Synthetic oligonucleotide separations by mixed-mode reversed-phase/weak anion-exchange liquid chromatography

• Reversed-phase/weak anion-exchanger was evaluated for synthetic oligonucleotide separations.
• This mixed-mode phase can be used in various (buffer, pH, organic modifier) gradient elution modes.
• Better separation between structurally related oligos than in ion-pair RPLC was observed.
• Single, double, triple nucleotide deletions were well resolved.
• Single nucleotide exchanges were mostly resolved, especially if guanine base was involved.

Synthetic oligonucleotides gain increasing importance in new therapeutic concepts and as probes in biological sciences. If pharmaceutical-grade purities are required, chromatographic purification using ion-pair reversed-phase chromatography is commonly carried out. However, separation selectivity for structurally closely related impurities is often insufficient, especially at high sample loads. In this study, a “mixed-mode” reversed-phase/weak anion exchanger stationary phase has been investigated as an alternative tool for chromatographic separation of synthetic oligonucleotides with minor sequence variations. The employed mixed-mode phase shows great flexibility in method development. It has been run in various gradient elution modes, viz. one, two or three parameter (mixed) gradients (altering buffer pH, buffer concentration, and organic modifier) to find optimal elution conditions and gain further insight into retention mechanisms. Compared to ion-pair reversed-phase and mere anion-exchange separation, enhanced selectivities were observed with the mixed-mode phase for 20–23 nucleotide (nt) long oligonucleotides with similar sequences. Oligonucleotides differing by 1, 2 or 3 nucleotides in length could be readily resolved and separation factors for single nucleotide replacements declined in the order Cytosine (C)/Guanine (G) > Adenine (A)/Guanine ∼ Guanine/Thymine (T) > Adenine/Cytosine ∼ Cytosine/Thymine > Adenine/Thymine. Selectivities were larger when the modification was at the 3′ terminal-end, declined when it was in the middle of the sequence and was smallest when it was located at the 5′ terminus. Due to the lower surface area of the 200 Å pore size mixed-mode stationary phase compared to the corresponding 100 Å material, lower retention times with equal selectivities under milder elution conditions were achievable. Considering high sample loading capacities of the mixed-mode anion-exchanger phase, it should have great potential for chromatographic oligonucleotide separation and purification.