A comparative study of ion exchange vs. ion pair chromatography for preparative separation of oligonucleotides

Oligonucleotides are commonly purified using either ion exchange chromatography (IEX) or ion-pair reversed-phase liquid chromatography (IP-RPLC). This study compares the purification of a crude 20-mer oligonucleotide (ON) using both methods under preparative conditions. Two variables were investigated during the separation: column load and gradient slope. Although the IEX purifications using agarose-based resins had longer cycle times, this was compensated by the high loadability compared to the silica-based IP-RPLC media. This resulted in both higher productivity and lower solvent consumption at all evaluated purities, ranging from 95 % to 99 %, at optimal productivity levels. At 95 % purity, IEX achieved more than twice the productivity, and at 99 % purity, the productivity was seven times higher. Additionally, solvent consumption was significantly reduced, with IEX consuming only one-third to one-tenth of the solvents compared to IP-RPLC at purities from 95 % to 99 %.