Gene expression analysis for high throughput screening applications

To meet growing needs for high throughput gene expression profiling, we established a new automated high throughput TaqMan RT-PCR method for quantitative mRNA expression analysis. In this method, the Allegro( trade mark ) (Zymark) system conducts all sample tracking and liquid handling steps, and ABI PRISM 7900 HT (Applied Biosystems) is used to conduct real-time determination of the C(t) value when amplification of PCR products is first detected and accumulation of inhibitory PCR products is unlikely to occur. The ABI PRISM 7900 HT Sequence Detection System features a real-time PCR instrument with 384-well-plate compatibility and robotic loading, and continuous wavelength detection, which enables the use of multiple fluorophores in a single reaction. The Allegro System offers an assembly line approach with a modular design that allows reconfiguration of the components to accommodate variations in the assay flow. In the present study, we have established and validated a new automated High Throughput (HT) TaqMan RT-PCR- based method for quantitative mRNA expression analysis. The data demonstrate that HT-Taqman PCR is a powerful tool that can be used for measuring low concentrations of mRNA, and is highly accurate, reproducible, and amenable to high throughput analysis. Results suggest that HT-TaqMan is a reliable method for the quantification of low-expression genes and a powerful tool with HT capability for target identification/validation, structure-activity relationship (SAR) study, compound selection for efficacy studies, and biomarker identification in drug discovery and development.     

Mechanistic studies on the formation and reactivity of dioxygen adducts of diiron complexes supported by sterically hindered carboxylates

Dioxygen activation by enzymes such as methane monooxygenase, ribonucleotide reductase, and fatty acid desaturases occurs at a nonheme diiron active site supported by two histidines and four carboxylates, typically involving a (peroxo)diiron(III,III) intermediate in an early step of the catalytic cycle. Biomimetic tetracarboxylatodiiron(II,II) complexes with the familiar "paddlewheel" topology comprising sterically bulky o-dixylylbenzoate ligands with pyridine, 1-methylimidazole, or THF at apical sites readily react with O(2) to afford thermally labile peroxo intermediates that can be trapped and characterized spectroscopically at low temperatures (193 K). Cryogenic stopped-flow kinetic analysis of O(2) adduct formation carried out for the three complexes reveals that dioxygen binds to the diiron(II,II) center with concentration dependences and activation parameters indicative of a direct associative pathway. The pyridine and 1-methylimidazole intermediates decay by self-decomposition. However, the THF intermediate decays much faster by oxygen transfer to added PPh(3), the kinetics of which has been studied with double mixing experiments in a cryogenic stopped-flow apparatus. The results show that the decay of the THF intermediate is kinetically controlled by the dissociation of a THF ligand, a conclusion supported by the observation of saturation kinetic behavior with respect to PPh(3), inhibition by added THF, and invariant saturation rate constants for the oxidation of various phosphines. It is proposed that the proximity of the reducing substrate to the peroxide ligand on the diiron coordination sphere facilitates the oxygen-atom transfer. This unique investigation of the reaction of an O(2) adduct of a biomimetic tetracarboxylatodiiron(II,II) complex provides a synthetic precedent for understanding the electrophilic reactivity of like adducts in the active sties of nonheme diiron enzymes.     

Rubidium dimolybdate,Rb2Mo2O7, and caesium dimolybdate,Cs2Mo2O7

The crystal structures of dirubidium hepta­oxodimolybdate, Rb₂Mo₂O₇, and dicaesium hepta­oxodimolybdate, Cs₂Mo₂O₇, in the space groups Ama2 and P2₁/c, respectively, have been determined for the first time by single‐crystal X‐ray diffraction. The structures represent two novel structure types of monovalent ion dimolybdates, A₂Mo₂O₇ (A = alkaline elements, NH₄, Ag or Tl). In the structure of Rb₂Mo₂O₇, Mo atoms are on a twofold axis, on a mirror plane and in a general position. One of the Rb atoms lies on a twofold axis, while three others are on mirror planes. Two O atoms attached to the Mo atom on a mirror plane are located on the same plane. Rubidium dimolybdate contains a new kind of infinite Mo–O chain formed from linked MoO₄ tetra­hedra and MoO₆ octa­hedra alternating along the a axis, with two terminal MoO₄ tetra­hedra sharing corners with each octa­hedron. The chains stack in the [001] direction to form channels of an approximately square section filled by ten‐coordinate Rb ions. Seven‐ and eight‐coordinate Rb atoms are located between chains connected by a c translation. In the structure of Cs₂Mo₂O₇, all atoms are in general positions. The MoO₆ octa­hedra share opposite corners to form separate infinite chains running along the c axis and strengthened by bridging MoO₄ tetra­hedra. The same Mo–O polyhedral chain occurs in the structure of Na₂Mo₂O₇. Eight‐ to eleven‐coordinate Cs atoms fill the space between the chains. The atomic arrangement of caesium dimolybdate has an ortho­rhom­bic pseudosymmetry that suggests a possible phase transition P2₁/c→Pbca at elevated temperatures.     

Heats of formation of [2.2]paracyclophane-1-ene and [2.2]paracyclophane-1,9-diene - an experimental study

The enthalpies of formation [Delta(g)] of tricyclo[8.2.2.2(4,7)]hexadeca-1(13),2,4(16),5,7(15),10(14),11-heptaene (2, 1,2-dehydro[2.2]paracyclophane or [2.2]paracyclophane-1-ene) and tricyclo[8.2.2.2(4,7)]hexadeca-1(13),2,4(16),5,7(15),8,10(14),11-octaene (3, 1,2,9,10-dehydro[2.2]paracyclophane or [2.2]paracyclophane-1,9-diene) have been determined by measuring their heats of combustion in a microcalorimeter and their heats of sublimation by the transpiration method. Values of the strain energies (SE) [SE(2) = 34.7 kcal mol(-)(1), SE(3) = 42.0 kcal mol(-)(1)] have been derived from the gas-phase heats of formation and are compared with those from MM3 and PM3 calculations and with the corresponding value SE(1) = 30.1 kcal mol(-)(1) for the parent tricyclo[8.2.2.2(4,7)]hexadeca-1(13),4(16),5,7(15),10(14),11-hexaene (1, [2.2]paracyclophane). The higher strain energies of 2 and 3 (by 4.6 and 11.9 kcal mol(-)(1)) are in accord with the well-known increased reactivities of their aromatic rings as a consequence of their increased bending. As revealed by an X-ray crystal structure analysis, the bending in the monoene 2 corresponds to that of 1 and 3 at one of two bridging corners.     

TeSe3]2- and [TeSe2]2- as synthons

The [Au2(TeSe2)2]2- anion has been prepared from the reaction of [TeSe3]2- with AuCN in DMF in the presence of PEt3 and from the reaction of [TeSe2]2- with AuCN in DMF. Reaction of [TeSe2]2- with AuCN in DMF in the presence of PEt3 leads ultimately to the [Au2(Te2)2]2- anion.     

Redetermination of hexa­carbonyl­(η5‐cyclo­penta­dienyl)­bis(μ3‐selenido)­diiron(II)­cobalt(II)

The structure of the title compound, hexa­carbonyl‐1κ³C,2κ³C‐[3(η⁵)‐cyclo­penta­dienyl]­bis(μ₃‐selenido)­diiron(II)­cobalt(II),[CoFe₂(μ₃‐Se)₂(C₅H₅)(CO)₆], was redetermined at room temperature and the correct C2/c space group was assumed instead of the previously reported P space group [Mathur et al. (1995). Organometallics, 14 , 2115–2118]. Analysis of the literature data showed that the previously reported triclinic parameters correspond to a primitive subcell of the actual monoclinic C‐centred cell with cell dimensions close to those found by us. The title compound appeared to be isostructural with the sulfur–selenium analogue.     

Non-trivial behavior of palladium(II) acetate

Reaction of activated palladium metal with a HNO3/acetic acid mixture produces both orange Pd3(OAc)6, 1, and purple Pd3(OAc)5(NO2), 2. Compound has a trinuclear structure derived from that of the well-known triangular complex 1 in which one acetate group has been replaced by a nitrite group which is bonded to one palladium atom by the nitrogen atom and to another Pd atom using one of the oxygen atoms. Highly pure 1 can be made by continuous removal of the nitric oxides from the reaction mixture using a flow of N2. 1H NMR spectra of solutions of 1 in CDCl3 and C6D6 show several signals of various intensities when a small amount of water is present in the deuterated solvents but only one signal when the solvents are thoroughly dried. These results are consistent with the occurrence of one or more hydrolysis processes when the solvents contain water and suggest that hypotheses about various [Pd(OAc)2]n aggregates that have previously been brought forward in the literature to explain the complexity of the spectrum of 1 are unnecessary, especially for nonpolar solvents. Compound 2 does not hydrolyze, and in wet or dried solvents shows a 1H NMR spectrum that consists of five equal-intensity signals due to the five nonequivalent acetate groups.     

Reactions of CF3-enones with ethyl nitroacetate and nitromethane: synthesis of CF3-γ-nitroketones

Reactions of α,β-unsaturated CF₃-ketones with nitromethane and ethyl nitroacetate have been investigated. We found that α,β-unsaturated trifluoromethylketones react with ethyl nitroacetate in the presence of calcinated potassium fluoride to form two classes of 1,4-conjugated addition products: CF₃-γ-nitroketones and 6,6,6-trifluoro-2-nitro-5-oxohexanoates in nearly quantitative yields. The products obtained are precursors for CF₃-pyrrolidine synthesis.     

Synthesis of the branched-chain sugar aceric acid: a unique component of the pectic polysaccharide rhamnogalacturonan-II

Described herein is the synthesis of 3-C-carboxy-5-deoxy-L-xylose (aceric acid), a rare branched-chain sugar found in the complex pectic polysaccharide rhamnogalacturonan-II. The key synthetic step in the construction of aceric acid was the stereoselective addition of 2-trimethylsilyl thiazole to 5-deoxy-1,2-O-isopropylidene-alpha-L-erythro-pentofuran-3-ulose (2), which was prepared from L-xylose. The thiazole group was efficiently converted into the required carboxyl group via conventional transformations. Aceric acid was also synthesized by dihydroxylation of a 3-C-methylene derivative of 2 followed by oxidation of the resulting hydroxylmethyl group. The C-2 epimer of aceric acid was also synthesized using thiazole addition chemistry, starting from L-arabinose.     

Preparation,structures, and redox and emission characteristics of the isothiocyanate complexes of hexarhenium(III) clusters [Re6(mu3-E)8(NCS)6]4- (E = S,Se)

Hexarhenium(III) complexes with terminal isothiocyanate ligands, [(n-C(4)H(9))(4)N](4)[Re(6)(mu(3)-S)(8)(NCS)(6)] (1) and (L)(4)[Re(6)(mu(3)-Se)(8)(NCS)(6)] (L(+) = PPN(+) (2a), (n-C(4)H(9))(4)N(+) (2b)), have been prepared by three different methods. Complex 1 was prepared by the reaction of [(n-C(4)H(9))(4)N](4)[Re(6)(mu(3)-S)(8)Cl(6)] with molten KSCN at 200 degrees C, while 2b was obtained by refluxing the chlorobenzene-DMF (2:1 v/v) solution of [Re(6)(mu(3)-Se)(8)(CH(3)CN)(6)](SbF(6))(2) and [(n-C(4)H(9))(4)N]SCN. The [Re(6)(mu(3)-Se)(8)(NCS)(6)](4)(-) anion was also obtained from a mixture of Cs(2)[Re(6)(mu(3)-Se)(8)Br(4)] and KSCN in C(2)H(5)OH by a mechanochemical activation at room temperature for 20 h and isolated as 2a. The X-ray structures of 1 and 2a.4DMF have been determined (1, C(70)H(144)N(10)S(14)Re(6), monoclinic, space group P2(1)/n (No. 14), a = 14.464(7) A, b = 22.059(6) A, c = 16.642(8) A, beta = 113.62(3) degrees, V = 4864(3) A(3), Z = 2; 2a.4DMF, C(162)H(144)N(14)O(4)P(8)S(6)Se(8)Re(6), triclinic, space group P1 (No. 2), a = 15.263(2) A, b = 16.429(2) A, c = 17.111(3) A, alpha = 84.07(1) degrees, beta = 84.95(1) degrees, gamma = 74.21(1) degrees, V = 4098.3(8) A(3), Z = 1). All the NCS(-) ligands in both complexes are coordinated to the metal center via nitrogen site with the Re-N distances in the range of 2.07-2.13 A. The redox potentials of the reversible Re(III)(6)/Re(III)(5)Re(IV) process in acetonitrile are +0.84 and +0.70 V vs. Ag/AgCl for [Re(6)(mu(3)-S)(8)(NCS)(6)](4)(-) and [Re(6)(mu(3)-Se)(8)(NCS)(6)](4)(-), respectively, which are the most positive among the known hexarhenium complexes with six terminal anionic ligands. The complexes show strong red luminescence with the emission maxima (lambda(max)/nm), lifetimes (tau(em)/micros), and quantum yields (phi(em)) being 745 and 715, 10.4 and 11.8, and 0.091 and 0.15 for 1 and 2b, respectively, in acetonitrile. The data reasonably well fit in the energy-gap plots of other hexarhenium(III) complexes. The temperature dependence of the emission spectra and tau(em) of 1 and [(n-C(4)H(9))(4)N](4)[Re(6)(mu(3)-S)(8)Cl(6)] are also reported.