Gram-scale purification of phosphorothioate oligonucleotides using ion-exchange displacement chromatography.

The purification of oligonucleotides by ion-exchange displacement chromatography is demonstrated on the gram-scale. Using a 50 mmD x 100 mmL (203 ml) column operated in the displacement mode, 1.2 g of a 24mer phosphorothioate oligonucleotide was purified. Product yield for this separation was 70% (780 mg) at a purity of 96.4% and the mass balance recovery of all oligonucleotide was 97.5%. The displacement purification of four additional phosphorothioate oligonucleotides ranging in length from 18 to 25 bases is also demonstrated on the semi-preparative (10-50 mg) scale. All of these oligonucleotides were purified using similar displacement conditions and typical results were 60% yield at 96% purity. The displacement portion of these separations required <15 min and total cycle time including equilibration, feed loading and regeneration can be performed in under 30 min. These results seem to indicate that displacement chromatography may be amenable to generalizations in separation protocol that would greatly reduce the effort required to obtain an optimized purification scheme for moderately long oligonucleotides.

Gibbs free energy of adsorption for biomolecules in ion-exchange systems.

The Gibbs free energy of adsorption (delta G0ads) was estimated for several amino acids, peptides and proteins in a cation-exchange system. Using the steric mass action formalism that describes biomolecular adsorption in ion-exchange systems, the delta G0ads was chromatographically determined under infinitely dilute conditions. The delta G0ads measured for seven globular proteins ranged from -5.7 to -13.9 kcal/mol. The average bond energy (defined as delta G0ads divided by the number of bonds formed between the protein and the surface) for these proteins varied from -1.1 to -1.7 kcal/mol. These bond energies were found to be comparable to the bond energies for lysine and arginine (-1.1 and -1.5 kcal/mol, respectively), the amino acids which primarily contribute to the cation-exchange of proteins. In contrast, an elevated average bond energy of -2.6 kcal/mol was observed for two peptides and protamine (a polypeptide) suggesting that synergistic binding may play a role for unstructured macromolecules, but not for globular proteins.

Cation-exchange displacement chromatography of proteins with protamine displacers: effect of induced salt gradients.

Protamine was investigated for its utility as a protein displacer in cation-exchange systems. Although the protamine solution contained several variants of the molecule, the high affinity of all of the components in this heterogeneous biopolymer enabled it to act as an efficient protein displacer. To facilitate parameter estimation of the protamine, a preliminary purification was carried out by preparative elution chromatography. Chromatographic parameters of both the feed proteins and protamine displacer were obtained for use in a multicomponent steric mass action ion-exchange displacement model. Model simulations were compared to displacement results under both moderate and intense induced salt gradient conditions. In both cases, excellent agreement was obtained between the displacement experiments and theoretical predictions. In addition, these studies serve to dramatize the importance of induced salt gradients in ion-exchange displacement systems.