)₁₃rG sequences.