Direct analysis in real time (DART) mass spectrometry of nucleotides and nucleosides: elucidation of a novel fragment [C<Subscript>5</Subscript>H<Subscript>5</Subscript>O]<Superscript>+</Superscript> and its in-source adducts

Direct analysis in real time (DART) mass spectrometry is a recently developed innovative technology, which has shown broad applications for fast and convenient analysis of complex samples. Due to the ease of sample preparation, we have recently initiated an investigation of the feasibility of detecting nucleotides and nucleosides using the DART-AccuTOF instrument, which we will refer to as the DART mass spectrometer. Our experimental results reveal that the ions representing the intact molecules of nucleotides are not detectable in either positive-ion or negative-ion mode. Instead, all four natural nucleotides fragment in the DART ion source, and a common fragment ion, [C₅H₅O]⁺ (1), is observed, which is probably formed via multiple-elimination reactions. Interestingly, 1 can form adducts with nucleobases in different molar ratios in the DART ion source. In contrast to nucleotides, the ions representing the intact molecules of nucleosides are detected in both positive-ion and negative-ion mode using DART mass spectrometry. Surprisingly, the fragmentation pattern of nucleosides is different from that of nucleotides in the DART ion source. In the cases of nucleosides (under positive-ion conditions), the production of 1 is not observed, indicating that the phosphate group plays an important role for the multiple eliminations observed in the spectra of nucleotides. The in-source reactions described in the present work show the complexity of the conditions in the DART ion source, and we hope that our results illustrate a better understanding about DART mass spectrometry.     

A Combined Experimental and Computational Study of Halogen and Hydrogen Bonding in Molecular Salts of 5-Bromocytosine

Although natural or artificial modified pyrimidine nucleobases represent important molecules with valuable properties as constituents of DNA and RNA, no systematic analyses of the structural aspects of bromo derivatives of cytosine have appeared so far in the literature. In view of the biochemical and pharmaceutical relevance of these compounds, six different crystals containing proton-transfer derivatives of 5-bromocytosine are prepared and analyzed in the solid-state by single crystal X-ray diffraction. All six compounds are organic salts, with proton transfer occurring to the N_imino atom of the pyridine ring. Experimental results are then complemented with Hirshfeld surface analysis to quantitively evaluate the contribution of different intermolecular interactions in the crystal packing. Furthermore, theoretical calculations, based on different arrangements of molecules extracted from the crystal structure determinations, are carried out to analyze the formation mechanism of halogen bonds (XBs) in these compounds and provide insights into the nature and strength of the observed interactions. The results show that the supramolecular architectures of the six molecular salts involve extensive classical intermolecular hydrogen bonds. However, in all but one proton-transfer adducts, weak to moderate XBs are revealed by C–Br^…O short contacts between the bromine atom in the fifth position, which acts as XB donor (electron acceptor). Moreover, the lone pair electrons of the oxygen atom of adjacent pyrimidine nucleobases and/or counterions or water molecules, which acts as XB acceptor (electron donor).     

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.     

The study and characterization of nucleosides by mass spectrometry—I: The mass spectra of pyrimidine 2,2′-anhydronucleosides and their derivatives

The mass spectra of 2,2′-anhydrouridine, 2,2′-anhydrothymidine and 2,2′-anhydro-4-thiouridine are reported. The acetyl, trifluoroacetyl, trityl, pivaloyl and trimethylsilyl ether derivatives were also studied. Deuterium labeling in acetyl and trimethylsilyl groups aided characterization of many ions in the spectra, as well as helping to clarify hydrogen migration processes. The anhydronucleosides and their derivatives are readily distinguished from natural nucleosides by the presence of an ion containing the base moiety plus the anhydro-ring plus one hydrogen atom from the rest of the molecule. As for natural nucleosides the [base + H]⁺ and [base + 2H]⁺ ions are usually prominent, but in contrast to natural nucleosides, ions characteristic of the sugar moiety do not retain the 2′-oxygen atom (i.e. the oxygen atom of the anhydro-ring). The mass spectra of deuterium labeled derivatives suggest a test for the presence of a 3′-O-acetyl function (the O-acetyl group is lost from the molecular ion much more readily from the 3′- than from the 5′-carbon atom). The trimethylsilyl derivatives showed evidence in their mass spectra for migration of trimethylsilyl groups in addition to hydrogen atoms.     

Mass spectra of sterically crowded trialkylsilyl derivatives of nucleosides

The electron impact mass spectra of tert-butyldimethylsilyl-, cyclo-tetramethylene-tert-butylsilyl and cyclo-tetramethylene-isopropylsilyl- ether derivatives of ribo- and 2′-deoxyribonucleosides are described in detail. The interpretation of fragmentation pathways of full and mixed derivatives was aided by metastable ion decomposition studies, precise mass and deuterium labelling measurements, and spectra of mixed derivatives containing the ‘passive’ (in these spectra) trimethylsilyl group. The sterically crowded silyl groups have a powerful fragmentation directing effect. Elimination of a bulky radical, R˙ (tert-butyl or isopropyl), from the molecular ion produces the siliconium ion [M? R]⁺, which is the precursor for most of the other prominent ions in the spectra. These arise from ‘siliconium ion rearrangements’ resulting from the interaction of the positively charged siliconium ion center with electron dense regions (i.e. oxygens) in the molecule, to form cyclic silyloxonium ions which subsequently decompose. Since the interacting oxygen and silicon must be sterically accessible, the fragment ion types and their abundances are very dependent upon structure. Consequently, [M? R]⁺ ions formed from 2′, 3′ or 5′-O-silyl groups give rise to different sets of daughter ions which, for the most part, are not found, or have very low abundances, in the mass spectra of underivatized or trimethylsilylated nucleosides. Detailed information on sugar and base moieties and isomeric substitution is readily obtained.     

Some Novel Thiopyrimidine Nucleoside Analogs: Synthesis and In Vitro Antimicrobial Evaluation

Some new S-alkyl derivatives of indeno[1′,2′:4,5]thieno[2,3-d]pyrimidine 2–8 were prepared starting with pyrimidine-2(1H)-thione derivative (1). Also, treatment of compound 1 with 2,3,4,6-tetra-O-acetyl-α-D-glucopyranosyl bromide or 1-O-acetyl-2,3,5-tri-O-benzoyl-β-D-ribofuranose afforded nucleosides 9 and 12, respectively. Furthermore, deprotection of the latter blocked nucleosides was achieved in methanolic ammonia to afford the desired free S-nucleoside derivatives 10 and 13, respectively. Some prepared products were screened for antimicrobial activity, and some of them showed promising activity.     

Type I Photosensitization of 2′‐deoxyadenosine 5′‐monophosphate (5′‐dAMP) by Biopterin and its Photoproduct Formylpterin

Biopterin (Bip) and its photoproducts 6‐formylpterin (Fop) and 6‐carboxypterin (Cap) accumulate in the skin of patients suffering from vitiligo, a chronic depigmentation disorder where the protection against UV radiation fails because of the lack of melanin. These compounds absorb in the UV‐A inducing a potential photosensitizing action that can cause damage to DNA and other biomolecules. In this work, we have investigated the capability of these pterin derivatives (Pt) to act as photosensitizers under UV‐A irradiation for the degradation of 2′‐deoxyadenosine 5′‐monophosphate (5′‐dAMP) in aqueous solutions, as model DNA target. Steady‐state and time‐resolved experiments were performed and the effect of pH was evaluated. The results showed that photosensitized degradation of 5′‐dAMP was only observed under acidic conditions, and a mechanistic analysis revealed the participation of the triplet excited state of the pterin derivatives (³Pt*) by electron transfer yielding the corresponding pair of radical ions (Pt^?? and 5′‐dAMP^?+), with successive photosensitizer recovery by electron transfer from Pt^?? to O₂. Finally, 5′‐dAMP^?+ participates in subsequent reactions to yield degradation products.     

Chemometrics for comprehensive analysis of nucleobases,nucleosides, and nucleotides in Siraitiae Fructus by hydrophilic interaction ultra high performance liquid chromatography coupled with triple‐quadrupole linear ion‐trap tandem mass spectrometry

A rapid and sensitive hydrophilic interaction ultra high performance liquid chromatography coupled with triple‐quadrupole linear ion‐trap tandem mass spectrometry method was validated for the simultaneous determination of 20 nucleobases, nucleosides, and nucleotides (within 3.5 min), and then was employed to test the functional food of Luo‐Han‐Guo samples. The analysis showed that the Luo‐Han‐Guo was rich in guanosine and uridine, but contained trace levels of the other target compounds. Chemometrics methods were employed to identify 40 batches of Luo‐Han‐Guo samples from different cultivated forms, regions and varieties. Unsupervised hierarchical cluster analysis and principal component analysis were used to classify Luo‐Han‐Guo samples based on the level of the 20 target compounds, and the supervised learning method of counter propagation artificial neural network was utilized to further separate clusters and validate the established model. As a result, the samples could be clustered into three primary groups, in which correlation with cultivated varieties was observed. The present strategy could be applied to the investigation of other edible plants containing nucleobases, nucleosides, or nucleotides.     

Synthesis and Structural Assignment of 1-O-Acetyl-2,3,5-tri-O-benzoyl-4-(thymin-1-yl)-α-l-lyxofuranose

Abstract

Analogues of nucleosides in which the nucleobase is fixed onto the C-4 of the sugar moiety are generally prepared either from 4,5-unsaturated sugar derivatives or via a formaldehyde condensation.¹ We tested the furanosyl bromide reactivity of 1 ² towards a series of nucleophiles, mostly azides or cyanides, without success. Conversely, the nucleosidation of 1 using 5-methyl-2,4-bis(trimethyl-silyloxy)pyrimidine in the presence of stannic chloride took place at the second anomeric position (C-4) and led to the isolation in acceptable yield (47%) of a unique anomer 2 (Scheme 1).     

Analysis of nucleic acid derivatives by micellar electrokinetic capillary chromatography

The use of micellar electrokinetic capillary chromatography (MECC) for the analysis of the major nucleobases, nucleosides, and nucleotides, and their chemically modified derivatives, has been developed and refined. The dimensions of the separating capillaries, the composition of the buffering systems, and the conditions used for electrophoresis were investigated in order to obtain the best performance. Particular emphasis was placed on the identification of the physiological constituents of nucleic acids and their chemically modified analogs: in vitro studies on calf thymus DNA exposed to genotoxic agents have demonstrated that adducted bases and nucleolides can be identified by MECC.     

MASS SPECTRA OF SULFUR COMPOUNDS. ASSESSMENT OF 1, X (X=2,3,4,5) HYDROGEN TRANSFER IN DIALKYL SULFIDES AND DISULFIDES UNDER ELECTRON IMPACT. A NOVEL 1,5-H SHIFT

Abstract

The transfer of hydrogen atoms from the gamma carbon of dialkyl disulfides upon electron impact is presented and its occurrence is formally shown by the electron ionization mass spectrum of 1-(2′,2′-dideuteriocyclohexyl)-2,3-dithiapent-1,1′-ene (4b). Also, the spectrum of 1-(2′,2′-dideuteriocyclohexyl)-2-thiahex-1-ene (3b) is analyzed in terms of hydrogen/deuterium transfer, where it is absent. This result is compared with selected mass spectral data of eighteen other dialkylthianes. Evidence is put forth to indicate that dialkyl sulfides are prone to undergo only 1,3-H shift upon electron inpact, whereas in dithianes 1,3- and 1,5-Hydrogen transfer take place. The evidence collected suggests that neither 1,2- nor 1,4-hydrogen transfer occurs in both sulfur derivatives.     

A novel 1,8-naphthalimide probe: synthesis and interactions with nucleic acid and its precursor

Three novel, water-soluble N-substituted 1,8-naphthalimides as the spectroscopic probes of nucleic acid, N-(2-hydroxyethyl)-1,8-naphthalimide (NI1), 1,8-naphthalimide-N-acetic acid (NI2) and 1,8-naphthalimide-N-caproic acid (NI3), were synthesized and photophysically characterized. The steady-state fluorescence quenching of the NI probes with nucleic acids (NA) and their precursors (nucleobases and nucleosides) were studied by Stern–Volmer correlation. The rate constants for bimolecular quenching were obtained in Tris buffer solution. The transient absorption spectroscopy by nanosecond laser flash photolysis were explored to identify the transient species and to determine the kinetics. The dynamic interaction mechanism was attributed to electron transfer (ET) and energy transfer via ³NI.     

Interrelationships between purine nucleotide degradation and radical formation during intestinal ischaemia and reperfusion: an application of ion-pair high-performance liquid chromatography of nucleotides, nucleosides and nucleobases

There are peroxidative changes during the reperfusion of the rat small intestine following a 1h period of total ischaemia. That is demonstrated by the increases of the concentrations of glutathione disulphide and of thiobarbituric acid-reactive substances. An important source of the active oxygen species leading to peroxidations is the degradation of purine nucleotides. The nucleotides and their derivatives were measured by an ion-pair reversed-phase high-performance liquid chromatographic separation in a single analysis within 40 min. Modification of the elution gradient resulted in a high resolution of nucleosides and nucleobases, including allopurinol and oxypurinol. The decrease of the nucleoside triphosphate concentration and the increase of nucleoside monophosphate concentration, followed by accumulations of nucleosides and nucleobases in the course of the ischaemia were measured. During reperfusion the nucleotide pools are filled up. Restoration of adenosine triphosphate and guanosine triphosphate can be accelerated by application of the xanthine oxidoreductase inhibitor allopurinol. Pretreatment of the animals with allopurinol also diminished the formation of glutathione disulphide and thiobarbituric acid-reactive substances.     

Nucleic-Acid Analogues with Constraint Conformational Flexibility in the Sugar-Phosphate Backbone (‘Bicyclo-DNA’). Part 1. Preparation of (3S,5′R)-2′-Deoxy-3′,5′-ethano-αβ-D-ribonucleosides (‘Bicyclonucleosides’)

We describe the synthesis of 2′-deoxy-3′,5′-ethano-D -ribonucleosides 1 – 8 (= (5′,8′-dihydroxy-2′-oxabicyclo-[3.3.0]oct-3′-yl)purines or -pyrimidines) of the nucleobases adenine, thymine, cytosine, and guanine. They differ from natural 2′-deoxyribonucleosides only by an additional ethylene bridge between the centers C(3′) and C(5′). The configuration at these centers (3S,5′R) was chosen as to match the geometry of a repeating nucleoside unit in duplex DNA as close as possible. These nucleosides were designed to confer, as constituents of an oligonucleotide chain, a higher degree of preorganization of a single strand for duplex formation with respect to natural DNA, thus leading to an entropic advantage for the pairing process. The synthesis of these ‘bicyclonucleosides’ was achieved by construction of an enantiomerically pure carbohydrate precursor 18 / 19 (Schemes 1), which was then converted to the corresponding nucleosides by known methods in nucleoside synthesis (Schemes 2 and 3). In all cases, both anomeric forms of the nucleosides were obtained in pure crystalline form, the relative configuration of which was established by ¹H-NMR-NOE spectroscopy. A conformational analysis of the nucleosides with β-configuration at the anomeric center by means of X-ray and ¹H-NMR (including NOE) spectroscopy show the furanose part of the molecules to adopt uniformly a 1′exo-conformation with the base substituents preferentially in the anti-range in the pyrimidine nucleosides (anti/syn ca. 2:1) distribution in the purine nucleosides (in solution).     

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.     

Fluorescence Quenching and Binding Interaction of l0-Methylacridinium Iodide to Nucleic Acids

Interaction of 10‐methylacridinium iodide (MAI) as fluorescence probe with nucleobases, nucleosides and nucleic acids has been studied by UV‐visible absorption and fluorescence spectroscopy. It was found that fluorescence of MAI is strongly quenched by the nucleobases, nucleosides and nucleic acids, respectively. The quenching follows the Stern‐Volmer linear equation. The fluorescence quenching rate constant (k_q) was measured to be 10^9‐10¹⁰ (L/mol)/s within the range of diffusion‐controlled rate limit, indicating that the interaction between MAI and nucleic acid and their precursors is characteristic of electron transfer mechanism. In addition, the binding interaction model of MAI to calf thymus DNA (ct‐DNA) was further investigated. Apparent hypochromism in the absorption spectra of MAI was observed when MAI binds to ct‐DNA. Three spectroscopic methods, which include (1) UV spectroscopy, (2) fluorescence quenching of MAI, (3) competitive dual‐probe method of MAI and ethidium bromide (EB), were utilized to determine the affinity binding constants (K) of MAI and ct‐DNA. The binding constants K obtained from the above methods gave consistent data in the same range (1.0–5.5) × 10⁴L/mol, which lend credibility to these measurements. The binding site number was determined to be 1.9. The influence of thermal denaturation and phosphate concentration on the binding was examined. The binding model of MAI to ct‐DNA including intercalation and outside binding was investigated.     

Intermolecular vs. intramolecular photoinduced electron transfer from nucleotides in DNA to acridinium ion derivatives in relation with DNA cleavage

Photoirradiation of various 10-methylacridinium ions (AcrR⁺, R = H, ⁱPr, and Ph) intercalated in DNA results in ultrafast intramolecular electron transfer, followed by rapid back electron transfer between AcrR⁺ and nucleotides in DNA. The electron-transfer dynamics in DNA were monitored by femtosecond time-resolved transient absorption spectroscopy. Both acridinyl radical and nucleotide radical cations, formed in the photoinduced electron transfer in DNA, were successfully detected in an aqueous solution. These transient absorption spectra were assigned by the comparison with those of DNA nucleotide radical cations, which were obtained by the intermolecular electron-transfer oxidation of nucleotides with the electron-transfer state of 9-mesityl-10-methylacridinium ion (Acr–Mes⁺) produced upon photoexcitation of Acr⁺–Mes. Photoinduced cleavage of DNA with various acridinium ions (AcrR⁺, R = H, ⁱPr, Ph, and Mes) has also been examined by agarose gel electrophoresis, which indicates that the rapid intramolecular back electron transfer between acridinyl radical and nucleotide radical cation in DNA suppresses the DNA cleavage as compared with the intermolecular electron-transfer oxidation of nucleotides with Acr–Mes⁺.     

Micellar electrokinetic capillary chromatography of nucleic acid constituents and dinucleoside monophosphate photoproducts

Micellar electrokinetic capillary chromatography has been explored as an efficient and rapid method of separating the photoproducts of 2′-deoxyuridylyl-(3′-5′)-thymidine (i.e., cis-syn and trans-syn cyclobutane dimers, (6–4) photoproduct, and the related Dewar valence isomer) from normal nucleosides and nucleotides. Three cationic surfactants, dodecyl-, tetradecyl-, and hexadecyltrimethy-lammonium bromide were evaluated and the separations compared with those obtainable with the anionic surfactant, sodium dodecylsulfate. Optimum resolution of the dinucleoside monophosphate photoproducts was obtained using tetradecyltrimethylammonium bromide. By use of this detergent the photoproducts could also be separated from other normal constituents in less than 6 min at ?25 kV. Dodecyl- and hexadecyltrimethylammonium bromide provided some separation between the various species but sodium dodecylsulfate did not separate the UV radiation-induced products from either the parent compound or other dinucleoside monophosphates. Increased interaction between negatively charged solutes and positively charged micelles accounts for the differences.