The aminomethylation of adenine,cytosine and guanine

Aminomethylated derivatives of adenine, cytosine and guanine have been isolated and characterized for the first time. These results are important because of the potential for similar adducts being formed transiently between nucleosides and nucleotides, and endogenous aldehydes and amines in vivo, and of the potential use of similar adducts for drug delivery. Mono-alkylated products obtained were from the reaction of adenine with one equivalent of aminomethylating agent derived from amines exhibiting lower basicity (e.g., morpholine and N-methylpiperazine); bis-alkylated products were obtained with agents derived from more basic amines regardless of the stoichiometry. On the other hand, only bis-alkylated products were obtained from the reaction of cytosine or guanine with the aminomethylating agent regardless of the basicity of the secondary amine used or the stoichiometry of the reaction. The mono-alkylated adenine products were alkylated on N-9 while the bis-alkylated cytosine products were alkylated on N-9 and N⁴ and the bis-alkylated adenine products were alkylated on N-9 and N⁶. The adenine and cytosine aminomethyl adducts hydrolyzed rapidly in dilute aqueous solution.     

Etheno derivatives of adenine and cytosine (review)

The method of modification of heterocyclic bases of nucleic acids with chloroacetaldehyde and other α-halo carbonyl compounds is examined in this review. The mechanism, kinetics, and scope of the reaction, the chemical properties of modified derivatives of adenine and cytosine, and the possibilities of the application of etheno derivatives of adenine and cytosine in biochemistry and molecular biology are discussed. Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 3, pp. 291–305, March, 1980.     

Ab initio Calculations on cytosine,thymine and adenine

An ab initio LCAO SCF calculation has been performed in a small contracted GTO basis set on three bases of ADN. A check of the representativity of the basis set is reported for formamide and pyrrole.

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Zusammenfassung Es wurde eine ab initio LCAO-SCF-Rechnung mit einem kleinen, kontrahierten GTO-Basissatz für drei ADN-Basen durchgeführt. Eine Prüfung des Einflusses dieses Basissatzes wird für Formamid und Pyrrol beschrieben.

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Résumé Un calcul ab initio dans une petite base de gaussiennes contractée a été fait pour trois bases de l'ADN. Un calcul-test sur la representativité de la base atomique est donné sur les exemples de la formamide et du pyrrole.

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This work was supported by grant 67-00-532 of the Délégation Générale à la Recherche Scientifique et Technique (Comité de Biologie Moléculaire).     

Spectroscopic study of protonation of oligonucleotides containing adenine and cytosine

Acidobasic properties of purine and pyrimidine bases (adenine, cytosine) and relevant nucleosides (adenosine, cytidine) were studied by means of glass-electrode potentiometry and the respective dissociation constants were determined under given experimental conditions (I = 0.1 M (NaCl), t = (25.0 ± 0.1) °C): adenine (pK _HL = 9.65 ± 0.04, pK _H2L = 4.18 ± 0.04), adenosine (pK _H2L = 3.59 ± 0.05), cytosine (pK _H2L = 4.56 ± 0.01), cytidine (pK _H2L = 4.16 ± 0.02). In addition, thermodynamic parameters for bases: adenine (ΔH ⁰ = (−17 ± 4) kJ mol⁻¹, ΔS ⁰ = (23 ± 13) J K⁻¹ mol⁻¹), cytosine (ΔH ⁰ = (−22 ± 1) kJ mol⁻¹, ΔS ⁰ = (13 ± 5) J K⁻¹ mol⁻¹) were calculated. Acidobasic behavior of oligonucleotides (5′CAC-CAC-CAC3′ = (CAC)₃, 5′AAA-CCC-CCC3′ = A₃C₆, 5′CCC-AAA-CCC3′ = C₃A₃C₃) was studied under the same experimental conditions by molecular absorption spectroscopy. pH-dependent spectral datasets were analyzed by means of advanced chemometric techniques (EFA, MCR-ALS) and the presence of hemiprotonated species concerning (C⁺-C) a non-canonical pair (i-motif) in titled oligonucleotides was proposed in order to explain experimental data obtained according to literature.     

Hydroxyethylation of uracil,adenine, and cytosine with ethylene carbonate

It was established that both 1-(2-hydroxyethyl)uracil and 3-(2-hydroxyethyl)-uracil, which are converted to 1, 3-bis (2-hydroxyethyl) uracil, are formed in the first step of the reaction of uracil with ethylene carbonate. The simultaneous formation of 9- (2-hydroxyethyl) adenine and 3- (2-hydroxyethyl) adenine occurs in the reaction of adenine with ethylene carbonate. The only product of hydroxyethylation of cytosine was 1-(2-hydroxyethyl) cytosine. Methods for the analytical separation of the hydroxyethylation products and the preparative isolation of the 1- and 9-hydroxyethyl derivatives are proposed.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 5, pp. 684–689, May, 1978.     

Cathodic stripping voltammetry of adenine nucleotides,polyriboadenylic acid and nicotinamide adenine dinucleotide coenzymes at the dropping mercury electrode

The inverse voltammetry of twelve adenine nucleotides, poly r-A and seven nicotinamide adenine dinucleotide coenzymes was performed in 0.1 M sodium phosphate buffer (pH 7.0) at the d.m.e. using high scan rates (10-100 V/s). The stripped phase formed at +0,15 V versus s.c.e. consists of insoluble mercurous salts (5′-AMP, ADP, ATP, d-AMP) with 1 : 1 nucleotide-Hg(I) stoichiometry or of mercuric complexes with 1:2 (adenosine, ADPR) or 1 : 1 (c-AMP) composition. 2′-AMP probably forms a thick polymeric layer, Poly r-A forms a surface salt with 1 : 1 composition in Hg(I) to the AMP monomer. Resolution of the adenine nucleotides in the mixture was not possible because of mixed phase formation. Nicotinamide adenine dinucleotide coenzymes form insoluble mercuric salts with 1 : 2 composition. The influence of adenine ring substitution on the electroactivity in the inverse voltammetry was studied in the case of 5′-AMP and of NAD⁺.     

Electrochemical oxidation-reduction paths for pyrimidine, cytosine, purine and adenine Correlation and application

In order to evaluate the striking discrepancy between the experimental ease of polarographic reduction of adenine and cytosine, and that predicted by molecular orbital calculation, the electrochemical oxidation-reduction behaviour of pyrimidine, cytosine, purine, adenine and related compounds was investigated at both mercury and graphite electrodes. Information was obtained on the specific adsorption of reactant and product species on the electrode, the reversibility of the energy-controlling electron-transfer step, and accompanying chemical reactions. Triangular sweep voltammetry, a.c. and d.c. polarography, and electrocapillary data, in particular, were utilized. The first three techniques were critically examined for their potential analytical utility. The results were compared with previously obtained electrochemical data and the sequence of electron-transfer and various non-electron transfer steps was more firmly established. It became clear that in order validly to correlate quantum mechanically calculated data for the energy required to add or remove an electron to or from the outermost electron level of each molecule (in the gas phase), with electrochemical redox potentials (in solution), the effects of adsorption, electron-transfer reversibility and solvation energy must be considered.     

Ultratrace determination of adenine in the presence of copper by adsorptive stripping voltammetry

An electrochemical stripping procedure for ultra-trace measurements of adenine is described based on the adsorption of the adenine-copper complex on a static mercury drop electrode. Cyclic voltammetry was used to characterize the interfacial and redox behavior. Optimum experimental conditions were found when using a 0.005 M NaOH solution containing 0.4 ppm of copper, an accumulation potential of -0.30 V, a scan rate of 100 mV s(-1) and a linear scan mode. There is a linear response to adenine concentration in the range of 0.1-1.0 ppb and the detection limit for 6 min accumulation time was of 4.0 ppt (3.0x10(-11) M). Proper conditions for measuring the adenine in presence of guanine, thymine and cytosine were also investigated. The method was applied for the determination of adenine in a sample of single-stranded calf thymus DNA.     

Time-resolved emission of flavin adenine dinucleotide in water and water-methanol mixtures

Time-resolved fluorescence decay of flavin adenine dinucleotide (FAD) was studied at room temperature in water and water-methanol mixtures by a fluorescence upconversion technique. The observations were focused on the most initial decay phase (200 ps), before the residual fluorescence assumes a single exponential decay, typical for an extended conformation of the fluorophore. Within the first few picoseconds, where most of the electron transfer coupled quenching takes place, the emission decay curves could be fitted by a stretched exponent, compatible with the inhomogeneous distance dependent electron transfer model. This implies that the population of the excited FAD molecules exhibits a large number of non-identical states, each with its own separation between the donor (adenine) and acceptor (isoalloxazine) moieties, having its own rate of electron transfer. To evaluate the distribution of the separation between the donor-acceptor pair, we carried out molecular dynamics simulations of closed conformation of the FAD in water and water-methanol mixtures, sampling the structure at 10 fs intervals. The analysis of the dynamics reveals that within the 4 ps time frame, where most of the nonexponential fluorescence relaxation takes place, the relative motion of the donor-acceptor pair is consistent with a one-dimensional Brownian motion, where the diffusion coefficient and the shape of the confining potential well are solvent dependent. The presence of methanol enhances the diffusion constant and widens the width of the potential well. On the basis of these parameters, the relaxation dynamics was accurately reconstructed as an electron transfer reaction in an inhomogeneous system where the reactants are diffusing within the time frame of the observation.     

Mixed-ligand palladium(II) complexes with amino acids,cytosine, and adenine

pH titration shows that 1 : 1 : 1 mixed-ligand complexes are formed in the systems palladium(II)-Cyt-Glu-H₂O (loggB = 19.73) and palladium(II)-Cyt-Lys-H₂O (logβ = 16.20). Complexes Pd(C₅H₅N₅)(C₅H₈NO₄)Cl, Pd(C₅H₅N₅)(C₆H₁₃N₂O₂)Cl, Pd(C₄H₅N₃O)(C₆H₁₃N₂O₂)Cl, and Pd(C₄H₅N₃O)(C₅H₈NO₄)Cl are synthesized and characterized by chemical analysis, X-ray powder diffraction, and thermogravimetry. The coordination mode of amino acids, cytosine, and adenine to the palladium(II) ion is determined.     

Simultaneous determination of guanine,adenine, thymine and cytosine with a simple electrochemical method

A simple method for simultaneous detection of guanine, adenine, thymine and cytosine was set up by using a bare glassy carbon electrode in acetate buffer solution of pH 4.5. The peak current responses of these four DNA bases in this supporting electrolyte were significantly increased comparing with those in phosphate buffer solution and Tris-HCl, moreover, the peak current values were linearly dependent on the concentration of four DNA bases, respectively. Individual and simultaneous determinations of four bases were performed by controlling certain experimental conditions, and broad linear ranges and low detection limits (S/N = 3) were obtained. The assay processes do not need any separation or pretreatment steps. In addition, this method showed good selectivity, reproducibility, and stability and can be used for determination of the four bases content in real DNA sample.     

Analysis of powder mixtures with the help of abrasive stripping voltammetry and coulometry

Summary Abrasive stripping voltammetry was applied to the quantitative analysis of the following powder mixtures: MnO₂-FeOOH, HgS-HgO, HgO-PbO. Therefore, g-amounts of the powder mixture were transferred onto a solid electrode and the electrochemical response of the solid sample is recorded. The calibration was made by measuring the percentage peak height of each component taking the sum of peak currents of both components as 100%. The relative standard deviation ranges from 3 to 15%. A calibration-free method based on microcoulometric measurements can be used in the case of powder mixtures of AgCl-AgI. The integration of staircase voltammograms directly yields the charges required to reduce AgCl and AgI and thus also gives the ratio of both components. The relative standard deviation was 10%. Microcoulometric measurements gave evidence that, in abrasive stripping voltammetry, the amount of electroactive substance ranges between 10^–12 and 10^–9 mole.On leave from University of Warsaw, Poland     

Elimination of iron interference in the differential pulse anodic stripping voltammetry of copper

The interference of iron(III) on the quantitation of copper(II) in citrate media by differential-pulse anodic stripping voltammetry can be completely removed by lowering the pH to 1.5 with 70% perchloric acid.     

Survey of the proton affinities of adenine, cytosine, thymine and uracil dideoxyribonucleosides, deoxyribonucleosides and ribonucleosides

The kinetic method was applied to the determination of the proton affinities (PAs) of modified deoxy- and dideoxyribonucleosides. A correlation between the measured PAs and the replacement of one of the three hydroxyl groups of the ribose unit is presented. A PA scale was obtained which shows that the replacement of the primary or of one or both secondary hydroxyl groups of a ribonucleoside with a hydrogen atom induces the lowering or the enhancement of the nucleoside PA, respectively. The scale extends over a very narrow range of approximately 2 kcal mol(-1), thus demonstrating the sensitivity of the kinetic method in the evaluation of small differences in thermodynamic parameters.     

Synthesis of polynucleotide analogs by grafting optically active adenine,cytosine, and hypoxanthine derivatives onto polytrimethylenimine

A new family of polynucleotide analogs were prepared by grafting nucleic acid base derivatives onto polytrimethylenimine. Several new optically pure α-nucleic acid base substituted propanoic acids were prepared as pendant groups. The (R)-ethyl adeninylpropanoate was obtained from adenine and (S)-ethyl lactate by utilizing a diethyl azodicarboxylate-triphenyl phosphine method. Subsequent hydrolysis of the ester in aqueous acid gave the (R)-adeninylpropanoic acid without racemization. The reaction of cytosine sodium salt with (S)-ethyl 2-[(methylsulfonyl)oxy] propanoate produced the 20% racemized (R)-ethyl 2-(cytosin-1-yl)propanoate. The optically pure ester was obtained by recrystallization from ethyl alcohol, which was hydrolyzed in aqueous acid to give the (R)-acid with 66% enantiomeric excess. The (R)-2-(hypoxanthin-9-yl)propanoic acid was prepared by reaction of (R)-2-(adenin-9-yl)propanoic acid with sodium nitrite. The pendant groups were allowed to react with N-hydroxy compounds in the presence of dicyclohexylcarbodiimide to give the active esters. These active esters underwent reaction with N,N-dipropylamine to provide monomer model compounds. The pendant groups were grafted onto polytrimethylenimine by using the active ester method. The racemization reactions were observed in the grafting reactions. The resulting polymers showed a range of percent grafting from 60 to 80%.     

Mechanism of epoxide hydrolysis in microsolvated nucleotide bases adenine, guanine and cytosine: a DFT study

Six water molecules have been used for microsolvation to outline a hydrogen bonded network around complexes of ethylene epoxide with nucleotide bases adenine (EAw), guanine (EGw) and cytosine (ECw). These models have been developed with the MPWB1K-PCM/6-311++G(3df,2p)//MPWB1K/6-31+G(d,p) level of DFT method and calculated S(N)2 type ring opening of the epoxide due to amino group of the nucleotide bases, viz. the N6 position of adenine, N2 position of guanine and N4 position of cytosine. Activation energy (E(act)) for the ring opening was found to be 28.06, 28.64, and 28.37 kcal mol(-1) respectively for EAw, EGw and ECw. If water molecules were not used, the reactions occurred at considerably high value of E(act), viz. 53.51 kcal mol(-1) for EA, 55.76 kcal mol(-1) for EG and 56.93 kcal mol(-1) for EC. The ring opening led to accumulation of negative charge on the developing alkoxide moiety and the water molecules around the charge localized regions showed strong hydrogen bond interactions to provide stability to the intermediate systems EAw-1, EGw-1 and ECw-1. This led to an easy migration of a proton from an activated water molecule to the alkoxide moiety to generate a hydroxide. Almost simultaneously, a proton transfer chain reaction occurred through the hydrogen bonded network of water molecules and resulted in the rupture of one of the N-H bonds of the quaternized amino group. The highest value of E(act) for the proton transfer step of the reaction was 2.17 kcal mol(-1) for EAw, 2.93 kcal mol(-1) for EGw and 0.02 kcal mol(-1) for ECw. Further, the overall reaction was exothermic by 17.99, 22.49 and 13.18 kcal mol(-1) for EAw, EGw and ECw, respectively, suggesting that the reaction is irreversible. Based on geometric features of the epoxide-nucleotide base complexes and the energetics, the highest reactivity is assigned for adenine followed by cytosine and guanine. Epoxide-mediated damage of DNA is reported in the literature and the present results suggest that hydrated DNA bases become highly S(N)2 active on epoxide systems and the occurrence of such reactions can inflict permanent damage to the DNA.     

Elimination of the interfering effect of hydrogen on the determination of palladium by stripping voltammetry

The effect of hydrogen on the electrooxidation current of a palladium–hydrogen precipitate is studied. It is shown that the UV irradiation of the solution changes the mechanism of the formation of molecular hydrogen in the electrochemical deposition of palladium. A procedure is developed for determining palladium in platinum metal preconcentrates by stripping voltammetry.     

Groebke-Blackburn-Bienaymé multicomponent reaction in scaffold-modification of adenine, guanine, and cytosine: synthesis of aminoimidazole-condensed nucleobases

A multicomponent method for scaffold-modification of nucleobases (adenine, guanine, and cytosine) was developed. This modification approach, as an alternative to usual synthetic routes involving protection-deprotection or S_NAr of halo (or leaving group-equivalent)-purines, affords in one step therapeutically-relevant substituted aminoimidazole-[i]-condensed adenine, [b]-condensed guanine, [c]-condensed cytosine. These derived nucleobases possess enhanced lipophilicity and solubility and contain the functionalities useful for further chemical manipulations.