The 9‐fluorenylmethyloxycarbonyl group as a 5′‐OH protection in oligonucleotide synthesis

Abstract

Oligo-DNAs are synthesized on a solid support using the 9-fluorenylmethyloxycarbonyl group as a 5'-OH base labile protection. The synthesis of the pure protected nucleotides, a relevant phosphoramidite-type strategy of coupling, and the optimization of the deprotection steps are described. This new synthetic method is an alternative to the standard protocol that avoids acidic conditions.

Solid-phase synthesis of oligonucleotides containing site-specific N-(2'-deoxyguanosin-8-yl)-2-(acetylamino)fluorene adducts using 9-fluorenylmethoxycarbonyl as the base-protecting group

“…As part of these initial studies, we also investigated the effect of the capping step on solid-phase assembly using the Fmoc phosphoramidites, since other studies reported an instability of Fmoc to (dimethylamino)pyridine (Ma & Sonveaux, 1989;Webb & Matteucci, 1986;Kuijpers et al, 1990), the capping catalyst used in our synthesizer. We conducted additional syntheses of the unmodified 6-mer and the AAF-6-mer by excluding the capping step from the standard CED cycle.…”

Wang Linker Free of Side Reactions

“…The first Fmoc-amino acid was incorporated into both resins using the symmetrical anhydride in the presence of catalytic amounts of DMAP, while DIPCDI-OxymaPure was used for the rest of the residues . The symmetrical anhydride was a satisfactory method for introducing the first amino acid on the OH-BTL resin (Table ), as demonstrated by means of UV analysis of the piperidine–dibenzofulvene adduct . The peptide content of the final peptide resin calculated by amino acid analysis (AAA) was shown to be superior for the OH-BTL resin for all three peptides (Table ).…”

Reactions at Oxygen Atoms

“…After each chain elongation using 98, the Fmoc group is removed in basic media such as Et 3 N/py [130],piperidine/MeCN (5:95) [34],morpholine/MeCN (3:7) [34], or 0.1 M DBU/MeCN [132] to give 99 (Scheme 51). In this deprotection, the efficacy has been studied by varying the combination of base and solvent [131]; it is concluded that DBU/MeCN (or py) is the best combination.…”

“…The base-catalyzed fragmentation of the Fmoc group is explained by an initial removal of the H-9 atom, which is acidic in nature (Scheme 50). A problem remaining in this protection is the liberation of highly reactive dibenzofulvene [131]. In the actual synthesis of ribonucleotides, the Fmoc group is introduced by treatment of alcohols with Fmoc chloride (Fmoc-Cl) (see 96~97) [132], and the resulting 5'-carbonates are phosphitylated (see Sect.…”