Glen Report 11.25: Alternatives to Expedite Monomers

Expedite Monomers

The monomers protected with t-butyl-phenoxyacetyl groups (Expedite monomers) have proved to be popular and are used predominantly for the two applications covered below. With their very base-labile protecting groups, oligonucleotides produced using Expedite monomers can be deprotected under mild conditions using ammonium hydroxide for 2 hours at room temperature, or rapidly in 15 minutes at 55°C. Glen Research supplies systems that are equivalent or superior in performance, as described below.

UltraMILD Deprotection

The synthesis of labelled oligonucleotides has become a standard procedure in many laboratories and many labelling reagents are now available as phosphoramidites. In some instances the labelling reagents are not stable to the alkaline conditions required for removal of the base protecting groups on the standard dA, dC and dG monomers. Glen Research is pleased to offer a set of monomers using phenoxyacetyl (Pac) protected dA, 4-isopropyl-phenoxyacetyl (iPr-Pac) protected dG, and acetyl (Ac) protected dC. These monomers can be used with sensitive labelling reagents such as TAMRA, Cy5 and HEX since cleavage and deprotection can be carried out in 2 hours at room temperature with ammonium hydroxide or 0.05M potassium carbonate in anhydrous methanol. For additional ordering information, see the Catalog under UltraMILD Synthesis.

Figure 1

UltraFAST Deprotection

The Glen Research line of reagents for DNA synthesis includes Ac-dC-CE Phosphoramidite and the corresponding Ac-dC support, the basis for the UltraFAST cleavage and deprotection system that allows 10 minute deprotection of oligonucleotides. This system requires that the normal benzoyl (Bz) protection of the dC monomer be replaced with acetyl (Ac). The three other monomers remain unchanged. This seemingly minor change in protecting group leads to oligonucleotides which can be cleaved and deprotected in 10 minutes using AMA which is a 50:50 mixture of aqueous Ammonium hydroxide and aqueous MethylAmine. With AMA the cleavage of the oligonucleotide from the support is accomplished in 5 minutes at room temperature. The deprotection step is carried out at 65°C for a further 5 minutes. Deprotection can also be carried out at lower temperatures as follows. In all cases, no base modification has been observed.

5 min 65°
10 min 55°
30 min 37°
90 min 25°

Please note the new lower prices for the UltraMILD dA and dG monomers.

Product Information

UltraMild Base Protection Phosphoramidites and Supports