Application of sample displacement techniques to the purification of synthetic oligonucleotides and nucleic acids: a mini-review with experimental results

Simultaneous analysis of multiple oligonucleotides by temperature-responsive chromatography using a poly(N-isopropylacrylamide)-based stationary phase

Oligonucleotide therapeutics have contributed remarkably to healthcare, being well suited for the treatment of intractable diseases that are difficult to approach using conventional drug modalities. However, as common techniques of oligonucleotide analysis rely on reversed-phase or ion-exchange liquid chromatography and thus employ toxic organic solvents and/or ion-pairing reagents, better alternatives are highly sought after. Poly(N-isopropylacrylamide) (PNIPAAm) is widely used in temperature-responsive chromatography (TRC), which relies on column temperature variation to control the physical properties of the stationary phase and, unlike conventional reversed-phase liquid chromatography, avoids the use of toxic organic solvents and complicated gradient methods. Herein, PNIPAAm copolymer hydrogel-modified silica beads were used for the simultaneous analysis of multiple synthetic oligonucleotides by TRC to recognize differences in the length of single nucleotides, single bases, and the number of phosphorothioated sites. Temperature-responsive elution was observed in all cases. Each separation of all combinations of multiple oligonucleotides was better at higher temperatures above the lower critical solution temperature and was performed without the use of organic solvents and gradient methods. In the case of multiply phosphorothioated oligonucleotides, good separation was achieved using an aqueous solvent and isocratic elution in the absence of ion-pairing reagents. Thus, the developed procedure was concluded to be well suited for oligonucleotide analysis.

Recent advances in chromatographic purification of plasmid DNA for gene therapy and DNA vaccines: A review

The wide spread of infectious diseases have provoked the scientists to develop new types of vaccines. Among the different types of vaccines, the recently discovered plasmid DNA vaccines, have gained tremendous attentions in the last few decades as a modern approach of vaccination. The scientific interest in plasmid DNA vaccines is attributed to their prominent efficacy as they trigger not only the cellular immune response but also the humoral immune responses. Moreover, pDNA vaccines are easily to be stored, shipped and produced. However, the purification of the pDNA vaccines is a crucial step in their production and administration, which is usually conducted by different chromatographic techniques. This review summarizes the most recent chromatographic purification methods provided in the literature during the last five years following our last review in 2013, including affinity chromatography, hydrophobic interaction chromatography, ion exchange chromatography, multimodal chromatography, sample displacement chromatography and miscellaneous chromatographic methods.

Analysis and Purification of Synthetic Nucleic Acids Using HPLC

Chromatographic methods have been essential tools for analysis and purification of synthetic oligonucleotides since the 1970s. Significant developments in terms of instruments and stationary phases (media) have been made during the past several decades; among the latest are sub-micron to micron particles for the media, as well as ultra performance liquid chromatography (UPLC). Micron and sub-micron particles have increased product resolution. Applications of recently developed methods such as IP-RP-HPLC and LC-MS have been discussed for analysis, along with use of various methods for purification. Utilization of UPLC has decreased analysis time, increasing the throughput for analysis. Commonly used methods for analysis and purification of synthetic oligonucleotides have been described in this unit.

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

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 200Å pore size mixed-mode stationary phase compared to the corresponding 100Å 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.

Purification of small interfering RNA using nondenaturing anion-exchange chromatography

A manufacturing and purification process for duplex oligonucleotides was established, which shortens and simplifies currently used procedures, yielding a product of higher purity. The reported procedure is based on nondenaturing anion-exchange (AEX) chromatography, which is performed on the annealed duplex rather than the individual single strands. The duplex is formed early in the process by annealing of the crude single strands directly after solid-phase synthesis. Two 30 μmol manufacturing runs using duplex purification were performed on 2 different AEX resins and compared with a manufacturing run of the same scale using conventional single-strand chromatography. The same pooling strategy was employed for all purifications. Content of optimal duplex (duplex exclusively comprising full-length single strands) was 90.5% and 90.2% for the batches obtained by duplex purification and 86.1% for the batch obtained by single-strand purification. Maximum chromatographic recoveries were 67% for the duplex purification and 68% for the single-strand purification. Hence, the manufacture of small interfering RNA (siRNA) using duplex purification was simpler and faster than conventional single-strand purification and provided better purity and similar yield of final siRNA.

New monolith technology for automated anion-exchange purification of nucleic acids

Synthetic nucleic acid analysis often employs pellicular anion-exchange (AE) chromatography because it supports very high efficiency separations while offering means to control secondary structure, retention and resolution by readily modifiable chromatographic conditions. However, these pellicular anion-exchange (pAE) phases do not offer capacity sufficient for lab-scale oligonucleotide (ON) purification. In contrast, monolithic phases produce fast separations at capacities exceeding their pellicular counterparts, but do not exhibit capacities typical of fully porous, bead-based, anion-exchangers. In order to further increase monolith capacity and obtain the selectivity and mass transfer characteristics of pellicular phases, a surface-functionalized monolith was coated with pAE nanobeads (latexes) usually employed on the pellicular DNAPac phase. The nanobead-coated monolith exhibited chromatographic behaviors typical of polymer AE phases. Based on this observation the monolithic substrate surface porosity and latex diameters were co-optimized to produce a hybrid monolith harboring capacity similar to that of fully porous bead-based phases and peak shape approaching that of the pAE phases. We tested the hybrid monolith on a variety of previously developed pAE capabilities including control of ON selectivity, resolution of derivatized ONs, the ability to resolve RNA ONs harboring aberrant linkages at different positions in a single sequence and separation of phosphorothioate diastereoisomers. We compared the yield and purity of an 8 mg ON sample purified on both the new hybrid monolith and a benchmark AE column based on fully porous monodisperse beads. This comparison included an assessment of the relative selectivities of both columns. Finally, we demonstrated the ability to couple AE ON separations with ESI-MS using an automated desalting protocol. This protocol is also useful for preparing ONs for other assays, such as enzyme treatments, that may be sensitive to high salt levels.

Capillary electrophoresis for capture and concentrating of target nucleic acids by affinity gels modified to contain single-stranded nucleic acid probes

Selective capture and pre-concentration of target nucleic acids from relatively complicated samples may provide a method to facilitate introduction to a microfluidic-based detection system to improve detection limits. An acrylamide polymer gel modified with Acrydite that contained 20mer oligonucleotide probe was prepared and loaded into a capillary column. The results indicated that the amount of probe DNA that was captured into the acrylamide was about 40% of the starting monomer, and different quantities of probe could therefore be coupled into the gel. The gel was passivated by pre-treatment with non-complementary DNA oligonucleotide to block non-selective adsorption sites, and the gel was determined to be stable for multiple cycles of use. The probe could hybridize with target sequences that were introduced by electrokinetic injection from a sample solution. The target could be freed from the polymer gel by use of a combination of heating, chaotropic salt and voltage conditions. Target capture efficiency was up to 90% when using samples that did not saturate probe sites in the columns, and recovery of target from the gel could be as high as 95%.

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.

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.

Chromatographic purification of some 3-hydroxy-3-methylglutaryl coenzyme A reductase inhibitors

The purification of pravastatin, simvastatin and lovastatin in the sodium salt or lactone form and of mevastatin in the lactone form by reversed-phase displacement chromatography is presented. The mobile phases consisted of water or mixtures of water-methanol and water-acetonitrile. Six different displacers were successfully used. Up to 0.14 g of raw sample per gram of stationary phase was loaded on a column packed with silica-based octadecyl phase. Crude substances from 85 to 88% chromatographic purity were purified and at least 99.5% purity was achieved.

Purification of antisense oligonucleotides

Chromatography is an effective tool for obtaining high-purity synthetic oligonucleotides for a variety of end uses, including antisense drug therapy. Reversed-phase and anion-exchange chromatographies are widely used techniques for this application. While selectivity of these techniques can be modified by methods such as ion-pair RP-HPLC or affinity chromatography, these are presently used only at small scales. RP chromatography makes use of terminal hydrophobic-protecting groups to increase retention and selectivity. The main advantages of the RP method are its utility for the purification of a wide variety of modified oligonucleotide structures, its applicability across a range of terminal hydrophobic groups, such as fluorescein, and its ready use from small scale to very large scale with a minimal requirement for process development. AX-HPLC can also give high-purity products at generally higher media capacities. A more extensive method development effort is typically required for the AX-HPLC purification of AO. The AX yield per unit operation can be lower, but the isolated yield of DMT-off desalted oligonucleotide can be equal to or higher than that from RP-HPLC. As additional AO drugs enter and mature in the market, there will be a potential need for ton-scale purification processes. AX provides a way to scale up production on somewhat less expensive equipment with reduced organic solvent requirements.