Advancements in the characterisation of oligonucleotides by high performance liquid chromatography-mass spectrometry in 2021: A short review

Optimisation of Heated Electrospray Ionisation Parameters to Minimise In-Source Generated Impurities in the Analysis of Oligonucleotide Therapeutics

RATIONALE

Oligonucleotides have emerged as an important new class of therapeutic. Due to their structural complexity, this presents significant challenges for the development of analytical methods to characterise and determine their impurity profile. In this study, we introduce a sensitive ion-pair reverse phase method interfaced with mass spectrometry for analysis of antisense oligonucleotides and small interfering RNAs.

METHODS

Liquid chromatography-mass spectrometry analysis of antisense oligonucleotides and small interfering RNAs was performed using hexylamine: hexafluoro-2-propanol mobiles phases. LC-MS analysis was performed in both negative and positive ion mode. Electrospray ionisation source conditions including collision energy and temperature were optimised to minimise in-source generated impurities and alkylamine adducts in the analysis of oligonucleotide therapeutics.

RESULTS

The results show that under low or no in-source collision energy the presence of hexylamine adducts are observed and are predominantly on the lowest charge states present. As the in-source collision energy is increased, a reduction of hexylamine adducts is observed in conjunction with an increase in nucleobase loss in the gas phase, therefore generating in-source impurities. In comparison to tributylammonium acetate, increased MS sensitivity, higher charge states and effective removal of hexylamine adducts using mild source conditions was achieved.

CONCLUSIONS

Optimisation of the mild source conditions in conjunction with high pH mobile phases was combined with high-resolution accurate mass spectrometry analysis and automated deconvolution workflows to develop a simplified and streamlined approach for characterising oligonucleotide therapeutics and their related impurities.

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.

Quantification of Epigenetic DNA and RNA Modifications by UHPLC-MS/MS Technologies: New Concepts and New Improvements for the Special Collections

Dynamic and reversible DNA and RNA modifications are essential for cell differentiation and development. Aberrant epigenetic modifications are closely associated with the occurrence and progression of diseases, serving as potential markers for cancer diagnosis and prognosis. Ultra-high-performance liquid chromatography coupled with tandem mass spectrometry (UHPLC-MS/MS) offers distinct advantages in the qualitative and quantitative analysis of various modifications due to its sensitivity, specificity, and accuracy. This review provides a comprehensive overview of the current knowledge regarding the liquid chromatography-mass spectrometry (LC-MS) analysis of DNA and RNA modifications, including analytical procedures, advancements, and biological applications, with a focus on tracing the source of (N6-2'-deoxy-adenosine) 6mdA in eukaryotes. Additionally, we examine the integration of UHPLC-MS/MS with other separation techniques to achieve accurate quantification of modifications in specific regions, certain fragments, and free nucleosides.

OligoDistiller: A Platform Agnostic Software Tool for MS and MS2 Data Analysis of Complex Oligonucleotides and Their Impurities

Oligonucleotides are currently one of the most rapidly advancing classes of therapeutic modalities. Understanding critical quality attributes, such as the impurity profile, stability, potential metabolites, and sequence conformity, is the key to their ultimate success. To obtain the information presented above, liquid chromatography-mass spectrometry (LC-MS) is often employed. However, data interpretation can be challenging due to multiple charge states, unknown species, chemical noises, and overlapping isotope envelopes (OIEs) of distinct but unresolved species. To address these challenges, we have developed an MS-platform agnostic, multifunctional R package and a web-tool for automated and interactive MS and MS2 data analysis, OligoDistiller. From the MS spectrum of a complex mixture of two synthetic strands, our tool OligoDistiller annotated and quantified 45 oligonucleotide-related features including 13 unknown impurities and 6 OIEs, which all together explained 90.8% of the detected peaks. Also, major product ions were assigned from the MS2 spectrum of a 47-mer DNA strand, covering 80.3% of the oligonucleotide sequence. We provide not only diverse isotope quality metrics for each annotated feature but also an interactive data review module allowing for direct inspection of the part of raw spectrum linked to a selected feature. This tool OligoDistiller is freely available at https://github.com/daniellyz/OligoDistiller.

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.

Separation of nucleobases, nucleosides, nucleotides and oligonucleotides by hydrophilic interaction liquid chromatography (HILIC): A state-of-the-art review

The polar nature of nucleobases, nucleosides and nucleotides makes hydrophilic interaction chromatography (HILIC) a good choice of technology for separation. Both naturally occurring and modified nucleosides and nucleotides have been successfully separated in HILIC. A wide range of stationary phases with different retention and selectivity are suitable for the separation of nucleobases, nucleosides and nucleotides; and a sufficient knowledge base is also available to guide method development. Although oligonucleotides are significantly different from nucleotides in terms of polarity and charges, HILIC has been shown to be a viable alternative to ion-pairing reversed-phase liquid chromatography (IP-RPLC). Only a few polar stationary phases have been shown to provide satisfactory performance; however, the requirements for the mobile phase composition including organic solvent, mobile phase pH and salt concentration are sufficiently understood. This review provides a comprehensive evaluation of the chromatographic conditions with a historical perspective on adopting and developing HILIC for the separation of nucleobases, nucleosides, nucleotides and oligonucleotides. The areas for more research and potential directions for future development activities are identified and discussed.

Triphenyl-Modified Mixed-Mode Stationary Phases With and Without Embedded Ion-Exchange Sites for High-Performance Liquid Chromatography

The present work reports on the preparation, characterization, and evaluation of a set of novel triphenyl-modified silica-based stationary phases without and with embedded ion-exchange sites for mixed-mode liquid chromatography. The three synthesized triphenyl phases differed in additionally incorporated ion-exchange sites. In one embodiment, allyltriphenylsilane was bonded to thiol-modified silica by thiol-ene click reaction, leading to particles with no ion-exchange sites. A second stationary phase was obtained by thiol-yne click reaction of thiol silica with 2-propinyl-triphenylphosphonium bromide, yielding a strong anion-exchanger (SAX). A third stationary phase was obtained from this SAX phase by the oxidation of residual thiols to sulfonic acid moieties, leading to a zwitterionic surface. All synthesized materials were subjected to elemental analysis, 13C and 29Si solid-state cross-polarization/magic angle spinning nuclear magnetic resonance (CP/MAS NMR) spectroscopy analysis, and pH-dependent ζ-potential determinations via electrophoretic light scattering. The prepared stationary phases were chromatographically evaluated under classical reversed-phase, ion-exchange, and hydrophilic interaction chromatography conditions and classified within a set of commercially available columns by principal component analysis of retention factors. Finally, the obtained stationary phases were applied for biomolecule separations (e.g., teicoplanin and siRNA patisiran). These LC tests proved the orthogonality of the three prepared stationary phases and indicated possible fields of application.

Development of a Versatile High-through-put Oligonucleotide LC-MS Method to Accelerate Drug Discovery

Liquid chromatography-mass spectrometry (LC-MS) is an effective tool for high-throughput quantification of oligonucleotides that is crucial for understanding their biological roles and developing diagnostic tests. This paper presents a high-throughput LC-MS/MS method that may be versatilely applied for a wide range of oligonucleotides, making it a valuable tool for rapid screening and discovery. The method is demonstrated using an in-house synthesized MALAT-1 Antisense oligonucleotide (ASO) as a test case. Biological samples were purified using a reversed liquid-liquid extraction process automated by a liquid handling workstation and analyzed with ion-pairing LC-MS/MS. The assay was evaluated for sensitivity (LLOQ = 2 nM), specificity, precision, accuracy, recovery, matrix effect, and stability in rat cerebrospinal fluid (CSF) and plasma. Besides some existing considerations such as column selection, ion-pairing reagent, and sample purification, our work focused on the following four subtopics: 1) selecting the appropriate Multiple Reaction Monitoring (MRM) transition to maximize sensitivity for trace-level ASO in biological samples; 2) utilizing a generic risk-free internal standard (tenofovir) to avoid crosstalk interference from the oligo internal standard commonly utilized in the LC-MS assay; 3) automating the sample preparation process to increase precision and throughput; and 4) comparing liquid-liquid extraction (LLE) and solid-phase extraction (SPE) as sample purification methods in oligo method development. The study quantified the concentration of MALAT-1 ASO in rat CSF and plasma after intrathecal injection and used the difference between the two matrices to evaluate the injection technique. The results provide a solid foundation for further internal oligonucleotide discovery and development.

Unveiling the intricacy of gapmer oligonucleotides through advanced tandem mass spectrometry approaches and scan accumulation for 2DMS

Antisense oligonucleotides (ASOs) are crucial for biological applications as they bind to complementary RNA sequences, modulating protein expression. ASOs undergo synthetic modifications like phosphorothioate (PS) backbone and locked nucleic acid (LNA) to enhance stability and specificity. Tandem mass spectrometry (MS) techniques were employed to study gapmer ASOs, which feature a DNA chain within RNA segments at both termini, revealing enhanced cleavages with ultraviolet photodissociation (UVPD) and complementary fragment ions from collision-induced dissociation (CID) and electron detachment dissociation (EDD). 2DMS, a data-independent analysis technique, allowed for comprehensive coverage and identification of shared fragments across multiple precursor ions. EDD fragmentation efficiency correlated with precursor ion charge states, with higher charges facilitating dissociation due to intramolecular repulsions. An electron energy of 22.8 eV enabled electron capture and radical-based cleavage. Accumulating multiple scans and generating average spectra improved signal intensity, aided by denoising algorithms. Data analysis utilised a custom Python script capable of handling modifications and generating unique mass lists.

Charge Detection Mass Spectrometry Enables Molecular Characterization of Nucleic Acid Nanoparticles

Nucleic acid nanoparticles (NANPs) are increasingly used in preclinical investigations as delivery vectors. Tools that can characterize assembly and assess quality will accelerate their development and clinical translation. Standard techniques used to characterize NANPs, like gel electrophoresis, lack the resolution for precise characterization. Here, we introduce the use of charge detection mass spectrometry (CD-MS) to characterize these materials. Using this technique, we determined the mass of NANPs varying in size, shape, and molecular mass, NANPs varying in production quality due to formulations lacking component oligonucleotides, and NANPs functionalized with protein and nucleic acid-based secondary molecules. Based on these demonstrations, CD-MS is a promising tool to precisely characterize NANPs, enabling more precise assessments of the manufacturing and processing of these materials.

Study of nusinersen metabolites in the cerebrospinal fluid of children with spinal muscular atrophy using ultra-high-performance liquid chromatography coupled with quadrupole-time-of-flight mass spectrometry

The study aimed to analyze nusinersen metabolites in the cerebrospinal fluid samples using ion-pair reversed-phase ultrahigh-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry. Three different sample preparation methods were tested for extraction and purification, but solid phase extraction appeared to be the most suitable, allowing a significant sample enrichment (40-fold). This step was necessary to detect and identify metabolites of nusinersen in the cerebrospinal fluid. The developed and applied analytical procedure enabled the identification of nusinersen metabolites: sequences shorter by several nucleotides from the 3' end; shorter by several nucleotides from both the 3' and 5' ends; and some depurination products. To the best of our knowledge, this is the first report on the analysis and identification of nusinersen metabolites in cerebrospinal fluid samples taken from children with spinal muscular atrophy treated with Spinraza.

Non-Targeted Detection of Synthetic Oligonucleotides in Equine Serum Using Liquid Chromatography-High-Resolution Mass Spectrometry

There is great concern in equine sport over the potential use of pharmaceutical agents capable of editing the genome or modifying the expression of gene products. Synthetic oligonucleotides are short, single-stranded polynucleotides that represent a class of agents capable of modifying gene expression products with a high potential for abuse in horseracing. As these substances are not covered by most routine anti-doping analytical approaches, they represent an entire class of compounds that are not readily detectable. The nucleotide sequence for each oligonucleotide is highly specific, which makes targeted analysis for these agents problematic. Accordingly, we have developed a non-targeted approach to detect the presence of specific product ions that are not naturally present in ribonucleic acids. Briefly, serum samples were extracted using solid-phase extraction with a mixed-mode cartridge following the disruption of protein interactions to isolate the oligonucleotides. Following the elution and concentration steps, chromatographic separation was achieved utilizing reversed-phase liquid chromatography. Following an introduction to a Thermo Q Exactive HF mass spectrometer using electrospray ionization, analytes were detected utilizing a combination of full-scan, parallel reaction monitoring and all ion fragmentation scan modes. The limits of detection were determined along with the accuracy, precision, stability, recovery, and matrix effects using a representative 13mer oligonucleotide. Following method optimization using the 13mer oligonucleotide, the method was applied to successfully detect the presence of specific product ions in three unique oligonucleotide sequences targeting equine-specific transcripts.

Multi-dimensional technology - Recent advances and applications for biotherapeutic characterization

This review provides an overview of the latest advancements and applications in multi-dimensional liquid chromatography coupled with mass spectrometry (mD-LC-MS), covering aspects such as inter-laboratory studies, digestion strategy, trapping column, and multi-level analysis. The shift from an offline to an online workflow reduces sample processing artifacts, analytical variability, analysis time, and the labor required for data acquisition. Over the past few years, this technique has demonstrated sufficient maturity for application across a diverse range of complex products. Moreover, there is potential for this strategy to evolve into an integrated process analytical technology tool for the real-time monitoring of monoclonal antibody quality. This review also identifies emerging trends, including its application to new modalities, the possibility of evaluating biological activity within the mD-LC set-up, and the consideration of multi-dimensional capillary electrophoresis as an alternative to mD-LC. As mD-LC-MS continues to evolve and integrate emerging trends, it holds the potential to shape the next generation of analytical tools, offering exciting possibilities for enhanced characterization and monitoring of complex biopharmaceutical products.

Decoding Complexity in Synthetic Oligonucleotides: Unraveling Coeluting Isobaric Impurity Ions by High Resolution Mass Spectrometry

Analyzing coeluting impurities with similar masses in synthetic oligonucleotides by liquid chromatography-mass spectrometry (LC-MS) poses challenges due to inadequate separation in either dimension. Herein, we present a direct method employing fully resolved isotopic envelopes, enabled by high resolution mass spectrometry (HRMS), to identify and quantify isobaric impurity ions resulting from the deletion or addition of a uracil (U) or cytosine (C) nucleotide from or to the full-length sequence. These impurities may each encompass multiple sequence variants arising from various deletion or addition sites. The method utilizes a full or targeted MS analysis to measure accurate isotopic distributions that are chemical formula dependent but nucleotide sequence independent. This characteristic enables the quantification of isobaric impurity ions involving sequence variants, a capability typically unavailable in sequence-dependent MS/MS methods. Notably, this approach does not rely on standard curves to determine isobaric impurity compositions in test samples; instead, it utilizes the individual isotopic distributions measured for each impurity standard. Moreover, in cases where specific impurity standards are unavailable, the measured isotopic distributions can be adequately replaced with the theoretical distributions (calculated based on chemical formulas of standards) adjusted using experiment-specific correction factors. In summary, this streamlined approach overcomes the limitations of LC-MS analysis for coeluting isobaric impurity ions, offering a promising solution for the in-depth profiling of complex impurity mixtures in synthetic oligonucleotide therapeutics.

Inquest for the interaction of canonical and non-canonical DNA/RNA bases with ternary based 2D Si2BN and doped Si2BN for biosensing applications

Density functional theory (DFT) is invoked to investigate the interaction between the canonical (CN) and non-canonical (NC) bases with pristine Si2BN (Si2BN) and Phosphorous-doped Si2BN (P-dop-Si2BN) sheets. Inquest for the better sensing substrate is decided through the adsorption energy calculation which reveals that doping of phosphorous atom enhances the adsorption strength of AT (-83.74 kcal/mol) AU (-82.77 kcal/mol) and GC (-96.36 kcal/mol) base pairs. The CN and NC bases have higher adsorption energy than the previous reported values which concludes that the P-dop-Si2BN sheet will be optimal substrate to sense the bases. Meanwhile, the selected CN and NC (except hypoxanthine) bases interact with sheet in parallel manner which infers the π-π interaction with Si2BN and P-dop-Si2BN sheets. The energy gap variation (ΔEg%) of the P-dop-Si2BN complexes has a noticeable change, ranging from -24.75 to -197.28% which thrust the sensitivity of the P-dop-Si2BN sheet over the detection of CN and NC bases. The natural population analysis (NPA) and electron density difference map (EDDM) confirms that charges are transferred from CN and NC bases to Si2BN and P-dop-Si2BN sheet. The optical property of the P-dop-Si2BN complexes reveals that the noticeable red and blue shift in the visible and near-infrared regions (778 nm to 1143 nm) has been observed. Therefore, the above results conclude that the P-dop-Si2BN sheet plays a potential candidate to detect the CN and NC bases which contribute to the development of biosensors and DNA/RNA sequencing devices.Communicated by Ramaswamy H. Sarma.

Review of fragmentation of synthetic single-stranded oligonucleotides by tandem mass spectrometry from 2014 to 2022

The fragmentation of oligonucleotides by mass spectrometry allows for the determination of their sequences. It is necessary to understand how oligonucleotides dissociate in the gas phase, which allows interpretation of data to obtain sequence information. Since 2014, a range of fragmentation mechanisms, including a novel internal rearrangement, have been proposed using different ion dissociation techniques. The recent publications have focused on the fragmentation of modified oligonucleotides such as locked nucleic acids, modified nucleobases (methylated, spacer, nebularine and aminopurine) and modification to the carbon 2'-position on the sugar ring; these modified oligonucleotides are of great interest as therapeutics. Comparisons of different dissociation techniques have been reported, including novel approaches such as plasma electron detachment dissociation and radical transfer dissociation. This review covers the period 2014-2022 and details the new knowledge gained with respect to oligonucleotide dissociation using tandem mass spectrometry (without priori sample digestion) during that time, with a specific focus on synthetic single-stranded oligonucleotides.

Polybutylene terephthalate-based stationary phase for ion-pair-free reversed-phase liquid chromatography of small interfering RNA. Part 2: Use for selective comprehensive two-dimensional liquid chromatography

With the increasing numbers of nucleic acid-based pharmaceuticals like antisense oligonucleotides (ASO), small interfering ribonucleic acid (siRNA) entering the market, research facilities, pharmaceutical industries and also regulatory authorities have been looking for efficient analytical methods for these synthetic oligonucleotides (ON). Besides of conventional one-dimensional (1D) reversed-phase liquid chromatography with or without ion-pairing (IP-RP-LC, RP-LC), hydrophilic liquid chromatography (HILIC) and mixed-mode chromatography (MMC), two-dimensional (2D) approaches combining two orthogonal chromatographic techniques also become more relevant due to the high structural complexity of oligonucleotides. Recently, we tested a polybutylene terephthalate(PBT)-based stationary phase under ion-pairing free RP mode for the liquid chromatography electrospray ionization mass spectrometry (LC-ESI-MS) analysis of siRNA (Patisiran). In this study, retention profile and chromatographic orthogonality, respectively, were compared to other LC-modes like HILIC, IP-RPLC, another ion-pair free cholesterol-bonded RPLC and MMC considering their normalized retention times. Finally, because of higher orthogonality, the ion-pairing free PBT-bonded RPLC as first dimension (¹D) was hyphenated with HILIC in the second dimension (²D) in a selective comprehensive 2D-LC setup leading to an enhanced resolution for peak purity evaluation of the main ON entities.

Advancements in the characterisation of oligonucleotides by high performance liquid chromatography-mass spectrometry in 2021: A short review

The first oligonucleotide therapeutic was approved by the Food and Drug Administration in 1998, and since then, 12 nucleic acids have been commercialised as medicines. To be approved, the oligonucleotides need to be identified and characterised as well as its related impurities. Different methods exist, but the most commonly used is ion-pairing reversed-phase liquid chromatography with tandem mass spectrometry. The separation obtained depends on the mobile phase and column used. Other methods have been developed, notably by using hydrophilic interaction chromatography and two-dimensional high performance liquid chromatography. Furthermore, ion-pairing reversed-phase high performance liquid chromatography ultra-violet spectroscopy detection and mass spectrometry has been optimised for the analysis of methylated nucleobases due to the utilisation of this modification in the drugs. This review covers the recent advancements in the analysis and characterisation of oligonucleotides in 2021 by high performance liquid chromatography mass spectrometry, notably by hydrophilic interaction chromatography and two-dimensional liquid chromatography but also the different parameters that influence the analysis by ion-pairing reversed-phase high performance liquid chromatography, the characterisation of methylated nucleobases, and the recent software developed for oligonucleotides.