Development of an ion pairing reversed-phase liquid chromatography-mass spectrometry method for characterization of clustered regularly interspaced short palindromic repeats guide ribonucleic acid

A platform method for simultaneous quantification of lipid and nucleic acid components in lipid nanoparticles

Nucleic acid-based medicines have achieved significant advancements in recent years, with lipid nanoparticles (LNPs) being a pivotal platform for their delivery. However, the complexity of LNP presents significant challenges, requiring analytical methods to identify and quantify individual components to guide formulation development and ensure quality and safety. Current approaches often perform nucleic acid and lipid analysis separately and focus on a single type of formulation, highlighting the need for a simple platform method that can be applied to diverse formulations. We present a platform ion-pair reversed-phase HPLC method with UV and charged aerosol detection (CAD) to simultaneously separate and quantify lipid and nucleic acid components in LNPs. The method separated and quantified 12 lipid species and three types of nucleic acids (antisense oligonucleotide, single-guide RNA, and mRNA), covering a broad range of therapeutic cargoes. Notably, this can be achieved for the first time by one HPLC run with one-step facile sample preparation. Specifically, we used a simple buffer containing Triton and heparin to enable the single-step, simultaneous extraction of both nucleic acid and lipid components from LNPs, achieving quantification recoveries of 90-110 %. We further applied this method and addressed process and quality control challenges of LNPs, including the recovery rate of individual LNP components after purification and simultaneous quantification of co-loaded, different nucleic acid species for potential gene editing applications. This new platform method offers a robust and widely applicable tool to assess the quality of lipid-based nucleic acid therapies.

Real-Time Monitoring of Higher-Order Structure of RNAs by Temperature-Course Size Exclusion Chromatography and Microfluidic Modulation Spectroscopy

Recently, there has been emerging interest in the characterization of the higher order structure (HOS) of oligonucleotide therapeutics because of its potential impact on the function. However, many existing experimental and computational methods face challenges with respect to throughput, cost, and resolution for large ribonucleic acids (RNAs). In this study, we present the use of two orthogonal analytical methods, size-exclusion chromatography (SEC) and microfluidic modulation spectroscopy (MMS), which are used to investigate conformational changes of two 100 mer single guide RNAs (sgRNAs) with complex HOS and aggregation specie profiles. SEC, coupled with multiangle light scattering (MALS), mass spectrometry (MS), and isothermal MMS revealed various forms of aggregation and potential interactions. We also developed temperature-course SEC and thermal ramping MMS methods to monitor real-time HOS changes from room temperature to the RNA melting point. Through the experiments, we observed two discrete steps of thermally induced dissociation of RNA aggregates, namely higher order aggregates (HOA) dissociation and dimer dissociation. Temperature-course SEC allows for thermodynamic analysis of the enthalpy and entropy of the reaction. We also identified two spectral regions in infrared (IR) spectra with thermal ramping MMS, 1665 cm-1 and between 1700 and 1720 cm-1, which closely correlated to the Watson-Crick base pairing and the related HOS change in RNA. The combination of SEC and MMS offers a comprehensive biophysical characterization toolkit for RNA HOS under native conditions, providing valuable insights for candidate optimization and formulation screening in the development of RNA therapeutics.

Retention mechanism in slalom chromatography: Perspectives on the characterization of large DNA and RNA biopolymers in cell and gene therapy

Significant progress has been made in the last two decades in producing small (<2μm), high-purity, and low-adsorption particles, columns and system hardware, for ultra-high pressure liquid chromatography (UHPLC). Simultaneously, the recent rapid expansion of cell and gene therapies for treating diseases necessitates novel analytical technologies for analyzing large (>2 kbp) plasmid double-stranded (ds) DNA (which encodes for the in vitro transcription (IVT) of single-stranded (ss) mRNA therapeutics) and dsRNAs (related to IVT production impurities) biopolymers. In this context, slalom chromatography (SC), a retention mode co-discovered in 1988, is being revitalized using the most advanced column technologies for improved determination of the critical quality attributes (CQAs) of such new therapeutics. In this review, we first recall non-exhaustively the main currently available analytical techniques (enzyme-linked immunosorbent assay (ELISA), agarose gel electrophoresis (AGE), pulse field gel electrophoresis (PFGE), capillary gel electrophoresis (CGE), mass photometry (MP), anion-exchange chromatography (AEX), ion-pairing reversed-phase liquid chromatography (IP-RPLC), hydrophobic interaction chromatography (HIC), size-exclusion chromatography (SEC), hydrodynamic chromatography (HDC), highly converging flow ultra-filtration (HCF-UF), asymmetrical flow field-flow fractionation (AF4), mass spectrometry (MS), and atomic force microscopy (AFM)) for analyzing mixtures containing large nucleic acid biopolymers, while assessing their strengths and weaknesses. We then focus comprehensively on the SC technique, report on its past applications since its birth, and review in detail the history and evolution of the proposed retention mechanisms accounting for the observations made in SC. This includes and emphasizes the latest physico-chemical insights (shear rates in packed HPLC columns, entropic elasticity and relaxation of dsDNA, dsRNA, and mRNA biopolymers) governing the retention behavior of such biopolymers in SC. Finally, based on the recent advancements in understanding the fundamentals of retention in SC, we provide some perspectives and recent proof-of-concept for the analytical characterization by SC of large dsDNAs (plasmid digests, polymerase chain reaction (PCR) verification), the separation of supercoiled/circular and linear dsDNAs (plasmid linearization), the isolation and quantification of large dsRNAs impurities present in mRNA samples produced by IVT, and the differentiation between dsRNA conformers.

sgRNA Single-Nucleotide Resolution by Ion-Pairing Reversed-Phase Chromatography

Single-stranded guide RNAs (sgRNAs) are important therapeutic modalities that facilitate selective genome editing by the CRISPR/Cas9 system. While these therapeutic modalities are synthesized through solid phase oligonucleotide synthesis similar to small interfering RNA (siRNAs) and antisense oligonucleotide (ASOs) therapeutics, their sequence length and complex secondary and tertiary structure hinder analytical characterization. The resulting current sgRNA methodologies have limited chromatographic selectivity near the FLP and limited MS compatibility. Here, we perform a systematic evaluation of chromatographic parameters to develop a highly selective ion-pairing reversed-phase chromatography separation for sgRNAs. We identify that stronger and more hydrophobic ion-pairing reagents promote the selectivity for long truncation impurities. Further, reduced flow rates and temperatures promote selectivity near the FLP. Together, this study reports the first single-nucleotide resolution chromatography method for an sgRNA modality while employing a highly MS-compatible mobile phase. This work provides further evidence that the sgRNA chromatographic selectivity is highly independent of on-column mass transfer. This methodology will enable the high-resolution characterization of sgRNA therapeutics, providing further insights into impurity profiles to facilitate toxicological studies and process development of these genetic medicines.

Quantitative Analysis of Phosphorothioate Isomers in CRISPR sgRNA at Single-Residue Resolution Using Endonuclease Digestion Coupled with Liquid Chromatography Cyclic Ion Mobility Mass Spectrometry (LC/cIMS)

Phosphorothioate (PS) modifications in single-guided RNA (sgRNA) are crucial for genome editing applications using the CRISPR/Cas9 system. These modifications may enhance sgRNA stability, pharmacokinetics, and binding to targets, thereby facilitating the desired genetic alterations. Incorporating multiple PS groups at varying positions may introduce chiral centers into the sgRNA backbone, resulting in a complex mixture of constitutional- and stereoisomers that challenges current analytical capabilities for reliable identification and quantification. In this study, we developed an innovative methodology that combines endonuclease digestion of sgRNA with ion pairing reversed-phase liquid chromatography coupled with cyclic ion mobility mass spectrometry (IPRP-LC/cIMS) to fully distinguish PS-induced isomers in a complex mixture. The relative abundance of each isomer was quantified using a two-step method, wherein the ion abundance was sequentially extracted from an LC/MS ion chromatogram and LC/cIMS two-dimensional ion mobiligram. This quantification method was thoroughly evaluated, demonstrating excellent sensitivity, precision, dynamic range, repeatability, and accuracy. In addition, this method enables the investigation of the kinetics of forming PS to phosphodiester (PO) impurities in sgRNA under oxidative stress conditions, offering unprecedented insights into PS stability at a single-residue resolution. In this context, this method highlights the in-depth characterization of PS, demonstrating its capability to support biomedical research, development, and production of sgRNA products.

Applications of hydrophilic interaction and mixed-mode liquid chromatography in pharmaceutical analysis

Hydrophilic Interaction Liquid Chromatography (HILIC) and Mixed-Mode Chromatography (MMC) excel in separating polar, hydrophilic, and charged analytes due to unique hydrophilic or mixed-mode retention mechanisms. They represent a complementary approach to the widely used Reversed Phase Liquid Chromatography (RPLC). Often, where RPLC struggles, HILIC and MMC thrive. The applications of HILIC and MMC in pharmaceutical analysis are expanding rapidly across a variety of drug modalities. This article reviews advances in the applications of HILIC and MMC in seven major areas of pharmaceutical analysis: synthetic small molecules, counterions and salts, lipids and surfactants, carbohydrates, amino acids and peptides, proteins, and nucleic acids in the past two decades. We aim to provide comprehensive information and strategic guidance to facilitate future research, development and applications in these areas.

Mass Spectrometry as a Quantitative Tool for SpCas9 sgRNA Quality Control

Mass spectrometry (MS) has long been used for quality control of oligonucleotide therapeutics, including single-guide RNAs (sgRNAs) for clustered regularly interspaced short palindromic repeats techniques. However, the application of MS is limited to qualitative assays in most cases. Here, we showed that electrospray-ionization quadrupole time-of-flight MS (ESI-QTOF-MS) assays can be quantitative for chemical species found in sgRNA samples. More specifically, using a 100-nt SpCas9 sgRNA as the example, we estimated that the limits of quantification for length variants in the range of N - 4 to N + 4 (i.e., 96-104 nucleotides) were equal to or lower than 1%. Our study highlighted the potential of ESI-QTOF in its application as a quality control method for sgRNA molecules.

Probing the higher order structure of oligonucleotides through anion exchange chromatography

Large synthetic oligonucleotides such as guide ribonucleic acid (gRNA), a critical reagent in clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 genome editing, have complex higher order structures (HOS) inherent in their design. In this study, we first developed a generic anion exchange chromatography (AEX) method for the comprehensive analysis of a 100mer single guide ribonucleic acid (sgRNA) impurity profiling. AEX demonstrated superior resolution compared to other common chromatographic methods employed for sgRNA analysis, such as Ion-Pairing Reversed Phase Liquid Chromatography (IP-RPLC) and Hydrophilic Interaction Chromatography (HILIC). Moreover, we discovered AEX's potential in probing the HOS of RNAs by adjusting the temperature and using organic additives. Our study also highlighted that sgRNA possesses a unique HOS distinctly different from other therapeutic nucleic acids, such as antisense oligonucleotides and messenger RNAs.

Characterization of mRNA therapeutics

Therapeutic messenger RNAs (mRNAs) have emerged as powerful tools in the treatment of complex diseases, especially for conditions that lack efficacious treatment. The successful application of this modality can be attributed to its ability to encode entire proteins. While the large nature of these molecules has supported their success as therapeutics, its extended size creates several analytical challenges. To further support therapeutic mRNA development and its deployment in clinical trials, appropriate methods to support their characterization must be developed. In this review, we describe current analytical methods that have been used in the characterization of RNA quality, identity, and integrity. Advantages and limitations from several analytical techniques ranging from gel electrophoresis to liquid chromatography-mass spectrometry and from shotgun sequencing to intact mass measurements are discussed. We comprehensively describe the application of analytical methods in the measurements of capping efficiency, poly A tail analysis, as well as their applicability in stability studies.

A dual methodology employing ion-pair chromatography and built-in UV spectrophotometry for quantifying recently approved combination of mometasone and indacaterol in a novel combined metered dose inhaler: assessing the greenness, carbon footprint, blueness, and whiteness

Developing analytical techniques that align with green and sustainable chemistry principles is crucial in today's scientific landscape. This work introduces two innovative approaches for the simultaneous quantification of indacaterol (IND) and mometasone (MOM), a recently approved combination therapy for chronic obstructive pulmonary disease. These methods-rapid isocratic ion pair chromatography (IPC) and UV-visible spectrophotometry-demonstrate improved environmental sustainability, cost-effectiveness, and versatility compared to existing techniques. The optimized 4-min IPC method achieved excellent resolution (retention times 2.18 ± 0.1 min for IND and 3.95 ± 0.1 min for MOM), peak symmetry, and sensitivity. It utilizes a low-cost ion pair mobile phase of acetonitrile and acidified water containing 0.025% sodium dodecyl sulfate (50:50% v/v), making it suitable for laboratories with standard chromatographic instruments. The spectrophotometric approach offers two procedures: first derivative and ratio derivative methods. These serve as simplified, low-cost alternatives for resource-limited laboratories without access to advanced instruments. Both techniques feature simplified protocols that minimize extraction and fractionation steps. Comprehensive validation confirmed outstanding accuracy (98-102%) and precision (%2 <). Sustainability assessments using ComplexGAPI, AGREE, carbon footprint, BAGI, and RGB12 tools demonstrated enhanced environmental performance compared to existing methods. The IPC and spectrophotometry methods achieved greenness scores of 0.81 and 0.85, respectively, surpassing the 0.63-0.67 range of reported techniques. Additionally, they showed lower carbon footprints of 0.035 and 0.022 kg CO2 equivalent emissions per sample, compared to 0.079-0.092 kg for conventional procedures. The application of novel "blueness" and "whiteness" concepts using BAGI and RGB12 algorithms further confirmed superior sustainability, with scores of 87.5 & 90 for blueness and 88.1 & 89.8 for whiteness. Successfully applied to quantify IND and MOM in combined capsules, this work provides a model for eco-friendly pharmaceutical analysis that maintains high analytical reliability while improving sustainability metrics.

Stability indicating ion-pair reversed-phase liquid chromatography method for modified mRNA

Modified messenger RNA (mRNA) represents a rapidly emerging class of therapeutic drug product. Development of robust stability indicating methods for control of product quality are therefore critical to support successful pharmaceutical development. This paper presents an ion-pair reversed-phase liquid chromatography (IP-RPLC) method to characterise modified mRNA exposed to a wide set of stress-inducing conditions, relevant for pharmaceutical development of an mRNA drug product. The optimised method could be used for separation and analysis of large RNA, sized up to 1000 nucleotides. Column temperature, mobile phase flow rate and ion-pair selection were each studied and optimised. Baseline separations of the model RNA ladder sample were achieved using all examined ion-pairing agents. We established that the optimised method, using 100 mM Triethylamine, enabled the highest resolution separation for the largest fragments in the RNA ladder (750/1000 nucleotides), in addition to the highest overall resolution for the selected modified mRNA compound (eGFP mRNA, 996 nucleotides). The stability indicating power of the method was demonstrated by analysing the modified eGFP mRNA, upon direct exposure to heat, hydrolytic conditions and treatment with ribonucleases. Our results showed that the formed degradation products, which appeared as shorter RNA fragments in front of the main peak, could be well monitored, using the optimised method, and the relative stability of the mRNA under the various stressed conditions could be assessed.

Comprehensive Impurity Profiling of mRNA: Evaluating Current Technologies and Advanced Analytical Techniques

In vitro transcription (IVT) of mRNA is a versatile platform for a broad range of biotechnological applications. Its rapid, scalable, and cost-effective production makes it a compelling choice for the development of mRNA-based cancer therapies and vaccines against infectious diseases. The impurities generated during mRNA production can potentially impact the safety and efficacy of mRNA therapeutics, but their structural complexity has not been investigated in detail yet. This study pioneers a comprehensive profiling of IVT mRNA impurities, integrating current technologies with innovative analytical tools. We have developed highly reproducible, efficient, and stability-indicating ion-pair reversed-phase liquid chromatography and capillary gel electrophoresis methods to determine the purity of mRNA from different suppliers. Furthermore, we introduced the applicability of microcapillary electrophoresis for high-throughput (<1.5 min analysis time per sample) mRNA impurity profiling. Our findings revealed that impurities are mainly attributed to mRNA variants with different poly(A) tail lengths due to aborted additions or partial hydrolysis and the presence of double-stranded mRNA (dsRNA) byproducts, particularly the dsRNA 3'-loop back form. We also implemented mass photometry and native mass spectrometry for the characterization of mRNA and its related product impurities. Mass photometry enabled the determination of the number of nucleotides of different mRNAs with high accuracy as well as the detection of their size variants [i.e., aggregates and partial and/or total absence of the poly(A) tail], thus providing valuable information on mRNA identity and integrity. In addition, native mass spectrometry provided insights into mRNA intact mass, heterogeneity, and important sequence features such as poly(A) tail length and distribution. This study highlights the existing bottlenecks and opportunities for improvement in the analytical characterization of IVT mRNA, thus contributing to the refinement and streamlining of mRNA production, paving the way for continued advancements in biotechnological applications.

Characterization of synthetic guide ribonucleic acids through hydrophilic interaction chromatography coupled with mass spectrometry

In this study, we aimed to develop a hydrophilic interaction liquid chromatography (HILIC) method for the analysis of single guide ribonucleic acid (sgRNA), a critical reagent used in CRISPR genome editing. Our results showed that effective profiling of sgRNA can be achieved by suppressing the surface charge of the stationary phase in HILIC. We identified hydrogen bonding as the primary retention mechanism with potential weak partitioning in HILIC separation of large oligonucleotides like 100-mer sgRNA. Moreover, we demonstrated that direct coupling of HILIC with mass spectrometry (MS) allows the intact mass analysis of sgRNA and its impurities with minimal adduct present. Finally, we characterized the post peak shown in the low temperature HILIC and identified it as sgRNA aggregates. Our findings provide valuable insight into the characterization of sgRNA and highlight the potential of HILIC-MS as a powerful analytical tool for relatively large oligonucleotide analysis.

Characterization of antisense oligonucleotide and guide ribonucleic acid diastereomers by hydrophilic interaction liquid chromatography coupled to mass spectrometry

Oligonucleotides have become an essential modality for a variety of therapeutic approaches, including cell and gene therapies. Rapid progress in the field has attracted significant research in designing novel oligonucleotide chemistries and structures. Beyond their polar nature, the length of large RNAs and presence of numerous diastereomers for phosphorothioate (PS)-modified RNAs pose heightened challenges for their characterization. In this study, the stereochemistry of a fully-modified antisense oligonucleotide (ASO) and partially-modified guide RNAs (gRNAs) was investigated using HILIC and orthogonal techniques. The profiles of three lots of a fully-modified ASO with PS linkages were compared using ion-pairing RPLC (IPRP) and HILIC. Interestingly, three isomer peaks were partially resolved by HILIC for two lots while only one peak was observed on the IPRP profile. Model oligonucleotides having the same sequence of the five nucleotides incorporated to the 3'-end of the gRNA but differing in their number and position of PS linkages were investigated by HILIC, IPRP, ion mobility spectrometry-mass spectrometry (IM-MS) and nuclear magnetic resonance (NMR). An strategy was ultimately designed to aid in the characterization of gRNA stereochemistry. Ribonuclease (RNase) T1 digestion enabled the characterization of gRNA diastereomers by reducing their number from 32 at the gRNA intact level to 4 or 8 at the fragment level. To our knowledge, this is the first time that HILIC has successfully been utilized for the profiling of diastereomers for various oligonucleotide formats and chemical modifications.

Middle-out sequence confirmation of CRISPR/Cas9 single guide RNA (sgRNA) using DNA primers and ribonuclease T1 digestion

Accurate sequencing of single guide RNAs (sgRNAs) for CRISPR/Cas9 genome editing is critical for patient safety, as the sgRNA guides the Cas9 nuclease to target site-specific cleavages in DNA. An approach to fully sequence sgRNA using protective DNA primers followed by ribonuclease (RNase) T1 digestion was developed to facilitate the analysis of these larger molecules by hydrophilic interaction liquid chromatography coupled with high-resolution mass spectrometry (HILIC-HRMS). Without RNase digestion, top-down mass spectrometry alone struggles to properly fragment precursor ions in large RNA oligonucleotides to provide confidence in sequence coverage. With RNase T1 digestion of these larger oligonucleotides, however, bottom-up analysis cannot confirm full sequence coverage due to the presence of short, redundant digestion products. By combining primer protection with RNase T1 digestion, digestion products are large enough to prevent redundancy and small enough to provide base resolution by tandem mass spectrometry to allow for full sgRNA sequence coverage. An investigation into the general requirements for adequate primer protection of specific regions of the RNA was conducted, followed by the development of a generic protection and digestion strategy that may be applied to different sgRNA sequences. This middle-out technique has the potential to expedite accurate sequence confirmation of chemically modified sgRNA oligonucleotides.

Top-Down Mass Spectrometry of Synthetic Single Guide Ribonucleic Acids Enabled by Facile Sample Clean-Up

In recent years, CRISPR-Cas9 genome editing has become an important technology in biomedical research and has demonstrated tremendous therapeutic potential. With Cas9 endonuclease, the use of single guide ribonucleic acids (sgRNAs) allows for sequence-specific cutting on target double-stranded deoxyribonucleic acids. Therefore, the design and quality of sgRNAs can greatly affect the efficiency and specificity of genome editing. Mass spectrometry (MS) has been a powerful tool to detect molecular features and sequence a variety of biomolecules; however, as the sizes of oligonucleotides get larger, it becomes more challenging to desalt samples and achieve high-quality intact spectra with effective fragmentation. Here, we develop a simple but effective online column-based clean-up method (reversed-phase column in a size exclusion mode) that removes formulation salts and metal adducts from larger oligonucleotides upon entering the mass spectrometer in a consistent manner. Using the top-down approach without any nuclease digestion, we characterized and sequenced 100-nucleotide-long sgRNAs by higher-energy collision dissociation (HCD), collision-induced dissociation (CID), ultraviolet photodissociation (UVPD), and activated electron photodetachment (a-EPD). In a single 10 min liquid chromatography-tandem MS (LC-MS/MS) run, CID yielded the best sequence coverage, of 67%. When adding complementary UVPD and a-EPD runs, we achieved 80% overall sequence coverage and 100% cleavages for the variable sequence, the first 20 nucleotides from the 5' end. This LC-MS/MS platform provides a facile top-down workflow to analyze and sequence larger chemically modified oligonucleotides with no sample treatment.

Characterization of Impurities in Therapeutic RNAs at the Single Nucleotide Level

The chemistry of guide RNA (gRNA) affects the performance of the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 genome editing technique. However, the literature is very scarce about the study of gRNA degradation and in particular at the single nucleotide level. In this work, we developed a workflow to characterize the impurities of large RNAs at the single nucleotide level and identified the residues prone to degradation. Our strategy involves (i) the reduction of RNA length, (ii) a chromatographic mode able to capture subtle changes in impurity polarity, and (iii) a streamlined data treatment. To illustrate the approach, stressed gRNA samples were analyzed by coupling an immobilized ribonuclease T1 cartridge to a hydrophilic interaction liquid chromatography (HILIC) column hyphenated with tandem mass spectrometry (MS/MS). Critical findings were made possible by the presented technology. In particular, the desulfurization of phosphorothioate (PS) linkages was the major degradation observed at the single nucleotide level while no change in purity profile could be observed when using conventional ion-pairing reversed-phase (IPRP) liquid chromatography. To our knowledge, this is the first time that several impurity types are screened for a large RNA molecule using an automated online digestion analysis approach.

Simultaneous quantification of multiple RNA cargos co-loaded into nanoparticle-based delivery systems

Robust, sensitive, and versatile analytical methods are essential for quantification of RNA drug cargos loaded into nanoparticle-based delivery systems. However, simultaneous quantification of multiple RNA cargos co-loaded into nanoparticles remains a challenge. Here, we developed and validated the use of ion-pair reversed-phase high-performance liquid chromatography combined with UV detection (IP-RP-HPLC-UV) for simultaneous quantification of single- and double-stranded RNA cargos. Complete extraction of RNA cargo from the nanoparticle carrier was achieved using a phenol:chloroform:isoamyl alcohol mixture. Separations were performed using either a C₁₈ or a PLRP-S column, eluted with 0.1 M triethylammonium acetate (TEAA) solution as ion-pairing reagent (eluent A), and 0.1 M TEAA containing 25 % (v/v) CH₃CN as eluent B. These methods were applied to quantify mRNA and polyinosinic:polycytidylic acid co-loaded into lipid-polymer hybrid nanoparticles, and single-stranded oligodeoxynucleotide donors and Alt-R CRISPR single guide RNAs co-loaded into lipid nanoparticles. The developed methods were sensitive (limit of RNA quantification < 60 ng), linear (R² > 0.997), and accurate (≈ 100 % recovery of RNA spiked in nanoparticles). Hence, the present study may facilitate convenient quantification of multiple RNA cargos co-loaded into nanoparticle-based delivery systems.

Diving into the Structural Details of In Vitro Transcribed mRNA Using Liquid Chromatography–Mass Spectrometry-Based Oligonucleotide Profiling

The production process of in vitro transcribed messenger RNA (IVT-mRNA)-based vaccines has matured in recent years, partly due to the fight against infectious diseases such as COVID-19. One key to success has been the use of modified, next to canonical, nucleotides and the efficient addition of a Cap-structure and poly A tail to the 5’ and 3’ end, respectively, of this massive biomolecule. These important features affect mRNA stability and impact translation efficiency, consequently boosting the optimization and implementation of liquid chromatography–mass spectrometry (LC–MS)-based oligonucleotide profiling methods for their characterization. This article will provide an overview of these LC–MS methods at a fundamental and application level. It will be shown how LC–MS is implemented in mRNA-based vaccine analysis to determine the capping efficiency and the poly A tail length, and how it allows, via RNA mapping, (i) to determine the mRNA sequence, (ii) to screen the fidelity of the manufactured modifications, and (iii) to identify and quantify unwanted modifications resulting from manufacturing or storage, and sequence variants resulting from mutation or transcription errors.