A Study on Synthesis and Upscaling of 2′-<i>O</i>-AECM-5-methyl Pyrimidine Phosphoramidites for Oligonucleotide Synthesis

Abstract

2′-O-(N-(Aminoethyl)carbamoyl)methyl-modified 5-methyluridine (AECM-MeU) and 5-methylcytidine (AECM-MeC) phosphoramidites are reported for the first time and prepared in multigram quantities. The syntheses of AECM-MeU and AECM-MeC nucleosides are designed for larger scales (approx. 20 g up until phosphoramidite preparation steps) using low-cost reagents and minimizing chromatographic purifications. Several steps were screened for best conditions, focusing on the most crucial steps such as N3 and/or 2′-OH alkylations, which were improved for larger scale synthesis using phase transfer catalysis (PTC). Moreover, the need of chromatographic purifications was substantially reduced by employing one-pot synthesis and improved work-up strategies.

Keywords

• 2′-<i>O</i>-(N-(aminoethyl)carbamoyl)methyl modification
• phase transfer catalysis (PTC)
• 5-methyluridine
• 5-methylcytidine
• oligonucleotides
• alkylation