High-performance liquid chromatography and studies of neurophysin-neurohypophysial hormone pathways

A definitive method to determine adenine compounds simultaneously was established by introducing a new fluorescent reagent into high-performance liquid chromatography. Bromoacetaldehyde was the best reagent among the haloacetaldehydes examined. A quantitative reaction was obtained even for unstable ADP and ATP. A high resolution of adenine nucleotides was obtained using a column of Hitachi gel No. 3012-N. The method was applied to the measurement of cyclic AMP in urine, and ADP and ATP in brain and blood. Further, the sensitivity of the method was increased by a new fluorescence spectrophotometer constructed for micro-HPLC. Femtomole amounts of the adenine nucleotides were clearly separated.     

Protonation studies of modified adenine and adenine nucleotides by theoretical calculations and (15)N NMR

The acid/base character of nucleobases affects phenomena such as self-association, interaction with metal ions, molecular recognition by proteins, and nucleic acid base-pairing. Therefore, the investigation of proton-transfer equilibria of natural and synthetic nucleos(t)ides is of great importance to obtain a deeper understanding of these phenomena. For this purpose, a set of ATP prototypes was investigated using (15)N NMR spectroscopy, and the corresponding adenine bases were investigated by theoretical calculations. (15)N NMR measurements provided not only acidity constants but also information on the protonation site(s) on the adenine ring and regarding the ratio of the singly protonated species in equilibrium. Substituents of different nature and position on the adenine ring did not change the preferred protonation site, which remained N1. However, for 2-thioether-ATP derivatives a mixed population of N1 and N7 singly protonated species was observed. Reduction of basicity of 0.4-1 pK(a) units relative to ATP was also observed for all evaluated ATP derivatives, except for 2-Cl-ATP, for which K(a) was ca. 10,000-fold lower. To explain the substitution-dependent variations in the experimental pK(a) values of the ATP analogues, gas-phase proton affinities (PA), Delta Delta G(hyd), and pK(a) values of the corresponding adenine bases were calculated using quantum mechanical methods. The computed PA and Delta Delta G(hyd) values successfully explained the experimental pK(a) values. A computational procedure for the prediction of accurate pK(a) values was developed using density functional theory and polarizable continuum model calculations. In this procedure, we developed a set of parameters for the polarizable continuum model that was fitted to reproduce experimental pK(a) values of nitrogen heterocycles. This method is proposed for the prediction of pK(a) values and protonation site(s) of purine analogues that have not been synthesized or analyzed.     

Simultaneous determination of myocardial creatine phosphate and adenine nucleotides by reversed-phase HPLC

An isocratic HPLC system has been developed which allows for the rapid (single run of 20 min) measurement of creatine phosphate (PCr) and adenine nucleotides (ATP, ADP and AMP) in extracts from freeze-clamped and freeze-dried myocardial tissues. The separation was achieved at room temperature by using a RP18 column and a dual variable wavelength spectrophotometer, set at 210 and 254 nm. The solvent was 30 mM potassium dihydrogen phosphate, 15 mM tetrabutylammonium hydrogen sulfate, pH 6.7, 19% (v/v) acetonitrile. A distinct separation (confirmed with the retention time of standard sample) of these high energy compounds was achieved. Standard curves were linear. In isolated rat hearts the following values were obtained (mumol/g dry wt, mean +/- SEM): ATP 21.5 +/- 1.3, ADP 4.6 +/- 0.2, AMP 1.5 +/- 1.1 and PCr 32.5 +/- 1.3; which are consistent with previously published values for high energy compounds in this tissue.     

Rapid determination of adenine nucleotides in brain tissue by ion-paired reversed-phase column liquid chromatography under isocratic conditions

A rapid method for analysis of adenine nucleotides (AMP, ADP and ATP) in nervous tissue based on ion-paired reversed-phase column liquid chromatography under isocratic conditions is described. An optimal composition of elution buffer was 25 mM potassium phosphate and 4% triethylamine adjusted to pH 6.5 with phosphoric acid. Typical separation time did not exceed 10 min with a 10-cm long compact glass cartridge packed with 5-microns silica C18. The method was employed to determine ATP, ADP and AMP concentrations in rat brain extracts and values thus obtained were compared with those published elsewhere.     

Multiple intermolecular interaction modes of positively charged residues with adenine in ATP-binding proteins

Adenosine 5'-triphosphate (ATP) plays an essential role in all forms of life. Molecular recognition of ATP in ATP-binding proteins is a subject of great importance for understanding enzymatic mechanisms and for drug design. We have carried out a large-scale data mining of the Protein Data Bank (PDB) to analyze molecular determinants for recognition of ATP, in particular, the adenine base, by ATP-binding proteins. A novel distribution pattern of charged residues around the adenine base was discovered: lysine residues tend to occupy the major groove N7 side of the adenine base, and the arginine residues situate preferentially above or below the adenine bases. Such an arrangement is advantageous because it facilitates multiple modes of intermolecular interactions, that is, cation-pi interactions and a hydrogen bond between lysine and adenine, and cation-pi and pi-pi stacking interactions between arginine and adenine. For the two representative Lys...Adenine and Arg...Adenine interactions, intermolecular interaction energies were subsequently analyzed by means of the supermolecular approach at the MP2 level with solvation free energy correction using the SM5.42R model of Cramer and Truhlar, which gave rise to significant interaction strengths.     

Cathodic reduction of nicotinamide adenine dinucleotide and other adenine-containing compounds in acidic media

Both nicotinamide adenine dinucleotide (NAD⁺) and acid-hydrated NADH, as well as adenine, adenosine, adenosine mono-, di-, and tri-phosphate and adenosine diphosphoribose, undergo four-electron reductions of the protonated adenine ring in acidic media. The values of αn_a (transfer coefficient times the number of electrons involved in the rate-determining step), n (total number of electron transferred), and p (number of protons involved in the rate-determining step) agree well with values previously reported for adenine. Cathodic stripping voltammetry of an adsorbed film can be applied to these compounds. Rapid scan rates are required to eliminate the slow desorption step at ?1.1 V vs. SCE for some of these compounds. Hydration of the nicotinamide ring of NADH appears to inhibit this desorption step, but does not appear to be related directly to the electroactivity of the hydration product.     

Synthesis of adenine derivatives containing an amino alcohol fragment

The alkylation of adenine and N(in6)-substituted adenine derivatives by 1, 2-dihaloethanes and the production of 9-(2-haloethyl)derivatives of adenine were studied. 1n the reaction of the derivatives with amino alcohols a series of adenine derivatives containing an amino alcohol fragment was synthesized.Latvian Institute of Organic Synthesis, Riga, LV-1006. Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 3, pp. 386–390, March, 1996. Original article submitted March 7, 1995.     

The determination of total nitrogen in plant materials with an automatic nitrogen analyser

An automatic analyser is used for the measurement of total nitrogen in chemical compounds and botanical material after the combustion method of Dumas in vacuum. The analyser is described and results for several chemical compounds and plant materials are given. The results have been statistically evaluated to compare the reproducibility and accuracy of the automatic analyser and the Kjeldahl method.     

Conformational flexibility of pyrimidine ring in adenine and related compounds

The structural non-rigidity of aromatic pyrimidine rings in adenine and selected related compounds has been investigated by quantum chemical non-empirical methods of calculation at the MP2 and DFT levels of theory. The results of the calculations demonstrate that the pyrimidine ring possesses a notable degree of conformational flexibility despite its aromatic character. The transition of the heterocycle from a planar equilibrium geometry to a non-planar structure with an endocyclic torsion angle of ±20° results in an energy increase of less than 2.8 kcal/mol. An analysis of the population of ground and excited vibrational levels for the lowest out-of-plane vibration of the ring indicates that in adenine 45% of the molecules have a non-planar pyrimidine ring with relevant torsion angle up to ±17° at any moment of time.     

ATPase inhibitor based luciferase assay for prolonged and enhanced ATP pool measurement as an efficient fish freshness indicator

The nucleotide degradation pathway in somatic cells leads to the accumulation of products such as hypoxanthine and inosine, which are commonly used as fish and meat freshness indicators. Assays based on these molecules cannot differentiate the postmortem time over a short period of time (5–10 h). Further, quantification of these degradation products is cumbersome, costly and time-consuming. For the proposed assay, optimal concentrations of 30 and 2 mM, respectively, for the ATPase inhibitors sodium orthovanadate and EDTA were found. Further, it was observed that a firefly luciferase based assay could enhance the sensitivity levels up to 165-fold at 30 °C. In addition, it was observed that the sensitivity for ATP assay was enhanced up to 60-fold even after 12 h. The limit of detection for the ATP assay was 1 pM, unlike other conventional methods, which are sensitive only up to micromolar levels. Moreover, as little as 0.044 g fish fillet was required for the assay, and no time-consuming sample preparation was necessary. Luminescence of prolonged duration was observed in harvested fish kept at -20 °C in comparison with fish kept at 4 and 30 °C, which reflects the shelf life of fish preserved at lower temperatures.

Quadracyclic adenine: a non-perturbing fluorescent adenine analogue

Fluorescent-base analogues (FBAs) comprise a group of increasingly important molecules for the investigation of nucleic acid structure and dynamics as well as of interactions between nucleic acids and other molecules. Here, we report on the synthesis, detailed spectroscopic characterisation and base-pairing properties of a new environment-sensitive fluorescent adenine analogue, quadracyclic adenine (qA). After developing an efficient route of synthesis for the phosphoramidite of qA it was incorporated into DNA in high yield by using standard solid-phase synthesis procedures. In DNA qA serves as an adenine analogue that preserves the B-form and, in contrast to most currently available FBAs, maintains or even increases the stability of the duplex. We demonstrate that, unlike fluorescent adenine analogues, such as the most commonly used one, 2-aminopurine, and the recently developed triazole adenine, qA shows highly specific base-pairing with thymine. Moreover, qA has an absorption band outside the absorption of the natural nucleobases (>300?nm) and can thus be selectively excited. Upon excitation the qA monomer displays a fluorescence quantum yield of 6.8?% with an emission maximum at 456?nm. More importantly, upon incorporation into DNA the fluorescence of qA is significantly less quenched than most FBAs. This results in quantum yields that in some sequences reach values that are up to fourfold higher than maximum values reported for 2-aminopurine. To facilitate future utilisation of qA in biochemical and biophysical studies we investigated its fluorescence properties in greater detail and resolved its absorption band outside the DNA absorption region into distinct transition dipole moments. In conclusion, the unique combination of properties of qA make it a promising alternative to current fluorescent adenine analogues for future detailed studies of nucleic acid-containing systems.     

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.     

Theoretical study of proton-catalyzed hydrolytic deamination mechanism of adenine

Water-assisted proton-catalyzed hydrolytic deamination of adenine to produce hypoxanthine has been studied using density functional theory method. Because adenine could be protonated at N1, N3, N7 and N10, four pathways initiated from the four different protonated adenines have been investigated. The first step of the four pathways is the nucleophilic attack of water with an assistant water to form a tetrahedral structure complex, and this is the rate-determining step. Including solvent effects decreased the relative energies of stationary points but have little effect on the structures. Pathway A is preferred due to the lowest energy barrier, and the relative free energy is 28.9 kcal/mol in vacuo. The outcomes show that adenine deamination under acidic condition is much easier to occur than under neutral condition due to lower energy barriers. The total atomic charge of C5 in the initial intermediate is correlated with the ease of deamination reaction. The more positive C5 atom is, the easier the deamination reaction is.     

Preincubation with cysteine prevents modification of sulfhydryl groups in proteins by unreacted acrylamide in a gel.

It has been found that the double bond of free, unreacted acrylamide in a gel can react with a free -SH group of proteins, forming a cysteinyl-S-propionamide adduct. When beta-lactoglobulin was incubated at concentration levels lower than those of free acrylamide, left after polymerizing a 5% T, 4% C gel (barely 12 mM), under anaerobic conditions in 0.1 M borate, pH 9.5, for 1 h and then the tryptic digests analyzed by high performance liquid chromatography (HPLC), two new peptides were detected. The two new peaks were recovered and sequenced by the Edman degradation procedure. They correspond to the sequence from Leu-149 to Ile-162. Residue No. 160 was found to be a cysteinyl-S-propionamide reaction product. Interestingly, only this residue, out of a total of 5 Cys residues, had reacted. No other amino acids (including -NH2 terminus and free -NH2 in Lys) reacted with free acrylamide. The addition of free acrylamide to the -SH group could be completely inhibited if: (i) the gel was extensively washed prior to sample application, or (ii) the gel was incubated for 1 h in 100 mM free Cys.     

Functional monomers and polymers. CII. Synthesis and properties of oligomer models of polyethyleneimine derivatives containing pendant adenine bases

A series of oligomer model compounds of polyethyleneimine derivatives with pendant adenine bases were prepared by the reaction of a carboxyethyl derivative of adenine with oligomeric amines, using an activated ester method. To evaluate the intramolecular interaction between pendant adenine bases in these compounds, ultraviolet spectra at various pH regions were measured. Ultraviolet hypochromicities and pK_a values depended linearly on the chain length of the oligomers. The results showed that the intramolecular interactions of adenine bases were realized less in their protonated than neutral forms.     

Investigations of mitochondrial adenine nucleotide translocation by means of nucleotide analogs.

ATP and ADP are transferred across the inner mitochondrial membrane by means of a carrier (translocator), an inner membrane integral lipoprotein. Translocation of the adenine nucleotides occurs in two steps: specific binding and transport. By using substrate analogs with modified adenine, phosphate, or ribose moieties it is possible to check which structural properties of the substrate are essential for binding and transport.     

Inhibition of the nicotinamide adenine dinucleotide-oxidoreductase reaction by herbicides and fungicides of various structures

The effect of herbicides (basagran, zenkor, kusagard, roundup, setoxidim, and lontrel and lontrel complexes with some doubly charged metal ions) and fungicides (tachigaren and tilt) on the activity of nicotinamide adenine dinucleotide (NADH)-oxidoreductase from the methylotroph Methylococcus capsulatus (strain M) was studied. All the herbicides and fungicides inhibit the enzyme, differing in the degree and type of inhibition. The inhibition constants K _i for these compounds and for lontrel complexes were determined. A correlation between the K _i values and the complexation constants of these pesticides with NADH was established. The studied compounds are toxic. __________ Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 1284–1289, May, 2005.     

Adenine radicals in the gas phase: an experimental and computational study of hydrogen atom adducts to adenine

The elusive hydrogen atom adduct to the N-1 position in adenine, which is thought to be the initial intermediate of chemical damage, was specifically generated in the gas phase and characterized by neutralization-reionization mass spectrometry. The N-1 adduct, 1,2-dihydroaden-2-yl radical (1), was generated by femtosecond electron transfer to N-1-protonated adenine that was selectively produced by electrospray ionization of adenine in aqueous-methanol solution. Radical 1 is an intrinsically stable species in the gas phase that undergoes specific loss of the N-1-hydrogen atom to form adenine, but does not isomerize to the more stable C-2 adduct, 1,2-dihydroaden-1-yl radical (5). Radicals 1 that are formed in the fifth and higher electronically excited states of DeltaE > or = 2.5 eV can also undergo ring-cleavage dissociations resulting in expulsion of HCN. The relative stabilities, dissociation, and transition state energies for several hydrogen atom adducts to adenine have been established computationally at highly correlated levels of theory. Transition state theory calculations of 298 K rate constants in the gas phase, including quantum tunnel corrections, indicate the branching ratios for H-atom additions to C-8, C-2, N-3, N-1, and N-7 positions in adenine as 0.68, 0.20, 0.08, 0.03, and 0.01, respectively. The relative free energies of adenine radicals in aqueous solution point to the C-8 adduct as the most stable tautomer, which is predicted to be the predominating (>99.9%) product at thermal equilibrium in solution at 298 K.     

One-dimensional oxalato-bridged Cu(II), Co(II), and Zn(II) complexes with purine and adenine as terminal ligands

The reaction of nucleobases (adenine or purine) with a metallic salt in the presence of potassium oxalate in an aqueous solution yields one-dimensional complexes of formulas [M(mu-ox)(H(2)O)(pur)](n) (pur = purine, ox = oxalato ligand (2-); M = Cu(II) [1], Co(II) [2], and Zn(II) [3]), [Co(mu-ox)(H(2)O)(pur)(0.76)(ade)(0.24)](n)(4) and ([M(mu-ox)(H(2)O)(ade)].2(ade).(H(2)O))(n) (ade = adenine; M = Co(II) [5] and Zn(II) [6]). Their X-ray single-crystal structures, variable-temperature magnetic measurements, thermal behavior, and FT-IR spectroscopy are reported. The complexes 1-4 crystallize in the monoclinic space group P2(1)/a (No. 14) with similar crystallographic parameters. The compounds 5 and 6 are also isomorphous but crystallize in the triclinic space group P (No. 2). All compounds contain one-dimensional chains in which cis-[M(H(2)O)(L)](2+) units are bridged by bis-bidentate oxalato ligands with M(.)M intrachain distances in the range 5.23-5.57 A. In all cases, the metal atoms are six-coordinated by four oxalato oxygen atoms, one water molecule, and one nitrogen atom from a terminal nucleobase, building distorted octahedral MO(4)O(w)N surroundings. The purine ligand is bound to the metal atom through the most basic imidazole N9 atom in 1-4, whereas in 5 and 6 the minor groove site N3 of the adenine nucleobase is the donor atom. The crystal packing of compounds 5 and 6 shows the presence of uncoordinated adenine and water crystallization molecules. The cohesiveness of the supramolecular 3D structure of the compounds is achieved by means of an extensive network of noncovalent interactions (hydrogen bonds and pi-pi stacking interactions). Variable-temperature magnetic susceptibility measurements of the Cu(II) and Co(II) complexes in the range 2-300 K show the occurrence of antiferromagnetic intrachain interactions.     

Formation of intrastrand cross-link products between cytosine and adenine from UV irradiation of d((Br)CA) and duplex DNA containing a 5-bromocytosine

Here, we showed that Pyrex-filtered UV light irradiation of d((Br)CA) gave rise to three types of intrastrand cross-link products, that is, d(C[5-N6]A), d(C[5-2]A), and d(C[5-8]A), where the C5 carbon atom of cytosine is covalently bonded to the N6 nitrogen atom, C2, and C8 carbon atoms of adenine, respectively. Furthermore, we demonstrated by LC-MS/MS that the UV irradiation of a 5-bromocytosine-containing duplex oligodeoxynucleotide (ODN) led to the formation of five cross-link products, that is, C[5-N6]A, C[5-2]A, C[5-8]A, A[2-5]C, and A[8-5]C, under both aerobic and anaerobic conditions. LC-MS/MS quantification results showed that the yields for the formation of these cross-link products are different. The presence of molecular oxygen reduces the yields for the formation of all cross-link products except A[2-5]C. To our knowledge, this is the first report about the formation of intrastrand cross-link products between cytosine and adenine in duplex DNA. The chemistry discovered here may facilitate the future preparations of oxidative cross-link lesion-bearing substrates for biochemical and biophysical studies.