Ultrafast Cleavage and Deprotection of Oligonucleotides Synthesis and Use of C^Ac Derivatives

Abstract

We have investigated the use of alkylamines as fast cleavage and deprotection reagents for the solid phase synthesis of oligonucleotides and found methylamine/ammonium hydroxide (or methylamine) as an efficient reagent. The transamination side product formed with the commonly used dC^bz has been eliminated by the use of dC^Ac phosphoramidite. This system has successfully been used in the synthesis of oligonucleotides and oligonucleoside phosphorothioates. DMT dC^Ac hydrogen phosphonate and DMT ribo C^Ac-2′-O Me phosphoramidite also have been prepared and used in the synthesis of oligonucleotides.

Notes

It is available from Beckman Instruments and Glen Research under the name “UltraFAST Cleavage and Deprotection System”

Ammonium hydroxide was used as one of the components to increase the solubiliy of DNA, especially, when a nonaqueous reagent such as propylamine was used

The reactivity of methylamine/ammonium hydroxide was very close to that of methylamine itself. However, we have chosen methylamine/ammonium hydroxide since this reagent was more compatible with certain polymer materials used in packaging

Phosphoramidites are usually stored at -20°C to 4°C. However, we performed the accelerated stability at 37°C in order to obtain quick results