A new approach to preparation of antisense oligonucleotide samples with microextraction by packed sorbent

A simple and green solid phase extraction method for oligonucleotides using adsorbent with amino and carboxylic moieties

The study aimed to use a material with amino and carboxylic moieties to extract unmodified and phosphorothioate oligonucleotides. The charge of amine and carboxyl groups at the surface has changed with the change in pH of the adsorption (pH 4.5) and desorption solution (pH 9.5). Thus, both the binding and elution of the oligonucleotides were based on electrostatic interactions, and the procedure required only 10 mM ammonium acetate, with the change of pH depending on the extraction step. The developed procedure was successfully applied to extract oligonucleotides from aqueous solutions and serum samples. The method is simple and fast, providing good reproducibility (SD between 1 and 4%) and relatively high oligonucleotide recovery (81-98% for standards, 60-71% for diluted serum samples, and 80-92 for LLE serum extracts). Moreover, only environmentally friendly solvents were used.

Development of the Method for Nusinersen and Its Metabolites Identification in the Serum Samples of Children Treated with Spinraza for Spinal Muscular Atrophy

The application of oligonucleotides as drugs for different genetic diseases is increasing rapidly. Since 2016 they are used during spinal muscular atrophy treatment with the use of nusinersen oligonucleotide. The purpose of this study was to improve methods for the analysis of serum samples of patients treated with nusinersen. The results showed that liquid-liquid extraction (with phenol/chloroform) is insufficient and an additional purification step using solid-phase extraction is necessary. The best results were obtained for microextraction by packed sorbents. Important parameters in the optimization of the method were mainly the type of amine in the mobile phase and the stationary phase. Both influenced the selectivity of metabolite separation and thus their correct identification; while amine type impacted also the intensity of signals. Finally, the highest resolution of separation and the highest peak areas were obtained for N,N-dimethylbutylamine or N,N-diisopropylthylamine with an octadecyl column with a terminal aryl group. Over a dozen of metabolites were successfully identified with the use of methods developed during the study. The 3′ exonucleases and 5′ exonucleases were mainly responsible for nusinersen metabolism, consequently, 3′end shortmers, and 5′end shortmers were observed, as well as metabolites with simultaneous loss of bases at both ends of the sequence. However, some depurination and depyrimidination products were also identified. To the best of our knowledge, this is the first report on nusinersen and its metabolite identification in serum samples by liquid chromatography and mass spectrometry.

Oligonucleotides Isolation and Separation—A Review on Adsorbent Selection

Oligonucleotides have many important applications, including as primers in polymerase chain reactions and probes for DNA sequencing. They are proposed as a diagnostic and prognostic tool for various diseases and therapeutics in antisense therapy. Accordingly, it is necessary to develop liquid chromatography and solid phase extraction methods to separate oligonucleotides and isolate them from biological samples. Many reviews have been written about the determination of these compounds using the separation technique or sample preparation for their isolation. However, presumably, there are no articles that critically review the adsorbents used in liquid chromatography or solid phase extraction. The present publication reviews the literature from the last twenty years related to supports (silica, polymers, magnetic nanoparticles) and their modifications. The discussed issues concern reversed phase (alkyl, aromatic, cholesterol, mixed ligands), ion-exchange (strong and weak ones), polar (silica, polyhydroxy, amide, zwitterionic), and oligonucleotide-based adsorbents.

[Research progress of microextraction by packed sorbent and its application in microvolume sample extraction]

Microextraction is a rapidly developing sample preparation technology in the field of analytical chemistry, which is seeing widespread application. Accurate sample preparation can not only save time but also improve the efficiency of analysis, determination, and data quality. At present, sample pretreatment methods must be rapid, allow for miniaturization, automation, and convenient online connection with analytical instruments. To meet the requirements of green analytical methods and improve the extraction efficiency, microextraction techniques have been introduced as suitable replacements to conventional sample preparation and extraction methods. Microextraction using a packed sorbent (MEPS) is a new type of sample preparation technology. The MEPS equipment was prepared using microsyringe with a volume of 50-500 μL, including MEPS syringes and MEPS adsorption beds (barrel insert and needle, BIN), which is essentially similar to a miniaturized solid phase extraction device. The BIN contains the adsorbent and is built into the syringe needle. A typical MEPS extraction procedure involves repeatedly pumping the sample solution in two directions (up and down) through the adsorbent multiple times in the MEPS syringe. The specific operation course of MEPS includes conditioning, loading, washing, elution, and introduction into the analysis instrument. The conditioning process is adopted to infiltrate the dry sorbent and remove bubbles between the filler particles. The adsorption process is accomplished by pulling the liquid plunger of the syringe so that the sample flows through the adsorbent in both directions multiple times. The washing process involves rinsing the sorbent to remove unwanted components after the analyte is retained. The elution process involves the use of an eluent to ensure that the sample flows through the adsorbent in both directions multiple times, so that elution can be realized by the pumping-pushing action. The target analyte is eluted with the eluent, which can be directly used for chromatographic analysis. However, when processing complex biological matrix samples by MEPS, pretreatment steps such as dilution of the sample and removal of proteins are commonly required. At present, the operation modes of the MEPS equipment are classified into three types: manual, semi-automated, and fully automated. This increase in the degree of automation is highly conducive to processing extremely low or extremely high sample volumes. Critical factors affecting the MEPS performance have been investigated in this study. The conditions for MEPS optimization are the operating process parameters, including sample flow rate, sample volume, number of sample extraction cycles, type and volume of the adsorbent, and elution solvents. It is also necessary to consider the effect of the sample matrix on the performance of MEPS. The MEPS sorbent should be cleaned by a solvent to eliminate carryover and reuse. The sorbent is a core aspect of MEPS. Several types of commercial and non-commercial sorbents have been used in MEPS. Commercial sorbents include silica-based sorbents such as unmodified silica (SIL), C2, C8, and C18. Unmodified silicon-based silica is a normal phase adsorption material, which is highly polar and can be used to retain polar analytes. C18, C8, and C2 materials are suitable for reversed-phase adsorption, while SCX, SAX, APS, and M1 (C8+SCX) adsorbents are suitable for the mixed-mode and ion-exchange modes. Noncommercial sorbents include molecularly imprinted materials, restricted-access molecularly imprinted materials, graphitized carbon, conductive polymer materials, modified silicon materials, and covalent-organic framework materials. The performance of MEPS has recently been illustrated by online with LC-MS and GC-MS assays for the analysis of biological matrices, environmental samples, and food samples. Pretreatment in MEPS protocols includes dilution, protein precipitation, and centrifugation in biological fluid matrices. Because of the small sample size, fast operation, etc., MEPS is expected to be more widely used in the analysis of bio-matrix samples. MEPS devices could also play an important role in field pretreatment and analysis.

Poly(ionic liquid)s as new adsorbents in dispersive micro-solid-phase extraction of unmodified and modified oligonucleotides

Cross-linked poly(ionic liquid)s were successfully used for the first time in the preparation of oligonucleotide biological samples. The adsorbents were prepared by co-polymerization of imidazolium-based ionic liquids and divinylbenzene. Consequently, the following three adsorbents were prepared and comprehenzively characterized: poly(3-butyl-1-vinylimidazolium bromide-co-divinylbenzene), poly(3-hexyl-1-vinylimidazolium bromide-co-divinylbenzene) and poly(2-(1-vinylimidazoliumyl)acetate-co-divinylbenzene). Oligonucleotides were adsorbed onto the surface of these materials at low pH values. Preliminary studies of the desorption of the analytes included testing the influence of different types of salts, as well as their concentrations and pH, and organic solvents on the recovery. This allowed for determining the adsorbent and the desorption conditions for further optimization with the use of central composition design. The chosen adsorbent was poly(2-(1-vinylimidazoliumyl)acetate-co-divinylbenzene), and the optimal desorption conditions (5 mM ammonium acetate (pH = 9.5)/methanol (50/50, v/v)) gave a recovery of 99.7 ± 0.3%. The dispersive micro-solid-phase extraction procedure was successfully applied for the extraction of oligonucleotides with various modifications and lengths. Finally, the developed method was used to extract 2'-O-methyl oligonucleotide and its two synthetic metabolites from enriched human plasma without any pre-purification, yielding recoveries over 80%.

Microextraction approaches for bioanalytical applications: An overview

Biological samples are usually complex matrices due to the presence of proteins, salts and a variety of organic compounds with chemical properties similar to those of the target analytes. Therefore, sample preparation is often mandatory in order to isolate the analytes from troublesome matrices before instrumental analysis. Because the number of samples in drug development, doping analysis, forensic science, toxicological analysis, and preclinical and clinical assays is steadily increasing, novel high throughput sample preparation approaches are calling for. The key factors in this development are the miniaturization and the automation of the sample preparation approaches so as to cope with most of the twelve principles of green chemistry. In this review, recent trends in sample preparation and novel strategies will be discussed in detail with particular focus on sorptive and liquid-phase microextraction in bioanalysis. The actual applicability of selective sorbents is also considered. Additionally, the role of 3D printing in microextraction for bioanalytical methods will be pinpointed.