Large-scale purification of antisense oligonucleotides by high-performance membrane adsorber chromatography

Chromatographic approaches for the characterization and quality control of therapeutic oligonucleotide impurities

Phosphorothioate (PS) oligonucleotides are a rapidly rising class of drugs with significant therapeutic applications. However, owing to their complex structure and multistep synthesis and purification processes, generation of low-level impurities and degradation products are common. Therefore, they require significant investment in quality control and impurity identification. This requires the development of advanced methods for analysis, characterization and quantitation. In addition, the presence of the PS linkage leads to the formation of chiral centers which can affect their biological properties and therapeutic efficiency. In this review, the different types of oligonucleotide impurities and degradation products, with an emphasis on their origin, mechanism of formation and methods to reduce, prevent or even eliminate their production, will be extensively discussed. This review will focus mainly on the application of chromatographic techniques to determine these impurities but will also discuss other approaches such as mass spectrometry, capillary electrophoresis and nuclear magnetic resonance spectroscopy. Finally, the chirality and formation of diastereomer mixtures of PS oligonucleotides will be covered as well as approaches used for their characterization and the application for the development of stereochemically-controlled PS oligonucleotides.

New Q membrane scale-down model for process-scale antibody purification

Process-scale antibody production requires polishing steps with extremely high product throughput and robust operation. In this communication, the Sartobind Q membrane adsorber for process-scale antibody production is evaluated as an alternative to Q column chromatography. Although the capacity seen with large-scale membrane adsorbers is competitive with column chromatography, the same throughput is not achieved with the current scale-down models. The operational issues currently found in membrane scale-down models, including backpressure, which significantly compromises the membrane's capacity, were examined. A new scale-down model was designed to mimic the liquid flow path found in the large-scale capsule, and a new process capacity equivalent at both small and large scale was successfully achieved. Results of a 4-model virus study with a redesigned Sartobind Q absorber scale-down model at the new process capacity are presented.

Characterization of therapeutic oligonucleotides using liquid chromatography with on-line mass spectrometry detection

A method for the analysis and characterization of therapeutic and diagnostic oligonucleotides has been developed using a combination of liquid chromatography and mass spectrometry (LC-MS). The optimized ion-pairing buffers permit a highly efficient separation of native and chemically modified antisense oligonucleotides (AS-ODNs) from their metabolites or failure synthetic products. The mobile phases were MS compatible, allowing for direct and sensitive analysis of components eluting from the column. The method was applied for the quantitation and characterization of AS-ODNs, including phosphorothioates and 2'-O-methyl-modified phosphorothioates. Tandem LC-MS analysis confirmed the identity of the oligonucleotide metabolites, failure products, the presence of protection groups not removed after synthesis, and the extent of depurination or phosphorothioate backbone oxidation.

Performance of a membrane adsorber for trace impurity removal in biotechnology manufacturing

Membrane adsorbers provide an attractive alternative to traditional bead-based chromatography columns used to remove trace impurities in downstream applications. A linearly scalable novel membrane adsorber family designed for the efficient removal of trace impurities from biotherapeutics, are capable of reproducibly achieving greater than 4 log removal of mammalian viruses, 3 log removal of endotoxin and DNA, and greater than 1 log removal of host cell protein. Single use, disposable membrane adsorbers eliminate the need for costly and time consuming column packing and cleaning validation associated with bead-based chromatography systems, and minimize the required number and volume of buffers. A membrane adsorber step reduces process time, floor space, buffer usage, labor cost, and improves manufacturing flexibility. This "process compression" effect is commonly associated with reducing the number of processing steps. The rigid microporous structure of the membrane layers allows for high process flux operation and uniform bed consistency at all processing scales.

Calorimetric investigation of the adsorption of nitrogen bases and nucleosides on a hydrophobic interaction sorbent

Heats of adsorption for nitrogen bases and nucleosides on Sepharose CL-6B, a hydrophobic interaction adsorbent, were collected through flow microcalorimetry in order to ascertain the thermodynamic driving force for adsorption in each case. It was determined that enthalpy changes associated with base stacking self-interactions can contribute significantly to the observed heats of adsorption. Accordingly, the observed heats were the net effect of the adsorbate/adsorbent interactions and the adsorbate stacking self-interactions. Since base stacking proceeds beyond the dimer stage, multi-layer adsorption of these compounds is possible, even at low solution concentrations.

Micropreparative fractionation of DNA fragments on metathesis-based monoliths: influence of stoichiometry on separation

Applying Grubbs' first generation benzylidene-type catalyst Cl2Ru(PCy3)2(CHPh) in ring opening metathesis polymerization (ROMP) of norborn-2-ene (NBE) and 1,4,5,8,8a-hexahydro-1,4,5,8, exo, endo-dimethanonapthalene (DMN-H6), various monoliths were prepared within the confines of silanized borosilicate columns (100x3 mm I.D.) and investigated for the micropreparative separation of pBR322 DNA-Hae III restriction fragments ranging in size from 51 to 587 base pairs (bp), as a sample of double-stranded (ds) DNA. The approach to good resolution of dsDNA on monolithic columns entailed the modulation of the polymer morphology in terms of structure and porosity to suit such an analysis. Structural variations were achieved by changing the relative ratios of comonomers (NBE+DMN-H6) at the expense of porogens, and by increasing the DMN-H6 to NBE mass ratio. For dsDNA separations, eluents comprised 0.1 M aqueous triethylammonium acetate, pH 7.0, and acetonitrile. Alternatively, methanol was introduced in this study as a less polar gradient former. In terms of column evaluation, each column prepared was first tested in the separation of 5'-phosphorylated oligodeoxythymidylic acids [p(dT)(12-18)], since good separation of oligodeoxynucleotides indicates the potential liability of the column tested for dsDNA analysis, and vice versa. It was noted that monoliths with combinations of 25:25:40:10, 28:28:35:9, and 30:30:32:8 (as weight% of NBE/DMN-H6/2-propanol/toluene) showed good resolution of p(dT)(12-18). Moreover, they demonstrated good separation of the first 12 fragments (51-267 bp) of the pBR322 DNA-Hae III digest; however, reduced resolution in the separation of the last five highest molecular mass fragments (434-587 bp) was experienced. The best separation of these fragments was accomplished on a 25:25:40:10 NBE/DMN-H6/2-propanol/toluene combination at a flow-rate of 2 ml/min, a temperature of 50 degrees C, and a gradient of 4-10% acetonitrile in 1 min, then 10-16% in 14 min. The total amount of pBR322 HaeIII digest that may be fractionated on these systems is 0.5-2.5 microg.

Ion-pair reversed-phase high-performance liquid chromatography analysis of oligonucleotides: retention prediction

An ion-pair reversed-phase HPLC method was evaluated for the separation of synthetic oligonucleotides. Mass transfer in the stationary phase was found to be a major factor contributing to peak broadening on porous C18 stationary phases. A small sorbent particle size (2.5 microm), elevated temperature and a relatively slow flow-rate were utilized to enhance mass transfer. A short 50 mm column allows for an efficient separation up to 30mer oligonucleotides. The separation strategy consists of a shallow linear gradient of organic modifier, optimal initial gradient strength, and the use of an ion-pairing buffer. The triethylammonium acetate ion-pairing mobile phases have been traditionally used for oligonucleotide separations with good result. However, the oligonucleotide retention is affected by its nucleotide composition. We developed a mathematical model for the prediction of oligonucleotide retention from sequence and length. We used the model successfully to select the optimal initial gradient strength for fast HPLC purification of synthetic oligonucleotides. We also utilized ion-pairing mobile phases comprised of triethylamine (TEA) buffered by hexafluoroisopropanol (HFIP). The TEA-HFIP aqueous buffers are useful for a highly efficient and less sequence-dependent separation of heterooligonucleotides.

Purification of an oligonucleotide at high column loading by high affinity, low-molecular-mass displacers

The development of efficient techniques for large-scale oligonucleotide purification is of great interest due to the increased demand for antisense oligonucleotides as therapeutics as well as their use for target validation and gene functionalization. This paper describes the use of anion-exchange displacement chromatography for the purification of 20-mer phosphorothioate oligonucleotide from its closely related impurities using low-molecular-mass amaranth as the displacer. Experiments were carried out to examine the effect of the feed load on the performance of the displacement chromatography. In contrast to prior work, displacement chromatography was successfully scaled-up to high column loadings while maintaining high purity and yields. Experiments carried out on a Source 15Q column indicated that crude oligonucleotide loading as high as 39.2 mg/ml of column were readily processed, resulting in product recovery of 86% and purity of 92%. These results demonstrate that anion-exchange displacement chromatography can indeed be employed for large-scale oligonucleotide separations at high column loading.