Ion-pair reversed phase HPLC determination of nucleotides, nucleosides and nucleobases — Application to nucleotide metabolism in hepatocytes

Discrimination of Ribonucleoside Mono-, Di-, and Triphosphates Using an Engineered Nanopore

Ribonucleotides, which widely exist in all living organisms and are essential to both physiological and pathological processes, can naturally appear as ribonucleoside mono-, di-, and triphosphates. Natural ribonucleotides can also dynamically switch between different phosphorylated forms, posing a great challenge for sensing. A specially engineered nanopore sensor is promising for full discrimination of all canonical ribonucleoside mono-, di-, and triphosphates. However, such a demonstration has never been reported, due to the lack of a suitable nanopore sensor that has a sufficient resolution. In this work, we utilized a phenylboronic acid (PBA) modified Mycobacterium smegmatis porin A (MspA) hetero-octamer for ribonucleotide sensing. Twelve types of ribonucleotides, including mono-, di-, and triphosphates of cytidine (CMP, CDP, CTP), uridine (UMP, UDP, UTP), adenosine (AMP, ADP, ATP), and guanosine (GMP, GDP, GTP) were simultaneously discriminated. A machine-learning algorithm was also developed, which achieved a general accuracy of 99.9% for ribonucleotide sensing. This strategy was also further applied to identify ribonucleotide components in ATP tablets and injections. This sensing strategy provides a direct, accurate, easy, and rapid solution to characterize ribonucleotide components in different phosphorylated forms.

Quantitative assessments of adenosine triphosphatase hydrolytic activity by ultrafiltration-coupled ion-pair reversed-phase high-performance liquid chromatography

Adenosine triphosphate is a universal energy currency that can directly provide energy required for a multitude of biochemical reactions and biophysical actions through adenosine triphosphatase catalyzed hydrolysis. Adenosine triphosphatase activity is thus one important feature for the characterization of protein function and cell activity. Herein, we optimized ion-pair reversed-phase high-performance liquid chromatography technique for highly efficient separation of adenosine triphosphate, adenosine diphosphate, and adenosine monophosphate, and the method demonstrated good linearity. Moreover, by coupling a protein-removable ultrafiltration, we developed a sensitive and robust approach for quantification of adenosine triphosphatase hydrolytic activity. By this assay, we demonstrated that RecA filaments-catalyzed adenosine triphosphate hydrolysis approached a second-order reaction, and its rate constant was estimated as 0.057 mM^-1  min^-1 . In addition, we explored the effects of DNA length on this reaction and revealed that the increase of the length of single-stranded DNA can promote the adenosine triphosphatase hydrolytic activity of RecA filaments. All these results confirm the feasibility of this new method in quantification of adenosine triphosphatase hydrolytic activity assays. Compared with previous complicated enzyme-coupled or homogeneous colorimetric measurements, the developed approach with high resolution separation allows a simple reaction system for adenosine triphosphatase assay and a sensitive detection free of interference from background noise.

Separation of highly charged compounds using competing ions with hydrophilic interaction liquid chromatography - Application to assay of cellular nucleotides

Separation of highly charged compounds has always been a challenge in chromatography. Ion-pair reversed phase chromatography has been the most successful approach to date. Although polar reversed phase and HILIC columns have been introduced, they have limitations with highly charged compounds. Competing ions have been used, in addition to ion-pair reagent, to achieve better resolution with reversed phase columns. Herein, we explored the use of competing ions with HILIC columns to demonstrate the effects on retention and separation of mono-, di-, and tri-nucleotides, introducing a new tool to improve resolution with HILIC columns. HILIC columns that had irreversibly retained highly charged tri-nucleotides became capable of successfully separating the same compounds, by using this approach. The optimised method was used to successfully resolve a mixture of 12 nucleotides with charges ranging from 1^- to 3^-. The method was applied to quantify nucleotides in blood cell extracts.

Allosteric regulation and substrate activation in cytosolic nucleotidase II from Legionella pneumophila

Cytosolic nucleotidase II (cN-II) from Legionella pneumophila (Lp) catalyzes the hydrolysis of GMP and dGMP displaying sigmoidal curves, whereas catalysis of IMP hydrolysis displayed a biphasic curve in the initial rate versus substrate concentration plots. Allosteric modulators of mammalian cN-II did not activate LpcN-II although GTP, GDP and the substrate GMP were specific activators. Crystal structures of the tetrameric LpcN-II revealed an activator-binding site at the dimer interface. A double mutation in this allosteric-binding site abolished activation, confirming the structural observations. The substrate GMP acting as an activator, partitioning between the allosteric and active site, is the basis for the sigmoidicity of the initial velocity versus GMP concentration plot. The LpcN-II tetramer showed differences in subunit organization upon activator binding that are absent in the activator-bound human cN-II structure. This is the first observation of a structural change induced by activator binding in cN-II that may be the molecular mechanism for enzyme activation.

DATABASE

The coordinates and structure factors reported in this paper have been submitted to the Protein Data Bank under the accession numbers 2BDE and 4G63. The accession number of GMP complexed LpcN-II is 4OHF.

STRUCTURED DIGITAL ABSTRACT

LpcN-II and LpcN-II bind by molecular sieving (View interaction) LpcN-II and LpcN-II bind by x-ray crystallography (View interaction) [Structured digital abstract was added on 5 March 2014 after original online publication].

Structure elucidation of the thermal degradation products of the nucleotide cofactors NADH and NADPH by nano-ESI-FTICR-MS and HPLC-MS

Redox cofactors like NADH and NADPH are essential for the catalytic activity of several oxidoreductases. Here, we describe a comparative study of the thermal degradation products of both cofactors in the dry and liquid states. The degradation products were first separated, detected, and quantified by high-performance liquid chromatography (HPLC). Subsequently, selected main fractions were investigated by nanoelectrospray ionization-Fourier transform ion cyclotron resonance mass spectrometry (MS). Additionally, HPLC-MS was used to elucidate the structure of all degradation products. From these data, degradation pathways for both the liquid and the solid states were elucidated. Thermal degradation in water is significantly faster compared to degradation in the solid state. Hydrolysis and oxidative ring opening of the reduced nicotinamide adenine dinucleotide (phosphate) were shown to be the main reaction paths. Surprisingly, no significant differences were observed between the degradation of both cofactors in solution and in the solid state. Our results demonstrate that the stability of both cofactors is not limiting at moderate temperatures if they are used in the dry state (e.g., solid/gas catalysis). Significant degradation of dry cofactors was only observed under conditions, which are usually not appropriate for biocatalysis (>95 °C). Besides, the situation is completely different in solution where degradation is already observed at moderate temperatures.

Development of a NACE method for simultaneous measurement of three adenosine monophosphate isomers in biomimicking prebiotic synthesis without sample pretreatment

A practical NACE method was developed for simultaneous determination of three adenosine monophosphate (AMP) isomers. Separation of three AMP isomers was achieved using 200 mM Tris/H(3)BO(3) in acetontrile/water (2:1 v/v) at pH* 10.0 as the running buffer and +25 kV as the applied voltage over a bare fused-silica capillary of 50 microm id x 375 microm od x 54.5 cm (46 cm to the detector window). At 260 nm, the calibration curves were linear in the range of 1-100 microg/mL. The detection limits were less than 0.70 microg/mL. The recovery ranged from 94.5 to 106.4%. The intraday RSDs of the migration times were between 2.1 and 3.0%. The developed NACE method has been successfully applied for the determination of three AMP isomers in the real samples of biomimicking prebiotic synthesis reaction between N-(O,O-diisopropyl) phosphoryl amino acid and adenosine.

Determination of fifteen nucleotides in cultured human mononuclear blood and umbilical vein endothelial cells by solvent generated ion-pair chromatography

The paper describes the development of a method for the determination of 15 nucleotides in cultured mononuclear blood and umbilical vein endothelial cell lysates by solvent generated ion-pair chromatography. The phase system is generated via a mobile phase of 100 mM phosphoric acid adjusted to pH 6.2 with triethylamine. Nucleotides are eluted by applying a linear magnesium ion gradient. The method is robust, highly reproducible and easily adaptable to other cell lysates and allows the separation and quantitation of the nucleotides with detection limits in the range from 17 (ADP) to 126 (CDP) pmol in 20-microl aliquots.

Influence of mycophenolic acid on inosine 5'-monophosphate dehydrogenase activity in human peripheral blood mononuclear cells

BACKGROUND

Inosine 5'-monophosphate dehydrogenase (IMPDH) catalyses the oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5'-monophosphate (XMP). Thus, this enzyme plays an important role in the rate-limiting step of the de novo guanine nucleotide biosynthesis, making it a potent target for immunosuppressive drugs. Mycophenolic acid (MPA) is the most potent and specific inhibitor of IMPDH.

METHOD

IMPDH activity is determined via evaluation of XMP formation and the inhibitory influence of MPA in human peripheral blood mononuclear cells (PBMCs) is assessed by means of high-performance liquid chromatography (HPLC). For this objective, we have optimised a method based on solvent-generated ion exchange chromatography by cautiously varying mobile phase parameters.

RESULTS

The optimised method renders it possible to separate 18 analytes in 54 min in a single isocratic experiment and to measure the IMPDH activity in the lysate of human PBMCs in dependence on incubation time, substrate, co-substrate and inhibitor concentrations. In this way, we have determined the Michaelis-Menten constants K(M) and V(max) for IMP and beta-NAD+ and the inhibitor constant K(i) for MPA.

CONCLUSIONS

The chromatographic method presented in this report allows a rapid, reliable and reproducible quantification of IMPDH activity in PBMCs and therefore represents an attractive tool for the pharmacodynamic monitoring of the effects of MPA in patients under immunosuppressive therapy.

Application of mixed partition-adsorption systems in high-performance liquid chromatography of purines and pyrimidines

Separation of the test mixtures of some purine and pyrimidine derivatives on silicas (types A and B) in adsorption normal-phase (A-NP) and mixed partition-adsorption normal-phase (MPA-NP) mode has been studied. When the A-NP mode is used the peak shapes are unsatisfactory (especially on type A silica). At the same time MPA-NP systems show a good peak symmetry on all silica types. The findings have demonstrated that the MPA-NP mode offers a specific selectivity. This allows MPA-NP systems to supersede reversed-phase systems in some application areas.

Postanoxic formation of aldehydic lipid peroxidation products in human renal tubular cells

The levels of the aldehydic lipid peroxidation products 4-hydroxynonenal and malondialdehyde and the levels of adenine nucleotides were measured during anoxia/reoxygenation studies with isolated human renal tubular cells in vitro. Energy depletion of renal cells was demonstrated by the decrease of ATP level. ATP could be restored completely and rapidly during postanoxic reoxygenation. 4-Hydroxynonenal and malondialdehyde levels increased during reoxygenation. In parallel, the breakdown of physiological 4-hydroxynonenal levels was estimated. The 4-hydroxynonenal formation rate was estimated from accumulation and metabolic breakdown rates of this compound.

Reversed-phase high-performance liquid chromatography of purine compounds for investigation of biomedical problems: application to different tissues and body fluids

An overview of high-performance liquid chromatographic separation techniques (reversed-phase and ion-pair reversed-phase) used in the analysis of purine ribonucleotides, ribonucleosides and nucleobases, including procedures for sample preparation, is given. Coverage of the separation techniques is extended to the measurement of specific radioactivities of these compounds in tracer kinetic experiments for metabolic flux rate analyses. This article is focused on the development and adaptation of reversed-phase separation techniques for nucleotides, nucleosides and bases that are used to examine a variety of biomedical problems. The investigation of purine nucleotide metabolic disorders or physiological transitions in the pathomechanisms of different diseases and syndromes or in cell maturation processes, respectively, requires the application of chromatographic separation to a multitude of tissues and body fluids. These samples vary greatly in concentrations of purine compounds with low molecular mass, from ca. 5 mM to ca. 0.5 microM. The advantages and disadvantages of different techniques are critically discussed.

Reversed-phase and ion-pair separations of nucleotides, nucleosides and nucleobases: analysis of biological samples in health and disease

Methods for the assay of nucleotides, nucleosides and nucleobases in biological samples in health and disease are reviewed, with emphasis on reversed-phase and ion-pair reversed-phase techniques for their determination. Modes of extraction from biological samples are discussed with respect of the determination of in vivo concentrations. Advantages and limitations of ion-pair reversed-phase chromatography are discussed with examples from biochemistry and clinical chemistry. The capacity of the high-performance capillary electrophoresis is compared with that of ion-pair reversed-phase chromatography.

High-performance liquid chromatographic separation of purine deoxyribonucleoside monophosphate-benzo[a]pyrene adducts

Chromatographic methods that allow the separation of adducts of purine nucleoside 3'-phosphates with the pure enantiomers of the anti-dihydrodiol epoxide of benzo[a]pyrene are developed. The optimization procedure includes evaluation of the effect of buffer molarity, the pH of the buffer, and the role of organic modifiers. The method can be utilized to prepare standards with known absolute configuration that can be further used in the Randerath 32P-postlabeling procedure.

Improved ion-pair high-performance liquid chromatographic method for the quantification of a wide variety of nucleotides and sugar-nucleotides in animal cells

An improved method including extraction procedures is presented for the analysis of nucleotides in suspension-cultivated animal cells. Quantification was performed by ion-pair high-performance liquid chromatography after perchloric acid extraction. It was found that the amount of perchloric acid taken for extraction influenced the yield and that cell washing procedures caused deterioration of the analysis results for triphosphates. More than thirty nucleotides and sugar-nucleotides were separated within 25 min using a Supelcosil reversed-phase column (3 microns) with tetrabutylammonium hydrogensulphate as pairing agent and methanol-pH gradient elution. Cultivated hybridoma cells showed variations in intracellular nucleotide concentrations as well as relative amounts during different growth phases, which could reflect the physiological state of a cell culture.

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.

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.

Balancing of energy-consuming processes of rat hepatocytes

A method for the quantification of energy consuming processes described by Siems et al. for reticulocytes and by Müller et al. for ascites tumour cells was applied to balance the ATP-consumption of isolated rat hepatocytes. On the basis of decreased coupled respiration rates following the specific inhibition of energy-requiring reactions, the energy demands of protein turnover, nucleic acid synthesis, Na+/K(+)-ATPase and Ca2(+)-transport of hepatocytes in different incubation media were assessed. These processes together with urea synthesis account for about 60 per cent of the total energy consumption in a glucose and amino acid-enriched Eagle/Borsook medium. The metabolic flux rates of total ATP-consumption and ATP-consumption of single energy-requiring processes in hepatocytes are compared with those in reticulocytes and different tumour cell types.