Amidites
Polymerizable deoxynucleoside (PdN including PdA, PdC, PdG and PdT) phosphoramidites are useful for the synthesis of long oligos. Isolation of full-length 400-mer oligos from the complex mixture of chemical synthesis using the catching-by-polymerization (CBP) technology enabled by PdN has been demonstrated recently (ChemRxiv). Many genes and genomes contain difficult elements such as long repeats and stable higher order structures, and thus are difficult or impossible to construct using known technologies such as PCR assembly. The long oligos made available by the PdN phosphoramidites and CBP oligo purification technology provide an opportunity to address the problem. We proudly offer the PdN phosphoramidites to the communities of synthetic biology, protein engineering, and beyond.
During oligo (i.e. oligodeoxynucleotide, ODN) synthesis, the failure sequences are capped with Ac2O and full-length sequences are tagged with a PdN phosphoramidite (Figure). After cleavage and deprotection, the crude contains the full-length ODN (the desired product) with a polymerizable group (i.e. methacryl amide group, red portion in PdN in the Figure), failure ODNs and small molecules. For purification, the full-length ODN is co-polymerized into a polyacrylamide gel. Failure ODNs and small molecules are washed away. The product is cleaved and extracted, and then precipitated with nBuOH.