Shuyuan Yu

Tandem oligonucleotide synthesis using linker phosphoramidites

Multiple oligonucleotides of the same or different sequence, linked end-to-end in tandem can be synthesized in a single automated synthesis. A linker phosphoramidite [R. T. Pon and S. Yu (2004) Nucleic Acids Res., 32, 623–631] is added to the 5′-terminal OH end of a support-bound oligonucleotide to introduce a cleavable linkage (succinic acid plus sulfonyldiethanol) and the 3′-terminal base of the new sequence. Conventional phosphoramidites are then used for the rest of the sequence. After synthesis, treatment with ammonium hydroxide releases the oligonucleotides from the support and cleaves the linkages between each sequence. Mixtures of one oligonucleotide with both 5′- and 3′-terminal OH ends and other oligonucleotides with 5′-phosphorylated and 3′-OH ends are produced, which are deprotected and worked up as a single product. Tandem synthesis can be used to make pairs of PCR primers, sets of cooperative oligonucleotides or multiple copies of the same sequence. When tandem synthesis is used to make two self-complementary sequences, double-stranded structures spontaneously form after deprotection. Tandem synthesis of oligonucleotide chains containing up to six consecutive 20mer (120 bases total), various trinucleotide codons and primer pairs for PCR, or self-complementary strands for in situ formation of double-stranded DNA fragments has been demonstrated.

An improved synthesis of 2-substituted-3-furoic acids leading to an intramolecular Diels–Alder reaction between a dienophile and furan diene both containing an electron withdrawing group

An improved preparation of various 2-substituted-3-furoic acids by lithiation of 2-methyl-3-furoic acid with 2.0 equiv. of butyllithium, and a successful intramolecular Diels–Alder reaction using 0.1 equiv. of methylaluminium dichloride between a dienophile and furan diene, which are both substituted with an electron withdrawing moiety, are described.

Reusable solid-phase supports for oligonucleotides and antisense therapeutics

A general method for oligonucleotide synthesis on reusable solid-phase supports has been developed which will significantly lower the cost of large-scale synthesis. It consists of five steps: 1, nucleoside attachment to an hydroxy derivatized support through a Q-linker (hydroquinone-O,O′-diacetic acid) linker arm; 2, chloro-acetylation of unreacted surface groups; 3, conventional phosphodiester or phosphorothioate oligonucleotide synthesis; 4, cleavage from the support with aqueous or anhydrous ammonia; and 5, support regeneration with methanolic potassium carbonate. The recycling process is fast, fully automatable, and does not require removal of the support from the synthesis column. Fifteen solid-phase supports were evaluated with glycerol-CPG providing the best results. Consecutive syntheses of ISIS 2302, a dGCCCAAGCTGGCATCCGTCA phosphorothioate sequence, on the same synthesis column were performed. A glycerol-CPG synthesis column was satisfactorily used six consecutive times when NH4OH was the cleavage reagent. However, anhydrous NH3 allowed twelve consecutive syntheses without any deterioration in support loading, product quality, or amount of product produced. An improved method for preparing the essential nucleoside-3′-hemiesters of the Q-Linker and an unexpectedly slower rate of cleavage for phosphorothioate DNA vs. phosphodiester DNA are also described.

The regiospecific C-4 lithiation of 2-(tert-butyldimethylsilyl)-3-furoic acid

2-(tert-Butyldimethylsilyl)-3-furoic acid 7 was regiospecifically lithiated at the C-4 position when treated with 2.5 equiv. of butyllithium (at –20 °C) in either tetrahydrofuran or 1,2-dimethoxyethane; trapping of the dianion with a variety of electrophiles provided 2,3,4-trisubstituted furans in good to excellent yield.