Chiral phosphorothioate analogues of B-DNA. The crystal structure of Rp-d[Gp(S)CpGp(S)CpGp(S)C]

The compound Rp-d[Gp(S)CpGp(S)CpGp(S)C], an analogue of the deoxyoligomer d(G-C)3, crystallizes in space group P2(1)2(1)2(1) with a = 34.90 A, b = 39.15 A and c = 20.64 A. The structure, which is not isomorphous with any previously determined deoxyoligonucleotide, was refined to an R factor of 14.5% at a resolution of 2.17 A, with 72 solvent molecules located. The two strands of the asymmetric unit form a right-handed double helix, which is a new example of a B-DNA conformation and brings to light an important and overlooked component of flexibility of the double helix. This flexibility is manifest in the alternation of the backbone conformation between two states, defined by the adjacent torsion angles epsilon and zeta, trans . gauche-(BI) and gauche-. trans (BII). BI is characteristic of classical of B-DNA and has an average C(1') to C(1') separation of 4.5 A. The corresponding separation for BII is 5.3 A. Each state is associated with a distinct phosphate orientation where the plane of the PO2 (or POS) group is alternately near horizontal or vertical with respect to the helix axis. The BI and BII conformations are out of phase on the two strands. As a consequence, on one strand purine-pyrimidine stacking is better than pyrimidine-purine, while the converse holds for the other strand. At each base-pair step, good and bad stacking alternate across the helix axis. The pattern of alternation is regular in the context of a fundamental dinucleotide repeat. Re-examination of the B-DNA dodecamer d(C-G-C-G-A-A-T-T-C-G-C-G) shows that the C-G-C-G regions contain the BI and BII conformations, and the associated dual phosphate orientation and asymmetric base stacking. Different mechanisms are used in the two structures to avoid clashes between guanine residues on opposite strands, a combination of lateral slide, tilt and helical twist in the present structure, and base roll, tilt and longitudinal slide (Calladine rules) in the dodecamer. The flexibility of the phosphate orientations demonstrated in this structure is important, since it offers a structural basis for protein-nucleic acid recognition.     

The S(2)-Ensemble Fusion Algorithm

This paper presents a novel model for performing classification and visualization of high-dimensional data by means of combining two enhancing techniques. The first is a semi-supervised learning, an extension of the supervised learning used to incorporate unlabeled information to the learning process. The second is an ensemble learning to replicate the analysis performed, followed by a fusion mechanism that yields as a combined result of previously performed analysis in order to improve the result of a single model. The proposed learning schema, termed S(2)-Ensemble, is applied to several unsupervised learning algorithms within the family of topology maps, such as the Self-Organizing Maps and the Neural Gas. This study also includes a thorough research of the characteristics of these novel schemes, by means quality measures, which allow a complete analysis of the resultant classifiers from the viewpoint of various perspectives over the different ways that these classifiers are used. The study conducts empirical evaluations and comparisons on various real-world datasets from the UCI repository, which exhibit different characteristics, so to enable an extensive selection of situations where the presented new algorithms can be applied.     

The reaction of H(2)S with oxidized thiols: generation of persulfides and implications to H(2)S biology

Hydrogen sulfide is an endogenously generated molecule with many reported physiological functions. Although several biological targets have been proposed, the biochemical mechanisms by which it elicits activity are not established. Thus, in an effort to begin to delineate the fundamental biological chemistry of H₂S, we have examined the reaction of H₂S with oxidized thiols and thiol proteins in order to determine whether persulfide formation occurs, is stable and how this may affect protein function. We have found that persulfides are easily generated, relatively stable and can alter enzyme activity. Moreover, we have begun to develop methodology for in situ generation of persulfides to facilitate further study of this potentially important species.     

A useful route to (R)- and (S)-tert-leucine

Resolution of 1-(2-furyl)-2,2-dimethylpropylamine, an intermediate on a synthetic route to tert-leucine, followed by oxidation of the respective enantiomers, constitutes an interesting and useful strategy to (R)- and (S)-tert-leucine.     

`Silk Route Disease' (Beh?et's Disease)

Behçet''s disease is a multisystem disorder in which orogenital ulceration is associated with troublesome generalized uveitis, erythema nodosum, pyoderma, dermatographism, seronegative arthritis, and neurologic and cardiovascular symptoms. There is no diagnostic laboratory test; the diagnosis is based on the disorder''s multisystem clinical features. A points scoring system is helpful in distinguishing it from other multisystem disorders that mimic it. It occurs most frequently in an area coinciding with the old Silk Route, between latitudes 30° and 45° north, in Asian and Eurasian populations, and it has an HLA-B51 affinity. The cause remains unknown, but a postulated trigger factor is a herpesvirus with cofactors that include ethnic group, human leukocyte antigen affinities, T-cell and autonomic imbalance, circulating immune complexes, autoimmunity, blood viscosity, decreased fibrinolysis, and zinc deficiency. Treatment includes administering corticosteroids, azathioprine, chlorambucil, cyclosporine, and colchicine, and fibrinolytic therapy.     

Facile entry to (-)-(R)- and (+)-(S)-mexiletine

The title compounds, 1a and 1b, have been synthesized in a three-step sequence starting from (-)-(S) and (+)-(R)-propylene oxide, respectively, in acceptable overall yields. The enantiomeric excess values for 1a and 1b were 96% and 93% respectively, as assessed by HPLC analysis on a chiral stationary phase of the corresponding N-acetyl derivatives. The synthetic route herein presented may represent a facile entry to highly enriched mexiletine enantiomers, alternative to those previously reported in the literature.     

The S(3) state of the oxygen-evolving complex in photosystem II is converted to the S(2)Y(Z)* state at alkaline pH

Here we report an EPR signal that is induced by a pH jump to alkaline pH in the S(3) state of the oxygen-evolving complex in photosystem II. The S(3) state is first formed with two flashes at pH 6. Thereafter, the pH is changed in the dark prior to freezing of the sample. The EPR signal is 90-100 G wide and centered around g = 2. The signal is reversibly induced with a pK = 8.5 +/- 0.3 and is very stable with a decay half-time of 5-6 min. If the pH is changed in the dark from pH 8.6 to 6.0, the signal disappears although the S(3) state remains. We propose that the signal arises from the interaction between the Mn cluster and Y(Z), resulting in the spin-coupled S(2)Y(Z)(*) signal. Our data suggest that the potential of the Y(Z)(*)/Y(Z) redox couple is sensitive to the ambient pH in the S(3) state. The alkaline pH decreases the potential of the Y(Z)(*)/Y(Z) couple so that Y(Z) can give back an electron to the S(3) state, thereby obtaining the S(2)Y(Z)(*) EPR signal. The tyrosine oxidation also involves proton release from Y(Z), and the results support a mechanism where this proton is released to the bulk medium presumably via a close-lying base. Thus, the equilibrium is changed from S(3)Y(Z) to S(2)Y(Z)(*) by the alkaline pH. At normal pH (pH 5.5-7), this equilibrium is set strongly to the S(3)Y(Z) state. The results are discussed in relation to the present models of water oxidation. Consequences for the relative redox potentials of Y(Z)(*)/Y(Z) and S(3)/S(2) at different pH values are discussed. We also compare the pH-induced S(2)Y(Z)(*) signal with the S(2)Y(Z)(*) signal from Ca(2+)-depleted photosystem II.     

Efficient route to (S)-azetidine-2-carboxylic acid

A new and efficient route to (S)-azetidine-2-carboxylic acid (>99.9% ee) in five steps and total yield of 48% via malonic ester intermediates was established. As the key step, efficient four-membered ring formation (99%) was achieved from dimethyl (S)-(1'-methyl)benzylaminomalonate by treating with 1,2-dibromoethane (1.5 eq) and cesium carbonate (2 eq) in DMF. Krapcho dealkoxycarbonylation of dimethyl (1'S)-1-(1'-methyl)benzylazetidine-2,2-dicarboxylate, the product of this cyclization procedure, proceeded with preferential formation (2.7:1, 78% total yield) of the desired (2S,1'S)-monoester, with the help of a chiral auxiliary which was introduced on the nitrogen atom. The undesired (2R,1'S)-isomer could be converted to that with proper stereochemistry, by a deprotonation and subsequent re-protonation step. Finally, lipase-catalyzed preferential hydrolysis of the (2S,1'S)-monoester and subsequent deprotection provided enantiomerically pure (S)-azetidine-2-carboxylic acid in a 91% yield from the mixture of (2S,1'S)- and (2R,1'S)-isomers.     

Inversion of (R)- to (S)-ketoprofen in eight animal species

The (R)-enantiomer of the NSAID ketoprofen was administered orally at 20 mg/kg to a series of 8 animal species. In all species, a highly significant degree of inversion occurred after 1 h which varied from 27% (gerbil) to 73% (dog) and persisted or increased in plasma samples obtained 3 h after drug administration. Although the (R)-enantiomer was inactive as an inhibitor of cyclooxygenase, the analgesic effects of that isomer was almost the same as the (S)-isomer in animal analgesic assays, following oral administration of the drugs to mice and rats. Taken together, the present results suggest that (R)-ketoprofen administered alone functioned primarily as a prodrug for (S)-ketoprofen under the experimental conditions of this study. © 1995 Wiley-Liss, Inc.     

Synthesis of Zeolites Using the ADOR (Assembly-Disassembly-Organization-Reassembly) Route

Zeolites are an important class of materials that have wide ranging applications such as heterogeneous catalysts and adsorbents which are dependent on their framework topology. For new applications or improvements to existing ones, new zeolites with novel pore systems are desirable. We demonstrate a method for the synthesis of novel zeolites using the ADOR route. ADOR is an acronym for Assembly, Disassembly, Organization and Reassembly. This synthetic route takes advantage of the assembly of a relatively poorly stable that which can be selectively disassembled into a layered material. The resulting layered intermediate can then be organized in different manners by careful chemical manipulation and then reassembled into zeolites with new topologies. By carefully controlling the organization step of the synthetic pathway, new zeolites with never before seen topologies are capable of being synthesized. The structures of these new zeolites are confirmed using powder X-ray diffraction and further characterized by nitrogen adsorption and scanning electron microscopy. This new synthetic pathway for zeolites demonstrates its capability to produce novel frameworks that have never been prepared by traditional zeolite synthesis techniques.     

The biosynthesis of papaverine proceeds via (S)-reticuline

Papaverine is one of the earliest opium alkaloids for which a biosynthetic hypothesis was developed on theoretical grounds. Norlaudanosoline (=tetrahydropapaveroline) was claimed as the immediate precursor alkaloid for a multitude of nitrogen containing plant metabolites. This tetrahydroxylated compound was proposed to be fully O-methylated. The resulting tetrahydropapaverine should then aromatize to papaverine. In view of experimental data, this pathway has to be revised. Precursor administration to 8-day-old seedlings of Papaver followed by direct examination of the metabolic fate of the stable-isotope-labeled precursors in the total plant extract, without further purification of the metabolites, led to elucidation of the papaverine pathway in vivo. The central and earliest benzylisoquinoline alkaloid is not the tetraoxygenated norlaudanosoline, but instead the trihydroxylated norcoclaurine that is further converted into (S)-reticuline, the established precursor for poppy alkaloids. The papaverine pathway is opened by the methylation of (S)-reticuline to generate (S)-laudanine. A second methylation at the 3′ position of laudanine leads to laudanosine, both known alkaloids from the opium poppy. Subsequent N-demethylation of laudanosine yields the known precursor of papaverine: tetrahydropapaverine. Inspection of the subsequent aromatization reaction established the presence of an intermediate, 1,2-dihydropapaverine, which has been characterized. The final step to papaverine is dehydrogenation of the 1,2-bond, yielding the target compound papaverine. We conclusively show herein that the previously claimed norreticuline does not play a role in the biosynthesis of papaverine.     

The role of Bcl-X(S) in radiation sensitivity

Bcl-X(S) is a pro-apoptosis member of the Bcl2 family that has been shown to induce cell death and enhance chemosensitivity. We have investigated the effect of Bcl-X(S) overexpression on radiation sensitivity. Using a tetracycline-repressible system, we found that removal of tetracycline for 16 h induced Bcl-X(S) and reduced the surviving fraction of NIH 3T3 cells to 25%. However, radiation sensitivity was not significantly affected by Bcl-X(S) expression; the mean inactivation doses for Bcl-X(S) repressed and Bcl-X(S) induced cells were 2.7 +/- 0.3 and 2.3 +/- 0.1 Gy, respectively. We conclude that Bcl-X(S) induces cell death without affecting radiation sensitivity. These results suggest that mitochondrial pathways to apoptosis may not have a significant role in survival after irradiation.     

The 5S DNA units ofAcacia species (Mimosaceae)

The DNA sequence structure of 5S DNA units inAcacia species, including representatives from the three subgenera ofAcacia, have been determined. The data was interpreted to suggest that at least three lineages of 5S DNA sequences exist inAcacia and the proposal was made that the lineages be named5S Dna-1, 5S Dna-2, and5S Dna-3. The5S Dna-1 lineage was represented by units fromA. boliviana andA. bidwilli, the5S Dna-2 lineage by units fromA. melanoxylon, A. pycnantha, A. ulicifolia, A. boliviana, A. bidwillii, andA. albida, and the5S Dna-3 lineage by units fromA. bidwillii, A. boliviana, andA. senegal. Based on this interpretation of the sequence data, the Australian species of subg.Phyllodineae grouped together as a cluster, quite separate from the subgeneraAculeiferum andAcacia. As expected from the analyses of morphological characters, the 5S DNA units fromAcacia albida (syn.Faidherbia albida) were quite separate from the otherAcacia spp.