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.     

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.     

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).     

Vacuum-ultraviolet photoionization studies of the microhydration of DNA bases (guanine, cytosine, adenine, and thymine)

In this work, we report on a photoionization study of the microhydration of the four DNA bases. Gas-phase clusters of water with DNA bases [guanine (G), cytosine (C), adenine (A), and thymine (T)] are generated via thermal vaporization of the bases and expansion of the resultant vapor in a continuous supersonic jet expansion of water seeded in Ar. The resulting clusters are investigated by single-photon ionization with tunable vacuum-ultraviolet synchrotron radiation and mass analyzed using reflectron mass spectrometry. Photoionization efficiency (PIE) curves are recorded for the DNA bases and the following water (W) clusters: G, GWn (n = 1-3); C, CWn (n = 1-3); A, AWn (n = 1,2); and T, TWn (n = 1-3). Appearance energies (AE) are derived from the onset of these PIE curves (all energies in eV): G (8.1 +/- 0.1), GW (8.0 +/- 0.1), GW2 (8.0 +/- 0.1), and GW3 (8.0); C (8.65 +/- 0.05), CW (8.45 +/- 0.05), CW2 (8.4 +/- 0.1), and CW3 (8.3 +/- 0.1); A (8.30 +/- 0.05), AW (8.20 +/- 0.05), and AW2 (8.1 +/- 0.1); T (8.90 +/- 0.05); and TW (8.75 +/- 0.05), TW2 (8.6 +/- 0.1), and TW3 (8.6 +/- 0.1). The AEs of the DNA bases decrease slightly with the addition of water molecules (up to three) but do not converge to values found for photoinduced electron removal from DNA bases in solution.     

Classification of organic molecules to obtain electron affinities from half-wave reduction potentials: cytosine, uracil, thymine, guanine and adenine

A procedure for obtaining the adiabatic electron affinities (AEA) of organic molecules from half-wave reduction potentials in aprotic solvents is presented. Molecules are placed into groups according to their structure. Each group has a different solution energy difference. Calculations of AEA and charge distributions with AM1-multiconfiguration configuration interaction are used to support the intuitive classification of the molecules. The procedure is illustrated for Vitamins A and E, riboflavin, the azines, polyenes, hydroxy-pyrimidine, oxo-guanine, the hydrogen bonded cytosine-oxo-guanine as well as the AEA, and vertical EA (VEA) of Cytosine (C), Uracil (U), Thymine (T), Guanine (G) and Adenine (A). The latter values are: (VEA) G, 0.10; A, -0.49; U, 0.33; T, 0.31; C, -1.48 and (AEA) G, 1.51 +/- 0.05; A, 0.95 +/- 0.05; U, 0.80 +/- 0.05; T, 0.79 +/- 0.05; C, 0.56 +/- 0.05 in eV.     

Interaction of adenine and thymine with aqueous sugar solutions

The solubility of the nucleic acid bases, adenine and thymine, in aqueous erythritol, xylose, glucose, and sucrose solutions has been studied. The solubility of adenine increases linearly with glucose and sucrose concentration, whereas with the other reagents a nonlinear increase is observed. Below 1.5M reagent concentration, the solubility of adenine increases in the order erythritol < robose, xylose < glucose < sucrose. The solubility of thymine in these solutions, on the other hand, decreases, increases, or does not change depending upon the reagent. The effect of temperature on the solubility of adenine and thymine in sugar solution indicates that the transfer of these molecules from water to sugar solution is exothermic.Presented in part at the VIIth All-India Symposium in Biophysics held at Visva Bharati University during October 1976.     

Adsorption of bovine serum albumin at solid/aqueous interfaces

Adsorption of soluble serum proteins on hydrophilic and hydrophobic solid surfaces is important for biomaterials and chromatographic separations of proteins. The adsorption of bovine serum albumin (BSA) from aqueous solutions was studied with in situ ATR-IR spectroscopy, and with ex situ ATR-IR, ellipsometry, and water wettablity measurements. The results were used to quantitatively determine the adsorbed film thickness and surface density of BSA on hydrophilic silicon oxide/silicon surfaces, and on these surfaces covered with a hydrophobic lipid monolayer of dipalmitoylphosphatidylcholine (DPPC). The water contact angles were 5° for silicon oxide, 47° ± 1° for the DDPC monolayer, and 53° ± 1° for the BSA monolayers. At 25 °C, and with 0.01–1 wt% BSA in water, the surface densities range from Γ = 2.6–5.0 mg/m², and the film thicknesses range from d = 2.0–3.8 nm, on the assumption that the film is as dense as bulk protein. These results, and certain changes in the IR amide I and II bands of the protein, indicate that the protein adsorbs as a side-on monolayer, with some flattening due to unfolding or denaturation. The estimated -helical content for protein in buffer solutions is 15% higher than for solutions in water. The adsorption density reaches a steady-state value within 10 min for the lowest concentration, but does not appear to reach a steady-state value after 3 h f‘or the higher concentrations. Adsorption of BSA on a silicon oxide surface covered with a monolayer of DPPC leads to an adsorbed protein film of about half the thickness and surface density than on silicon oxide, but the same contact angle, indicating more protein unfolding on the hydrophobic than on the hydrophilic surface.     

Depletion at solid/liquid interfaces: flowing hexadecane on functionalized surfaces

We present a neutron reflectivity study on interfaces in contact with flowing hexadecane, which is known to exhibit surface slip on functionalized solid surfaces. The single crystalline silicon substrates were either chemically cleaned Si(100) or Si(100) coated by octadecyl-trichlorosilane (OTS), which resulted in different interfacial energies. The liquid was sheared in situ and changes in reflectivity profiles were compared to the static case. For the OTS surface, the temperature dependence was also recorded. For both types of interfaces, density depletion of the liquid at the interface was observed. In the case of the bare Si substrate, shear load altered the structure of the depletion layer, whereas for the OTS covered surface no effect of shear was observed. Possible links between the depletion layer and surface slip are discussed. The results show that, in contrast to water, for hexadecane the enhancement of the depletion layer with temperature and interfacial energy reduces the amount of slip. Thus a density depletion cannot be the origin of surface slip in this system.     

Protonation of thymine,cytosine, adenine,and guanine DNA nucleic acid bases: Theoretical investigation into the framework of density functional theory

Gradient-corrected density functional computations with triple-zeta-type basis sets were performed to determine the preferred protonation site and the absolute gas-phase proton affinities of the most stable tautomer of the DNA bases thymine (T), cytosine (C), adenine (A), and guanine (G). Charge distribution, bond orders, and molecular electrostatic potentials were considered to rationalize the obtained results. The vibrational frequencies and the contribution of the zero-point energies were also computed. Significant geometrical changes in bond lengths and angles near the protonation sites were found. At 298 K, proton affinities values of 208.8 (T), 229.1 (C), 225.8 (A), and 230.3 (G) kcal/mol were obtained in agreement with experimental results. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 989–1000, 1998     

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.     

Simultaneous determination of adenine guanine and thymine at multi-walled carbon nanotubes incorporated with poly(new fuchsin) composite film

A composite film (MWCNTs-PNF) which contains multi-walled carbon nanotubes (MWCNTs) along with the incorporation of poly(new fuchsin) (PNF) has been synthesized on glassy carbon electrode (GCE), gold (Au) and indium tin oxide (ITO) by potentiostatic methods. The presence of MWCNTs in the composite film enhances surface coverage concentration (Γ) of PNF to ≈176.5%, and increases the electron transfer rate constant (k_s) to ≈346%. The composite film also exhibits promising enhanced electrocatalytic activity towards the mixture of biochemical compounds such as adenine (AD), guanine (GU) and thymine (THY). The surface morphology of the composite film deposited on ITO has been studied using scanning electron microscopy and atomic force microscopy. These two techniques reveal that the PNF incorporated on MWCNTs. Electrochemical quartz crystal microbalance study reveals the enhancement in the functional properties of MWCNTs and PNF. The electrocatalytic responses of analytes at MWCNTs and MWCNTs-PNF films were measured using both cyclic voltammetry (CV) and differential pulse voltammetry (DPV). From electrocatalysis studies, well separated voltammetric peaks have been obtained at the composite film for AD, GU and THY, with the peak separation of 320.3 and 132.7 mV between GU-AD and AD-THY respectively. The sensitivity of the composite film towards AD, GU and THY in DPV technique is 218.18, 12.62 and 78.22 mA M⁻¹ cm⁻² respectively, which are higher than MWCNTs film. Further, electroanalytical studies of AD, GU and THY present in single-strand deoxyribonucleic acid (ssDNA) have been carried out using semi-derivative CV and DPV.     

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.     

Single-crystalline platinum nanosheets from nonionic surfactant 2-D self-assemblies at solid/aqueous solution interfaces

Single-crystalline platinum nanosheets have been prepared via a new methodology based on the chemical reduction of a platinum salt (H2PtCl6) with hydrazine at a graphite/solution interface, using polyoxyethylene (20) sorbitan monostearate (Tween 60) based self-assembly (hemicylindrical micelle) templates. The platinum nanosheets with a uniform thickness of as thin as 3.5 +/- 1 nm are surface-smooth and continuous over relatively large length scales of micrometer sizes. In striking contrast to the Tween 60 based system, no Pt nanosheets are obtained with nonaethylene glycol monododecyl ether (C12EO9) and polyoxyethylene (23) dodecyl ether (C12EO23). No Pt nanosheets are also obtainable with a laterally homogeneous layer of Tween 60 formed at the silica/solution interface. These results indicate that surfactant Tween 60 molecules with a triple polyoxyethylene structure, as well as their hemicylindrical micelle templates, play an essential role for the formation of the Pt nanosheets. It is also suggested that the interfacially directed growth of Pt metals within the aqueous shells of the Tween 60 hemicylindrical micelles induces the thin Pt crystals as thick as the aqueous shells. The present approach could be extended to prepare a wide range of novel nanostructures of noble metals, using various micelle-like self-assemblies at interfaces.     

Mesomorphic phases obtained through molecular recognition of complementary adenine and thymine nucleobases functionalized with long aliphatic chains

Abstract

Complementary adenine and thymine nucleobases were functionalized with long aliphatic chains. The materials exhibited a mesomorphic character which was attributed to the formation of supramolecular architectures. Molecular recognition through hydrogen bonding of the complementary ends of the molecules was the driving force for their formation. It was also found that these structures are affected by the crystallization medium.     

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.     

Mucin at solution/air and solid/solution interfaces

In this paper the surface activity of protein mucin at solution/air interface has been studied. The experiments of the adsorbed protein at solution/air interface have been carried out with a range of protein concentrations at a defined pH. The adsorption of the protein to solid surfaces and the degree of hydrophobicity at solid/solution interface of mucin have been evaluated at different pH and in the presence of Hofmeister electrolyte. The results from these studies have been further substantiated by surface potential measurements of mucin covered surface on stainless steel. Quartz crystal microbalance (QCM) has been used to follow the protein adsorption kinetics from solution to solid surface. The results from these measurements show that the adsorption behavior has a remarkable dependence on the degree of maximum coverage and is almost independent of the ionic strength. Other characteristic features such as maximum adsorption values at the protein isoelectric point (IEP4.7) and low-affinity isotherms that showed surface saturation even under unfavorable electrostatic conditions have been observed. The amount of mucin adsorbed in the presence of electrolytes has been estimated using electron spectroscopy for chemical analysis (ESCA). The study clearly shows that there exists an inverse relationship between the hydrophobicity and surface tension of the protein and also on the hydrated radius of Hofmeister electrolyte used.     

Synthesis,physicochemical characteristics,and biocompatibility of self‐assemble polymers bearing guanine,cytosine, uracil,and thymine moieties

We synthesized chemically well‐defined brush (i.e., comb‐like) polymers bearing guanine, cytosine, uracil, or thymine moieties at the bristle ends. The polymers were stable up to 220 °C and were readily solution‐processable, yielding high‐quality films. Interestingly, the brush polymers favorably self‐assembled to form molecular multibilayer structures stabilized by hydrogen bonding interactions among the nucleobase moieties at the bristle ends, which provided nucleobase‐rich surfaces. The multibilayer‐structured polymer films showed high water affinity. They also displayed selective protein adsorption, suppressed bacterial adherence, facilitated cell adhesion, and exhibited good biocompatibility in mice. The brush polymer DNA‐mimicking comb‐like polymers are suitable as biomaterials and in protein separation applications. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2015 , 53, 1151–1160     

Mesomorphic phases obtained through molecular recognition of complementary adenine and thymine nucleobases functionalized with long aliphatic chains

Complementary adenine and thymine nucleobases were functionalized with long aliphatic chains. The materials exhibited a mesomorphic character which was attributed to the formation of supramolecular architectures. Molecular recognition through hydrogen bonding of the complementary ends of the molecules was the driving force for their formation. It was also found that these structures are affected by the crystallization medium.     

On NO3--H2O interactions in aqueous solutions and at interfaces

The constrained molecular-dynamics technique was employed to investigate the transport of a nitrate ion across the water liquid/vapor interface. We developed a nitrate-ion-water polarizable potential that accurately reproduces the solvation properties of the hydrated nitrate ion. The computed free-energy profile for the transfer of the nitrate ion across the air/water interface increases monotonically as the nitrate ion approaches the Gibbs dividing surface from the bulk liquid side. The computed density profiles of 1M KNO(3) salt solution indicate that the nitrate and potassium ions are both found below the aqueous interface. Upon analyzing the results, we conclude that the probability of finding the nitrate anion at the aqueous interface is quite small.     

Electrophoretic studies of polygalacturonate oligomers and their interactions with metal ions

Polygalacturonic acid, a linear homopolysaccharide, was investigated by capillary electrophoresis (CE) using linear polyacrylamide-coated capillaries and laser-induced fluorescence (LIF) detection. A successful separation of its fluorescently labeled oligomers was achieved through sieving in polyacrylamide entangled matrices. The reaction conditions for the derivatization of polygalacturonic acid were optimized. In studying the interactions between polygalacturonic acid and various metal ions, the end-label, free-solution electrophoretic (ELFSE) technique, developed earlier in our laboratory (Sudor, J., Novotny, M. V., Anal. Chem. 1995, 67, 4205-4209) was found preferable to the sieving method. ELFSE is fast and convenient in that no polymer solutions are needed for the separation. The investigation showed that for the moderately large oligomers, the strongest binding occurred with calcium and cadmium ions, while the smallest interaction was observed with magnesium ions.