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.     

Isoindole Cycloadditions. Part III: The Synthesis of "Windscreen Wiper" and Other N-Bridged Cavity Systems

The thermal addition of N-carbobenzyloxyisoindole (N-Z isoindole) 11a, generated by the reaction of 3,6-di(2-pyridyl)-s-tetrazine 9 with N-Z 7-azabenzonorbornadiene 8a, onto dimethyl tricyclo[4.2.1.0^2.5]nona-3,7-diene-3,4-dicarboxylate 17 occurred site selectively at the cyclobutene -bond to form a stereoisomeric mixture of 1 : 1-adducts 18 and 19, in which the bent-frame isomer 19 was dominant (ratio 5 : 1). In contrast, N-benzyl tetrafluoroisoindole 11c reacted with 17 only under high-pressure conditions (14 kbar, RT, 4 days) to afford 1 : 1-adducts at the cyclobutene site, in which the extended-frame isomer 18c was dominant and the accompanying bent-frame product 19c reverted to starting materials soon after isolation. These same stereoselectivities were used to prepare "windscreen wiper" compound 28c having two mobile N-benzyl substituents attached to a rigid scaffold by the reaction of N-benzyl tetrafluoroisoindole 11c with tetramethyl tetracyclo[4.4.1.0.^2,5.0^7.10]undeca-3,8-diene-3,4,7,8-tetracarboxylate 23. Cavity bis-(cyclobutene-1,2-diester) 6 reacted with N-benzyl tetrafluoroisoindole 11c twice over to produce cavity structure 36 with two O- and two N-benzyl bridges on the inner face, whereas the narrower cavity bis-alkene 32 stopped at the 1 : 1-addition stage. The dynamics of the Z-group in the dual adducts 26a–28a are discussed briefly and key adducts and cavity systems have been structurally evaluated by X-ray crystallography, VT NMR, and molecular modeling.     

Synthesis and characterization of the new 22-π aromatic furan-containing macrocycle, “ozaphyrin”

The new 22-π, aromatic “pentaplanar” macrocycle, ozaphyrin ( 6 ), has been synthesized by a McMurry coupling of 5,5′-diformyl-4,4′-dipropyl-2,2′-bipyrrole ( 1 ) with 2,5-bis(5-formyl-4-propyl-2-pyrrolyl)furan ( 5 ). This synthetic pathway to ozaphyrin and its characterization by ¹H nmr spectroscopy, uv-visible spectroscopy, cyclic voltammetry, and X-ray crystallography are described. The structure consists of layers of planar, staggered macrocycles stacked perpendicular to the α-axis. Ozaphyrin crystallizes with four formula units in the monoclinic space group C⁵_2h-P2₁/n in a cell of dimensions a = 10.481(7) Å, b = 17.353(17) Å, c = 18.726(12) Å, and β = 102.84(5)° (108 K). The structure has been refined on F² (5171 unique reflections, 411 variables) to R_w(F_o²) = 0.165. The conventional agreement index R(F) is 0.074 for the 3289 reflections have F_o²>2o(F_o²).     

Determination of retinyl palmitate (vitamin A) in fortified fluid milk by liquid chromatography: collaborative study

A liquid chromatographic (LC) method was developed for fast and simple measurement of retinyl palmitate (vitamin A) in fortified milk. Retinyl acetate internal standard was added to a test portion of milk followed by extraction into hexane. The hexane extract was analyzed by LC using a normal-phase silica gel column equilibrated with mobile phase (conditioned hexane-isopropanol, 99.85 + 0.15, v/v) about 1 h before injections. The retinyl palmitate concentration was calculated by using a relative response factor determined with calibration standards. In the collaborative study, 11 laboratories analyzed 13 pairs of fluid milk materials in blind duplicate. Twelve of the materials were composed of skim milk (< 0.5% fat), 1% fat milk, 2% fat milk, and 1% fat chocolate milk. Each material was fortified at 3 concentrations of retinyl palmitate of approximately 581 microg/L (1000 IU/qt), 1163 microg/L (2000 IU/qt), and 2236 microg/L (4000 IU/qt). The 13th material, unfortified skim milk, served as a matrix blank. Repeatability standard deviations (RSDr) without outliers ranged from 1.5 to 5.7% and reproducibility standard deviations (RSDR) without outliers ranged from 5.0 to 22.7%. cis-Isomers co-eluted with the predominant trans-retinyl palmitate isomer and were included in the results reported by all the collaborative laboratories. Endogenous long-chain esters from milk fat were also measured with the retinyl palmitate additive. The Study Director recommends that this method for determination of retinyl palmitate in fluid milk by LC be adopted First Action.     

Five-coordinate Fe(III)NO and Fe(II)CO porphyrinates: where are the electrons and why does it matter?

Recent years have seen dramatic growth in our understanding of the biological roles of nitric oxide (NO). Yet, the fundamental underpinnings of its reactivities with transition metal centers in proteins and enzymes, the stabilities of their structures, and the relationships between structure and reactivity remains, to a significant extent, elusive. This is especially true for the so-called ferric heme nitrosyls ([FeNO](6) in the Enemark-Feltham scheme). The Fe-CO and C-O bond strengths in the isoelectronic ferrous carbonyl complexes are widely recognized to be inversely correlated and sensitive to structural, environmental, and electronic factors. On the other hand, the Fe-NO and N-O bonds in [FeNO](6) heme complexes exhibit seemingly inconsistent behavior in response to varying structure and environment. This report contains resonance Raman and density functional theory results that suggest a new model for FeNO bonding in five-coordinate [FeNO](6) complexes. On the basis of resonance Raman and FTIR data, a direct correlation between the nu(Fe)(-)(NO) and nu(N)(-)(O) frequencies of [Fe(OEP)NO](ClO(4)) and [Fe(OEP)NO](ClO(4)).CHCl(3) (two crystal forms of the same complex) has been established. Density functional theory calculations show that the relationship between Fe-NO and N-O bond strengths is responsive to FeNO electron density in three molecular orbitals. The highest energy orbital of the three is sigma-antibonding with respect to the entire FeNO unit. The other two comprise a lower-energy, degenerate, or nearly degenerate pair that is pi-bonding with respect to Fe-NO and pi-antibonding with respect to N-O. The relative sensitivities of the electron density distributions in these orbitals are shown to be consistent with all published indicators of Fe-N-O bond strengths and angles, including the examples reported here.     

Component B binding to the soluble methane monooxygenase hydroxylase by saturation-recovery EPR spectroscopy of spin-labeled MMOB

Spin-labeled Cys89 of the soluble methane monooxygenase regulatory protein (MMOB) from Methylococcus capsulatus (Bath) binds within 15 +/- 4 A of the hydroxylase (MMOH) diiron center, placing the MMOB docking site in the MMOH "canyon" region on iron-coordinating helices E and F of the alpha-subunit.     

Ab initio MRD-CI calculations for breaking a chemical bond in a molecule in a crystal or other solid environment. III. Me2N?NO2 decomposition of dimethylnitramine in a large crystalline environment

Recently we extended our strategy for MRD-CI (multireference double excitation-configuration interaction) calculations, based on localized/local orbitals and an “effective” CI Hamiltonian, for molecular decompositions of large molecules to breaking a chemical bond in a molecule in a crystalline or other solid environment. Our technique begins with an explicit quantum chemical SCF calculation for a reference molecule surrounded by a number of other molecules in the multipole environment of more distant neighbors. The resulting canonical molecular orbitals are then localized, and the localized occupied and virtual orbitals in the region of interest are included explicitly in the MRD-CI with the remainder of the occupied localized orbitals being folded into an “effective” CI Hamiltonian. The MRD-CI calculations are then carried out for breaking a bond in the reference molecule. This method is completely general in that the space treated explicitly, as well as the surrounding space, may contain voids, defects, deformations, dislocations, impurities, dopants, edges and surfaces, boundaries, etc. Dimethylnitramine is the smallest prototype of the energetic R₂N—NO₂ nitramines, such as the 6-member ring RDX or the 8-member ring HMX. Decomposition of energetic compounds is initiated in the solid by a breaking of the target bond. Thus, it is crucial to know the difference in energy between breaking a bond in an isolated energetic molecule versus in the molecule in a solid. In the present study, we have carried out MRD-CI calculations for the Me₂N—NO₂ dissociation of dimethylnitramine in a dimethylnitramine crystal. The cases we investigated were one dimethylnitramine molecule (surrounded by 53 and 685 neighboring dimethylnitramine molecules represented by multipoles), three dimethylnitramine molecules, and three dimethylnitramine molecules (surrounded by 683 neighbors). All multipoles were cumulative atomic multipoles up through quadrupoles. The MRD-CI calculations on dimethylnitramine required large numbers of reference configurations from which were allowed all single and double excitations.     

Copper(II) and nickel(II) complexes of 2-formylpyridine 3-piperidinyl-, 3-hexamethyleneiminyl- and 3-azabicyclo[3.2.2]nonylthiosemicarbazones

Summary Copper(II) and nickel(II) complexes of 2-formylpyridine 3-piperidinyl-, 3-hexamethyleneiminyl- and 3-azabicyclo-[3.2.2]nonylthiosemicarbazones were prepared and characterized spectroscopically. ¹H and ¹³C n.m.r. spectra of the thiosemicarbazones and a diamagnetic nickel(II) complex are reported, together with i.r., electronic and e.s.r. spectra of the metal complexes. The thiosemicarbazones and their copper(II) and nickel(II) complexes exhibit considerable growth inhibitory activity against Paecilomyces variotii, but show minimal activity against Aspergillus niger.