Synthesis of acyclic and macrocyclic analogs of Di-, Tri-, and tetranucleotides

Compounds consisting of two or three uracil fragments were synthesized by reaction of methyl-substituted uracil sodium salts with 1-(6-bromohexyl)-3,6-dimethyluracil or 1,6-dibromohexane. Treatment of these compounds with paraformaldehyde gave the corresponding pyrimidinophanes and acyclic compounds in which the uracil fragments are linked through methylene bridges. Uracil derivatives having no substituent on N³ were synthesized by reactions of silylated uracils with 1,3-bis(6-bromohexyl)uracil or 4,4′-(6-bromohexyloxy)diphenylmethane. The acyclic compound was converted into pyrimidinophane containing uracil fragments with N³H groups. A trinucleotide analog including uracil and two adenine fragments was synthesized from 1,3-bis(6-bromohexyl)uracil.     

Synthesis of 3-O-aryl esters of (R,S)-9-(2,3-dihydoxypropyl)adenine and its pyrimidine analogs as new potential inhibitors ofS-adenosyl-L-homocysteine hydrolase

With the aim of searching for new antiviral agents of the acyclonucleoside type, 3-O-arly esters of (R,S)-9-(2,3-dihydroxypropyl)adenine adenine and its pyrimidine analogs have been synthesized. Alkylation of adenine and cytosine by aryl glycidyl ethers in the presence of potassium carbonate affords 46–76% yields of the corresponding N⁹- and N¹-substituted derivatives. The interaction of aryl glycidyl ethers with trimethylsilyl derivatives of uracil and thymine also results in 41–57% yields of N¹-monosubstituted products with identical acyclic chain structure.Scientific-Research Institute of Pharmacology at the Volgograd Medical Academy, Volgograd 400066, Russia.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 1, pp. 82–86, January, 1999.     

Intramolecular interactions in acyclic and macrocyclic compounds containing nucleotide bases

Acyclic and cyclic counterparts containing thymine and two 3,6-dimethyluracil fragments bridged by methylene chains have been prepared and studied by UV and NMR spectroscopy; in water the uracil units of the acyclic counterpart form an intramolecular stack but arrange in a linear array in chloroform while the fragments of the uracilophane form an intramolecular stack both in chloroform and water; uracil units of bis(3,6-dimethyluracil-1-yl)butane and the macrocyclic counterpart form a stack in chloroform.     

Interaction of the mutagenic base analogs O6-methylguanine and N4-hydroxycytosine with potentially complementary bases

Infrared spectroscopy has been employed to study possible base pair interactions, in nonpolar media, between O⁶-methylguanine and uracil, cytosine and adenine; and between derivatives of N⁴-hydroxycytosine and adenine. The association constants of O⁶-methylguanine with uracil, cytosine, and adenine are well below 1M^–1, whereas those for interaction of 1-methyl-N⁴-methoxycytosine and its 5-methyl derivative with adenine are identical, K = 14M^–1. The significance of the latter finding is discussed in relation to the conformation of the exocyclic N⁴-methoxy group. Quantum chemical calculations, with the aid of the perturbation method, were carried out for the interaction of O⁶-methylguanine with uracil, cytosine, and adenine, to establish the most energetically favoured configurations for interactions of the free bases, and of the same base pairs in the B form of DNA. The role of the conformation of the exocyclic —OCH₃ group in O⁶-methylguanine is discussed. The relevance of both the experimental and theoretical results to mutagenesis by O⁶-methylguanine and N⁴-hydroxycytosine is examined.     

α,ω-Bis(3,6-dimethyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)alkanes and products of their cyclization, pyrimidinophanes: intra- and intermolecular interaction in crystals and in solutions

Reaction of α,ω-bis(3,6-dimethyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)alkanes with paraformaldehyde leads to pyrimidinophanes, which contain four 3,6-dimethyluracil fragments, connected to each other by the methylene chains. A comparative study of intra- and intermolecular interactions of “open” and macrocyclic uracil derivatives in the crystal state and in solution was performed. According to the NMR spectroscopy data, there is no self-association of “open” and macrocyclic compounds in chloroform solutions, whereas the X-ray data revealed the intermolecular π-π contacts between the 3,6-dimethyluracil fragments in the crystals of these compounds. Conclusions on the presence of intramolecular interactions in chloroform solutions of α,ω-bis(3,6-dimethyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)alkanes and pyrimidinophanes were made based on the UV spectra, which were interpreted in terms of hypo- and hyperchromic effects relatively to the model uracil derivative. These conclusions correlate with the X-ray data: there are no intramolecular π-π contacts between the 3,6-dimethyluracil fragments both in the crystals and in solutions of “open” compounds, positions of these fragments relatively to each other in the molecules of pyrimidinophanes are defined by the lengths of the polymethylene bridges. The intramolecular stacking effect between the opposite uracil rings is observed for the macrocycles with trimethylene and hexamethylene chains, whereas there is no such interactions in pyrimidinophanes with tetramethylene chains. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 119–131, January, 2008.     

Functional monomers and polymers. CXXI. Methylation and interaction studies on adenine containing polymethacrylate derivatives

Studies of the methylation of polymethacrylate derivatives with adenine bases were made in comparison to those with uracil bases. The polymethacrylate derivatives with adenine bases were methylated by using methyl iodide in dimethyl sulfoxide solution to produce polymers that contained N¹-methyladenine and N¹, N⁶-dimethyladenine units. The products were identified by spectroscopic data and by preparing their model compounds. The methylated polymers obtained were further applied in a study of polymer complex formation with uracil-base polymers.     

Functional monomers and polymers. CIV. Synthesis and properties of oligomer models of polyethyleneimine derivatives with spacer-separated nucleic acid bases

A series of polyethyleneimine derivatives and their oligomer models with pendant thymine or adenine bases separated by β-alanyl groups as spacers were prepared by an activated ester method. To elucidate the nature of intramolecular interaction of thymine and adenine bases ultraviolet (UV) spectrophotometric studies were undertaken for the series of compounds and the results were compared with those obtained for the corresponding oligomers without spacers. In the thymine derivatives, the nature of the intramolecular interaction resembled that of the corresponding compounds without β-alanyl units, although larger hypochromicities were found in the series with β-alanyl units. In the adenine derivatives, contrary to the corresponding thymine systems, UV hypochromicities of the compounds decreased by incorporation of the spacer group into side chains. It became evident that the intramolecular interaction of adenine bases was due to stacking neutral species, hydrogen bonding, and residual hypochromicity for the protonated species.     

Nonglycoside analogs of nucleotides

N¹-(2′,3′-Dihydroxypropyl)uracil, -thymine, -cytosine, and N⁹-(2′,3′-dihydroxypropyl)adenine were synthesized by alkylation of nucleic bases with 2,3-O-isopropylideneglycerol chlorohydrin, subsequent separation of the resulting mixtures, and removal of the protective groupings. Phosphorylation of these compounds or of their selectively substituted derivatives gave 2′(3′)-monophosphates, which were converted to 2′,3′-cyclophosphates by reaction with N,N′-dicyclohexylcarbodiimide. Thionation of the corresponding cytosine derivatives gave N¹-(2′,3′-dihydroxypropyl)-4-thiouracil and its 2′(3′) phosphate.     

An electrochemical evidence of free radicals formation from flutamide and its reactivity with endo/xenobiotics of pharmacological relevance

This paper reports the feasibility of free radicals formation from flutamide by using cyclic voltammetry. The electrochemical characteristics and the reactivity of the one-electron reduction product from flutamide in mixed media with thiol compounds and the nuclei acid bases are characterized. Results from this paper show the thermodynamic feasibility of free radical formation expressed for both the cathodic peak potential and the second-order rate constant values. The reactivity of the radical towards thiol compounds (glutathione, cysteamine, N-acetylcysteine) and the nuclei acid base, adenine, thymine and uracil were quantitatively assessed through the calculation of the respective interaction rate constants. Based on these results, the following tentative order of reactivity towards the xeno/endobiotics is as follows: cysteamine > uracil > glutathione > adenine > N-acetylcysteine > thymine. The stability of the nitro radical anion electrochemically generated from flutamide showed a linear dependence with pH.     

An electron-impact mass spectral (EIMS) study of N-1 and C-6 carboxyalkyl- and alkoxycarbonylalkyl-substituted derivatives of uracil

The electron impact (EI) induced mass spectral fragmentation of seventeen, including seven newly synthesized, N-1 and C-6 carboxyalkyl- and alkoxycarbonylalkyl-substituted derivatives of uracil and thymine was investigated. Fragmentation pathways are proposed on the basis of accurate mass and metastable transition measurements. The correlation between the intensities of the M⁺* and selected fragment ions of these compounds is discussed. The data obtained provide the basis for distinguishing isomers and metamers.     

Determination of Bromide Production in Radiolysis of Nucleobases,Nucleosides, and Nucleotides Using HPLC

Abstract

Determination of the formation of bromide ions in intermolecular electron transfer in 5-bromouracil (BrUr) and its nucleoside and nucleotide derivatives with nucleobases, nucleosides, and nucleotides was carried out with high performance liquid chromatography (HPLC). Initial electron attachment, at high concentration of nucleobases, nucleosides, or nucleotides, is mainly on these molecules; intermolecular electron transfer then occurs between theses molecules and BrUr and the derivatives. The elimination of bromide ions from BrUr and the derivatives then follows. It is concluded that in neutral and basic solution (pH 6 to 10) there is a significant electron transfer from thymine (T), uracil (Ur), thymidine (dT), 2′-deoxyuridine (dU), or 2′-deoxyuridine-5′-monophosphate (dUMP) to BrUr and the derivatives. For example, at a concentration ratio of BrUr and T of 1 : 100, the yield of bromide ions is about 1.6, amounting to 59% of hydrated electron (e^{aq .}) yield in the radiolysis, in which the pseudo-first-order rate constants predict a bromide yield of less than 0.03.     

N1-(2-furoylmethyl) and N1-(5-nitro-2- furoylmethyl) derivatives of uracil and its 5-substituted derivatives

The corresponding N₁-(2-furoylmethyl) and N₁-(5-nitro-2-furoylmethyl) derivatives of uracil and its 5-substituted derivatives were obtained by the reaction of 2-bromo- and 5-nitro-2-bromoacetylfurans with uracil, 5-fluorouracil, and thymine. The structures of these compounds as N₁-substituted uracils were proved by a study of the UV spectra at various pH values. The computational method of expanding the UV spectra into individual bands was used.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 9, pp. 1268–1270, September, 1971.     

Functional monomers and polymers. XCIV. Photochemical reactions on the synthetic polymers containing thymine bases in the presence of adenine derivatives

Photodimerization reactions of polyacrylate and polymethacrylate derivatives and the dimer model compound containing thymine bases were studied in the presence of adenine derivatives in dimethyl sulfoxide; N,N-dimethylformamide; and dimethyl sulfoxide–ethylene glycol solutions. The photodimerization of thymine bases both in the polymers and in the dimer model compound was found to be quenched by the addition of adenine derivatives. Base-base interaction in the ground state was also studied by ultraviolet (UV) spectroscopy in the three solvents. The quenching of the photodimerizationof thymine bases in the presence of adenine derivatives was discussed in terms of the specific interaction between adenine and thymine bases both in ground and excited states.     

m-Diethynylbenzene macrocycles: syntheses and self-association behavior in solution

m-Diethynylbenzene macrocycles (DBMs), buta-1,3-diyne-bridged [4(n)]metacyclophanes, have been synthesized and their self-association behaviors in solution were investigated. Cyclic tetramers, hexamers, and octamers of DBMs having exo-annular octyl, hexadecyl, and 3,6,9-trioxadecyl ester groups were prepared by intermolecular oxidative coupling of dimer units or intramolecular cyclization of the corresponding open-chain oligomers. The aggregation properties were investigated by two methods, the (1)H NMR spectra and the vapor pressure osmometry (VPO). Although some discrepancies were observed between the association constants obtained from the two methods, the qualitative view was consistent with each other. The analysis of self-aggregation by VPO revealed unique aggregation behavior of DBMs in acetone and toluene, which was not elucidated by the NMR method. Namely, the association constants for infinite association are several times larger than the dimerization constant, suggesting that the aggregation is enhanced by the formation of dimers (a nucleation mechanism). In polar solvents, DBMs aggregate more strongly than in chloroform due to the solvophobic interactions between the macrocyclic framework and the solvents. Moreover, DBMs self-associate in aromatic solvents such as toluene and o-xylene more readily than in chloroform. In particular, the hexameric DBM having a large macrocyclic cavity exhibits extremely large association constants in aromatic solvents. By comparing the aggregation properties of DBMs with the corresponding acyclic oligomers, the effect of the macrocyclic structure on the aggregation propensity was clarified. Finally, it turned out that DBMs tend to aggregate more readily than the corresponding phenylacetylene macrocycles, acetylene-bridged [2(n)]metacyclophanes, owing to the withdrawal of the electron density from the aromatic rings by the butadiyne linkages which facilitates pi-pi stacking interactions.     

Supramolecular architectures and crystal structures of gold(III) compounds with semicarbazones

The synthesis and crystal structures of two novel semicarbazones and four gold(III) compound derivatives of these semicarbazones are presented. A pattern in the formation of the semicarbazones shows the association of Cl^– ions held together by intra- and intermolecular forces. [AuCl₄]^? and [AuBr₄]^? anions are co-crystallised with these semicarbazone ligands, and the packing architectures revealed by a single-crystal X-ray diffraction analysis showed the different influences of the anions and the association of these chemical species by intermolecular forces on the crystal packing. Crystal engineering led to gold(III) compounds that are stabilised by relevant hydrogen bonding networks, which demonstrated their importance to the supramolecular organisation of the studied compounds. Interestingly, Cl???Br interactions are observed and contribute to the formation of the supramolecular structures. Elemental analysis data and spectroscopic properties in the solid state and solution are also described.     

Functional monomers and polymers. XXXXVI. A copolymerization study of methacryloyl-type monomers containing nucleic acid bases in chloroform solution

Behavior of the free radical copolymerization of N-β-methacryloyloxyethyl derivatives of adenine with that of thymine was studied in chloroform solution, taking account of the specific base-base interaction of these monomers. Hydrogen bonding interaction between such monomers was observed by NMR spectroscopy. The acceleration of copolymerization was found to be greater either at lower monomer concentration or at lower polymerization temperature. When N-β-methacryloyloxyethylcarbazole was used as a comonomer, the rate of copolymerization showed a similar trend as in the case of usual free radical copolymerizations. From r₁ and r₂ values obtained, the copolymerization was found to be alternating, particularly in the case of copolymerization between monomers having complementary nucleic acid bases. The results suggest that the hydrogen bonding interaction between adenine and thymine plays a role in the propagation step.     

Reactions of OH* and eaq − with uracil and thymine in the presence of Cu(II) ions in dilute aqueous solutions: A pulse radiolysis study

The reactions of OH^* and e_aq ^? adducts of uracil and thymine with Cu(II) ions in aqueous solutions were followed by pulse radiolysis. The transient absorption spectra of the OH^* adducts of uracil when followed in the presence of Cu(II) ions show growth in absorption at wavelengths 420 and 350 nm at 15 μs and 65 μs after the pulse respectively. Similar transient absorption spectra of thymine showed growth in absorption at wavelengths 390 and 320 nm at 38 μs and 65 μs after the pulse respectively. The rates of electron transfer from the OH^* adducts of uracil and thymine to various Cu(II) compounds when monitored at 360 nm lie between 10⁶ and 10⁸ mol^?1 dm³ s^?1 this implies that the electron transfer process is not an efficient process. Low rate constants coupled with the spectral changes suggest formation of a radical copper adduct which decays by water insertion to give cis-glycols as the major product. The electron transfer from the electron adducts of uracil and thymine to various copper(II) compounds takes place more efficiently (rate constants of the order of 10⁸ and 10⁹ mol^?1 dm³ s^?1) compared with that from the OH^* adducts. The t-butanol radicals formed on scavenging the OH^* radicals also produce adducts with Cu(I) ions which are formed on oxidation of the electron adducts by Cu(II) ions. This adduct has absorption around 400 nm both in the case of uracil and thymine.     

Investigation of proton transport tautomerism in clusters of protonated nucleic acid bases (cytosine, uracil, thymine, and adenine) and ammonia by high-pressure mass spectrometry and ab initio calculations

The energetics of the ion-molecule interactions and structures of the clusters formed between protonated nucleic acid bases (cytosine, uracil, thymine, and adenine) and ammonia have been studied by pulsed ionization high-pressure mass spectrometry (HPMS) and ab initio calculations. For protonated cytosine, uracil, thymine, and adenine with ammonia, the measured enthalpies of association with ammonia are -21.7, -27.9, -22.1, and -17.5 kcal mol-1, respectively. Different isomers of the neutral and protonated nucleic acid bases as well as their clusters with ammonia have been investigated at the B3LYP/6-31+G(d,p) level of theory, and the corresponding binding energetics have also been obtained. The potential energy surfaces for proton transfer and interconversion of the clusters of protonated thymine and uracil with ammonia have been constructed. For cytosine, the experimental binding energy is in agreement with the computed binding energy for the most stable isomer, CN01-01, which is derived from the enol form of protonated cytosine, CH01, and ammonia. Although adenine has a proton affinity similar to that of cytosine, the binding energy of protonated adenine to ammonia is much lower than that for protonated cytosine. This is shown to be due to the differing types of hydrogen bonds being formed. Similarly, although uracil and thymine have similar structures and proton affinities, the binding energies between the protonated species and ammonia are different. Strikingly, the addition of a single methyl group, in going from uracil to thymine, results in a significant structural change for the most stable isomers, UN01-01 and TN03-01, respectively. This then leads to the difference in their measured binding energies with ammonia. Because thymine is found only in DNA while uracil is found in RNA, this provides some potential insight into the difference between uracil and thymine, especially their interactions with other molecules.     

Selective determination of guanine and its nucleosides and nucleotides by reaction with phenylglyoxal as a fluorogenic reagent

A fluorimetric method is described for determining guanine in its nucleosides and nucleotides. The method is based on the reaction of the compounds with phenylglyoxal as a fluorogenic reagent in a weakly acidic solution (pH 4.0). The fluorescences produced show excitation and emission maxima around 365 and 510 nm, respectively. The conditions established for the reaction do not produce fluorescence from other nucleic acid bases such as adenine, cytosine, uracil and thymine, and their nucleosides and nucleotides. The method is sensitive and selective for guanine and its derivatives, with a detection limit of 47–310 pmol ml^?1 in the reaction mixture.     

Detection of hydrogen-bonded adenine-thymine base-pair complexes by electrospray mass spectrometry

Abstract

Bibracchial lariat ether compounds having three-carbon sidearms terminated in either adenine or thymine have the potential to form a molecular box in which the “ends” are crown ethers and the “sides” are hydrogen-bonded base pairs. Previous solution studies relying upon NMR and vapor pressure osmometry confirmed the formation of complexes. In the present study, four diaza-18-crown-6 derivatives having either one or two sidearms each terminated in either adenine or thymine have been studied in a mixture of CHCl₃ and CH₃OH. Either acetic acid or sodium chloride was added to the solutions. For the two-armed systems, the preferred complex was the dimer involving adenines on one monomer and thymines on the other. Homodimers and other complexes were detected as well. The preferred single-armed complex was that occurring between the monomer whose sidearm was terminated in thymine and either H⁺ or Na⁺.