Analysis of normal and modified nucleosides in urine by capillary electrophoresisa)

Summary Modified nucleosides excreted in urine have been studied as potential diagnostic markers for cancer and AIDS, and as indicators for the whole-body turnover of RNA. Until now, reversed-phase (RP) HPLC and, to some extent, immunoassays are the preferred analytical methods for urinary nucleosides. A new capillary electrophoretic method for the analysis of normal and modified nucleosides in urine has been developed and optimized in our laboratory. The separation of nucleosides extracted from normal human urine on phenyl boronic acid affinity chromatography columns was performed in uncoated 565 mm (500 mm to detection window) × 50 μm i.d. capillary tubing using a 300 mM SDS—25 mM borate—50 mM phosphate buffer (pH 6.7), a 45-s load, a voltage of 7.5 kV (41 μA) and UV detection at 260 and 210 nm. The average recovery of the nucleosides was 91 %. The calibration curves were linear over all physiological and pathophysiological concentration ranges and the limits of detection were at micromolar levels. Reproducibility of migration times were better than 1 % (coefficient of variation,CV), and the reproducibilities of the determined concentrations were better than 5 % for standards and 6–15 % for extracted urine. The developed method was used to quantify 15 normal and modified nucleosides in 25 normal urines to establish reference ranges. The analysis time was less than 45 min. Dedicated to Professor E. Bayer on the occasion of his 70th birthday. Presented at the 21^st ISC held in Stuttgart, Germany, 15^th–20^th September, 1996.     

Migration mechanism of bases and nucleosides in oil-in-water microemulsion capillary electrophoresis.

The electrophoretic behaviors of five bases and corresponding nucleosides in the oil in water (o/w) microemulsion capillary electrophoresis, microemulsion electrokinetic chromatography (MEEKC), were examined in comparison with those in normal capillary zone electrophoresis (CZE). The microemulsion systems were composed of heptane, sodium dodecyl sulfate (SDS), 1-butanol and 10 mM phosphate buffer (pH 7.0) or toluene, SDS, 1-butanol and 5 mM carbonate buffer (pH 10.0). CZE was carried out in the range of pH 9.7-10.9, and the dissociation constants, pKa, of the bases and nucleosides and the electrophoretic mobilities of the anionic forms were determined. The electrophoretic behaviors of the solutes in the microemulsion systems were analyzed from their pKa, the electrophoretic mobilities of the anions determined by CZE, and the distribution constants, K(D), of the neutral forms between the microemulsion droplets and the outer aqueous phase. The importance of adsorption mechanism in MEEKC system was suggested from the correlation between log K(D) and log P.     

Determination of the ultraviolet absorbance and radioactivity of purine compounds separated by high-performance liquid chromatography. Application to metabolic flux rate analysis.

A double detection system for the determination of adenine metabolism in biological tissues using isocratic ion-pair reversed-phase chromatography is presented. Two isocratic ion-pair separations were used: (i) 10 mM NH4H2PO4, 2 mM tetrabutylammonium phosphate (PIC reagent A) and 18% acetonitrile for the determination of nucleotides and (ii) 50 mM KH2PO4, 1 mM PIC reagent A and 1% acetonitrile for the determination of monophosphorylated nucleotides, nucleosides and nucleobases. The parallel detection of ultraviolet absorbance at 254 nm and the radioactivity of separated purine compounds allows the detection of pool sizes and of the specific radioactivities in tracer kinetic experiments. The high-performance liquid chromatography methods were applied to the determination of flux rates during adenine nucleotide metabolism in suspensions of Ehrlich mouse ascites tumour cells. The pathways of adenine metabolism in cells during the proliferation and plateau phases of tumour growth were compared.     

Separation of nucleosides using capillary electrochromatography

The analysis of nucleosides and nucleotides have in most cases been performed by HPLC using either reversed-phase HPLC with gradient elution or using reversed-phase ion-pair chromatography. In this paper we have explored the possibility of using capillary electrochromatography (CEC) in order to avoid the use of gradients or ion-pairing reagents. CEC is in many ways comparable to HPLC, but CEC is theoretically able to provide better separations due to the higher efficiency caused by the flowfront being more plug-like as also is the case in CE, which is to be compared to the more parabolic flow observed in HPLC. The separation of six nucleosides (adenosine, cytidine, guanosine, inosine, thymidine and uridine) was investigated with respect to concentration of buffers, pH, amount of acetonitrile, temperature and voltage in order to optimise the separation. Baseline separation was achieved for the six nucleosides in less than 13 min using a background electrolyte consisting of (5 mM acetic acid, 3 mM triethylamine, pH 5.0)-acetonitrile (92:8, v/v).     

Determination at ppb level of an anti-human immunodeficiency virus nucleoside drug by capillary electrophoresis-electrospray ionization tandem mass spectrometry

Capillary electrophoresis coupled with tandem mass spectrometry was used to indirectly separate and quantify the active metabolite of the anti-human immunodeficiency virus (anti-HIV) didanosine drug. The influence of several parameters (pH and ionic strength of volatile formic acid-ammonia buffer) upon electroosmotic flow, electrophoretic mobility and peak efficiency of several nucleosides (A, dA, ddA, C) has been studied. This paper illustrates the current importance in CE-MS technique as a complementary or substituted method to the known HPLC-radioimmunoassay or HPLC-UV method to measure levels of anti-HIV drugs. The limit of detection for 2',3'-dideoxyadenosine by this method is 2 microg 1(-1) in a formic acid-ammonia buffer (pH 2.5, 10 mM ionic strength).This methodology could be used to perform simultaneous detection of two or more anti-HIV nucleosides, such as stavudine or didanosine in combination therapy.     

Simultaneous Determination of Ten Nucleosides and Related Compounds by MEEKC with [BMIM]PF6 as Oil Phase

In the present study, four nucleobases (adenine, cytosine, uracil, thymine), four nucleosides (adenosine, cytidine, uridine, thymidine), and two nucleotides (adenosine-5′-monophosphate, and cytidine-5′-monophosphate) were simultaneously determined by MEEKC with ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM]PF₆) as oil phase. Experimental parameters including the microemulsion compositions (surfactant, co-surfactant, and oil phase), pH, and concentration of borate buffer were intensively investigated. Finally, the ten compounds were well separated within 11 min using the running buffer composed of 140 mM SDS, 1.8 M n-butanol, and 10 mM [BMIM]PF₆ in 20 mM borate buffer of pH 9.0. The developed method was successfully applied to determine the contents of investigated compounds in three different widely used traditional Chinese medicines (cultured Cordyceps sinensis, Radix Astragali, and Radix Isatidis). The results indicated that the developed MEEKC method could be used for the rapid determination of nucleobases, nucleosides, and nucleotides in herbal medicines or other complex matrices.     

Simultaneous Determination of Ten Nucleosides and Related Compounds by MEEKC with [BMIM]PF6 as Oil Phase

In the present study, four nucleobases (adenine, cytosine, uracil, thymine), four nucleosides (adenosine, cytidine, uridine, thymidine), and two nucleotides (adenosine-5′-monophosphate, and cytidine-5′-monophosphate) were simultaneously determined by MEEKC with ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM]PF₆) as oil phase. Experimental parameters including the microemulsion compositions (surfactant, co-surfactant, and oil phase), pH, and concentration of borate buffer were intensively investigated. Finally, the ten compounds were well separated within 11 min using the running buffer composed of 140 mM SDS, 1.8 M n-butanol, and 10 mM [BMIM]PF₆ in 20 mM borate buffer of pH 9.0. The developed method was successfully applied to determine the contents of investigated compounds in three different widely used traditional Chinese medicines (cultured Cordyceps sinensis, Radix Astragali, and Radix Isatidis). The results indicated that the developed MEEKC method could be used for the rapid determination of nucleobases, nucleosides, and nucleotides in herbal medicines or other complex matrices.

     

Changes of nucleotide patterns in liver, muscle and blood during the growth of Ehrlich ascites cells: application of the reversed-phase and ion-pair reversed-phase high-performance liquid chromatography with radial compression column

The pool of purine compounds was analysed in liver, skeletal muscle and blood of mice during the growth of Ehrlich ascites tumour cells. Three fast isocratic high-performance liquid chromatographic methods were used. (1) Determination of nucleotides by an isocratic ion-pair reversed-phase chromatography with a 10 mM ammonium phosphate buffer containing acetonitrile and tetrabutylammonium phosphate. (2) Separation of nucleosides and nucleobases in cell extracts by a reversed-phase system with methanol and 50 mM potassium phosphate buffer as eluent. (3) Nucleosides and nucleobases in body fluids were analysed by a reversed-phase system with 10 mM potassium phosphate containing methanol. These methods allow the rapid determination of purine compounds in small biological samples from various cell types and body fluids, with high accuracy and sensitivity. The pool of cellular nucleotides increased during the exponential phase of tumour growth. Adenosine accumulated significantly in all tissues in the stationary phase of tumour growth.     

硅胶基硝化苯硼酸亲和色谱材料的合成及应用

合成了硅胶基硝化苯硼酸亲和色谱材料,首先对间氨基苯硼酸进行硝基化,制得3-氨基-4-硝基苯硼酸功能基团,通过γ-缩水甘油醚氧丙基三甲氧基硅烷把功能基团键合到硅胶基体上,在20.7MPa压力下装成亲和色谱预柱(35mm×4.6mmi.d.)。用该预柱通过六通阀后接ODS分析柱(250mm×4.6mmi.d.),构成中心切割二维HPLC。该系统能对含有顺二羟基结构的化合物进行在线富集,实现生物复杂样品直接进样分离分析。使用该系统对尿中多种修饰核苷进行了分离分析,以pH值7.95的0.25mol/LNH4Ac碱性缓冲液把实际尿样(100μL)中核苷保留在预柱上,生物大分子无保留通过,再切换六通阀,以pH4.50的25mmol/LKH2PO4酸性洗脱液把保留在预柱上的核苷洗脱,进样到下一级ODS分析柱柱头上聚焦,然后用梯度洗脱法(pH4.50的25mmol/LKH2PO4缓冲液与体积比60∶40的甲醇-水梯度混合构成洗脱液)完成核苷在ODS分析柱上的分离(紫外检测260nm),11种目标核苷的分离分析取得了良好的定性定量结果。     

A Nano-Chip-LC/MS<Superscript><Emphasis Type="Italic">n</Emphasis></Superscript> Based Strategy for Characterization of Modified Nucleosides Using Reduced Porous Graphitic Carbon as a Stationary Phase

LC/MS analysis of ribonucleosides is traditionally performed by reverse phase chromatography on silica based C18 type stationary phases using MS compatible buffers and methanol or acetonitrile gradients. Due to the hydrophilic and polar nature of nucleosides, down-scaling C18 analytical methods to a two-column nano-flow setup is inherently difficult. We present a nano-chip LC/MS ion-trap strategy for routine characterization of RNA nucleosides in the fmol range. Nucleosides were analyzed in positive ion mode by reverse phase chromatography using a 75 μ × 150 mm, 5 μ particle porous graphitic carbon (PGC) chip with an integrated 9 mm, 160 nL trapping column. Nucleosides were separated using a formic acid/acetonitrile gradient. The method was able to separate isobaric nucleosides as well as nucleosides with isotopic overlap to allow unambiguous MS ⁿ identification on a low resolution ion-trap. Synthesis of 5-hydroxycytidine (oh⁵C) was achieved from 5-hydroxyuracil in a novel three-step enzymatic process. When operated in its native state using formic acid/acetonitrile, PGC oxidized oh⁵C to its corresponding glycols and formic acid conjugates. Reduction of the PGC stationary phase was achieved by flushing the chip with 2.5 mM oxalic acid and adding 1 mM oxalic acid to the online solvents. Analyzed under reduced chromatographic conditions oh⁵C was readily identified by its MH⁺ m/z 260 and MSⁿ fragmentation pattern. This investigation is, to our knowledge, the first instance where oxalic acid has been used as an online reducing agent for LC/MS. The method was subsequently used for complete characterization of nucleosides found in tRNAs using both PGC and C18 chips.     

Fast simultaneous determination of 14 nucleosides and nucleobases in cultured Cordyceps using ultra-performance liquid chromatography

Determination of nucleosides and their metabolic compounds is important for physiological and pharmacological studies. Herein, a rapid ultra-performance liquid chromatography (UPLC) method was developed for the simultaneous determination of 14 nucleosides and nucleobases, namely adenine, adenosine, cytosine, cytidine, uracil, uridine, guanine, guanosine, hypoxanthin, inosine, thymine, thymidine, 2′-deoxyuridine and cordycepin. The separation was performed on Waters Acquity UPLC system with Acquity UPLC BEH C₁₈ column and gradient elution of 0.5 mM acetic acid and acetonitrile in 5 min. The correlation coefficients of 14 analytes were high (R² > 0.9995) within the test ranges. The LOD and LOQ were lower to 11.9 and 47.0 ng/ml with 1 μl of injection volume, respectively. The overall R.S.D. for intra- and inter-day of 14 analytes were less than 1.8%. The developed method was applied for the analysis of nucleosides and nucleobases in cultured Cordyceps, which also could be used for the fast determination of the analytes in pharmaceutical products and biological fluids.     

Counter-current chromatographic separation of nucleic acid constituents with a hydrophilic solvent system

Nucleic acid constituents such as nucleobases, nucleosides and nucleotides were separated by counter-current chromatography using type J coil planet centrifuge. The separation was performed with a hydrophilic solvent system composed of 1-propanol/800 mM potassium phosphate buffer (pH 7.4) (1:1, v/v) by eluting the lower aqueous phase at a flow-rate of 0.5 ml/min. Eight selected nucleic acid constituents (4.0 mg, 0.5 mg of each), uridine monophosphate (UMP), adenosine monophosphate (AMP), deoxyadenosine monophosphate (dAMP), uridine, urasile, deoxy uridine, adenosine and adenine were well resolved within 160 min.     

Novel approach for developing urinary nucleosides profile by capillary electrophoresis-mass spectrometry

A simple, rapid and efficient capillary electrophoresis-mass spectrometry (CE-MS) method was developed to analyze urinary nucleosides for the first time. The composition of CE buffer and MS parameters were systematically optimized. The optimum buffer was 150 mM acetic acid containing 15% methanol and 15% ethanol. The optimum MS parameters were: methanol containing 0.5% acetic acid was selected as the sheath liquid and the flow rate was 5 microL/min; the flow rate and temperature of drying gas were 6L/min and 150 degrees C, respectively; the pressure of nebulizing gas was 2 psig; and the fragmentor and ESI voltage were 100 V and 4000 V, respectively. Under the optimum CE-MS conditions, the urinary nucleosides were separated within 18 min. The linearity between the relative peak areas and the corresponding concentration of nine nucleosides markers were excellent. The limits of detection (S/N=3) of markers were 0.00862-3.82 nmol/mL. The optimum CE-MS method was applied to analyze urine from 20 bladder cancer patients and 20 healthy volunteers. Considering the standards of many nucleosides cannot be obtained, it is not the ratios of the concentrations of nucleosides to that of creatinine in the literatures, but the ratios of the relative peak area of nucleosides to the concentration of creatinine that used for pattern recognition. And, the statistical analysis result indicated this method was feasible.     

Simple ethers as models of sugar molecules in calculations of vertical excitation energies of DNA and RNA nucleosides

The ribose and deoxyribose molecules of RNA and DNA nucleosides are substituted with simple model compounds 1-methoxy-2-ethanol and 1-methoxypropane to mimic the effect of binding to sugars on the vertical excitation energies of purine and pyrimidine bases. The (R)-1-methoxy-2-ethanol, CH(3)OC*HCH(2)OH, for model ribose nucleosides and (R)-1-methoxypropane, CH(3)OC*HC(2)H(5), for model deoxyribose nucleosides have minimal structural characteristics of ribose and deoxyribose molecules when attached to nucleic acid purine and pyrimidine bases. The bases are attached to the C1 carbon atom designated by the asterisk. The vertical excitation energies of these model nucleosides are calculated with the time-dependent density functional theory method at the B3LYP level with 6-311++G(d,p) and aug-cc-pVDZ basis sets. The attachment of the ether molecules qualitatively and quantitatively modifies the excited state energy levels of the model nucleosides when compared to the free bases. These changes can affect the deexcitation mechanisms for photoexcited nucleosides.     

Rapid simultaneous determination of 15 nucleosides and nucleobases in marine medicinal organism Anthopleura lanthogrammica Berkly by micellar electrokinetic capillary chromatography

In this study, a rapid and reliable micellar electrokinetic capillary chromatography (MECC) method has been developed and validated for the separation and quantification of 15 nucleosides and nucleobases in a kind of marine medicinal animal Anthopleura lanthogrammica Berkly. Factors such as micelle concentration, pH, concentration of buffer, etc. were investigated in order to obtain the optimum conditions for the separation. The optimized separation procedure employed 25 mM disodium hydrogen phosphate buffer containing 70 mM sodium dodecyl sulfate (SDS) at pH 8.7 as background electrolyte, 25°C of capillary temperature and 20 kV of separation voltage. UV detection was at 260 nm and injection was hydrodynamic at 50 mbar for 3 s. The whole analysis was completed within 13 min. The relative standard deviations (RSDs) of the peak areas for method precision ranged from 1.4 to 7.6%, and the recovery was between 80.2 and 112.9%. The limit of detection (LOD) for 15 nucleosides and nuleobases was between 0.25 and 0.75 μg/mL. According to the evaluation study, the method was shown to be precise, accurate and reproducible. The proposed MECC method was successfully applied for determination of nucleosides and nucleobases in Chinese Anthopleura lanthogrammica Berkly. The result showed that the species and content of nucleosides and nucleobases in Anthopleura lanthogrammica Berkly samples were abundant.     

Probing the Binding Requirements of Modified Nucleosides with the DNA Nuclease SNM1A

SNM1A is a nuclease that is implicated in DNA interstrand crosslink repair and, as such, its inhibition is of interest for overcoming resistance to chemotherapeutic crosslinking agents. However, the number and identity of the metal ion(s) in the active site of SNM1A are still unconfirmed, and only a limited number of inhibitors have been reported to date. Herein, we report the synthesis and evaluation of a family of malonate-based modified nucleosides to investigate the optimal positioning of metal-binding groups in nucleoside-derived inhibitors for SNM1A. These compounds include ester, carboxylate and hydroxamic acid malonate derivatives which were installed in the 5′-position or 3′-position of thymidine or as a linkage between two nucleosides. Evaluation as inhibitors of recombinant SNM1A showed that nine of the twelve compounds tested had an inhibitory effect at 1 mM concentration. The most potent compound contains a hydroxamic acid malonate group at the 5′-position. Overall, our studies advance the understanding of requirements for nucleoside-derived inhibitors for SNM1A and indicate that groups containing a negatively charged group in close proximity to a metal chelator, such as hydroxamic acid malonates, are promising structures in the design of inhibitors.     

Qualitative and quantitative determination of nucleosides, bases and their analogues in natural and cultured Cordyceps by pressurized liquid extraction and high performance liquid chromatography-electrospray ionization tandem mass spectrometry (HPLC-ESI-MS/MS)

A simple and rapid pressurized liquid extraction (PLE) and high performance liquid chromatography-electrospray ionization tandem mass spectrometry (HPLC-ESI-MS/MS) method was developed for qualitative and quantitative determination of nucleosides, bases and their analogues in natural and cultured Cordyceps. The samples were extracted using PLE. The separation was achieved on a ZORBAX Eclipse XDB-C₁₈ column with gradient elution of methanol and 5 mM aqueous ammonium acetate as mobile phase. Target compounds were identified by characterizing their product ions, precursor ions and retention times. Quantitative analysis of investigated compounds were performed using time programmed selective ion monitoring (SIM) or selective reaction monitoring (SRM) with 10 segments in positive (negative for uridine) ion mode. The results showed that 43 bases, nucleosides and their analogues were detected in Cordyceps, of these 16 compounds were identified. The simultaneous determination of seven nucleosides and six bases in Cordyceps was achieved using PLE and HPLC-ESI-MS/MS method described above, which afforded good linearity, selectivity, precision, recovery, short analysis time as well as LOD and LOQ in the ng/ml range.     

Optimization of CEC for simultaneous determination of eleven nucleosides and nucleobases in Cordyceps using central composite design

A CEC method is described for the simultaneous determination of 11 nucleosides and nucleobases including cytosine, uracil, uridine, hypoxanthine, 2'-deoxyuridine, inosine, guanosine, thymidine, adenine, adenosine, and cordycepin in Cordyceps using 5-chlorocytosine arabinoside as internal standard (IS). Chemometric optimization based on central composite design was employed to find the optimum conditions. The factors for optimization were defined as three parameters: voltage, pH, and concentration of ACN as organic modifier. The resolution (R(s)) between inosine and guanosine, as well as the entire run time were employed to evaluate the response function. A running buffer composed of 4 mM ammonium acetate and 2 mM triethylamine (TEA) adjusted to pH 5.3 using acetic acid, and containing 3% ACN as modifier, with gradient voltage (0-4 min: 20 kV, 4-12 min: linear gradient from 20 to 30 kV; 12-16 min: 30 kV) were found to be the optimum conditions for the separation. Separation of the 11 investigated compounds and 5-chlorocytosine arabinoside was achieved within 16 min. The contents of the 11 compounds in natural and cultured Cordyceps sinensis, and cultured Cordyceps militaris were also compared. The result showed that CEC is an efficient method for analysis of nucleosides and nucleobases in Cordyceps, which is helpful to control the quality of this valued traditional Chinese medicine.     

Analysis of modified nucleosides in the urine of patients with malignant cancer by liquid chromatography/electrospray ionization mass spectrometry

As modified nucleosides reflect altered tRNA turnover which seems to be impaired in the body of cancer patients, they have been evaluated as potential tumor markers. High-performance liquid chromatography/electrosprary ionization quadrupole time-of-flight mass spectrometry (HPLC/ESI-Q-TOFMS) was used to identify nucleosides purified from urine in positive ionization mode. Potential nucleosides were assessed by their evident UV absorbance in HPLC and then further examined by mass spectrometric techniques. In this manner, 21 nucleosides were detected in the urine of a patient with lymphoid cancer including three modified nucleosides 5'-dehydro-2-deoxyinosine, N1,N2,N7-trimethylguanosine and N1-methyl-N2-ethylguanosine, which had never been reported previously.     

A Dual-Column HPLC Method for the Simultaneous Measurement of 6-Thioguanine and Adenine in RNA or DNA

Abstract

A sensitive method for measuring 6-thioguanine incorporation into DNA and RNA utilizing a dual column system is presented. The measurement of the 6-thioguanine deoxyribo-or ribonucleosides and deoxyadenosine or adenosine is made simultaneously, thereby allowing for direct calculation of the incorporation per nucleic acid base. The separation utilizes a strong anion-exchange column connected in series with an octadecylsilane column. Prior to high pressure liquid chromatography, the sample is partially purified and oxidized with potassium permanganate. Following a 10-min delay, a 10-min linear gradient from 2% to 20% methanol in 30 mM NH₄H₂PO₄, pH 3.7, is employed. Detection of eluting material is by fluorescence and by UV absorbance at 254 nm. Recovery of the 6-thioguanine nucleosides was determined using [8-¹⁴C]-6-thioguanine. The sensitivity of the method for the oxidized 6-thioguanine compounds is approximately 1 pmole (fluorescence) whereas that for the adenine nucleosides (UV absorbance) is about 100 pmoles. This sensitivity is adequate to determine the incorporation in less than 10⁶ (about 1 mg) Chinese hamster ovary cells exposed to a cytotoxic concentration of 6-thioguanine.