High-Throughput Chromatographic Separation of Oligonucleotides: A Proof of Concept Using Ultra-Short Columns

Selected new approaches and future perspectives in liquid chromatography for the analysis of emerging modalities

Emerging biopharmaceutical modalities, such as genetic medicines and RNA therapies, offer transformative potential for treating previously intractable diseases. However, these complex drugs present unique analytical challenges due to their intricate structures, sophisticated manufacturing processes, and modality-specific product quality attributes. Liquid chromatography (LC) has emerged as a versatile tool for addressing these challenges, enabling precise characterization and quality control strategies. This review highlights recent advancements in LC technologies, including low-adsorption hardware, ultra-wide pore size exclusion chromatography (SEC) columns, and innovative separation modes such as slalom chromatography and pressure-enhanced liquid chromatography (PELC). These developments tackle issues such as non-specific adsorption, carryover, and inadequate selectivity while improving resolution and robustness for large biomolecules like mRNA, adeno-associated viruses (AAVs), and lipid nanoparticles (LNPs). Novel approaches, such as tandem SEC systems, gradient SEC columns, and dual stationary phase gradients, further expand the scope of LC techniques by enhancing separations for diverse analyte sizes and complexities. Additionally, practical innovations like bracketed injection methods and new enzymatic tools for oligo-mapping improve reproducibility, efficiency, and confidence in RNA sequence analysis. These advancements not only address current analytical limitations but also pave the way for regulatory-compliant approaches, which will support the broader adoption of LC in both discovery and quality control settings. As the field continues to evolve, these innovations are poised to play a pivotal role in ensuring the safety, efficacy, and consistency of next-generation therapeutics.

Does column length still matter? A case study of the effect of column length on resolution of therapeutic oligonucleotides

As the importance of therapeutic oligonucleotides (ONs) continues to grow in the pharmaceutical industry, the importance of high performing analytical methods needed to characterize them also grows. The characteristics of these molecules (e.g., highly charged phosphate backbone, and small but important modifications such as methylation and fluorination) make them difficult to analyze thoroughly using conventional liquid chromatography (LC) conditions. Recently, other research groups have been emphasizing the utility of ultra-short (<< 50 mm) columns for proteins and other large biomolecules, and have remarked that long columns only add unnecessary peak dispersion without providing additional resolution over short columns. These statements naturally call into question the long-established theory for small molecule LC separations that asserts that separation performance is maximized by working at the highest available operating pressure, and then choosing the longest column possible while working at the van Deemter optimum flow rate. This apparent contradiction in turn raises the question - for which types of large biomolecule does the established chromatographic theory no longer apply? In this study we have carried out experiments and calculations aimed at answering this question for ion-pairing reversed-phase separations of therapeutic ONs with masses on the order of 6 kDa. This included measuring isocratic plate heights for these molecules after establishing an empirical relationship between retention, mobile phase composition, and flow rate, because retention of the ONs is extremely sensitive to pressure (20 % increase in k per bar pressure drop), and thus retention varies with flow rate at a constant mobile phase composition. After taking these factors into account, we find that resolution of the oligonucleotides does increase with the square root of column length, as predicted by the well-established theory for small molecules. However, we also find that this relationship is only found when the gradient slope is held constant while varying the column length, and that if this is not done it is actually possible to observe that resolution decreases with increasing column length. Thus, the design of experiments used to evaluate the role of column length in separation performance is critical. In addition to the importance of these findings to development of LC methods for ON separations in general, they will be especially impactful in two-dimensional (2D) separations of ONs where there is more or less freedom to choose parameters from a wide range of possibilities depending on the mode of 2D separation that is used.

A dilute-and-shoot LC-MS/MS determination of low-dosage third-generation antipsychotics and their metabolites in urine using an ultra-short column

Third-generation atypical antipsychotics, known for their enhanced efficacy and reduced side effects compared to previous generations, are now extensively utilized in the treatment of schizophrenia. Due to their chemical properties and low dosages, these drugs are present at low concentrations in urine, making it challenging to monitor medication compliance among probationers. In this study, a liquid chromatography-tandem mass spectrometric (LC-MS/MS) method was developed and validated for the determination of three third-generation antipsychotics and their main metabolites in urine. A dilute-and-shoot approach was employed for rapid urine sample preparation. All compounds were separated on an ultra-short column (2.1 × 5 mm, 1.7 μm) and detected rapidly within a span of two minutes, thereby enhancing the efficiency in handling increased workloads. The limits of detection ranged from 0.01 to 0.23 ng/mL for all compounds, with correlation coefficients exceeding 0.997. The analytical method was validated using various parameters, including selectivity, precision and accuracy, matrix effect, and stability, ensuring its reliability for forensic applications. This newly developed LC-MS/MS method was successfully applied to analyze 86 urine samples obtained from probationers undergoing antipsychotic medication. Consequently, this method proves to be useful in verifying medication compliance among probationers, and effectively managing the recent increase in the number of urine drug testing.

Evaluation of ion pairing reversed-phase liquid chromatography for the separation of large RNA molecules

The rapid development of mRNA-based therapeutics, especially post-COVID-19, has necessitated the precise characterization of mRNA quality attributes, including sequence integrity. Ion-pairing reversed-phase liquid chromatography (IP-RPLC) has been widely accepted as a reference method for the characterization of small oligonucleotides. Some studies have already investigated the use of IP-RPLC for RNA, but no systematic approach has been developed to assess the impact of ion-pairing agents (IPAs) on the separation of large RNA molecules. This study addresses this gap by investigating the potential of IP-RPLC for the separation and characterization of large RNA molecules, with a specific focus on optimizing the use of IPAs to enhance retention and selectivity. Thirteen different IPAs, varying in hydrophobicity, were systematically tested using a supermacroporous polymeric (divinylbenzene) column with a very broad pore size range under various conditions, including different temperatures, pH, and IPA concentrations. The results demonstrate that moderately hydrophobic IPAs provide superior resolution for RNA species up to 6000 nucleotides. An optimized combination of 100 mM butylammonium acetate and 50 mM tripropylammonium acetate achieved the best overall separation, significantly improving resolution by 35% compared to individual IPAs. The study also identifies optimal conditions for RNA separation, including a mobile phase pH of 7.0, acetonitrile as the organic solvent, and a column temperature of 65 °C. In a second step, a solution to increase the retention of small nucleotides and thereby separate nucleic acids ranging from 1 to 6000 nucleotides allowing to characterize IVT-mRNA differing in length and study their integrity and fragmentation or monitor the presence of in-process impurities (nucleotides) was investigated by combining two different LC columns. These findings enhance the analytical toolbox for evaluating the critical quality attributes of RNA, supporting the development of reliable and efficient RNA-based therapeutics.

Mixed-mode separation of antisense oligonucleotides using a single column with complementary anion-exchange and hydrophobic interaction chromatography approaches

The current study investigates the use of mixed-mode chromatography as a combination of anion-exchange (AEX) and hydrophobic interaction chromatography (HIC) for the analysis and purification of single-stranded antisense oligonucleotides with stereo-controlled phosphorothioate inter- nucleotide linkages. Initially a Scherzo-SS-C18 trimodal stationary phase with reversed-phase/AEX/ cation-exchange (CEX) functionalities is systematically evaluated to reveal the presence of U-shaped retention composed of two retention modes namely AEX and HIC, where the latter was also observed on related trimodal Scherzo SM and SW analogues. For the first time, retention and separation of deprotected oligonucleotides was described on a single mixed-mode column using a combination of AEX and HIC. This methodology was later applied to an alternative reversed-phase/AEX support, Newcrom BH, displaying similar retention trends under dual salt / organic modifier gradients. The merit of the method was assessed on the basis of separations between a phosphodiester (PO) impurity and phosphorothioate (PS) target for an assortment of selected 2'-O-methoxyethyl 18- to 20-mer single-stranded antisense oligonucleotides. Various parameters were evaluated mostly under HIC conditions including organic modifier percentage, type of salt, temperature, pH and type of buffer in the mobile phase. Retention of the oligonucleotides was significantly affected by the acetonitrile composition and the type of salt ((NH4)2SO4, NaBr, NaCl) where the latter NaCl also afforded resolution between the PS target and closely eluting PO impurities. Small changes in pH between 6.5 and 7 using MES and TRIS respectively demonstrated notable differences in retention and resolution. The optimized methods were compared against a range of traditional supports and applied to various mixed-mode analogues, possessing embedded amino acid, complex forming weak cation-exchange and terminal strong cation-exchange functionalities. The mixed-mode supports displayed HIC retention and better resolution between PS target and PO impurity was evident with a more focused 5 % acetonitrile gradient over its 10 % counterpart. Overall, throughout the study AEX and HIC demonstrated comparable resolution trends. Finally, the optimized HIC method was applied to a selected 18-mer antisense oligonucleotide at semi-preparative scale using the Newcrom BH column, affording purities of 60-80 % and recoveries of 52-76 %. Although HIC does not provide better separations between PS and PO than AEX, it opens possibilities to operate under non-denaturing conditions and allows purification of samples containing high salt content, as a standalone method or post AEX without a prior desalting step, which can result in 20-30 % sample loss.

Understanding the fundamentals of the on-off retention mechanism of oligonucleotides and their application to high throughput analysis

Ion-pair reversed-phase liquid chromatography (IP-RPLC) is clearly recognized as the gold standard for analyzing therapeutic oligonucleotides (ONs). Recent studies have shown that ONs exhibit an on-off retention behavior in IP-RPLC, meaning that minor changes in acetonitrile (ACN) proportion can significantly impact retention. However, this behavior was initially demonstrated with only a single mobile phase condition. The aim of this study is to gain a deeper understanding of ON elution behavior by measuring the S values (slope of the retention model, log k vs.%ACN) across a broad range of mobile phase conditions. We systematically calculated the S values for both a 20-mer and 100-mer model ON under various conditions, including different IP reagents, IP concentrations, mobile phase pH, column temperatures, and two different buffering acids. We demonstrated that these mobile phase conditions impact the S values in the following order: IP hydrophobicity > IP concentration > column temperature > buffering acid > mobile phase pH. The main explanation for this trend is that mobile phase conditions that reduce the ion-pair retention mechanism (such as low IP hydrophobicity or concentration) will enhance the impact of% ACN on retention, leading to higher S values. In the second part of the study, this knowledge was used to develop ultra-fast separations for two therapeutic oligonucleotides: a 20-mer antisense oligonucleotide (ASO) without phosphorothioate (PS) modifications and a large single guide RNA (sgRNA) that includes certain PS modifications. The mobile phase conditions were optimized to maximize S values, while preventing the separation of diastereomers. It is important to notice that an S-value of at least 30 is required to benefit from the use of ultra-short columns. This approach allows the successful separation of the main species (ASO and sgRNA) and related impurities in less than one minute using a 5 mm length column.

Current state of hydrophilic interaction liquid chromatography of oligonucleotides

There has been a significant increase in the use of hydrophilic interaction liquid chromatography (HILIC) to separate oligonucleotides. This rise in the use of HILIC has correlated to the increasing success of oligonucleotides as therapeutic treatments and reagents in biomedical research. As more scientists need to routinely analyze oligonucleotides in addition to small molecules, peptides, and proteins using the same analytical instruments, it becomes difficult to use traditional types of analyses such as ion-pair reversed-phase chromatography. This increased use has led to new approaches that have improved the utility of HILIC to the point where it has become a legitimate alternative approach to ion-pair reversed-phase chromatography. This review highlights recent advances in HILIC separations of oligonucleotides with a focus on the underlying mechanisms of action. While HILIC has made significant gains in performance, there still remain challenges, which if properly addressed will continue to propel this approach forward.

Influence of theoretical and semi-empirical peak models on the efficiency calculation in chiral chromatography

Height equivalent to theoretical plate (H) equations, such as the van Deemter or Knox-Saleem equations, and other efficiency vs. linear velocity equations (u), provide kinetic insights into chromatographic separations phenomena and column performance. In enantioselective separations, the peak shape of the two enantiomers can differ significantly and are often asymmetric. The peak efficiency calculations heavily impact these efficiency-flow profiles, leading to erroneous estimations of eddy diffusion, longitudinal diffusion, and mass transfer terms. In this work, new asymmetric peak functions are employed for modeling enantiomer peaks based on the Haarhoff-Van der Linde function, its generalized variant (GHVL), once Generalized Asymmetric Gaussian (AGN), and Twice Generalized Gaussian (TGN). The new models (AGN, TGN, and GHVL) incorporate higher statistical moments besides the zeroth, first, and second moments to account for two-sided asymmetry (fronting or tailing). The fit results are compared with the traditional efficiency calculation methods endorsed by official pharmacopeia and numerical estimation of moments from the raw data. Enantiomeric separations of ibuprofen and dl-homophenylalanine were chosen as probe molecules. The results demonstrate that non-linear least squares fitted functions provide better estimations of peak efficiency data even in the presence of high noise. In particular, the generalized models consistently offered the best quality fits for various peak shapes in chiral separations. Conversely, the half-height Gaussian method greatly overpredicted skewed peak efficiencies. This investigation reveals that the commonly held assumptions of peak shape and numerical integration of raw data are highly insufficient for chiral chromatography. The impact of asymmetry on plate height should not be overlooked when accurate data from efficiency-flow rate curves is derived. We advocate for the broader adoption of these new generalized peak (AGN, TGN, GHVL) models because they provide robustness at various SNRs that account for right or left asymmetry while accurately representing peak geometry.

Two-dimensional sequential selective comprehensive chiral×reversed-phase liquid chromatography of synthetic phosphorothioate oligonucleotide diastereomers

In recent years, many nucleic acid-based pharmaceuticals have been approved and entered the market, and even a larger number are in late stage clinical trials. Conventional oligonucleotides are facing issues in vivo like fast renal clearance and nuclease degradation. Therefore, to increase their stability, phosphorothioation is a frequent modification of therapeutic oligonucleotides (ONs) which also leads to improved binding affinity facilitating cell internalization and intracellular distribution. At the same time, by replacing a phosphodiester linkage with a phosphorothioate group, a phosphorous stereogenic center is generated which causes the formation of Rp- and Sp-diastereomers. It increases the structural diversity. For example, with 15 of those phosphorothioate (PS) linkages, 32,768 different diastereomers are expected. Since the phosphorothioate is introduced non-stereoselectively, the molecular complexity of the resultant phosphorothioate ON products is tremendously increased impeding the chromatographic separation in the course of quality control. Since distinct phosphorothioate diastereomers have different bioactivities and pharmacological properties, there is increasing interest in implications of stereoisomerism of phosphorothiate oligonucleotides. From a quality and regulatory viewpoint, batch-to-batch reproducibility of the diastereomer profile may be of significant concern. In order to address this issue, this study investigates the stereoselectivity of LC methods for two phosphorothioate oligonucleotide (PSO) compounds differing in their molecular size and numbers of PS linkages. Diastereoselectivity of ion-pairing reversed-phase liquid chromatography (IP-RPLC), RPLC without ion-pairing agents and LC with chiral polysaccharide-based column were evaluated for model PSOs and an active pharmaceutical ingredient (API) of PSO with trivalent N-acetylgalactosamine (GalNAc) conjugate. Due to the structural complexity of PSOs, the separation power for the diastereomer mixture was increased by using sequential selective comprehensive two-dimensional chromatography with an amylose tris(α-methylbenzylcarbamate)-immobilized chiral stationary phase (CSP) in the first dimension and ion-pair RPLC with ethylammonium acetate in the second dimension. Improved diastereomer selectivity was obtained and a larger number of peaks could be separated.

Development of multiple heartcutting two-dimensional liquid chromatography with ion-pairing reversed-phase separations in both dimensions for analysis of impurities in therapeutic oligonucleotides

Oligonucleotides constitute an emerging and highly complex bioanalytical challenge and it is becoming increasingly clear that 1D methodologies are unable to fully resolve all possible impurities present in these samples. 2D-LC therefore constitutes a perfect solution wherein critical pairs can be sampled from a steep gradient 1D and separated in a shallower 2D gradient. Herein, we provide a facile 2D-LC method development approach to quickly generate high selectivity gradients utilizing ion pairing reverse phase (IPRP-IPRP). In particular we demonstrate how to iteratively generate a 12 % gradient from two training runs and then to utilize that data to predict retentions of analytes with a 2 % gradient with retention prediction errors as low as 3 and 11 %, respectively. This iterative method development workflow was applied to impurity profiling down to 1:1000 for the full-length product and phosphorothioate modified impurities. Additionally, we demonstrated the elucidation of critical pairs in complex crude pharmaceutical oligonucleotide samples by applying tailored high selectivity gradients in the second dimension. It was found that the iterative retention modeling approach allows fast and facile 2D-LC method development for complex oligonucleotide separations.

Rapid Intact Mass Analysis and Evaluation of the Separation Potential of Microfluidic Capillary Electrophoresis Mass Spectrometry for Oligonucleotides

Oligonucleotide characterization is a rapidly advancing field in the biopharmaceutical industry. Understanding critical quality attributes, such as intact mass and impurities, requires a toolbox of analytical techniques, which commonly includes liquid chromatography-mass spectrometry (LC-MS). Oligonucleotide LC-MS analysis frequently requires sample run times upward of 15 min to achieve separation of multiple oligonucleotide species. Additionally, LC methods frequently employ mobile phase additives such as triethylamine and 1,1,1,3,3,3-hexafluoro-2-propanol that are not always desired for use in MS instrumentation. Here, microfluidic capillary electrophoresis mass spectrometry (CE-MS) via ZipChip technology was employed to enable rapid intact mass analysis of oligonucleotide single strands. Baseline separation of equal length oligonucleotides was achieved in less than 4 min. Additionally, the potential of the ZipChip platform for separation of oligonucleotide full-length products (FLPs) and their impurities was evaluated.

Ultra-short columns for the chromatographic analysis of large molecules

Today, reverse phase liquid chromatography (RPLC) analysis of proteins is almost exclusively performed on conventional columns (100-150 mm) in gradient elution mode. However, it was shown many years ago that large molecules present an on/off retention mechanism, and that only a very short inlet segment of the chromatographic column retains effectively the large molecules. Much shorter columns - like only a few centimetres or even a few millimetres - can therefore be used to efficiently analyse such macromolecules. The aim of this review is to summarise the historical and more recent works related to the use of very short columns for the analysis of model and therapeutic proteins. To this end, we have outlined the theoretical concepts behind the use of short columns, as well as the instrumental limitations and potential applications. Finally, we have shown that these very short columns were also possibly interesting for other chromatographic modes, such as ion exchange chromatography (IEX), hydrophilic interaction chromatography (HILIC) or hydrophobic interaction chromatography (HIC), as analyses in these chromatographic modes are performed in gradient elution mode.