Separation of purine and pyrimidine bases by capillary zone electrophoresis with carbonate buffers

Electrokinetic identification of ribonucleotide monophosphates (rNMPs) using thermoplastic nanochannels

With advances in the design and fabrication of nanofluidic devices during the last decade, there have been a few reports on nucleic acid analysis using nanoscale electrophoresis. The attractive nature of nanofluidics is the unique phenomena associated with this length scale that are not observed using microchip electrophoresis. Many of these effects are surface-related and include electrostatics, surface roughness, van der Waals interactions, hydrogen bonding, and the electric double layer. The majority of reports related to nanoscale electrophoresis have utilized glass-based devices, which are not suitable for broad dissemination into the separation community because of the sophisticated, time consuming, and high-cost fabrication methods required to produce the relevant devices. In this study, we report the use of thermoplastic nanochannels (110 nm x 110 nm, depth x width) for the free solution electrokinetic analysis of ribonucleotide monophosphates (rNMPs). Thermoplastic devices with micro- and nanofluidic networks were fabricated using nanoimprint lithography (NIL) with the structures enclosed via thermal fusion bonding of a cover plate to the fluidic substrate. Unique to this report is that we fabricated devices in cyclic olefin copolymer (COC) that was thermally fusion bonded to a COC cover plate. Results using COC/COC devices were compared to poly(methyl methacrylate), PMMA, devices with a COC cover plate. Our results indicated that at pH = 7.9, the electrophoresis in free solution resulted in an average resolution of the rNMPs >4 (COC/COC device range = 1.94 - 8.88; PMMA/COC device range = 1.4 - 7.8) with some of the rNMPs showing field-dependent electrophoretic mobilities. Baseline separation of the rNMPs was not possible using PMMA- or COC-based microchip electrophoresis. We also found that COC/COC devices could be assembled and UV/O3 activated after device assembly with the dose of the UV/O3 affecting the magnitude of the electroosmotic flow, EOF. In addition, the bond strength between the substrate and cover plate of unmodified COC/COC devices was higher compared to PMMA/COC devices. The large differences in the electrophoretic mobilities of the rNMPs afforded by nanoscale electrophoresis will enable a new single-molecule sequencing platform we envision, which uses molecular-dependent electrophoretic mobilities to identify the constituent rNMPs generated from an intact RNA molecule using a processive exonuclease. With optimized nanoscale electrophoresis, the rNMPs could be identified via mobility matching at an accuracy >99% in both COC/COC and PMMA/COC devices.

Study on potential toxic material base and mechanisms of hepatotoxicity induced by Dysosma versipellis based on toxicological evidence chain (TEC) concept

Dysosma Versipellis (DV), a traditional Chinese medicine, has the functions of eliminating phlegm, detoxification, dispersing knots . However, its serious toxicity limits its further use. Therefore, it is necessary to conduct a comprehensive toxicity study of DV, screen the basis of potential toxic substances and understand its toxic mechanism. Based on the concept of toxicological evidence chain (TEC), this study utilizes the technologies and means of chemomics, metabolomics, molecular docking and network toxicology flexibly, step by step to find the evidence of potential toxic components in the development of hepatotoxicity induced by DV, evidence of critical toxicity events, evidence of adverse outcomes, thus, a chain of toxicity evidence with reference and directivity can be organized. It further confirmed the toxic damage and potential molecular mechanism of DV. 5 potential toxic components were identified, namely, Podophyllotoxin-4-O-D-glucoside, Podorhizol, Podophyllotoxin, Podophyllotoxone and 3',4'-O,O-Didemethylpophyllotoxin. These chemical constituents affect phenylalanine metabolism, glycerophospholipid metabolism, energy metabolism and other related pathways by regulating PAH, SOD1, SOD2 and other related targets, then it induces oxidative stress, cell apoptosis, inflammatory reaction and energy consumption, which ultimately induces the occurrence of liver injury. The results of this study provide some reference for the follow-up analysis of toxicity mechanism of DV.

Application of Carbon Nanotubes in Chiral and Achiral Separations of Pharmaceuticals, Biologics and Chemicals

Carbon nanotubes (CNTs) possess unique mechanical, physical, electrical and absorbability properties coupled with their nanometer dimensional scale that renders them extremely valuable for applications in many fields including nanotechnology and chromatographic separation. The aim of this review is to provide an updated overview about the applications of CNTs in chiral and achiral separations of pharmaceuticals, biologics and chemicals. Chiral single-walled carbon nanotubes (SWCNTs) and multi-walled carbon nanotubes (MWCNTs) have been directly applied for the enantioseparation of pharmaceuticals and biologicals by using them as stationary or pseudostationary phases in chromatographic separation techniques such as high-performance liquid chromatography (HPLC), capillary electrophoresis (CE) and gas chromatography (GC). Achiral MWCNTs have been used for achiral separations as efficient sorbent objects in solid-phase extraction techniques of biochemicals and drugs. Achiral SWCNTs have been applied in achiral separation of biological samples. Achiral SWCNTs and MWCNTs have been also successfully used to separate achiral mixtures of pharmaceuticals and chemicals. Collectively, functionalized CNTs have been indirectly applied in separation science by enhancing the enantioseparation of different chiral selectors whereas non-functionalized CNTs have shown efficient capabilities for chiral separations by using techniques such as encapsulation or immobilization in polymer monolithic columns.

Chiral analysis of anti-acquired immunodeficiency syndrome drug, 9-(R)-[2-(phosphonomethoxy)propyl]adenine (tenofovir), and related antiviral acyclic nucleoside phosphonates by CE using beta-CD as chiral selector

A new CZE method has been developed for chiral analysis of an important anti-acquired immunodeficiency syndrome drug, 9-(R)-[2-(phosphonomethoxy)propyl]adenine ((R)-PMPA, tenofovir), and six related antiviral acyclic nucleoside phosphonates using beta-CD as a chiral selector. The influence of the composition, concentration and pH of the BGE and the type and concentration of chiral selector on enantiomer resolution was investigated. Complete separations of (R,S)-enantiomers of PMPA with very good resolution (R(s)=1.50-3.64) were achieved within a short time (4-15 min) in 20-50 mM sodium borate or sodium tetraborate BGEs, pH 10.0, at 20 mg/mL concentration of beta-CD. (R,S)-enantiomers of five similar PMPA analogs containing purine bases (adenine, diaminopurine or guanine) and hydroxyl or fluor substituents at C3 carbon atom of propyl chain were baseline separated within 10-17 min in 35 mM sodium tetraborate BGE, pH 10.0, at 20 mg/mL beta-CD concentration. Another important antiviral used by acquired immunodeficiency syndrome patients, derived from pyrimidine base cytosine, 1-(S)-[3-hydroxy-2-(phosphonomethoxy)propyl]cytosine (cidofovir), and the (R)-enantiomer of this drug were successfully separated in 50 mM sodium tetraborate BGE, pH 10.5, at 20 mg/mL beta-CD concentration within 45 min. Using the UV-absorption detection at 206 nm, the concentration detection limits of the analyzed acyclic nucleoside phosphonates were determined in the submicromolar to micromolar range (0.15-2.51 microg/mL level).

Investigations on the migration behaviour of purines and pyrimidines in capillary electromigration techniques with UV detection and mass spectrometric detection

Different approaches for the separation of a set of nucleosides and nucleobases using capillary zone electrophoresis (CZE) and micellar electrokinetic chromatography (MEKC) are described. Several electrolyte compositions have been tested for this purpose. The addition of appropriate amounts of borate to the carrier electrolyte allowed manipulating migration orders in CZE and MEKC by selective complexation of the nucleosides. For detection either UV or two different modes of mass spectrometric (MS) detection were employed. The latter approach included a comparison of two ion sources namely electrospray ionization (ESI) and atmospheric pressure photoionization (APPI) with respect to their potential in the detection of the selected compounds. Thereby it could be demonstrated that, in particular when it comes to the analysis of real samples, APPI-MS is the better choice if MS detection of purines and pyrimidines after separation by CZE is required.

Application of CE for determination of DNA base composition

DNA base composition expressed as mol% of guanine plus cytosine (% GC) or GC content is a key parameter of bacterial taxonomy and genomic analyses. Direct chemical determination methods such as HPLC as well as indirect methods based on physical properties of deoxyribonucleic acid (DNA), melting point (T(m)), and buoyant density (B(d)) have been conventionally applied to determine the GC content. However, these methods require relatively large amounts of sample DNA, time, and labor. We have developed a protocol to determine the GC content by fine separation of nucleosides with CZE. Genomic DNAs with known GC content from 23 bacterial strains were determined by CE at the optimized conditions of 27 degrees C, 20 kV in 50 mM of NaHCO(3) (pH 9.0) and 70 mM SDS added. Nucleosides from <1 microg of DNA hydrolyzed with nuclease-P1 and bacterial alkaline phosphatase were separated in a 75 microm wide and 80 cm long silica capillary. The nucleoside peak areas were determined at 254 nm in less than 12 min. The CE-based determination of GC content requires only small amounts of DNA, and thus should be applicable to environmental genomics (metagenomics), as >90% of environmental micro-organisms are nonculturable and produce only small amounts of genomic DNA.

Enhanced separation of purine and pyrimidine bases using carboxylic multiwalled carbon nanotubes as additive in capillary zone electrophoresis

This paper describes the enhanced separation of adenine (A), hypoxanthine (HX), 8-azaadenine (8-AA), thymine (T), cytosine (C), uracil (U) and guanine (G) by CZE dispersing carboxylic multiwalled carbon nanotubes (c-MWNTs) into the running buffer. The effect of important factors such as c-MWNT nanoparticle concentration, the acidity and concentration of running buffer, and separation voltage were investigated to acquire the optimum conditions. The seven purine and pyrimidine bases could be well separated within 16 min in a 35 cm effective length fused-silica capillary at a separation voltage of +8.0 kV in a 23 mM tetraborate buffer (pH 9.2) containing 8.0 x 10(-5) g/mL c-MWNTs. Under the optimal conditions, the linear ranges were of 2-250 microg/mL for A (R2 = 0.995), 3-200 microg/mL for U (R2 = 0.990) and G (R2 = 0.992), 3-250 microg/mL for T (R2 = 0.998), 2-200 microg/mL for C (R2 = 0.985) and 4-200 microg/mL for HX (R2 = 0.988) and 8-AA (R2 = 0.990). The detection limits were 0.9 microg/mL for A (S/N = 3), 2.4 microg/mL for U, 2.0 microg/mL for T, 1.5 microg/mL for C, 2.5 microg/mL for G and 3.0 microg/mL for HX and 8-AA. The proposed method was successfully applied for determining five purine and pyrimidine bases in yeast RNA.

Separation of caffeine and theophylline in poly(dimethylsiloxane) microchannel electrophoresis with electrochemical detection

A method for the rapid separation and sensitive determination of caffeine and theophylline was presented in poly(dimethylsiloxane) (PDMS) microchannel electrophoresis integrated with electrochemical detection. By using methanol as an additive, the peak shape and resolution were essentially improved. The analytes were well separated within only 40s in the running buffer of 5.0mM borate solution (pH 9.2) containing 10% (v/v) methanol. The linear ranges were from 6microM to 0.6mM and the detection limits were 4microM for caffeine and theophylline, respectively. The proposed method has been successfully applied to determine caffeine and theophylline in rat serum and urine.

Capillary electrophoresis-electrospray-mass spectrometry of nucleosides and nucleotides: application to phosphorylation studies of anti-human immunodeficiency virus nucleosides in a human hepatoma cell line

We report the use of capillary electrophoresis-electrospray ionization-mass spectrometry (CE-ESI-MS) for the determination of antiretroviral dideoxynucleosides (ddNs), their nucleotides, and a set of ribonucleosides and ribonucleotides. A CE system for separation of most commonly used antiretroviral ddNs has been developed based on a basic buffer with a volatile electrolyte suitable for ESI-MS detection in an untreated capillary column. Positive and negative ionization modes are investigated and compared for sensitive and stable electrospray performance. A 14-compound mixture of nucleosides and nucleotides is profiled in a single capillary zone electrophoresis separation with a distinct elution order: electroosmotic flow, ddNs, mononucleotides, dinucleotides, and trinucleotides in less than 18 min. The fragmentation pathways of the nucleosides and nucleotides in ESI-MS have been interpreted. Concentration limits of detection are 100 to 200 nM with an injection volume of approximately 10 nL. This technique has been used to detect naturally occurring nucleotides and to study the metabolism of lamivudine (3TC) in the human hepatoma cell line Hep G2. 3TC and its metabolites 3TC-monophosphate, 3TC-diphosphate, and 3TC-triphosphate were detected after 10 h of incubation of 3TC with the cells.

Simultaneous determination of multiple constituents in real beer samples of different origins by capillary zone electrophoresis

Simultaneous determination of alcohols, amines, amino acids, flavonoids, and purine and pyrimidine bases in bottled beer samples directly without any pre-treatment was carried out by capillary zone electrophoresis with diode-array detection. Electrolyte conditions such as pH, composition and concentration of the buffer, working voltage and type and time of injection were checked. The best separation of the cited analytes was achieved in 70 mM sodium borate solution and pH 10.25. The detection limits were from 2.1 to 5.6 mg L(-1) for the 18 compounds studied. The developed method is rapid, sensitive and quantitative and has been applied to seven types of international bottled beers of different origins bought locally.

Microchip capillary electrophoresis with a boron-doped diamond electrode for rapid separation and detection of purines

Microchip capillary electrophoresis (CE) coupled with a boron-doped diamond (BDD) electrode has been employed for the separation and detection of several purines and purine-containing compounds. The BDD end-channel amperometric detector offers favorable signal-to-noise (S/N) characteristics at the high detection potential (+ 1.3 V) essential for detecting purine-related compounds. Factors influencing the separation and detection processes were examined and optimized. Five purines (guanine, hypoxanthine, guanosine, xanthine, and uric acid) have been separated within 6 min at a separation voltage of 1000V using a borate/phosphate run buffer (pH 8.2). Linear calibration plots are observed for micromolar concentrations of the purine compounds. Good stability and reproducibility (R.S.D. < 5%) are obtained reflecting the minimal adsorption of purines at the BDD surface. Applicability for the detection of nucleosides, nucleotides, and oligonucleotides is illustrated. The new microchip protocol offers great promise for a wide range of bioanalytical applications involving assays of purines and purine-containing compounds.

Separation of purine and pyrimidine bases by capillary electrophoresis using β-cyclodextrin as an additive

Capillary electrophoresis was applied to separate purine and pyrimidine bases in the basis of their partial ionization in the alkaline buffer. The effects of buffer pH, buffer and beta-cylclodextrin concentration were systematically investigated using a commercial capillary electrophoresis instrument with UV detector at 254nm. We found that the resolutions of bases (especially for adenine and thymine) were significantly improved in the presence of beta-cylclodextrin. The satisfactory separation of five bases such as cytosine, thymine, adenine, guanine and uracil were achieved by capillary electrophoresis using beta-cylclodextrin as an additive. Under the optimal conditions, the linear range was from 2 to 200microg/ml for bases (R= 0,991-0,9977 ) and the detection limits were from 0.8 to 1.8microg/ml (S/N = 2). The detection limit of 0.05microg/ml ( S/N=2 ) for uracil was obtained by stacking injection mode. The assay was used to determine the deamination of cytosine to uracil by heating in the presence of sodium hydroxide. Our primarily results show that capillary electrophoresis is a very useful tool for determination of purine and pyrimidine bases and study on nucleic acids.

Capillary electrophoresis with amperometric detection of curcumin in Chinese herbal medicine pretreated by solid-phase extraction

In the present study, curcumin from Chinese herbal medicine turmeric was determined by capillary electrophoresis with amperometric detection (CE-AD) pretreated by a self-designed, simple, inexpensive solid-phase extraction (SPE) cartridge based on the material of tributyl phosphate resin. An average concentration factor of 9 with the recovery of > 80% was achieved when applied to the analysis of curcumin in extracts of tumeric. Under the optimized CE-AD conditions: a running buffer composed of 15 mM phosphate buffer at a pH 9.7, separation voltage at 16 kV, injection for 6 s at 9 kV and detection at 1.20 V, CE-AD with SPE exhibited low detection limit as 3 x 10(-8) mol/l (S/N = 3), high efficiency of 1.0 x 10(5) N, linear range of 7 x 10(-4) -3 x 10(-6) mol/l (r = 0.9986) for curcumin extracted from light petroleum. The method developed resulted in enhancement of the detection sensitivity and reduction of interference from sample matrix in complicated samples and exhibited the potential application for routine analysis, especially in food, because a relatively complete process of sample treatment and analysis was described.

Screening method for inherited disorders of purine and pyrimidine metabolism by capillary electrophoresis with reversed electroosmotic flow

Capillary electrophoresis with electroosmotic flow reversed by cationic surfactant for diagnosis of purine and pyrimidine inherited enzyme deficiencies is reported. Final separation conditions consist of 45 mM borate, 55 mM N-tris[hydroxymethyl]methylglycine, 10 mM tartrate, 1 mM cetyltrimethylammonium bromide and 0.44% tetrabutylammonium hydroxide-2-amino-2-methyl-1,3-propanediol (pH 8.6). Average sensitivity (2.51 microM), reproducibility of migration times (run-to-run C.V. < or = 0.6%, day-to-day C.V. < or = 2.5%), linearity (R2>0.994) and imprecision (mean intra-assay RSD 4.7% and inter-assay RSD 6.6%) of the method are acceptable for diagnostic purposes. Applicability of the method is demonstrated on urine samples from patients with enzymatically proven enzyme deficiencies.

Electrophoretic behaviour of oligonucleotides and mono-, di- and triphosphate nucleotides by capillary zone electrophoresis

A systematic investigation has been made into the mechanisms of the capillary zone electrophoresis (CZE) separation of 12 common nucleotides (mono-, di- and triphosphorylated) and polydeoxythymidylic acid oligonucleotides (pd(T)5-18) using electrophoretic mobility values calculated from migration time data. Relationships between electrophoretic mobility and the physicochemical characteristics of the analytes (charge, dissociation constants, charge-to-mass ratio) and the background electrolyte conditions (buffer strength, percentage organic modifier and buffer pH) were characterised. Nucleotide migration was dominated by the negatively charged phosphate groups. Additionally, there were important contributions to migration behaviour from the ionised amide groups of the nucleobases guanine and uracil at higher buffer pH values or with the presence of methanol in the electrolyte. Calculated electrophoretic mobility values for the nucleotides showed a substantially improved (5-fold) inter-run repeatability compared with migration time data. These studies show the value of representing nucleotide migration data as electrophoretic mobility in CZE for obtaining a more thorough analysis of separation mechanisms and to compensate for variation in migration time data caused by small changes in electrosmotic flow. Oligonucleotides pd(T)5-11 could be adequately resolved from their nearest neighbour, but the limit of single-base separation was pd(T)10 from pd(T)11 under the conditions used. It was calculated that a difference in charge-to-mass ratio of 2.64 x 10(-5) was required for resolution under the CZE conditions used.