Polymerizable phosphoramidites with an acid-cleavable linker for eco-friendly synthetic oligodeoxynucleotide purification

Abstract

Methacrylation phosphoramidites containing a linker cleavable with acetic acid were synthesized, and used for synthetic oligodeoxynucleotide (ODN) purification. During automated synthesis, the full-length ODN was tagged with the phosphoramidite. The failure sequences were not. In purification, the full-length ODN was co-polymerized into a polyacrylamide gel, and the failure sequences and other impurities were removed by washing. Pure ODN was cleaved from the gel with 80% acetic acid. Using this method, purification of sequences as long as a 197-mer, which are from the phi29 DNA polymerase gene, and at scales as large as 50 μmol was demonstrated. The products have high purity and the recovery yields are high. The method does not use any type of chromatography and purification is achieved through simple manipulations such as shaking and filtration. Compared with gel electrophoresis and HPLC purification methods, the new technology is less labor-demanding and more amendable for automation, consumes a smaller amount of environmentally harmful organic solvents and requires little energy for solvent evaporation. Therefore, it is ideal for high throughput purification and large scale ODN-based drug purification as well as small scale purification.