Quantitative determination of short single-stranded oligonucleotides from blood plasma using capillary electrophoresis with laser-induced fluorescence

Investigating the Merits of Microfluidic Capillary Zone Electrophoresis-Mass Spectrometry (CZE-MS) in the Bottom-Up Characterization of Larger RNAs

Established bottom-up approaches for the characterization of nucleic acids (NAs) rely on the strand-cleavage activity of nucleotide-specific endonucleases to generate smaller oligonucleotides amenable to gas-phase sequencing. The complexity of these hydrolytic mixtures calls for the utilization of a front-end separation to facilitate full mass spectrometric (MS) characterization. This report explored the merits of microfluidic capillary zone electrophoresis (CZE) as a possible alternative to common liquid chromatography techniques. An oligonucleotide ladder was initially employed to investigate the roles of fundamental analyte features and experimental parameters in determining the outcome of CZE-MS analyses. The results demonstrated the ability to fully resolve the various rungs into discrete electrophoretic peaks with full-width half-height (FWHH) resolution that was visibly affected by the overall amount of material injected into the system. Analogous results were obtained from a digestion mixture prepared by treating yeast tRNAPhe (75 nt) with RNase T1, which provided several well-resolved peaks in spite of the increasing sample heterogeneity. The regular shapes of such peaks, however, belied the fact that most of them contained sets of comigrating species, as shown by the corresponding MS spectra. Even though it was not possible to segregate each species into an individual electrophoretic peak, the analysis still proved capable of unambiguously identifying a total of 29 hydrolytic products, which were sufficient to cover 96% of the tRNAPhe's sequence. Their masses accurately reflected the presence of modified nucleotides characteristic of this type of substrate. The analysis of a digestion mixture obtained from the 364 nt HIV-1 5'-UTR proved to be more challenging. The electropherogram displayed fewer well-resolved peaks and significantly greater incidence of product comigration. In this case, fractionating the highly heterogeneous mixture into discrete bands helped reduce signal suppression and detection bias. As a result, the corresponding MS data enabled the assignment of 248 products out of the possible 513 predicted from the 5'-UTR sequence, which afforded 100% sequence coverage. This figure represented a significant improvement over the 36 total products identified earlier under suboptimal conditions, which afforded only 57% coverage, or the 83 observed by direct infusion nanospray-MS (72%). These results provided a measure of the excellent potential of the technique to support the bottom-up characterization of progressively larger NA samples, such as putative NA therapeutics and mRNA vaccines.

Analysis of therapeutic nucleic acids by capillary electrophoresis

Nucleic acids are getting increased attention to fulfill unmet medical needs. The past five years have seen more than ten FDA approvals of nucleic acid based therapeutics. New analytical challenges have been posed in discovery, characterization, quality control and bioanalysis of therapeutic nucleic acids. Capillary electrophoresis (CE) has proven to be an efficient separation technique and has been widely used for analyzing oligonucleotides and nucleic acids. This review discusses the recent technical advances of CE in nucleic acid analysis such as polymeric matrices, separation conditions and detection methods, and the applications of CE to various therapeutic nucleic acids including antisense oligonucleotide (ASO), small interfering ribonucleic acid (siRNA), messenger RNA (mRNA), gene editing tools such as clustered regularly interspaced short palindromic repeats (CRISPR)-based gene and cell therapy, and other nucleic acid related therapeutics.

Recent advances in therapeutic nucleic acids and their analytical methods

Therapeutic nucleic acids are various chemically modified RNA or DNA with different functions, which mainly play roles at the gene level. Owing to its accurately targeting at pathogenic genes, nucleic acid based therapeutics have a wide range of application prospects. Recently, the improvement on chemical synthesis and delivery materials accelerated the development of therapeutic nucleic acids rapidly. Up to now, 17 nucleic acid based therapeutics approved by Food and Drug Administration (FDA) or European Medicines Agency (EMA). The development of therapeutics raised higher requirements for analytical methods, both in quality control and in clinical research. The first part of this review introduces different classes of therapeutic nucleic acids, including antisense oligonucleotide (ASO), RNA interference (RNAi) therapy, mRNA, aptamer and other classes which are under research. The second part reviews the therapeutic nucleic acids commercialized from 2019 to now. The third part discusses the analytical methods for nucleic acid based therapeutics, including liquid chromatography-based methods, capillary gel electrophoresis (CGE), hybridization enzyme-linked immunosorbent assay (ELISA) and other infrequently used methods. Finally, the advantages and shortcomings of these methods are summarized, and the future development of analysis methods are prospected.

Studies of DNA Aptamer OliGreen and PicoGreen Fluorescence Interactions in Buffer and Serum

Spectrofluorometric and emission peak titration and timed studies of OliGreen (OG) and PicoGreen (PG) were conducted in Tris EDTA (TE) buffer, pooled rat and fetal bovine serum with two different aptamers of 72 and 192 bases in length to determine if OG or PG were suitable for aptamer pharmacokinetic (PK) studies in sera. Results indicated that OG and PG detected the single-stranded (ss) and double-stranded (ds) stem-loop structures of the two aptamers quite well in TE with reliable standard curves having exponential character (or several linear detection regions) up to 1 μg/ml of aptamer DNA with detection limits of ~1 ng/ml. The intensity of OG and PG staining appeared to correlate with the number and percentage of ss and ds bases in each aptamer. OG and PG fluorescence in pooled rat serum or fetal bovine serum (FBS) did not titer as a function of DNA aptamer concentration from 1 μg/ml to 1 ng/ml. This lack of OG or PG aptamer assays in serum is contrary to most published reports of OG or PG assays for ss antisense oligonucleotides, ds PCR amplicons or other types of DNA in serum or plasma. Further studies suggested that the lack of OG and PG assay titration in serum might not be entirely due to aptamer degradation from nucleases in serum since the fluorescence signals in serum appeared relatively stable over time from 30 min to 4 hours. A hypothesis is presented which attributes the inability of OG or PG to assay aptamers in serum to a combination of high blue-green autofluorescence in serum with possible serum nuclease degradation of aptamers over time and the changing aptamer to serum protein ratio coupled to nonspecific binding of serum proteins to aptamers thereby possibly changing aptamer conformations as a function of aptamer concentration during titration experiments.

Determination of therapeutic oligonucleotides using capillary gel electrophoresis

Oligonucleotides have developed into highly versatile and selective therapeutics over the past 20 years. More than five discrete mechanisms of action have been reported and more than 10 different chemical modifications have been used to extend their in vivo half-life and reduce their toxicity. Capillary gel electrophoresis (CGE) has been used extensively for the quantitative analysis of oligonucleotide therapeutics in both preclinical and clinical studies since the 1990s. The success of CGE is based on its extraordinary resolving power, which allows for the simultaneous determination of the parent drug and its metabolites. More recently, capillary gel electrophoresis has seen renewed interest with the emergence of replaceable gels with single-base resolving power and new capillary electrophoresis-mass spectrometry interfaces. This review discusses the bioanalysis of therapeutic oligonucleotides showing the evolution of the field over the past two decades leading to the current new approaches. Included in this review are topics such as different gel types, sample introduction modes, sample extraction procedures, separation conditions and detection methods used in CGE, along with discussions of the successes and limitations associated with each.

Bioanalysis of siRNA and oligonucleotide therapeutics in biological fluids and tissues

This article summarizes bioanalytical avenues for the determination of siRNA and oligonucleotide therapeutics, with an emphasis on hybridization methods. Aspects of the chemistry and delivery of investigational oligonucleotide therapeutics are considered. The nature of the oligonucleotide under investigation will dictate the best analytical course of action; each method has its advantages and disadvantages, depending upon the oligonucleotide test article and the anticipated toxicokinetic and pharmacokinetic study parameters. Stringent method development and specific validation criteria are essential to attain the best quality results in support of a regulatory filing.

Real-time PCR to study the sequence specific magnetic purification of DNA

The performance of various molecular techniques using complex biological samples greatly depends on the efficient separation and purification of DNA targets. In recent years, magnetic separation technology making use of small magnetic beads, has gained immense popularity. Most of these methods rely on the non-specific adsorption of DNA/RNA. However, as presented here, when functionalizing the beads with complementary DNA probes, the target of interest can selectively be isolated. Such sequence specific purification was evaluated for short DNA targets by means of simple fluorescent measurements, resulting in purification efficiencies around 80%. Besides standard fluorescent techniques, a real-time PCR (qPCR) method was applied for monitoring the purification of longer DNA targets. This qPCR method was specifically optimized for directly quantifying the purification efficiency of low concentrated DNA targets bound to magnetic beads. Additionally, parameters possibly affecting the magnetic isolation, including the length of the used capture probe or the hybridization location, were investigated. Using optimized conditions in combination with qPCR, purification efficiencies between 60% and 80% were observed and this over a large concentration window. These data also show the power of a direct qPCR approach to monitor the magnetic isolation of DNA at very low concentrations.

Sequential loss of tumor vessel pericytes and endothelial cells after inhibition of platelet-derived growth factor B by selective aptamer AX102

Inhibition of platelet derived growth factor (PDGF) can increase the efficacy of other cancer therapeutics, but the cellular mechanism is incompletely understood. We examined the cellular effects on tumor vasculature of a novel DNA oligonucleotide aptamer (AX102) that selectively binds PDGF-B. Treatment with AX102 led to progressive reduction of pericytes, identified by PDGF receptor beta, NG2, desmin, or alpha-smooth muscle actin immunoreactivity, in Lewis lung carcinomas. The decrease ranged from 35% at 2 days, 63% at 7 days, to 85% at 28 days. Most tumor vessels that lacked pericytes at 7 days subsequently regressed. Overall tumor vascularity decreased 79% over 28 days, without a corresponding decrease in tumor size. Regression of pericytes and endothelial cells led to empty basement membrane sleeves, which were visible at 7 days, but only 54% remained at 28 days. PDGF-B inhibition had a less pronounced effect on pancreatic islet tumors in RIP-Tag2 transgenic mice, where pericytes decreased 47%, vascularity decreased 38%, and basement membrane sleeves decreased 21% over 28 days. Taken together, these findings show that inhibition of PDGF-B signaling can lead to regression of tumor vessels, but the magnitude is tumor specific and does not necessarily retard tumor growth. Loss of pericytes in tumors is an expected direct consequence of PDGF-B blockade, but reduced tumor vascularity is likely to be secondary to pericyte regression.

Automated capture and on-column detection of biotinylated DNA on a disposable solid support

This work comprises the development of a technique for the capture of single-stranded DNA on a solid support combined with in situ quantification. The capture is based on the strong and selective interaction between biotinylated DNA and streptavidin-coated agarose beads. Sequential Injection in the lab-on-valve format allows for automated manipulation of all components including the building and disposal of bead columns. Detection was accomplished using the OliGreen fluorescent dye and optimization of the assay achieved a limit of detection of 111 pg ssDNA, with a total assay time of roughly 2.5 min per sample.

Response surface methodology in the development of a stacking-sensitive capillary electrophoresis method by field-amplified injection for the analysis of tricyclic antidepressants in the presence of salts

The work presented here explores the possibilities of the electrokinetic injection (EK) to achieve sensitive methods for the determination of tricyclic antidepressants in biological samples (serum). The addition of ACN to the sample, with high content in salts, causes stacking at the tip of the capillary, in a similar way as for hydrodynamic injection. An experimental design with the response surface methodology has been used to find the optimum composition of the matrix of the sample (sodium chloride and ACN percentages) and the conditions for the EK (water-plug length, time, and voltage of injection) in few experiments. The composition of the separation buffer was the same as utilized in a previous paper. The use of a bubble capillary to reach lower detection limits implies a loss of the resolution and requires a new optimization. Finally, a comparison between electrokinetic and hydrodynamic injections is made.

Fast separation of single-stranded oligonucleotides by capillary electrophoresis using OliGreen as fluorescence inducing agent

The fast separation of oligonucleotide (oligos) sizing marker by CE using OliGreen and including effects due to the concentration of separation medium and urea denaturant is presented. OliGreen dye is found to be more sensitive than ethidium bromide (by a factor of about 6 based on S/N considerations) for the oligos' separations. Higher concentration of F127 in 1xTris-boricacid-EDTA (TBE) up to 30% w/v leads to better resolution of oligos separations. The addition of urea into the separation medium decreases the sensitivity. With an optimized running condition, the oligos sizing marker could be successfully separated with 1-base resolution within 1.3 min by using 30% w/v F127/1xTBE solution as the separation medium at an applied electric field of 800 V/cm in a 3 cm long capillary, the fastest capillary gel electrophoresis separation with high resolution reported to date for oligos in the similar size range.

Quantification of Oligodeoxynucleotides in Human Plasma with a Novel Hybridization Assay Offers Greatly Enhanced Sensitivity over Capillary Gel Electrophoresis

Capillary gel electrophoresis using UV detection (CGE-UV) has been used to quantify oligodeoxynucleotides (ODN) in human plasma. Although the sensitivity of this method is adequate to detect antisense ODN, which are administered in daily doses up to 10 mg/kg, CGE-UV is not sensitive enough to detect the much lower quantities of ODN administered for other purposes, such as immune stimulation by CpG ODN. We have developed a very sensitive colorimetric hybridization assay that increases the sensitivity of detection by more than four logs compared with CGE-UV. The hybridization assay uses sequence-specific capture and detection ODN probes complementary to portions of the ODN sequence. Herein we provide a prototype for assay development and validation using a 24- mer immunostimulatory phosphorothioate ODN. Probes were locked nucleic acids (LNA), resulting in increased sensitivity and specificity. The linear range of the assay is 7.8-1000 pg/ml, with a 7.8 pg/ml lower limit of quantification (LLOQ) and a detection limit of 2.8 pg/ml. This translates to detection of 40 attamoles. Intraassay and interassay precision were < or =5.0% CV and < or =12.9% CV, respectively, for quality control samples. The assay is suitable for a variety of matrices, including monkey and rat plasma, allowing application to toxicokinetic samples. The methodology is highly specific, with the ability to distinguish almost all single-base mismatched ODN. The assay detects 100% of the parent as well as some metabolites up to N-4, which are known to be the primary metabolites forming in the first hours after in vivo administration and are physiologically active with in vitro assays.

Quantitative nuclear and cytoplasmic localization of antisense oligonucleotides by capillary electrophoresis with laser-induced fluorescence detection

We demonstrate the use of simple extraction procedures to separate nuclear and cytoplasmic material from cell extracts, which have been scrape-loaded with a 2-O-methyl phosphorothioate antisense oligonucleotide. Separation and quantitation of the fluorescein-labeled antisense and the flourescein isothiocyanate (FITC)-dextran (molecular weight 40000) as an internal standard is done using capillary electrophoresis coupled with laser-induced fluorescence detection (CE-LIF). The bulky FITC-dextran is unable to penetrate the nuclear membrane thereby making it a quantitative indicator of any overlap between the nuclear and cytoplasmic materials during separation of the two phases. Using this procedure, the fluorescein-labeled phosphorothioate oligomer was quantitated at 4.1 x 10(-13) and 3.4x 10(-14) mol antisense/microg-total cellular protein in the nuclear and cytoplasmic extracts respectively following scrape-load delivery of the phosphorothioate to a batch of confluent HeLa cells at a concentration of 0.5 microM (5 x 10(-10) total moles of oligomer). Additionally, gene expression was monitored by measurement of the luciferase reporter protein activity. Scrape-load, spontaneous and liposomal delivery were investigated and compared for subcellular distribution of the oligomer and subsequent gene expression.

Quantitation of intracellular concentration of a delivered morpholino oligomer by capillary electrophoresis-laser- induced fluorescence: correlation with upregulation of luciferase gene expression

Antisense oligonucleotides have shown great promise over the past several years as viable drugs to combat various forms of cancer and viral diseases. However, quantitative detection to monitor cellular association is difficult using conventional methods such as radiolabeling of the oligonucleotide or fluorescence confocal microscopy. In this paper quantitation of intracellular concentration of the morpholino oligonucleotide is investigated using capillary electrophoresis coupled with laser-induced fluorescence detection (CE-LIF). HeLa cells, which produce luciferase as the antisense oligomer enters the cell, were scrape-loaded with varying concentrations of the morpholino antisense. The intracellular antisense concentration measured by CE-LIF was found to correlate with those obtained with the cellular functional assay based on upregulation of luciferase. Intracellular concentrations of the antisense were found to be in the range of 6 to 29 nmol/g total cell protein, depending on the amounts that were scrape-loaded. To our best knowledge, this is the first reported quantitative correlation between delivered antisense concentration in a cell extract and the subsequent antisense upregulation of gene expression.

Coupling continuous separation techniques to capillary electrophoresis

One of the weak points of capillary electrophoresis is the need to implement rigorously sample pretreatment because its great impact on the quality of the qualitative and quantitative results provided. One of the approaches to solve this problem is through the symbiosis of automatic continuous flow systems (CFSs) and capillary electrophoresis (CE). In this review a systematic approach to CFS-CE coupling is presented and discussed. The design of the corresponding interface depends on three factors, namely: (a) the characteristics of the CFS involved which can be non-chromatographic and chromatographic; (b) the type of CE equipment: laboratory-made or commercially available; and (c) the type of connection which can be in-line (on-capillary), on-line or mixed off/on-line. These are the basic criteria to qualify the hyphenation of CFS (solid-phase extraction, dialysis, gas diffusion, evaporation, direct leaching) with CE described so far and applied to determine a variety of analytes in many different types of samples. A critical discussion allows one to demonstrate that this symbiosis is an important topic in research and development, besides separation and detection, to consolidate CE as a routine analytical tool.

Utilization of the non-covalent fluorescent dye, NanoOrange, as a potential clinical diagnostic tool. Nanomolar human serum albumin quantitation

The commercially available dye, NanoOrange, has been investigated as a potential tool for clinical diagnostics due to its low cost, ease of use, and ability to detect nanomolar concentrations of protein. Virtually non-fluorescent in dilute aqueous solutions, NanoOrange fluorescence is enhanced by at least an order of magnitude upon non-covalent interaction with proteins. These features, coupled with the requirement for high throughput assays in the clinical laboratory has prompted the development of two orthogonal NanoOrange approaches. Human serum albumin (HSA) was used as a model protein for the development of both 96-well microplate and capillary electrophoresis laser-induced fluorescence (CE-LIF) assay formats. Dye performance in five commonly used buffers of various concentrations and pH indicated considerable flexibility in assay buffer selection, with optimal performance at pH 9.0. A salt concentration study indicated that increasing NaCl concentration generally decreases fluorescence emission and can be minimized by pre-diluting biological samples to a final salt concentration of 20-80 mM. Titration of protein with NanoOrange resulted in optimal HSA-NanoOrange complex formation utilizing 1 x and 2 x NanoOrange in the 96-well microplate and CE-LIF approaches, respectively. A NanoOrange binding model based on rapid signal enhancement and zero order fluorescence emission kinetics is proposed. The utilization of NanoOrange in CE-LIF based human serum analysis results in a signal-to-background ratio improvement of up to two orders of magnitude.

Derivatization trends in capillary electrophoresis

This survey gives an overview of recent derivatization protocols, starting from 1996, in combination with capillary electrophoresis (CE). Derivatization is mainly used for enhancing the detection sensitivity of CE, especially in combination with laser-induced fluorescence. Derivatization procedures are classified in tables in pre-, on- and postcapillary arrangements and, more specifically, arranged into functional groups being derivatized. The amine and reducing ends of saccharides are reported most frequently, but examples are also given for derivatization of thiols, hydroxyl, carboxylic, and carbonyl groups, and inorganic ions. Other reasons for derivatization concern indirect chiral separations, enhancing electrospray characteristics, or incorporation of a suitable charge into the analytes. Special attention is paid to the increasing field of research using on-line precapillary derivatization with CE and microdialysis for in vivo monitoring of neurotransmitter concentrations. The on-capillary derivatization can be divided in several approaches, such as the at-inlet, zone-passing and throughout method. The postcapillary mode is represented by gap designs, and membrane reactors, but especially the combination of separation, derivatization and detection on a chip is a new emerging field of research. This review, which can be seen as a sequel to our earlier reported review covering the years 1991-1995, gives an impression of current derivatization applications and highlights new developments in this field.

Quantitative determination of a chemically modified hammerhead ribozyme in blood plasma using 96-well solid-phase extraction coupled with high-performance liquid chromatography or capillary gel electrophoresis

Versatile bioanalytical assays to detect chemically stabilized hammerhead ribozyme and putative ribozyme metabolites from plasma are described. The extraction protocols presented are based on serial solid-phase extractions performed on a 96-well plate format and are compatible with either IEX-HPLC or CGE back-end analysis. A validation of both assays confirmed that both the HPLC and the CGE methods possess the required linearity, accuracy, and precision to accurately measure concentrations of hammerhead ribozyme extracted from plasma. These methods should be of general use to detect and quantitate ribozymes from other biological fluids such as serum and urine.

On-column amperometric detection in capillary electrophoresis with an improved high-voltage electric field decoupler

An improved fabrication method for a decoupler for on-column amperometric detection in capillary electrophoresis (CE) is described. The decoupler is fabricated by etching one side-wall of the capillary with hydrofluoric acid after the polymer coating had been etched by laser, then the etched hole is sealed with adhesive. The steady time, electric conductivity efficiency and performance are investigated. On-column amperometric detection by CE of para-substituted phenols was carried out by coupling with a carbon-fiber microelectrode (10-microm diameter) and a practical small electrochemical detection cell.

Real-time monitoring of the hybridization reaction: application to the quantification of oligonucleotides in biological samples

We describe here a competitive hybridization assay using TRACE technology which can be used for real-time monitoring of oligonucleotide hybridization. This assay quantifies all kinds of oligonucleotides in biological fluids without extraction. The assay makes use of two different probes and involves a fluorescent transfer process. As fluorescence measurements are not destructive, they can be sequentially repeated, thereby allowing comparison of the hybridization kinetics and binding strength of chemically modified backbone oligonucleotides (>0.5 nM) in biological media. The assay was validated for pharmacokinetic analysis of phosphodiester and phosphorothioate oligonucleotides in plasma and in different organs (liver, kidneys, lungs, spleen) at low concentrations (0.4 mg/kg, corresponding to clinical doses). Respective sensitivities for phosphodiester and phosphorothioate were 0.2 and 0.8 pmol/ml in plasma and 2 and 8 pmol/g in tissues, which allow to recover intact phosphorothioate sequences in some organs even after 24 h.

Pharmacokinetic applications of capillary electrophoresis

This review briefly discusses the use of capillary electrophoretic (CE) methods for the investigations of different aspects of pharmacokinetics. In most investigations, CE was the method of choice because of its unique features, including high resolving power for chiral or metabolite separation, small sample volume for pediatric pharmacokinetics or for cell-based investigations, in situ microdialysis sampling for rapid eliminations, low UV wavelength detection for nonderivatized analytes, fast and simplified sample processing for existing methods that require tedious sample preparation, or as a second method for verifications. Moreover, instrumental aspects of CE-based assays for pharmacokinetic studies, such as different modes of CE methods for analyzing biological samples, sample stacking for increasing detection sensitivity, and coupling techniques with microdialysis and mass spectrometry, are also discussed in this review. Furthermore, the advantages and limitations of CE methods as well as the future outlook for pharmacokinetic studies are summarized.

Characterization of SYBR Gold nucleic acid gel stain: a dye optimized for use with 300-nm ultraviolet transilluminators

The highest sensitivity nucleic acid gel stains developed to date are optimally excited using short-wavelength ultraviolet or visible light. This is a disadvantage for laboratories equipped only with 306- or 312-nm UV transilluminators. We have developed a new unsymmetrical cyanine dye that overcomes this problem. This new dye, SYBR Gold nucleic acid gel stain, has two fluorescence excitation maxima when bound to DNA, one centered at approximately 300 nm and one at approximately 495 nm. We found that when used with 300-nm transillumination and Polaroid black-and-white photography, SYBR Gold stain is more sensitive than ethidium bromide, SYBR Green I stain, and SYBR Green II stain for detecting double-stranded DNA, single-stranded DNA, and RNA. SYBR Gold stain's superior sensitivity is due to the high fluorescence quantum yield of the dye-nucleic acid complexes ( approximately 0.7), the dye's large fluorescence enhancement upon binding to nucleic acids ( approximately 1000-fold), and its capacity to more fully penetrate gels than do the SYBR Green gel stains. We found that SYBR Gold stain is as sensitive as silver staining for detecting DNA-with a single-step staining procedure. Finally, we found that staining nucleic acids with SYBR Gold stain does not interfere with subsequent molecular biology protocols.

Preconcentration and separation of antisense oligonucleotides by on-column isotachophoresis and capillary electrophoresis in polymer-filled capillaries

Small, single-stranded, chemically modified oligonucleotides, complementary to a specific gene section, commonly referred to as antisense compounds, are being investigated as potential therapeutic drugs. A number of modified oligonucleotides, in particular phosphorothioates, are in clinical development. Shorter fragments are found as metabolic products. Isotachophoresis (ITP) allows the introduction of large, diluted sample plugs into the separation capillary. In this work, ITP and capillary electrophoresis (CE) in polymer solutions were successfully coupled in a single capillary in a commercial instrument to increase sensitivity with UV detection and to shorten the time for sample pretreatment. It was shown that ITP-CE can be used as a preconcentration and clean-up method for phosphodiester- and phosphorothioate-containing samples. Up to 3 microL sample could be injected into the capillary without significantly disturbing the separation performance. ITP-CE of phosphodiesters directly out of salt- and protein-containing samples could be demonstrated. For phosphorothioates in serum samples an additional sample clean-up was necessary, due to oligonucleotide-protein binding. An optimized replaceable polymer solution was developed to increase the separation performance for heterogeneous phosphorothioates. A dextran-based sieving medium showed a good separation performance in ITP-CE of phosphorothioates. A concentration detection limit of 8.10(-9) mol/L for the 20-mer phosphorothioate ISIS5132, isolated from rat serum, was found.

Pharmacokinetics and biodistribution of a nucleotide-based thrombin inhibitor in rats

PURPOSE

To characterize the pharmacokinetic and tissue distribution profiles of a nucleotide-based thrombin inhibitor (GS522, phosphodiester oligonucleotide, GGTTGGTGTGGTTGG) following intravenous administration to rats.

METHODS

Pharmacokinetic study: 10 mg/kg, 20 mg/kg, 30 mg/kg (6 animals/dose) were administered to rats by rapid injection into the femoral vein. Blood samples were collected over a 45 minute period. Plasma concentrations of GS522 were determined using capillary gel electrophoresis with laser-induced fluorescence detection. Biodistribution Study: 10 mg/kg (400 microl, 31.46 microCi/ml) of 3H-GS522 was administered to rats by rapid injection into the femoral vein. The animals were sacrificed by decapitation at 1, 5, 10, 30, 60, 360 minutes post-dose (3 rats/point). Brain, blood, duodenum, eyes, heart, kidney, liver, lungs, muscle, pancreas, skin, spleen and vein samples were collected, processed and quantitated using liquid scintillation counting.

RESULTS

The pharmacokinetic profile declines in multiexponential manner, exhibiting extremely fast distribution and elimination (t1/2 = 7.6-9.0 min, Cl = 22.0-28.0 ml/min, V = 83.9-132.4 ml/kg). GS522 follows linear pharmacokinetics, with the area under the curve being proportional to the dose (Rsq = 0.9744). Highest radioactivity levels were detected in kidney, liver and blood (39.7, 15.7 and 15.3% dose/ respective organ). Less than 1% of the dose was detected in the heart, spleen and lungs, and >0.3% of the dose was found in the brain and eyes. The oligonucleotide associated radioactivity was uniformly distributed between the brain regions (left and right lobe and cerebellum). Six hours following the dose administration a statistically significant increase (p < 0.05) in radioactivity levels was observed in the brain, eyes, skin, liver, pancreas and vein.

CONCLUSIONS

The pharmacokinetic and biodistribution profiles of GS522 following intravenous administration to rats at three doses were characterized. The oligonucleotide associated radioactivity was widely distributed in tissues. The amount of radioactivity sharply decreased with time in most tissues. Kidney, liver and muscle were the main sites of accumulation. The oligonucleotide associated radioactivity did not cross the blood brain barrier to an appreciable extent. In addition, a statistically significant increase (p < 0.05) in the radioactivity levels observed in select tissues suggested a re-uptake mechanism for intact oligonucleotide or its degradation products.