Oxalyl-CPG: a labile support for synthesis of sensitive oligonucleotide derivatives

Abstract

A procedure is described for linking nucleosides covalently to controlled pore glass or cross-linked polystyrene supports by means of an oxalyl anchor. Though stable to triethylamine and diisopropylamine, the nucleoside-oxalyl link can be cleaved within a few minutes at room temperature with ammonium hydroxide in methanol. This new anchor can be used in automated synthesis of conventional oligonucleotides. The primary value, however, is that it enables one to employ solid support methodology to synthesize a variety of base-sensitive oligonucleotide derivatives, as illustrated here by synthesis of oligomers with base protecting groups intact and with methyl phosphotriester groups at the internucleoside links.

Pyrenylmethyldeoxyadenosine: A 3′‐Cap for Universal DNA Hybridization Probes

“…The sarcosine linker prevents loss of oligonucleotide chains from the support through intramolecular attack of the deprotonated linker amide on the 3'-ester functionality under the basic conditions required for the onsupport nucleophilic displacement. An oxalyl linker ( Figure S2, Supporting Information) [35] proved too labile towards these conditions. Support 31 was treated with 1-(aminomethyl)pyrene (Py), 2-(hydroxymethyl)anthraquinone, and 4-hydroxystilbene in the presence of DIEA, yielding supports of general structure 32.…”

Synthesis and properties of oligonucleotides containing aminodeoxythymidine units

“…for 11-13) or concentrated ammonium hydroxide, 55°C, 20 min (when a succinyl anchor was used, for [14][15]. In cases where phosphoryl protecting groups (preparation of 6-10 and precursors of 18,19) or base protecting groups (preparation of 22,23) were to be removed, the solid supported oligomers were treated with concentrated ammonium hydroxide at 55°C for 17 h. The methyl phosphonate derivatives (20, and precursors of 21, 24) were cleaved from the support by successive treatment with hydrazine/acetic acid/pyridine and ethylenediamine/ethanol as described by Miller.28 This treatment also removed the ,B-cyanoethyl protecting group at the phosphoramidate linkage. After filtration and concentration, the anionic oligonucleotides were isolated by ion exchange chromatography and further purified by reversed Labelling with Fluorescein A solution of fluorescein isothiocyanate (Aldrich) (10 1l of 10% solution in DMF) was added to the aminooligonucleotide (0.25 A260 units) in 0.2 M borate buffer, pH 8.6, 100 il).…”

Vinyldeoxyadenosine in a Sarcin−Ricin RNA Loop and Its Binding to Ricin Toxin A-Chain

“…This was reduced by allowing the deprotection reaction for 4 hrs at room temperature instead of the standard 16-18 hrs. This problem was also encountered in our initial synthesis but was circumvented by using a 3'-end nucleoside that was derivatized on an oxalyl-controlled pore glass (CPG) solid support (26) instead of the standard succinyl-CPG. The former has the advantage of being labile to ammonia-free cleavage with basic reagents like triethylamine which are not nucleophilic.…”