Separation of purine bases, nucleosides and nucleotides by a column-switching technique combining reversed-phase and anion-exchange high-performance liquid chromatography

An on-line two-stage column chromatographic technique is described which combines reversed-phase and anion-exchange chromatography for the separation of purine nucleic acid components. The elution program applied, consisting of two gradient programmes, provides a separation of bases and nucleosides on the octadecyl silica column and a separation of the nucleotides on the anion-exchange column to which they have been switched at the beginning of the elution. This method is easy to modify for special problems and can be used when establishing a complete profile of purines.     

Perspectives on analyses of nucleic acid constituents: the basis of genomics

The recent mapping of the human genome was a tremendous achievement made possible to a large degree by the development of analytical methods for sequencing purine and pyrimidine bases in nucleic acids. In the last 3 decades, the number of analyses of nucleic acids and their constituents by HPLC and capillary electrophoresis (CE) has exploded. These techniques have been used not only for genomics, but also for the determination of free nucleotides, nucleosides and their bases in body fluids and tissues. Although a large number of HPLC and CE papers have been published on nucleic acid constituent applications, relatively little has been written on the mechanisms of the separations. However, to optimize analytical conditions knowledgeably and rapidly, it is important to know why and how these separations occur and the factors that affect them. The HPLC methods for the analysis of nucleic acid constituents and the information available on some of the mechanisms of separation of nucleotides, nucleosides and their bases, as well as the analysis of these compounds by CE and the factors that affect these separations are discussed.     

Application of reversed-phase and ion-pair HPLC for investigation of nucleotide metabolism in erythrocytes,reticulocytes and tumour cells

Summary The determination of nucleotides, nucleosides, and nucleobases was carried out in cells of different metabolic complexity: in mature and immature red blood cells, in Ehrlich ascites tumour cells from different proliferation stages, and in other tumour cells. The maturation of reticulocytes to erythrocytes is accompanied by loss of organelles and energy-requiring processes as well as the switch from aerobic to anaerobic ATP production. The profile of purine nucleotides, nucleosides, bases, and pyridine dinucleotides, by reversed-phae HPLC, shows large concentration changes during the maturation of red blood cells. The concentrations of purine mono and triphosphates are two to four times greater in reticulocytes in comparison with erythrocytes; the difference in the concentrations of nucleosides and nucleobases between reticulocytes and erythrocytes is even greater. Application of ion-pair HPLC showed that the Ehrlich ascites cells loose major portions of purine mono-, diand triphosphates between the 7th and 11th day after inoculation. Fast growing solid sarcoma tumours of rats (MV 202 Ner) contain higher amounts of nucleotides than slowly growing tumours of identical cell type.     

Reversed-phase and cation-exchange chromatography on a new poly(styrene-divinylbenzene) high capacity,weak cation-exchanger

Summary A weak cation-exchanger for high-performance liquid chromatography is obtained by oxidation of either poly(methylstyrene-divinylbenzene) or of poly(chloromethylstyrene-divinylbenzene). Reaction conditions were optimised to yield an exchange capacity of about 4meqg^–1 dry resin. The material was evaluated chromatographically as a function of pH, organic modifier, temperature and flow rate. A combination of ionexchange and hydrophobic interaction between the solutes and the packing material was observed. This could be used to provide more options for realising chromatographic separations. Some chromatograms of heterocyclic bases, nucleosides, nucleotides and amino acids are shown.     

New operational modes for multidimensional and comprehensive gas chromatography by using cryogenic modulation

Historically, hardware and method-related concerns have limited the use of multidimensional gas chromatography in the routine laboratory. This paper presents a new approach that offers the potential to significantly alter the manner in which multidimensional gas chromatography is conducted, based on the use of a modulated cryogenic trap which can be moved longitudinally along the column. Two columns are directly coupled, and no switching valves are used. It is demonstrated that a heartcut section can be cryofocused and zone-compressed, and then rapidly remobilized at the prevailing column oven temperature without any supplementary heating. A short second dimension column is used, giving fast second dimension analysis. This allows a large number of heartcuts to be programmed for any one analysis. The 'ultimate' manifestation of multidimensional gas chromatography is the comprehensive GC technique (GC X GC). This is now simply effected by performing very rapid heartcuts at intervals on the order of 1/5th of the peak width of primary dimension peaks, and requires that the second dimension be able to complete the analysis of each collected zone on a similar timeframe. This paper uses a semi-volatile aromatic mixture to demonstrate these selected operational modes, that can be achieved with the longitudinal modulation method. The flexibility that arises from this approach is shown by the ability to swap between selected whole-peak enhancement and comprehensive modes during the one analytical run. The increased sensitivity that follows from peak compression is a further advantage, which would be beneficial for trace analysis.     

Particle beam glow discharge mass spectrometry: spectral characteristics of nucleobases

Use of a particle beam glow discharge (PB-GD) source for mass spectrometric determinations of deoxy- and ribonucleosides and nucleotides is described. Use of this combination of sample introduction and ion source decouples the vaporization and ionization steps, leading to very simple spectral structure. The mass spectra of these compounds are EI-like in nature, with clearly identified molecular ions and fragmentation patterns that are easily rationalized. The PB-GDMS combination can be operated in a flow injection mode wherein the analyte is injected directly into the solvent flow, or can also be coupled to a high-performance liquid chromatography (HPLC) system allowing LC/MS analysis of mixtures. Mass spectra obtained for nucleic acid bases, nucleosides, and nucleotides are readily obtained with injections of low-nanomole quantities. Representative PB-GDMS spectra for deoxy- and ribonucleosides, nucleotides, and mixed-base oligonucleotides are presented to demonstrate the capabilities of the GD source. Characteristic fragmentation peaks from the spectra of adenine, cytosine, guanine, and thymine were identified in 22-base sequences of single-stranded DNA. The PB-GD source is capable of producing spectra that may be used to identify the individual bases present in mixed-base DNA and RNA fragments.     

Rapid Chromatographic Analysis of Nucleosides and N-Bases in Physiologic Fluids

Abstract

A high-resolution anion-exchange system has been developed to analyze specifically for the nucleosides and bases present in physiologic fluids. This sytem employs a unique coupled-column operation that allows rapid column stripping and regeneration on completion of each run. Results obtained in the analysis of urine for nucleosides and bases are presented.     

Interaction of low-energy electrons with the purine bases, nucleosides, and nucleotides of DNA

The authors report results from computational studies of the interaction of low-energy electrons with the purine bases of DNA, adenine and guanine, as well as with the associated nucleosides, deoxyadenosine and deoxyguanosine, and the nucleotide deoxyadenosine monophosphate. Their calculations focus on the characterization of the pi* shape resonances associated with the bases and also provide general information on the scattering of slow electrons by these targets. Results are obtained for adenine and guanine both with and without inclusion of polarization effects, and the resonance energy shifts observed due to polarization are used to predict pi* resonance energies in associated nucleosides and nucleotides, for which static-exchange calculations were carried out. They observe slight shifts between the resonance energies in the isolated bases and those in the nucleosides.     

A Sulfonic‐Azobenzene‐Grafted Silica Amphiphilic Material: A Versatile Stationary Phase for Mixed‐Mode Chromatography

A novel sulfonic‐azobenzene‐functionalized amphiphilic silica material was synthesized through the preparation of a new sulfonic azobenzene monomer and its grafting on mercaptopropyl‐modified silica by a surface‐initiated radical chain‐transfer reaction. The synthesis was confirmed by infrared spectra, elemental analysis, and thermogravimetric analysis. This new material was successfully applied as a new kind of mixed‐mode stationary phase in liquid chromatography. This allows an exceptionally flexible adjustment of retention and selectivity by tuning the experimental conditions. The distinct separation mechanisms were outlined by selected examples of chromatographic separations in the different modes. In reversed‐phase liquid chromatography, this new stationary phase presented specific chromatographic performance when evaluated using a Tanaka test mixture. Seven dinitro aromatic isomers, four steroids, and seven flavonoids were separated successfully in simple reversed‐phase mode. This stationary phase can also be used in hydrophilic interaction chromatography because of the existing polar functional groups; for this, nucleosides and their bases were used as a test mixture. Interestingly, the same nucleosides and bases can also be separated in per aqueous liquid chromatography using the same stationary phase. Three ginsenosides including Rg1, Re, and Rb1 were successfully separated in hydrophilic mode. There is the potential for more applications to benefit from this useful column.     

Monolithic silica columns with mixed mode of hydrophilic interaction and weak anion-exchange stationary phase for pressurized capillary electrochromatography

A silica-based monolithic column as polar stationary phase is proposed for pressurized CEC (pCEC). The monolithic silica matrix from a sol-gel process was chemically modified by 3-aminopropyltrimethoxysilane to produce a column for hydrophilic interaction applications. The amino groups on the surface of the polar stationary phase generated anodic EOF under acidic conditions and served at the same time as a weak anion-exchanger. The anion solutes such as nucleotides were separated by the mixed mode mechanism, which comprised hydrophilic interaction, weak anion-exchange, and electrophoresis. The influences of buffer concentration and organic modifier content on the separation of nucleotides by pCEC have been investigated. In addition, the monolithic silica columns were also able to separate various polar compounds such as phenols, nucleic acid bases, and nucleosides in the hydrophilic interaction CEC mode.     

Adsorption and oxidation of purine bases and their derivatives on electrodes modified with carbon nanotubes

The electrochemical behavior of nitrogen bases and their derivatives is studied on electrodes modified with carbon nanotubes. On these electrodes, the strong adsorption of purines and their oxidation is observed at potentials in the vicinity of +0.8 V for guanine and +1.0 V (vs. Ag/AgCl) for guanine nucleosides/nucleotides and adenine. At more positive potentials, the high background current prevents the detection of adenine nucleotides and pyrimidines. The peculiarities of oxidation of the most easily detectable DNA components, namely, guanine and deoxyguanosinemonophosphate, on modified electrodes are elucidated and the corresponding reaction scheme is proposed. The results can be used in the development of biosensors based on electroactive properties of nucleic acids and their components.     

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.     

Dual Retention Mechanism in Two-Dimensional LC Separations of Barbiturates,Sulfonamides, Nucleic Bases and Nucleosides on Polymethacrylate Zwitterionic Monolithic Micro-Columns

In-house prepared zwitterionic polymethacrylate micro-columns using in situ polymerization of N,N-dimethyl-N-metacryloxyethyl-N-(3-sulfopropyl) ammonium betaine (MEDSA) functional monomer with bisphenol A glycerolate dimethacrylate (BIGDMA) cross-linker provided excellent stability and reproducibility of preparation and separation efficiency of 60,000–70,000 theoretical plates m⁻¹ for small molecules under isocratic conditions. The column showed a dual retention mechanism, reversed-phase (RP) in highly aqueous mobile phases and aqueous normal-phase (HILIC) in acetonitrile-rich mobile phases. This property can be used to obtain complementary separation and combined information on the sample from repeated injections of a sample on a single column, in different mobile phases characteristic for the HILIC and for the RP modes, which is in fact a form of offline two-dimensional chromatography on a single column. The dual retention mechanism has been observed with a variety of columns, however, often with impractically narrow retention range in one of the two modes. To take full advantage from the combined single-column RP–HILIC experiments, the column should provide a sufficiently broad mobile phase interval both in the RP and in the HILIC mode. The BIGDMA-MEDSA micro-columns proved suitable earlier for the combined RP–HILIC separations of some phenolic compounds and flavonoids. In the present work, we investigated the effects of the mobile phase composition on the retention of a variety of polar compounds over full retention range of buffered aqueous acetonitrile mobile phases, to find potentially useful HILIC and RP retention ranges for barbiturates, sulfonamides, nucleosides and nucleic bases. In the HILIC mode, proton donor–acceptor interactions show a major effect on retention and selectivity of separation, whereas the size of the non-polar hydrocarbon part of the sample molecule is the most important factor in the water-rich mobile phases. The sample structure strongly affects the composition of aqueous–organic mobile phases at which the transition between the two retention modes occurs. Of the investigated sample types, barbiturates show better separation under reversed-phase conditions, whereas nucleosides and nucleic bases in the HILIC mode. Aromatic carboxylic acids and sulfonamides can be separated either in the reversed phase or under HILIC conditions, the two separation modes showing complementary selectivity of separation.

     

A SPECTROPHOTOFLUOROMETER FOR MEASURING VERY WEAK FLUORESCENCES FROM BIOLOGICAL MOLECULES

Abstract —A spectrophotometer using the photon-counting method is described. The sample cuvette is mounted on a table which can be displaced in the X and Y directions, permitting investigation of absorption and self-absorption processes within the cuvette. Fluorescence detection is performed at right angles to the direction of the exciting beam, the analysis grating being driven by a stepping motor. The apparent spectrum is fed into a multichannel analyser and printed. Corrections are made to the data provided by the printer. Signal-to-noise ratio, fluorescence spectra and fluorescence excitation spectra are discussed in more detail for the case of more concentrated solutions. This very high sensitivity device allows room-temperature investigation of the fluorescent emission from neutral aqueous solutions of nucleic acid bases, nucleosides, nucleotides, dinucleotides etc., quantum yields for these molecules being of the order of 10^-4. A table of minimum concentration values of some commonly used fluorescent probes is given.     

Reversed-phase high-performance liquid chromatographic analysis of endogenous purine ribonucleotide pools in BHK monolayer cultures

A rapid, sensitive, and reproducible separation of purine bases, nucleosides and nucleotides by reversed-phase high-performance liquid chromatography is described. A multi-step gradient of acetonitrile in 0.1 _M potassium phosphate was used to detect picomole amounts of each compound within 22 min. The high sensitivity of the method made it suitable for the analysis of purine nucleotide pools extracted from 1--2 × 10⁶ hamster fibroblasts grown as monolayer (BHK line) and for the detection of purine bases and nucleosides leaked form the cells into the incubation media. The chromatographic procedure was applied to study the effects of hexavalent chromium (potassium dichromate) on purine metabolism. Several steps are affected by this treatment, causing a marked unbalance of both the guanylate and adenylate pool, which was seen as a strong decrease in the level of triphosphates and accumulation of their precursors.     

Self-assembly of nucleoamphiphiles: investigating nucleosides effect and the mechanism of micrometric helix formation

A new family of self-assembling systems based on nucleoamphiphiles is described. Nano to micrometric left-handed helix formation in aqueous solution was induced simply by complexing a GMP or an AMP with a nonchiral monocationic amphiphile. The assembling behavior such as micellar formation, monolayer at air-water interface, as well as the aggregates in solution of these nucleoamphiphiles are strongly influenced by the presence of nucleosides in solution. The observed effects depend on the properties of complexed nucleotides and nucleosides with a complex mixture of pi stacking, hydrophobicity of the bases, and hydrogen bonding.     

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.     

Determination Of Nucleic Acid Bases At Nanomolar Concentrations By Means Of Cathodic Stripping Voltammetry

Abstract

It is shown that nucleic acid bases and some of their derivatives can be determined by means of cathodic stripping voltammetry (CSV). The limit of detection of adenine is about 2 × 10^?9 M. Presence of an excess of DNA does not interfere with the determination of free bases. CSV may be used also for the determination of nucleosides and nucleotides derived from purine bases.     

HPLC Separation of Different Groups of Small Polar Compounds on a Novel Amide-Embedded Stationary Phase

Retention behaviors of an amide-embedded silica base stationary phase, which was recently developed by our group, were studied by using six different groups of small polar compounds including phenolic compounds, substituted anilines, chlorinated herbicides, Sudan dyes and some nucleotides and nucleosides in HPLC. The chromatographic behaviors of the prepared stationary phase for these analytes were compared with those of a commercially available reversed-phase column ACE C18 under same conditions. Among the six groups of analytes studied, the amide-silica stationary phase showed enhanced selectivity towards phenolic compounds, substituted anilines, Sudan dyes and herbicides under reversed-phase conditions and satisfactory selectivity towards nucleosides and nucleotides which could not be separated with ACE C18 column under HILIC conditions. Experimental data provided some evidence that functional groups on the stationary phases might have certain degrees of influence on selectivity possibly through secondary interactions with the model compounds. The retentions of the moderately polar compounds such as phenolic acids, anilines and herbicides on the stationary phase are higher than highly polar compounds such as nucleotides and nucleosides due to both the hydrophobic and hydrophilic interactions between the stationary phase and analytes. The quantitative determination of Sudan dyes (I, II, III, and IV) in red chilli peppers was performed. Many red chilli peppers were screened and three of them contained Sudans dyes.     

HPLC Separation of Different Groups of Small Polar Compounds on a Novel Amide-Embedded Stationary Phase

Retention behaviors of an amide-embedded silica base stationary phase, which was recently developed by our group, were studied by using six different groups of small polar compounds including phenolic compounds, substituted anilines, chlorinated herbicides, Sudan dyes and some nucleotides and nucleosides in HPLC. The chromatographic behaviors of the prepared stationary phase for these analytes were compared with those of a commercially available reversed-phase column ACE C18 under same conditions. Among the six groups of analytes studied, the amide-silica stationary phase showed enhanced selectivity towards phenolic compounds, substituted anilines, Sudan dyes and herbicides under reversed-phase conditions and satisfactory selectivity towards nucleosides and nucleotides which could not be separated with ACE C18 column under HILIC conditions. Experimental data provided some evidence that functional groups on the stationary phases might have certain degrees of influence on selectivity possibly through secondary interactions with the model compounds. The retentions of the moderately polar compounds such as phenolic acids, anilines and herbicides on the stationary phase are higher than highly polar compounds such as nucleotides and nucleosides due to both the hydrophobic and hydrophilic interactions between the stationary phase and analytes. The quantitative determination of Sudan dyes (I, II, III, and IV) in red chilli peppers was performed. Many red chilli peppers were screened and three of them contained Sudans dyes.