Oxa-enediynes: probing the electronic and stereoelectronic contributions to the Bergman cycloaromatization

Efficient routes to three classes of 10-membered oxa-enediynes are presented. The electronic and stereoelectronic contributions to half-lives are supported by density functional theory calculations. One member of this class cyclizes to give an isochroman which binds to and degrades the aryl hydrocarbon receptor (AhR).     

Halo-enediynes: probing the electronic and stereoelectronic contributions to the Bergman cycloaromatization

A series of halogen-substituted cyclic enediynes were prepared with use of carbenoid coupling strategy. DFT analysis, initially used to identify synthesis candidates, was also employed to rationalize the propensity for cycloaromatization of the compounds. In all cases studied the halogen atom had a strongly retardative effect on the thermal Bergman cycloaromatization reaction. The isolation of the first C-9 monochloroenediyne is noteworthy, and may find application in prodrug design.     

Synthesis of novel analogs of aromatic peptide nucleic acids (APNAs) with modified conformational and electrostatic properties

Aromatic peptide nucleic acid analogs having an N-(2-aminobenzyl)glycine backbone (APNA 1) were previously identified as promising new leads for the design of polyaromatic DNA mimics. Structural modifications of 1, which lock the aromatic backbone into a unique conformation, while maintaining the same space distribution between the nucleobases as in 1, were investigated. The electrostatic potential of the aromatic backbone was also modified in an attempt to improve the solubility of these compounds in aqueous media and to evaluate how the quadrapole of the aromatic backbone may influence the biophysical properties of the APNA oligomers. PNA hexamers containing a single monomer insert of each new APNA monomer were used to explore the hybridization properties of these analogs with poly rA and poly dA. Preliminary results indicated that these modifications do not seriously alter the molecular recognition properties of APNAs towards DNA and RNA.     

Systematic evaluation of the conformational properties of aliphatic omega-hydroxy acids

A systematic conformational study of omega-hydroxy acids, HO-(CH(2))(n)()-COOH with n ranging from 2 to 5, has been performed using quantum mechanical calculations at the MP2 level. To distinguish between intrinsic and environmentally induced conformational preferences, calculations have been carried out in both gas phase and chloroform solution, a polarizable continuum solvation model being used to represent the latter. Results indicate a consistent conformational behavior, as reflects the feature that the lowest energy minimum for n = 2, 3, 4, and 5 corresponds to the g+g-t, g+g+g-t, g-g+g+g-t, and g+g-g+g+g-t conformations, respectively. Furthermore, the stability of the extended and semi-extended conformations increases systematically with the size of the central aliphatic segment. The relationship between the size of the aliphatic segment and the stability of folded conformations is analyzed and discussed.     

Polyunsaturated fatty acids in lipid bilayers: intrinsic and environmental contributions to their unique physical properties.

Polyunsaturated lipids are an essential component of biological membranes, influencing order and dynamics of lipids, protein-lipid interaction, and membrane transport properties. To gain an atomic level picture of the impact of polyunsaturation on membrane properties, quantum mechanical (QM) and empirical force field based calculations have been undertaken. The QM calculations of the torsional energy surface for rotation about vinyl-methylene bonds reveal low barriers to rotation, indicating an intrinsic propensity toward flexibility. Based on QM and experimental data, empirical force field parameters were developed for polyunsaturated lipids and applied in a 16 ns molecular dynamics (MD) simulation of a 1-stearoyl-2-docosahexaenoyl-sn-glyerco-3-phosphocholine (SDPC) lipid bilayer. The simulation results are in good agreement with experimental data, suggesting an unusually high degree of conformational flexibility of polyunsaturated hydrocarbon chains in membranes. The detailed analysis of chain conformation and dynamics by simulations is aiding the interpretation of experimental data and is useful for understanding the unique role of polyunsaturated lipids in biological membranes. The complete force field is included as Supporting Information and is available from http://www.pharmacy.umaryland.edu/faculty/amackere/research.html.     

Synthesis and properties of peptide nucleic acids containing a psoralen unit

We prepared the psoralen PNA unit from 8-methoxypsoralen and synthesized various PNAs containing psoralen by a typical (t)()Boc method. PNAs containing psoralen (P-PNA) at strand end formed a stable duplex with complementary DNA. The hybridization of P-PNA with complementary DNA resulted in a considerable decrease of the psoralen fluorescence.     

Electronic structure and conformational properties of (carboxy-alkenyl)-phosphonic acids

The general conformational properties and electronic structure of (carboxy-alkenyl)-phosphonic derivatives were determined at RHF/STO-3G^* level. In all the series, low rotation barriers were found for the two C=C/P=O conformers. In the compounds in which the interactions between the carboxylic and phosphonic moieties are smaller, the most stable conformers are the C=C/P=O s-cis ones. In most of the conformers, the C=C/C=O system presents the disposition s-cis. The Z-(2-carboxy-vinyl) and Z-(2-carboxy-propenyl) phosphonic acids present intramolecular hydrogen bonds, existing in at least four conformer with internal hydrogen bonds. These last compounds were more rigorously studied at RHF/3-21G^* and RHF/6-31G^** levels. The most stable conformer shows a trans structure for the C=C/P=O angle, with an intramolecular hydrogen bond located between the hydroxylic hydrogen of phosphonic group and the carbonyl oxygen of carboxylic moiety. A secondary conformer is found with a double intramolecular hydrogen bond between two hydroxylic hydrogens of the phosphonic moiety and the oxygen of carboxylic bond. Another secondary conformer appears with an intramolecular hydrogen bond between the oxygen of the phosphoryl bond and the hydroxylic hydrogen of the carboxylic group. A study of the topology of charge densities is carried out. This analysis reveals bonds with an ionic participation. A very weak π conjugation, variable with the conformers, is found in the C=C/P=O system, as well as a strongly polarized P=O partial triple bond. The intramolecular hydrogen bonds give rise to cyclic structures.     

Voltammetric study of the interaction of ciprofloxacin-copper with nucleic acids and the determination of nucleic acids

The behavior of the ciprofloxacin (CPFX) complex with copper, Cu(II)L₂, at a mercury electrode has been investigated in borax–boric acid buffer. The adsorption phenomena were observed by linear sweep voltammetry. The mechanism of the electrode reaction was found to be reduction of Cu(II)L₂ adsorbed on the surface of the electrode by an irreversible charge transfer to metal amalgam, Cu(0)(Hg). In the presence of DNA, the formation of the electrochemically non-active complexes Cu(II)L₂–DNA results in the decrease of the equilibrium concentration of Cu(II)L₂ and its peak current. Under the optimum conditions, the decrease of the peak current is proportional to DNA concentration. The linear ranges are 6.67×10⁻⁸ to 1.20×10⁻⁵ g ml⁻¹ for calf thymus DNA (ctDNA), 3.30×10⁻⁸ to 2.33×10⁻⁶ g ml⁻¹ for fish sperm DNA (fsDNA) and 1.0×10⁻⁸ to 1.2×10⁻⁶ g ml⁻¹ for yeast RNA. The detection limits are 5.00×10⁻⁹, 3.00×10⁻⁹ and 2.50×10⁻⁹ g ml⁻¹, respectively. This method exhibits good recovery and high sensitivity.     

Photochemistry of nucleic acids in cells.

A survey of the recent aspects of the main photoreactions induced by far-UV radiation in cellular DNA is reported. This mostly includes the formation of cyclobutadipyrimidines, pyrimidine(6-4)pyrimidone photoadducts and related Dewar valence isomers in various eukaryotic and prokaryotic cells, as monitored by using either specific or more general assays. Information is also provided on mechanistic aspects regarding the formation of 5,6-dihydro-5-(alpha-thyminyl) thymine, the so-called "spore photoproduct" within far-UV-irradiated bacterial spores. The second major topic of the review deals with the effects of near-UV radiation and visible light on cellular DNA which are mostly mediated by photosensitizers. The main photoreactions of furocoumarins with DNA, one major class of photosensitizers used in the phototherapy of skin diseases, involve a [2 + 2] cycloaddition to the thymine bases according to an oxygen-independent mechanism. In contrast a second type of photosensitized reaction which appears to play a major role in the genotoxic effects of both near-UV and visible light requires the presence of oxygen. The photodynamic effects which are mediated by either still unidentified endogenous photosensitizers or defined exogenous photosensitizers lead to the formation of a wide spectrum of DNA modifications including base damage, oligonucleotide strand breaks and DNA-protein cross-links.     

Synthesis and properties of trans-3',4'-bridged nucleic acids having typical S-type sugar conformation

The synthesis of nucleoside analogues with a conformationally restricted sugar moiety is of great interest. The present research describes the synthesis of BNA (bridged nucleic acid) monomers 1 and 2 bearing a 4,7-dioxabicyclo[4.3.0]nonane skeleton and a methoxy group at the C2' position. Conformational analysis showed that the sugar moiety of these monomers is restricted in a typical S-type conformation. It was difficult to synthesize the phosphoramidite derivative of the ribo-type monomer 1, while the phosphoramidite of the arabino-type monomer 2 was successfully prepared and incorporated into oligodeoxynucleotides (ODNs). The hybridization ability of the obtained ODN derivatives containing 2 with complementary strands was evaluated by melting temperature (T(m)) measurements. As a result, the ODN derivatives hybridized with DNA and RNA complements in a sequence-selective manner, though the stability of the duplexes was lower than that of the corresponding natural DNA/DNA or DNA/RNA duplex.     

Solution structure and conformational dynamics of deoxyxylonucleic acids (dXNA): an orthogonal nucleic acid candidate

Orthogonal nucleic acids are chemically modified nucleic acid polymers that are unable to transfer information with natural nucleic acids and thus can be used in synthetic biology to store and transfer genetic information independently. Recently, it was proposed that xylose-DNA (dXNA) can be considered to be a potential candidate for an orthogonal system. Herein, we present the structure in solution and conformational analysis of two self-complementary, fully modified dXNA oligonucleotides, as determined by CD and NMR spectroscopy. These studies are the initial experimental proof of the structural orthogonality of dXNAs. In aqueous solution, dXNA duplexes predominantly form a linear ladderlike (type-1) structure. This is the first example of a furanose nucleic acid that adopts a ladderlike structure. In the presence of salt, an equilibrium exists between two types of duplex form. The corresponding nucleoside triphosphates (dXNTPs) were synthesized and evaluated for their ability to be incorporated into a growing DNA chain by using several natural and mutant DNA polymerases. Despite the structural orthogonality of dXNA, DNA polymerase β mutant is able to incorporate the dXNTPs, showing DNA-dependent dXNA polymerase activity.     

Synthesis and conformational studies of peptides from new C-linked carbo-beta-amino acids (beta-Caas) with anomeric methylamino- and difluorophenyl moieties

New C-linked carbo-beta-amino acids (beta-Caas), Cbz-(S)-beta-Caa-(NHBoc)-OMe (1) and Cbz-(R)-beta-Caa-(NHBoc)-OMe (2), with an additional amine group (methylamino group of NHBoc) at the C-1 position of the lyxofuranoside side chain and Boc-(S)-beta-Caa-(diFP)-OMe (3) and Boc-(R)-beta-Caa-(diFP)-OMe (4), with a C-difluorophenyl (diFP) moiety at the anomeric position of the lyxofuranoside side chain were prepared from D-mannose. Beta-peptides [tetra- and hexapeptides] were synthesized from these beta-Caas, 'epimeric' [at the amine stereocentre (C(beta))], using the concept of 'alternating chirality' to carry out their conformational studies [NMR (CDCl(3)), CD and MD]. In the monomer design, it was envisaged that the presence of an additional amine group in 1 or 2 would help in solubilizing the peptides in water, while, the C-difluorophenyl (diFP) moiety of 3 and 4 is expected to enhance the biological activity. The peptides having 1 and 2, though could not retain their 12-10-mixed helices in water, have shown moderate activity against gram positive and gram negative bacterial strains. The peptides prepared from 3 and 4, much against our expectations, did not display any biological activity.     

Theoretical study of the electronic properties of the purine and pyrimidine components of the nucleic acids

A semi-empirical self-consistent field calculation has been carried out for the purine and pyrimidine bases of the nucleic acids after an appropriate optimization of the integral values using reference compounds. Special emphasis has been laid upon results concerned with the ionization potentials, electron affinities, spectral transitions, triplet states, dipole moments and basicities of the compounds. They enable in particular a detailed interpretation of both the individual ultra-violet absorption spectra of the bases and of their interrelations.

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Zusammenfassung Ein semiempirisches SCF-Verfahren wurde zur Berechnung von Purin- und Pyrimidinbasen von NucleinsÄuren herangezogen, wobei besonderes Gewicht auf Ionisierungspotentiale, ElektronenaffinitÄten, spektrale übergÄnge, TriplettzustÄnde, Dipolmomente und BasizitÄten gelegt wurde. Insbesondere ist eine eingehende Interpretation der UV-Absorptions-spektren möglich, und zwar sowohl hinsichtlich der einzelnen Basen als auch deren Beziehungen untereinander.

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Résumé Un calcul self-consistent semi-empirique a été effectué pour les bases puriques et pyrimidiques des acides nucléiques, à l'aide d'un jeu d'intégrales déterminées de facon optimum pour une série de molécules de référence. L'accent a été mis en particulier sur les résultats relatifs aux potentiels d'ionisation, affinités électroniques, transitions ^*, états triplets, moments dipolaires et basicités. Il a été possible d'interpréter tant les spectres individuels des bases que leurs interrelations.

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This work was supported by grant No. GM 12289–01 of the United States Public Health Service (National Institute of General Medical Sciences).     

以核酸为作用靶的内源性活性物质的研究

(Sp)-8-Cl-cAMP-辛酯通过调节细胞信号传导系统而抑制肿瘤细胞生长,其代谢产物8-Cl-腺苷也同样具有诱导分化和启动肿瘤细胞程序死亡的作用。从D(L)-木糖、D-葡萄糖和2-氨基-2-脱氧-D-葡萄糖出发合成了五种不同形式的异核苷,由异核苷组成的反义寡核苷酸能有效拮抗磷酸二酯酶的降解,它们对互补序列的杂交能力与异核苷的结构及磷酸二酯键的连接方式密切相关。     

Synthesis and conformational properties of 2,6-bis-anilino-3-nitropyridines

The synthesis of 2,6-bis-anilino-3-nitropyridines that are alkylated or acylated at the anilino nitrogen atoms is described. These derivatives show characteristic differences in the 1H-NMR spectra compared with the unsubstituted parent compound. These differences are used to determine structure-conformation relationships of this type of compounds. The conclusions drawn from the 1H-NMR spectra in this respect are supported by X-ray crystallographic data and by 1H-NMR data of conformationally restricted analogues. Preliminary investigations indicate that these relationships can in principle be extended to other diarylamines.     

Microanalysis of nucleic acids using the limulus G test.

The limulus G test has been used as a quantitative analysis of (1-->3)-beta-D-glucans, including schizophyllan (SPG) and curdlan. The present work extended the limulus G test to detect polynucleotide/SPG complexes. The complex showed an extremely sensitive response to the test, compared with SPG itself. The minimum concentration of the complex to show the response is almost 10-times as small as that of SPG itself, indicating the possibility to detect (1-->3)-beta-D-glucans or/and polynucleotides on the pico gram/ml scale.     

Poly(β-Amino acids). VI. Synthesis and conformational properties of poly[(r)-3-pyrrolidinecarboxylic acid]

Racemic and optically active 3-pyrrolidinecarboxylic acids (β-proline) were synthesized, and their polymers, poly[(RS)-β-proline] and poly[(R)-β-proline], were prepared by the polycondensation reaction of the p-nitrophenyl esters. Model compounds, N-cyclopentylcarboxylic acid pyrrolidide and N-cyclopentylcarbonyl-(R)-3-pyrrolidinecarboxylic acid pyrrolidide, were synthesized to elucidate the conformation of the polymer. The solution properties of poly[(R)-β-proline] and the model compounds were investigated by means of circular dichroism (CD) and NMR spectroscopy. The spectral patterns of the polymer and model compounds were similar in various solvents. Poly[(R)-β-proline] and poly[(RS)-β-proline] showed identical NMR spectra. These results suggest that poly[(R)-β-proline] may exist in a random conformation consisting of mixtures of cis and trans amide bonds. The conformational study of cyclopentanecarboxylic acid pyrrolidide by NMR spectroscopy with a shift reagent, Eu(fod)₃, in CDCl₃ implied that the plane containing the amide group bisects the cyclopentane ring. This suggests that each amide plane in the polymer in chloroform may also bisect the pyrrolidine ring.