Theoretical Models of Ion Pair Chromatography: A Close Up of Recent Literature Production

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

Ion-pairing reversed-phase liquid chromatography (IP-RPLC) is the reference separation technique for characterizing oligonucleotides (ONs) and their related impurities. The aim of this study was to better understand the retention mechanism of ONs, evaluate the applicability of the linear solvent strength (LSS) retention model, and explore the potential of ultra-short columns having a length of only 5 mm for the separation of model ONs. First, the validity of the LSS model was evaluated for ONs having sizes comprised between 3 and 30 kDa, and the accuracy of retention time predictions was assessed. It was found that ONs in IP-RPLC conditions follow an "on-off" elution behavior, despite a molecular weight lower than that of proteins. For most linear gradient separation conditions, a column length between 5 and 35 mm was found to be appropriate. Ultra-short columns of only 5 mm were therefore explored to speed up separations by considering the impact of the instrumentation on the efficiency. Interestingly, the impacts of injection volume and post-column connection tubing on peak capacity were found to be negligible. Finally, it was demonstrated that longer columns would not improve selectivity or separation efficiency, but baseline separation of three model ONs mixtures was enabled in as little as 30 s on the 5 mm column. This proof-of-concept work paves the way for future investigations using more complex therapeutic ONs and their related impurities.

The impact of low adsorption surfaces for the analysis of DNA and RNA oligonucleotides

As interest in oligonucleotide (ON) therapeutics is increasing, there is a need to develop suitable analytical methods able to properly analyze those molecules. However, an issue exists in the adsorption of ONs on different parts of the instrumentation during their analysis. The goal of the present paper was to comprehensively evaluate various types of bioinert materials used in ion-pairing reversed-phase (IP-RPLC) and hydrophilic interaction chromatography (HILIC) to mitigate this issue for 15- to 100-mer DNA and RNA oligonucleotides. The whole sample flow path was considered under both conditions, including chromatographic columns, ultra-high-performance liquid chromatography (UHPLC) system, and ultraviolet (UV) flow cell. It was found that a negligible amount of non-specific adsorption might be attributable to the chromatographic instrumentation. However, the flow cell of a detector should be carefully subjected to sample-based conditioning, as the material used in the UV flow cell was found to significantly impact the peak shapes of the largest ONs (60- to 100-mer). Most importantly, we found that the choice of column hardware had the most significant impact on the extent of non-specific adsorption. Depending on the material used for the column walls and frits, adsorption can be more or less pronounced. It was proved that any type of bioinert RPLC/HILIC column hardware offered some clear benefits in terms of adsorption in comparison to their stainless-steel counterparts. Finally, the evaluation of a large set of ONs was performed, including a DNA duplex and DNA or RNA ONs having different base composition, furanose sugar, and modifications occurring at the phosphate linkage or at the sugar moiety. This work represents an important advance in understanding the overall ON adsorption, and it helps to define the best combination of materials when analyzing a wide range of unmodified and modified 20-mer DNA and RNA ONs.

Analytical techniques for characterizing diastereomers of phosphorothioated oligonucleotides

Oligonucleotides have emerged as powerful therapeutics for treating diverse diseases. To fully unlock the therapeutic potential of oligonucleotides, there is still a great need to further improve their drug-like properties. Numerous chemical modifications have been explored to achieve this goal, with phosphorothioation being one of the most widely used strategies. However, phosphorothioate modification produces diastereomers that are reported to have different properties and performances, demanding detailed characterization of these diastereomers. Here we provide an overview of phosphorothioated oligonucleotide diastereomers, covering their origin and configurations, physicochemical and pharmacological properties, and stereo-selective chemical synthesis, followed by a summary of currently available analytical techniques for characterizing these diastereomers, with a focus on liquid chromatography-based approaches, including ion-pair reversed-phase liquid chromatography, anion exchange chromatography, mixed-mode chromatography, and hybrid approaches. Non-chromatographic techniques, such as capillary electrophoresis, spectroscopy and other methods, are also being reviewed.

Performance of ion pairing chromatography and hydrophilic interaction liquid chromatography coupled to charged aerosol detection for the analysis of underivatized amino acids

The charged aerosol detector (CAD) is frequently employed in liquid chromatography for the analysis of small polar and ionizable compounds such as amino acids and amino sugars, which provide a weak chromophore only. Separation of these compounds is achieved by means of ion pair chromatography (IPC), and, more recently, hydrophilic interaction chromatography (HILIC) techniques. However, as the CAD's response is highly dependent on the mobile phase composition, the substantial differences in the mobile phase composition of IPC and HILIC have a distinct impact on the detector's performance. This study was aimed at systematically comparing the performance of IPC and HILIC when coupled to the CAD. Therefore, the separation techniques characterized by their specific mobile phase compositions were evaluated for their influence on the CAD response and the signal-to-noise ratio (S/N) of the amino acids L-alanine, L-leucine, and L-phenylalanine applying the response surface methodology (RSM). The RSM results derived from flow injection analysis (FIA) indicated that the CAD response and thus the obtainable S/N are significantly higher in HILIC compared to IPC where the S/N decreased with the chain length of the applied ion-pairing reagent. In addition, an IPC and a HILIC method, respectively, were developed for the impurity profiling of the branched-chain amino acids (BCAAs) L-leucine, L-isoleucine, and L-valine. The beneficial effects of the HILIC conditions on the S/N observed under FIA conditions were partly offset by moderate column bleed effects when using an amide functionalized column, which facilitates the separation in the HILIC method. Satisfactory LOQs (3-10 ng on column) were obtained with both methods; however, the HILIC method was found to be slightly superior in terms of sensitivity and separation efficiency.

Selectivity limits of and opportunities for ion pair chromatographic separation of oligonucleotides

Here it was investigated how oligonucleotide retention and selectivity factors are affected by electrostatic and non-electrostatic interactions in ion pair chromatography. A framework was derived describing how selectivity depends on the electrostatic potential generated by the ion-pair reagent concentration, co-solvent volume fraction, charge difference between the analytes, and temperature. Isocratic experiments verified that, in separation problems concerning oligonucleotides of different charges, selectivity increases with increasing surface potential and analyte charge difference and with decreasing co-solvent volume fraction and temperature. For analytes of the same charge, for example, diastereomers of phosphorothioated oligonucleotides, selectivity can be increased by decreasing the co-solvent volume fraction or the temperature and has only a minor dependency on the ion-pairing reagent concentration. An important observation is that oligonucleotide retention is driven predominantly by electrostatic interaction generated by the adsorption of the ion-pairing reagent. We therefore compared classical gradient elution in which the co-solvent volume fraction increases over time versus gradient elution with a constant co-solvent volume fraction but with decreasing ion-pair reagent concentration over time. Both modes decrease the electrostatic potential. Oligonucleotide selectivity was found to increase with decreasing ion-pairing reagent concentration. The two elution modes were finally applied to two different model antisense oligonucleotide separation problems, and it was shown that the ion-pair reagent gradient increases the selectivity of non-charge-based separation problems while maintaining charge-difference-based selectivity.

Determination of individual oligonucleotide impurities by small amine ion pair-RP HPLC MS and MS/MS: n - 1 impurities

Ion pair-reversed phase (IP-RP) HPLC is one of the most widely used methods for the analysis of oligonucleotide impurities. The method is compatible with mass spectrometry and has been used to guide the development of improved synthesis and purification approaches. The ability to detect and characterize impurities depends on the reagents and the IP buffer system employed, as each can directly affect the degree of chromatographic separation and the sensitivity of detection by MS. Previous work in our laboratory has shown that small alkyl amines are suitable IP reagents for the analysis of impurities in phosphate diester oligonucleotides and can be used to differentiate among individual members of composite impurity families. The addition of an alkyl acid often further enhances peak separation, but at the detriment of ion signal. An improved method with increased chromatographic performance and sensitivity of detection is presented here. Improvements were mainly realized through the use of lower concentrations of small alkyl amine (i.e., 5 mM) and acid (0.5 mM) IP reagents, and ammonium bicarbonate (20 mM) as a buffer. The improved capabilities of the new method are demonstrated by separation of the individual components of the composite n - 1 impurity in a set of four production-scale batches of a single oligonucleotide. Addition of the alkyl acid resulted in resolution of most individual n - 1 impurities. The observed enhanced sensitivity of detection allowed multiple reaction monitoring (MRM) experiments, which were used to differentiate among unresolved impurities.

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.

Fluoroalkylamines: Novel, Highly Volatile, Fast-Equilibrating, and Electrospray Ionization-Mass Spectrometry Signal-Enhancing Cationic Ion-Interaction Reagents

A new class of cationic ion-interaction reagents for reversed-phase chromatography is introduced in the present work. Compounds belonging to a homologous series of linear fluoroalkyl chains including trifluoroethylamine (TFEAm), pentafluoropropylamine (PFPAm), heptafluorobutylamine (HFBAm), and nonafluoropentylamine (NFPAm) were tested and compared with ammonia and triethylamine (TEA) for the separation of selected organic acids of general interest such as the herbicides glyphosate, ethephon, and fosamine and arsenic metabolites methylarsonic acid and dimethylarsinic acid as well as other compounds. Depending on the carbon and fluorine atom number, the fluoroalkylamines were shown to be effective cationic ion-interaction reagents, significantly enhancing the retention of organic acids on a C18 reversed-phase column. Contrary to the general behavior of ion-interaction reagents (a broader term than ion-pairing reagent), significant (up to 5-fold) and consistent enhancement in the electrospray ionization mass spectrometry signal (ESI-MS) was observed relative to ammonia and triethylamine. Overall, among the tested series HFBAm was found to offer the best overall properties among the tested series as it provided a good compromise between column equilibration time (ca. 25 column volumes) and retention behavior (up to a 10-fold increase in the retention factor of acids relative to ammonia) while providing the same general advantages found for the fluoroalkylamines such as fast washout times from the ESIMS system (ca. 30 min) and a 3–5-fold signal enhancement. The fluoroalkylamines are a new class of cationic ion-interaction reagents with clear advantages over the currently employed alkylamines and may revive the general interest in ion-interaction chromatography.

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.

Simultaneous Determination of Trigonelline, Caffeine, Chlorogenic Acid and Their Related Compounds in Instant Coffee Samples by HPLC Using an Acidic Mobile Phase Containing Octanesulfonate

In order to analyze trigonelline, caffeine, chlorogenic acid, and their related compounds simultaneously, an HPLC method using an InertSustain C18 column and a mobile phase containing octanesulfonate as an ion-pairing reagent under an acidic condition was developed. The optimum mobile phase conditions were determined to be 0.1% phosphoric acid, 4 mM octanesulfonate, and 15% methanol at 35°C. Using the proposed method, trigonelline, nicotinic acid, caffeine, theophylline, chlorogenic acid, and caffeic acid in ten instant coffee samples were analyzed. These analytes except for theophylline were detected in all samples. An increase in the caffeine content in instant coffee samples tended to decrease in both trigonelline and chlorogenic acid contents, and the trigonelline content was found to be correlated well with the chlorogenic acid content (R(2) = 0.887).