Capillary monoliths for the analysis of nucleic acids by high-performance liquid chromatography–electrospray ionization mass spectrometry

Styrene-based polymerised high internal phase emulsions using monomers in the internal phase as co-surfactants for improved liquid chromatography

Poly(styrene-co-divinylbenzene)-based monoliths were prepared from the polymerisation of water-in-monomer high internal phase emulsions, where the water-soluble monomers acrylamide (AAm) or poly(ethylene glycol) diacrylate (PEGDA) (M w 258) were also included in the 90 vol% internal phase. Both AAm and PEGDA were found to act as co-surfactants, resulting in the obtainment of monoliths with greater homogeneity in some cases. As a result these materials demonstrated significantly improved chromatographic performance for the separation of a standard mixture of proteins using reversed-phase liquid chromatography, in comparison to monoliths prepared with no internal phase monomer. In particular, the columns grafted with PEGDA were capable of separating a more complex mixture consisting of seven components. The inclusion of monomers in the internal phase also allowed for the functionalisation of the monolith's surface where the degree of polymerisation that occurred in the internal phase, which was governed by the monomer content in the internal phase and initiation location, determined whether polymeric chains or a hydrogel were grafted to the surface. A monolith grafted with AAm was also found to be capable of retaining polar analytes as a result of the increase in surface hydrophilicity.

Evaluation of micropillar array columns for chromatographic separation of phosphorothioated oligonucleotides and their diastereomers

Chromatographic analysis of therapeutic oligonucleotides is challenging due to the presence of closely related impurities, degradants or metabolites and due to the presence of phosphorothioate bonds, which introduce chiral centers. In the present study, ion pair reversed phase chromatography of oligonucleotides on micropillar array columns was investigated. Two commonly used mobile phase conditions were included. With 16.3 mM triethylamine and 400 mM hexafluoroisopropanol, the separation of 16-mer oligonucleotides differing in the number and positions of phosphorothioate linkages as well as some n-1 and n-2 truncations demonstrated complete suppression of diastereoselectivity. Although the positional phosphorothioate isomers evaluated could not be resolved, an increase in phosphorothioate bonds resulted in more retention. A therapeutic 19-mer RNA sequence with 2'-fluor and 2'-O-methyl modifications showed partial separation of some very close impurities. When using 15 mM triethyl ammonium acetate in the mobile phase, diastereomer selectivity was clearly observed for all analytes. The best result was obtained for the 19-mer RNA therapeutic mimic with four phosphorothioate bonds, since all 16 theoretical diastereomers were clearly observed under the conditions tested. A limited benchmark exercise demonstrated the improved capability of the new micropillar array columns. Therefore, these columns can be positioned as a valuable alternative when challenging oligonucleotide separations are expected.

Performance of functionalized monolithic silica capillary columns with different mesopore sizes using radical polymerization of octadecyl methacrylate

We report on the possibility to enhance the phase ratio and retention factor in silica monoliths. According to pioneering work done by Núñez et al. [1], this enhancement is pursued by applying a stationary phase layer via radical polymerization with octadecyl methacrylate (ODM) as an alternative to the customary octadecylsilylation (C18-derivatization). The difference in band broadening, retention factor and separation selectivity between both approaches was compared. Different hydrothermal treatment temperatures for the column preparation were applied to produce monolithic silica structures with three different mesopore sizes (resp. 10, 13, and 16 nm, as determined by argon physisorption) while maintaining similar domain size (sum of through-pore and skeleton size). It has been found that the columns with the poly(octadecyl methacrylate)-phase (ODM columns) provided a 60 to 80% higher retention factor in methanol-water mixture compared to the octadecylsilylated (ODS) columns produced by starting from similar silica backbone structures. In acetonitrile-water mixture, the enhancement is smaller (15 to 30% times higher), yet significant. By adjusting the fabrication conditions (for both the preparation of the monolithic backbones and the surface functionalization), the achieved retention factors (up k = 4.89 for pentylbenzene in 80:20% (v/v) methanol/water) are obviously higher than obtained in the pioneering study on ODM monoliths of Núñez et al. [1], and column clogging could be completely avoided. In addition, also separation efficiencies were significantly higher than shown in Ref. [1], with plate heights as low as 5.8 μm. These plate heights are however inferior to those observed on the ODS-modified sister columns. The difference can be explained by the slower intra-skeleton diffusion displayed by the ODM-modified columns, in turn caused by the larger obstruction to diffusion originating from the thicker stationary phase layer.

Silica-Based Monolithic Columns as a Tool in HPLC-An Overview of Application in Analysis of Active Compounds in Biological Samples

Monolithic fillings used in chromatography are of great interest among scientists since the first reports of their synthesis and use were published. In the 20 years since silica-based monolithic columns were introduced into the commercial market, numerous papers describing their chromatographical properties and utility in various branches of industry and scientific investigations were presented. This review is focused on possible applications of commercially available silica-based HPLC monolithic columns in the analysis of biological samples.

Monolithic carbon xerogel with co-continuous hierarchical porosity via one-step, template- and catalyst-free hydrothermal reaction with resorcinol and formaldehyde

Monolithic carbon xerogel (MCX) with co-continuous hierarchical porosity was prepared via a one-step, template- and catalyst-free hydrothermal polycondensation reaction with resorcinol, formaldehyde and distilled water.

Template-free synthesis of monolithic carbon xerogels with hierarchical porosity from resorcinol and formaldehyde via hydrothermal reaction

Monolithic carbon xerogels with hierarchical porosity were prepared from resorcinol (R) and formaldehyde (F) via a base-catalysed hydrothermal polycondensation reaction, without a template and supercritical drying. First, an aqueous solution of resorcinol, formaldehyde and sodium carbonate was prepared by varying R/W (25–45) and R/C (1–10k) ratios to produce monolithic RF gels. The reaction was carried out in a pressurized Teflon mould at 100 °C for 6 h to give a co-continuous pore structure via spinodal decomposition and a tenacious gel to avoid supercritical drying. Next, the RF gels were dried for 42 h at 60 °C and another 6 h at 100 °C to produce RF xerogels without cracks, followed by pyrolysis in a tube furnace at 900 °C for 2 h under N₂ flow, and then activation at 1000 °C for 2, 4 or 6 h under CO₂ flow. Finally, the carbon xerogels were characterized by SEM and N₂ adsorption–desorption measurements. Monolithic RF gels were obtained from all combinations of R/W and R/C, but the gels from R/W = 45 exhibited a co-continuous large-pore structure, providing a specific surface area (SSA) of ∼650 m² g⁻¹, which increased to 3311 m² g⁻¹ (for R/C = 10k) at 6 h of CO₂ activation without exhibiting cracks. N₂ isotherms demonstrated that micro- and meso-pores were introduced via activation, forming hierarchical porosity in combination with large pores from spinodal decomposition without using a template.

Monolithic porous carbon with hierarchical porosity via a one-step template-free hydrothermal polycondensation reaction with resorcinol and formaldehyde.

Nucleic acid separations using superficially porous silica particles

Ion pair reverse-phase liquid chromatography has been widely employed for nucleic acid separations. A wide range of alternative stationary phases have been utilised in conjunction with ion pair reverse-phase chromatography, including totally porous particles, non-porous particles, macroporous particles and monolithic stationary phases. In this study we have utilised superficially porous silica particles in conjunction with ion pair reverse-phase liquid chromatography for the analysis of nucleic acids. We have investigated a range of different pore-sizes and phases for the analysis of a diverse range of nucleic acids including oligonucleotides, oligoribonucleotides, phosphorothioate oligonucleotides and high molecular weight dsDNA and RNA. The pore size of the superficially porous silica particles was shown to significantly affect the resolution of the nucleic acids. Optimum separations of small oligonucleotides such as those generated in RNase mapping experiments were obtained with 80Å pore sizes and can readily be interfaced with mass spectrometry analysis. Improved resolution of larger oligonucleotides (>19mers) was observed with pore sizes of 150Å. The optimum resolution for larger dsDNA/RNA molecules was achieved using superficially porous silica particles with pore sizes of 400Å. Furthermore, we have utilised 150Å pore size solid-core particles to separate typical impurities of a fully phosphorothioated oligonucleotide, which are often generated in the synthesis of this important class of therapeutic oligonucleotide.

Genotyping of Toxic Pufferfish Based on Specific PCR-RFLP Products As Determined by Liquid Chromatography/Quadrupole-Orbitrap Hybrid Mass Spectrometry

A method based on liquid chromatography-electrospray mass spectrometric analysis of the enzymatically digested amplicons derived from the mitochondrial 16S rRNA gene was established for the discrimination of toxic pufferfish. A MonoBis C18 narrow-bore silica monolith column (Kyoto Monotech) and a Q Exactive mass spectrometer (Thermo Fisher) were employed for separation and detection, respectively. Monoisotopic masses of the oligonucleotides were calculated using Protein Deconvolution 3.0 software (Thermo Fisher). Although a lock mass standard was not used, excellent accuracy (mass error, 0.83 ppm on average) and precision (relative standard deviation, 0.49 ppm on average) were achieved, and a mass accuracy of <2.8 ppm was maintained for at least 180 h without additional calibration. The present method was applied to 29 pufferfish samples, and results were consistent with Sanger sequencing.

Simultaneous Determination of Five Alkaloid Compounds in a Drug Based on a Hydrophilic Monolithic Column by Capillary Electrochromatography

A novel capillary electrochromatography (CEC) method was developed by using a hydrophilic monolithic column for the simultaneous determination of five alkaloids in a drug. The monolithic stationary phase was first prepared via in situ polymerization of acrylamide (AM), glycidyl methacrylate (GMA), N,N'-methylenebisacrylamide (MBA) and 2-acrylamido-2-methyl-1-propane-sulfonic acid (AMPS) in a ternary porogen solvent system consisting of cyclohexanol, dodecanol and toluene. The obtained monolithic stationary phase was subsequently modified by 0.1 mol/L ammonia water for opening epoxide groups of GMA. The separation performance and efficiency of the resulting monolithic column were investigated by the use of five compounds (thiourea, aniline, naphthylamine, diphenylamine and dimethyl acetamide) by CEC. The optimized monolithic column has obtained high column efficiencies with 74,000-121,000 theoretical plates/m. Finally, the prepared monolithic column was used to separate and determine five alkaloids (piperine, nuciferine, kukoline, berberine and tetrandrine) using CEC. Under the conditions of acetonitrile/10 mM phosphate buffer solution (65/35, v/v, pH 8.5) and 15 kV applied voltage, the baseline separation of five alkaloids was achieved. The proposed method has been successfully applied to the determination of berberine in a tablet sample. The percentage of recovery of spiked tablet samples ranged from 93.4 to 108.0% with relative standard deviations (RSDs) <9.20%.

Synthetic oligonucleotide separations by mixed-mode reversed-phase/weak anion-exchange liquid chromatography

Synthetic oligonucleotides gain increasing importance in new therapeutic concepts and as probes in biological sciences. If pharmaceutical-grade purities are required, chromatographic purification using ion-pair reversed-phase chromatography is commonly carried out. However, separation selectivity for structurally closely related impurities is often insufficient, especially at high sample loads. In this study, a "mixed-mode" reversed-phase/weak anion exchanger stationary phase has been investigated as an alternative tool for chromatographic separation of synthetic oligonucleotides with minor sequence variations. The employed mixed-mode phase shows great flexibility in method development. It has been run in various gradient elution modes, viz. one, two or three parameter (mixed) gradients (altering buffer pH, buffer concentration, and organic modifier) to find optimal elution conditions and gain further insight into retention mechanisms. Compared to ion-pair reversed-phase and mere anion-exchange separation, enhanced selectivities were observed with the mixed-mode phase for 20-23 nucleotide (nt) long oligonucleotides with similar sequences. Oligonucleotides differing by 1, 2 or 3 nucleotides in length could be readily resolved and separation factors for single nucleotide replacements declined in the order Cytosine (C)/Guanine (G)>Adenine (A)/Guanine∼Guanine/Thymine (T)>Adenine/Cytosine∼Cytosine/Thymine>Adenine/Thymine. Selectivities were larger when the modification was at the 3' terminal-end, declined when it was in the middle of the sequence and was smallest when it was located at the 5' terminus. Due to the lower surface area of the 200Å pore size mixed-mode stationary phase compared to the corresponding 100Å material, lower retention times with equal selectivities under milder elution conditions were achievable. Considering high sample loading capacities of the mixed-mode anion-exchanger phase, it should have great potential for chromatographic oligonucleotide separation and purification.

Comparison of mobile-phase systems commonly applied in liquid chromatography-mass spectrometry of nucleic acids

LC-MS represents an important technology for the qualitative and quantitative analysis of nucleic acids. For MS, ESI in negative ion mode is used. The chromatographic method of choice is ion-pair (IP) RP chromatography. Chromatographic separations are usually accomplished by gradients of an organic modifier in aqueous solutions of IP reagents. Commonly applied IP reagents are 2.3 mM triethylamine/400 mM 1,1,1,3,3,3-hexafluoro-2-propanol (TEA/HFIP, pH 7.0) and 10-25 mM cyclohexyldimethylammonium acetate (CycHDMAA, pH 8.4). Direct comparison of mass spectrometric performance of the two solvent systems revealed that the TEA/HFIP system offers better detection sensitivity than the CycHDMAA system. This is mainly attributable to the depletion of HFIP during droplet formation and solvent evaporation. Removal of the anionic counterion facilitates oligonucleotide ionization, and the oligonucleotides are desorbed as highly charged ions into the gas phase. TEA/HFIP-based mobile phases are recommended for developing quantitative assays targeting defined oligonucleotides. The CycHDMAA system allows the formation of cyclohexyldimethylammonium adducts. These adducts are cleaved in the gas phase, and this decomposition gives rise to charge state reduction. Ammonium adduct formation is of particular importance in preventing adducting with metal ions. Thus, adducts with metal ions are efficiently suppressed with CycHDMAA. For the TEA/HFIP system, however, such adducting represents a severe problem particularly if large oligonucleotides are analyzed. Thus, CycHDMAA-based mobile phases are recommended for qualitative assays such as LC-MS-based genotyping.

Preparation and characterization of alkyl methacrylate-based monolithic columns for capillary gas chromatography applications

Gas chromatography (GC) is considered the least common application of both polymer and silica-based monolithic columns. This study describes the fabrication of alkyl methacrylate monolithic materials for use as stationary phases in capillary gas chromatography. Following the deactivation of the capillary surface with 3-(trimethoxysilyl)propyl methacrylate (TMSM), the monoliths were formed by the co-polymerization of either hexyl methacrylate (HMA) or lauryl methacrylate (LMA) with different percentage of ethylene glycol dimethacrylate (EDMA) in presence of an initiator (azobisisobutyronitrile, AIBN) and a mixture of porogens include 1-propanol, 1,4-butanediol and water. The monoliths were prepared in 500mm length capillaries possessing inner diameters of 250μm. The efficiencies of the monolithic columns for low molecular weight compounds significantly improved as the percentage of crosslinker was increased, because of the greater proportion of pores less than 50nm. The columns containing lower percentages of crosslinker were able to rapidly separate a series of 8 alkane members in 0.7min, but the separation was less efficient for the light alkanes. Columns prepared with the lauryl methacrylate monomer yielded a different morphology for the monolith-interconnected channels. The channels were more branched, which increased the separation time, and unlike the other columns, allowed for temperature programming.

Phosphorothioate oligonucleotide quantification by μ-liquid chromatography-mass spectrometry

Phosporothioate oligonucleotides represent an important class of therapeutic oligonucleotides, in which none-bridging oxygen atoms of the phosphate groups are replaced by sulfur. These oligonucleotides are designed to treat disease by modulating gene expression of an affected individual. As the development and application of these therapeutical oligonucleotides require analytical support, the development, validation, and application of an assay for the quantitative analysis of a phosporothioate oligonucleotide in rat plasma is described. The method employs ion-pair reversed-phase chromatography on a monolithic capillary column with acetonitrile gradients in cyclohexyldimethylammonium acetate for separation and high-resolution tandem mass spectrometry for detection of nucleic acids. Chromatographic parameters (i.e. column temperature, mobile phase composition) as well as mass spectrometric parameters (i.e. spray voltage, gas flow, and capillary position, scan mode) have been optimized for sensitive oligonucleotide quantification. Furthermore, a solid-phase extraction method was developed which enabled processing of 10 μl of plasma. The five-point calibration curve showed linearity over the range of concentrations from 100 to 1,000 nM of the oligonucleotide. The limit of detection was 50 nM. The intra- and inter-day precision and accuracies were always better than 10.2 %. Using this assay, we performed a pharmacokinetic study of the phosporothioate oligonucleotide in rat treated with a single intravenous dose of 0.39 μmol/kg. The assay sensitivity was sufficient to study the early phase elimination of the oligonucleotide. Small amounts of the oligonucleotide were detectable up to 3 h after dosing.

Surfactant-bound monolithic columns for CEC

A novel anionic surfactant bound monolithic stationary phase based on 11-acrylaminoundecanoic acid is designed for CEC. The monolith possessing bonded undecanoyl groups (hydrophobic sites) and carboxyl groups (weak cationic ion-exchange sites) were evaluated as a mixed-mode stationary phase in CEC for the separation of neutral and polar solutes. Using a multivariate D-optimal design the composition of the polymerization mixture was modeled and optimized with five alkylbenzenes and seven alkyl phenyl ketones as test solutes. The D-optimal design indicates a strong dependence of electrochromatographic parameters on the concentration of 11-acrylaminoundecanoic acid monomer and porogen (water) in the polymerization mixture. A difference of 6, 8 and 13% RSD between the predicted and the experimental values in terms of efficiency, resolution and retention time, respectively, indeed confirmed that the proposed approach is practical. The physical (i.e. morphology, porosity and permeability) and chromatographic properties of the monolithic columns were thoroughly investigated. With the optimized monolithic column, high efficiency separation of N-methylcarbamates pesticides and positional isomers was successfully achieved. It appears that this type of mixed-mode monolith (containing both chargeable and hydrophobic sites) may have a great potential as a new generation of CEC stationary phase.

Porous polymer monoliths: amazingly wide variety of techniques enabling their preparation

The porous polymer monoliths went a long way since their invention two decades ago. While the first studies applied the traditional polymerization processes at that time well established for the preparation of polymer particles, creativity of scientists interested in the monolithic structures has later led to the use of numerous less common techniques. This review article presents vast variety of methods that have meanwhile emerged. The text first briefly describes the early approaches used for the preparation of monoliths comprising standard free radical polymerizations and includes their development up to present days. Specific attention is paid to the effects of process variables on the formation of both porous structure and pore surface chemistry. Specific attention is also devoted to the use of photopolymerization. Then, several less common free radical polymerization techniques are presented in more detail such as those initiated by gamma-rays and electron beam, the preparation of monoliths from high internal phase emulsions, and cryogels. Living processes including stable free radicals, atom transfer radical polymerization, and ring-opening metathesis polymerization are also discussed. The review ends with description of preparation methods based on polycondensation and polyaddition reactions as well as on precipitation of preformed polymers affording the monolithic materials.

Surfactant-bound monolithic columns for separation of proteins in capillary high performance liquid chromatography

A surfactant-bound monolithic stationary phase based on the co-polymerization of 11-acrylamino-undecanoic acid (AAUA) is designed for capillary high performance liquid chromatography (HPLC). Using D-optimal design, the effect of the polymerization mixture (concentrations of monomer, crosslinker and porogens) on the chromatographic performance (resolution and analysis time) of the AAUA-EDMA monolithic column was evaluated. The polymerization mixture was optimized using three proteins as model test solutes. The D-optimal design indicates a strong dependence of chromatographic parameters on the concentration of porogens (1,4-butanediol and water) in the polymerization mixture. Optimized solutions for fast separation and high resolution separation, respectively, were obtained using the proposed multivariate optimization. Differences less than 6.8% between the predicted and the experimental values in terms of resolution and retention time indeed confirmed that the proposed approach is practical. Using the optimized column, fast separation of proteins could be obtained in 2.5 min, and a tryptic digest of myoglobin was successfully separated on the high resolution column. The physical properties (i.e., morphology, porosity and permeability) of the optimized monolithic column were thoroughly investigated. It appears that this surfactant-bound monolith may have a great potential as a new generation of capillary HPLC stationary phase.

GenoMass--a computer software for automated identification of oligonucleotide DNA adducts from LC-MS analysis of DNA digests

In the investigation of oligonucleotides, DNA and their adducts by LC-MS, a myriad of data are generated that make manual data processing quite difficult. This paper describes a 'reversed pseudo-combinatorial' approach for fragment identification and the software implementation of this approach. Combinatorial isomer libraries are generated in silico to represent the digestion products of oligonucleotides, DNA or DNA adducts of various sizes. The software automatically calculates ion masses of each isomeric segment of the library, searches for them in complicated LC-MS data, lists their intensities and plots extracted ion chromatograms (EIC). This customized new data analysis tool has enabled a study of the enzymatic behavior of a nuclease system in the digestion of normal and adducted DNA, and in the recognition of oligomers containing a carcinogen bound to a nucleobase. The software program potentially can be further expanded to postulate unknown DNA sequences and recognize the adduction sites.

A model of flow-through pore formation in methacrylate ester-based monolithic columns

The main factors affecting the porosity of methacrylate-ester based monolithic columns were investigated. We prepared 23 monolithic capillary columns with porosity controlled by varying the proportions of butyl methacrylate and ethylene dimethacrylate monomers and of 1,4-butanediol and 1-propanol as the porogen solvent in the polymerization mixtures by thermally initiated in-situ polymerization in fused-silica capillaries. Using mixture design software, we systematically varied the composition of the polymerisation mixtures to find significant factors affecting flow-through pore formation. Multivariate analysis of the experimental data obtained for the fabricated columns yielded a model for prediction of the flow-through porosity in monolithic beds as a function of the composition of the polymerization mixture used to prepare polymethacrylate monolithic capillary columns. The mean error of prediction was lower than 8% for eight columns prepared independently of the original set of 15 columns used to derive the flow-through model. The flow-through porosity increases with increasing concentration of the binary porogen solvent mixture, the concentration of 1,4-butanediol being the main factor enhancing flow-through pore formation. On the other hand, increasing concentrations of the hydrophobic monomer butyl methacrylate and increasing concentrations of 1-propanol have a negative effect on flow-through pore formation. The capillary columns prepared with a high proportion of flow-through pores and a minimum amount of mesopores can be used for fast gradient separations of both low-molecular weight compounds and biopolymers.