Ion-pairing reversed-phase liquid chromatography (IP-RPLC)
is the
reference separation technique for characterizing oligonucleotides
(ONs) and their related impurities. The aim of this study was to better
understand the retention mechanism of ONs, evaluate the applicability
of the linear solvent strength (LSS) retention model, and explore
the potential of ultra-short columns having a length of only 5 mm
for the separation of model ONs. First, the validity of the LSS model
was evaluated for ONs having sizes comprised between 3 and 30 kDa,
and the accuracy of retention time predictions was assessed. It was
found that ONs in IP-RPLC conditions follow an “on–off”
elution behavior, despite a molecular weight lower than that of proteins.
For most linear gradient separation conditions, a column length between
5 and 35 mm was found to be appropriate. Ultra-short columns of only
5 mm were therefore explored to speed up separations by considering
the impact of the instrumentation on the efficiency. Interestingly,
the impacts of injection volume and post-column connection tubing
on peak capacity were found to be negligible. Finally, it was demonstrated
that longer columns would not improve selectivity or separation efficiency,
but baseline separation of three model ONs mixtures was enabled in
as little as 30 s on the 5 mm column. This proof-of-concept work paves
the way for future investigations using more complex therapeutic ONs
and their related impurities.