Strategies for predictive modeling of overloaded oligonucleotide elution profiles in ion-pair chromatography

Due to their potential for gene regulation, oligonucleotides have moved into focus as one of the preferred modalities modulating currently undruggable disease-associated targets. In the course of synthesis and storage of oligonucleotides a significant number of compound-related impurities can be generated. Purification protocols and analytical methods have become crucial for the therapeutic application of any oligonucleotides, be they antisense oligonucleotides (ASOs), small interfering ribonucleic acids (siRNAs) or conjugates. Ion-pair chromatography is currently the standard method for separating and analyzing therapeutic oligonucleotides. Although mathematical modeling can improve the accuracy and efficiency of ion-pair chromatography, its application remains challenging. Simple models may not be suitable to treat advanced single molecules, while complex models are still inefficient for industrial oligonucleotide optimization processes. Therefore, fundamental research to improve the accuracy and simplicity of mathematical models in ion-pair chromatography is still a necessity. In this study, we predict overloaded concentration profiles of oligonucleotides in ion-pair chromatography and compare relatively simple and more advanced predictive models. The experimental system consists of a traditional C18 column using (dibutyl)amine as the ion-pair reagent and acetonitrile as organic modifier. The models were built and tested based on three crude 16-mer oligonucleotides with varying degrees of phosphorothioation, as well as their respective n - 1 and (P = O)1 impurities. In short, the proposed models were suitable to predict the overloaded concentration profiles for different slopes of the organic modifier gradient and column load.

Evaluating orthogonality between ion-pair reversed phase, anion exchange, and hydrophilic interaction liquid chromatography for the separation of synthetic oligonucleotides

The orthogonality of separation between ion-pair reversed phase (IP-RP), anion exchange (AEX), and hydrophilic interaction liquid chromatography (HILIC) was evaluated for oligonucleotides. A polythymidine standard ladder was first used to evaluate the three methods and showed zero orthogonality, where retention and selectivity were based on oligonucleotide charge/size under all three conditions. Next, a model 23-mer synthetic oligonucleotide containing 4 phosphorothioate bonds with 2' fluoro and 2'-O-methyl ribose modifications typical of small interfering RNA was used for evaluating orthogonality. The resolution and orthogonality were evaluated between the three modes of chromatography in terms of selectivity differences for nine common impurities, including truncations (n-1, n-2), addition (n + 1), oxidation, and de-fluorination. We first evaluated different ion-pairing reagents that provided the best separation of the key impurities while suppressing diastereomer separation due to phosphorothioate linkages. Although different ion-pairing reagents affected resolution, very little orthogonality was observed. We then compared the retention times between IP-RP, HILIC, and AEX for each impurity of the model oligonucleotide and observed various selectivity changes. The results suggest that coupling HILIC with either AEX or IP-RP provide the highest degree of orthogonality due to the differences in retention for hydrophilic nucleobases and modifications under HILIC conditions. IP-RP provided the highest overall resolution for the impurity mixture, whereas more co-elution was observed with HILIC and AEX. The unique selectivity patterns offered by HILIC provides an interesting alternative to IP-RP or AEX, in addition to the potential for coupling with multidimensional separations. Future work should explore orthogonality for oligonucleotides with subtle sequence differences such as nucleobase modifications and base flip isomers, longer strands such as guide RNA and messenger RNA, and other biotherapeutic modalities such as peptides, antibodies, and antibody-drug-conjugates.

Development of a unified gradient theory for ion-pair chromatography using oligonucleotide separations as a model case

Ion-pair chromatography is the de facto standard for separating oligonucleotides and related impurities, particularly for analysis but also often for small-scale purification. Currently, there is limited understanding of the quantitative modeling of both analytical and overloaded elution profiles obtained during gradient elution in ion-pair chromatography. Here we will investigate a recently introduced gradient mode, the so-called ion-pairing reagent gradient mode, for both analytical and overloaded separations of oligonucleotides. The first part of the study demonstrates how the electrostatic theory of ion-pair chromatography can be applied for modeling gradient elution of oligonucleotides. When the ion-pair gradient mode is used in a region where the electrostatic surface potential can be linearized, a closed-form expression of retention time can be derived. A unified retention model was then derived, applicable for both ion-pair reagent gradient mode as well as co-solvent gradient mode. The model was verified for two different experimental systems and homo- and heteromeric oligonucleotides of different lengths. Quantitative modeling of overloaded chromatography using the ion-pairing reagent gradient mode was also investigated. Firstly, a unified adsorption isotherm model was developed for both gradient modes. Then, adsorption isotherms parameter of a model oligonucleotide and two major synthetic impurities were estimated using the inverse method. Secondly, the parameters of the adsorption isotherm were then used to investigate how the productivity of oligonucleotide varies with injection volume, gradient slope, and initial retention factor. Here, the productivity increased when using a shallow gradient slope combined with a low initial retention factor. Finally, experiments were conducted to confirming some of the model predictions. Comparison with the conventional co-solvent gradient mode showed that the ion-pairing reagent gradient leads to both higher yield and productivity while consuming less co-solvent.

Retention behaviors of pre-column derivatized mono-, di- and oligosaccharides in various modes of high performance liquid chromatography

Three LC-based methods, including reversed-phase chromatography (RPC), ion-pair RPC and weak anion-exchange chromatography (WAX), were examined in the separations of precolumn derivatized mono- and oligosaccharides with the following three tagging agents: 1-naphthylamine (1-NA), 2-aminoanthracene (2-AA), and 3-amino-2,7-naphthalenedisulfonic acid (ANDSA). Due to differences in their charges and polarity, the three tagging agents imparted the sugar derivatives varying elution patterns in the three, just mentioned, chromatographic modes. While RPC yielded high resolution separations for 1-NA- and 2-AA-sugar derivatives, ion-pair RPC in the presence of the ion-pairing agent dodecyl trimethylammonium bromide (DTAB) in the mobile phase exhibited far more resolution and selectivity than WAX in the separation of ANDSA-sugar derivatives. This finding portrays the fact that an octadecyl column operating in ion-pair RPC mode can eliminate in most cases the need for an ion-exchange column for bioanalytical separations of ionic or ionizable species. Lastly, the characteristics of each chromatographic mode in the analysis of derivatized sugars are described using various mobile phase compositions.

A closer study of overloaded elution bands and their perturbation peaks in ion-pair chromatography

There is strong renewed interest in ion-pair chromatography (IPC) because of its great importance for separating new-generation biosimilar pharmaceuticals such as oligonucleotides. Due to the complexity of the IPC process, its mathematical modeling is challenging, especially in preparative mode. In a recent study, Leśko et al. (2021) developed a mathematical model for predicting, with good accuracy, overloaded concentration profiles for sodium benzenesulfonate, describing how the overloaded solute concentration profiles change from Langmuirian to complicated U-shaped, and then back again to Langmuirian profiles, with increasing concentration of the ion-pair reagent in the mobile phase. This study identifies and explains the underlying mechanism generating these complex peak shapes and band-shape transformations; this was only possible by visualizing and modeling the underlying equilibrium perturbations that occur upon injection in preparative IPC. In the 2021 study, the model was derived based on the concentration profiles obtained using a conventional UV detector principle, so the concentration gradients and perturbation zones of the mobile-phase components were not visualized. In this study, the necessary mechanistic information was obtained via complementary experiments combining two detection principles, i.e., refractive index detection and UV detection, with modeling efforts. The models correctly described the invisible equilibrium perturbations and how these formed internal gradients of the mobile-phase components. The models also explained the complex overloaded solute-band deformations reported in the recent study. In addition, a rule of thumb was developed for predicting experimental conditions that could result in deformed solute elution profiles and/or for avoiding these deformations. The latter is crucial for the practical chromatographer, since such U-shaped solute-band profiles are undesirable in preparative separation due to the broader elution zones, resulting in lower productivity than that of normal band shapes.

Fluorinated carboxylic acids as "ion repelling agents" in reversed-phase chromatography

Fluorinated carboxylic acids have been in use as ion-pairing reagents for over three decades. It has been observed that ion-pairing reagents not only increase the retention of oppositely charged analytes on reversed-phase HPLC columns but also decrease the retention of similarly charged analytes; these latter effects, however, have not been thoroughly investigated for the fluorinated carboxylic acids, and the application of these reagents has been rather restricted to their ion-pairing capacity to separate basic analytes. In the present study, we report a systematic investigation about the effects of three fluorinated carboxylic acids (trifluoroacetic acid (TFA), pentafluoropropionic acid (PFPA), and heptafluorobutyric acid (HFBA)) on the retention and selectivity of the separation of halogenated carboxylic acids and sulfonic acids by reversed-phase chromatography with an inductively coupled plasma mass spectrometry detector (ICPMS). Several eluents were tested and compared at different concentrations (0-100 mM) and pH values, including sulfate, nitrate, phosphate, oxalate, TFA, PFPA, and HFBA. The fluorinated carboxylic acids resulted in a consistent decrease in the retention factors (up to ca. 9-fold with HFBA) in a concentration dependent manner, which plateaued at around 50 mM. Significant improvement of the peak symmetry of the chromatographed acids was also observed. We highlight the advantages of incorporating the fluorinated carboxylic acids in modifying the selectivity and retention of organic acids in reversed phase chromatography in general, and particularly when employing chromatographic detectors with limited compatibility with organic mobile phases such as the ICPMS.

Low pressure ion pair chromatography with amperometric detection for the determination of trigonelline in coffee samples

In this work, the use of ion pair chromatography strategy in low pressure chromatographic flow systems is explored for the first time. The straightforward flow manifold encompassed a peristaltic pump, an injection valve and a 1 cm-length C₁₈ monolithic column. The amperometric detection system relied on a boron-doped diamond electrode, used as working electrode. The determination of trigonelline in coffee samples was the case-study selected. This alkaloid is an important quality marker for this commodity and is usually determined using HPLC-UV methodologies. The proposed methodology, based on ion-pair chromatography with amperometric detection, enabled the quantitative resolution of the studied analyte from the matrix compounds by adding to the mobile phase the ion pair reagent, 1-tetradecanosulfonate sodium. The present work, following the recent developments of the low pressure chromatography approach, demonstrates the potentialities of coupling monolithic columns to traditional flow analysis systems for separation and quantification of ionic or ionisable compounds.

Alkylamine ion-pairing reagents and the chromatographic separation of oligonucleotides

Alkylamines are commonly used to improve both chromatographic and mass spectral performance of electrospray ionization liquid chromatography mass spectrometry based methods for the analysis of oligonucleotides. Recently several new alkylamines have been introduced to enhance the electrospray mass spectral response for oligonucleotides; however, the chromatographic properties of these new alkylamines have not been rigorously assessed. We have investigated the retention, peak width, resolution and general chromatographic performance of fifteen different alkylamines for the separation of a model DNA, RNA and an antisense therapeutic oligonucleotide. Eleven of the fifteen alkylamines were shown to provide similar chromatographic performance across all three classes of oligonucleotides. Based on these findings, a model for the mechanism of retention of oligonucleotides using alkylamines and hexafluoroisopropanol mobile phases is proposed. Depending on the concentrations of alkylamines and pH adjustment, oligonucleotides can be retained by micellar chromatography and not the generally held ion-pairing mechanism. This conclusion is supported by light scattering, transmission electron microscopy and ion mobility experiments detecting three micron aggregates in the mobile phase at concentrations that are routinely used for LC-MS analysis of oligonucleotides. These aggregates are not detected at lower alkylamine concentrations where the retention mechanism follows an ion-pairing mechanism. The formation of these aggregates appears to be dependent on the pH of the mobile phase.

Quantification of nucleotides and their sugar conjugates in biological samples: Purposes, instruments and applications

Nucleotides and their sugar conjugates are fundamental molecules in life, participating in processes of DNA/RNA composition, cell wall build-up, glycosylation reactions, and signal conduction. Therefore, the quantification of these compounds in biological samples significantly benefits the understanding of their functions. However, nucleotides and nucleotide sugars are extremely hydrophilic, causing bad retention and peak symmetry on regular C18 chromatographic columns. To solve this problem, ion-pair (IP) chromatography, ion-exchange (IE) chromatography and hydrophilic interaction chromatography (HILIC) were applied, of which differentiated mechanisms were utilized to increase the retention of the analytes on the stationary phases. IP-HPLC and HILIC were convenient for coupling with many kinds of detectors (ultraviolet, UV or mass spectrometry, MS). Combining these two kinds of techniques, the advantages of better separation and retention were increased, while disadvantages like irreversible adsorption by stationary phases were greatly decreased. Due to the high concentrations of nonvolatile buffer salts used, IE-HPLC was not suitable for MS detectors. Protein precipitation and solid phase extraction were the common methods for sample treatment in the analysis of nucleotides and nucleotide sugars. By carefully optimizing the LCUV or LCMS conditions, high sensitivities could be achieved, and the methods could be applied to the analysis of many kinds of biological samples (cells, tissues, plants, bacteria, etc.). Developing new analyzing techniques may help the utilization of nucleotides and nucleotide sugars in the diagnosis and therapy of diseases.

Degradation product characterization of therapeutic oligonucleotides using liquid chromatography mass spectrometry

Synthetic antisense phosphorothioate oligonucleotides (PS) have undergone rapid development as novel therapeutic agents. The increasing significance of this class of drugs requires significant investment in the development of quality control methods. The determination of the many degradation pathways of such complex molecules presents a significant challenge. However, an understanding of the potential impurities that may arise is necessary to continue to advance these powerful new therapeutics. In this study, four different antisense oligonucleotides representing several generations of oligonucleotide therapeutic agents were evaluated under various stress conditions (pH, thermal, and oxidative stress) using ion-pairing reversed-phase liquid chromatography tandem mass spectrometry (IP-RPLC-MS/MS) to provide in-depth characterization and identification of the degradation products. The oligonucleotide samples were stressed under different pH values at 45 and 90 °C. The main degradation products were observed to be losses of nucleotide moieties from the 3'- and 5'-terminus, depurination, formation of terminal phosphorothioates, and production of ribose, ribophosphorothioates (Rp), and phosphoribophosphorothioates (pRp). Moreover, the effects of different concentrations of hydrogen peroxide were studied resulting in primarily extensive desulfurization and subsequent oxidation of the phosphorothioate linkage to produce the corresponding phosphodiester. The reaction kinetics for the degradation of the oligonucleotides under the different stress conditions were studied and were found to follow pseudo-first-order kinetics. Differences in rates exist even for oligonucleotides of similar length but consisting of different sequences. Graphical abstract Identification of degradation products across several generations of oligonucleotide therapeutics using LC-MS.

Offline comprehensive liquid chromatography in combination with a Deoxyribonuclease I immobilized enzymatic reactor for selective screening of oligonucleotide mixtures

The development of a comprehensive ion-pair chromatography-immobilized enzyme reactor×ion-pair chromatography (IPC-IMER×IPC) methodology for the advanced characterization of DNA/RNA oligonucleotides (ONs) mixtures has been carried out. More in detail, a DNase I IMER has been coupled to IPC in the post column configuration, followed by the collection of the eluting fractions and reanalysis by IPC. The effect of the mobile phase over the IMER activity was qualitatively evaluated. The methodology proved to generate relevant ON degradation profiles that might be correlated with the ON stability towards nucleases. Moreover, this platform shows potential for its further implementation in selective analysis of ON mixtures and in mapping studies.

Hyphenation of a Deoxyribonuclease I immobilized enzyme reactor with liquid chromatography for the online stability evaluation of oligonucleotides

The stability of antisense oligonucleotides (ONs) toward nucleases is a key aspect for their possible implementation as therapeutic agents. Typically, ON stability studies are performed off-line, where the ONs are incubated with nucleases in solution, followed by their analysis. The problematics of off-line processing render the detailed comparison of relative ON stability quite challenging. Therefore, the development of an online platform based on an immobilized enzyme reactor (IMER) coupled to liquid chromatography (LC) was developed as an alternative for improved ON stability testing. More in detail, Deoxyribonuclease I (DNase I) was immobilized on epoxy-silica particles of different pore sizes and packed into a column for the construction of an IMER. Subsequently, the hyphenation of the IMER with ion-pair chromatography (IPC) and ion-exchange chromatography (IEC) was evaluated, leading to the successful development of two online methodologies: IMER-IPC and IMER-IEC. More specifically, natural and modified DNA and RNA oligonucleotides were used for testing the performance of the methodologies. Both methodologies proved to be simple, automatable, fast and highly reproducible for the quantitative and qualitative evaluation of ON degradation. In addition, the extended IMER life time in combination with a more straightforward control of the reaction kinetics substantiate the applicability of the IMER-LC platform for ON stability tests and its implementation in routine and research laboratories.

Different approaches to quantitative structure-retention relationships in the prediction of oligonucleotide retention

Quantitative structure-retention relationships studies were performed for cholesterol and alkylamide stationary phases, which were previously applied in the analysis of nucleotides and oligonucleotides. An octadecyl column was also tested. Twenty-four oligonucleotides of various sequences and length were chosen; next, their structural descriptors were determined with the use of quantum-mechanics method. The sequence features were related mainly to their surface area, hydrophobicity, and the nature of nucleobases. Moreover, for the first time models employing experimentally derived descriptors (the sum of retention factor for individual nucleotides) were developed in the quantitative structure-retention relationship studies of these compounds. The retention of oligonucleotides for alkylamide and cholesterol stationary phases may be effectively predicted with the use of quantitative structure-retention relationship models based only on molecularly modeled descriptors, as well as with models employing experimentally derived descriptors. Therefore, we recommend the first approach, since descriptors may be easily and quickly calculated. However, oligonucleotide retention prediction for octadecyl phases gives better results, when individual nucleotide retention factors are known and utilized for the creation of a mathematical model.

Combining liquid chromatography with multiplexed capillary gel electrophoresis for offline comprehensive analysis of complex oligonucleotide samples

Offline two dimensional liquid chromatography (LC)×capillary gel electrophoresis (CGE) and LC×(24) multiplexed-CGE methodologies were developed for the separation of oligonucleotides of therapeutic size. Both ion-pair chromatography (IPC) and ion-exchange chromatography (IEC) were studied as methods for the first dimension and single and multiplexed capillary electrophoresis methods in entangled polymer solutions were used for the second dimension separations. Electrokinetic and pressure injection were evaluated for the analysis of the collected LC fractions. The comprehensive separation was optimized with standard mixtures of poly adenosine, thymidine, cytosine and uracil homodeoxyoligonucleotides up to 35 bases long. Highly orthogonal methodologies and overall peak capacities of 6435 and 6993 for IPC×CGE and IEC×CGE, respectively, were obtained within a few hours analysis time.