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.     

Hyperoxygenation enhances the tumor cell killing of photofrin-mediated photodynamic therapy

Tumor hypoxia, either preexisting or as a result of oxygen depletion during photodynamic therapy (PDT) light irradiation, can significantly reduce the effectiveness of PDT-induced cell killing. To overcome tumor hypoxia and improve tumor cell killing, we propose using supplemental hyperoxygenation during Photofrin-PDT. The mechanism for the tumor cure enhancement of the hyperoxygenation-PDT combination is investigated using an in vivo-in vitro technique. A hypoxic tumor model was established by implanting mammary adenocarcinoma in the hind legs of mice. Light irradiation (200 J/cm2 at either 75 or 150 mW/cm2), under various oxygen supplemental conditions (room air, carbogen, 100% normobaric or hyperbaric oxygen), was delivered to animals that received 12.5 mg/kg Photofrin 24 h before light irradiation. Tumors were harvested at various time points after PDT and grown in vitro for colony formation analysis. Treated tumors were also analyzed histologically. The results show that when PDT is combined with hyperoxygenation, the hypoxic condition could be improved and the cell killing rate at various time points after PDT could be significantly enhanced over that without hyperoxygenation, suggesting an enhanced direct and indirect cell killing associated with high-concentration oxygen breathing. This study further confirms our earlier observation that when a PDT treatment is combined with hyperoxygenation it can be more effective in controlling hypoxic tumors.     

Theoretical study of the spin trapping of hydroxyl radical by cyclic nitrones: a density functional theory approach

The hydroxyl radical (*OH) is an important mediator of biological oxidative stress, and this has stimulated interest in its detection. 5,5-Dimethyl-1-pyrroline N-oxide (DMPO) and its alkoxycarbonyl and alkoxyphosphoryl analogues have been employed as spin traps for electron paramagnetic resonance (EPR) spectroscopic radical detection. Energies of optimized geometries of nitrones and their corresponding *OH adducts were calculated using density functional theory (DFT) at the B3LYP/6-31+G//B3LYP/6-31G level. Calculations predict that the trans adduct formation is favored in alkoxycarbonyl nitrones, while cis adducts with intramolecular H-bonding is favored for alkoxyphosphoryl nitrones. Addition of *OH to a phosphoryl-substituted nitrone is more exoergic than the carbonylated nitrones. Charge and spin densities on the nitrone spin traps were correlated with their rates of addition with *OH, and results show that the charge density on the nitronyl C, the site of *OH addition, is more positive in phosphorylated nitrones compared to DMPO and the alkoxycarbonyl nitrones. The dihedral angle between the beta-H and nitroxyl O bonds is smaller in phosphorylated nitrones, and that aspect appears to account for the longer half-lives of the spin adducts compared to those in DMPO and alkoxycarbonyl nitrones. Structures of nitrones with trifluoromethyl-, trifluoromethylcarbonyl-, methylsulfonyl-, trifluoromethylsulfonyl-, amido-, spiropentyl-, and spiroester substituents were optimized and their energies compared. Amido and spiroester nitrones were predicted to be the most suitable nitrones for spin trapping of *OH due to the similarity of their thermodynamic and electronic properties to those of alkoxyphosphoryl nitrones. Moreover, dimethoxyphosphoryl substitution at C-5 was found to be the most efficient substitution site for spin trapping of *OH, and their spin adducts are predicted to be the most stable of all of the isomeric forms.     

Spectroscopy and reactivity of a photogenerated tryptophan radical in a structurally defined protein environment

Near-UV irradiation of structurally characterized [Re(I)(CO)3(1,10-phenanthroline)(Q107H)](W48F/Y72F/H83Q/Y108W)AzM(II) [Az = Pseudomonas aeruginosa azurin, M = Cu, Zn]/[Co(NH3)5Cl]Cl2 produces a tryptophan radical (W108*) with unprecedented kinetic stability. After rapid formation (k = 2.8 x 106 s-1), the radical persists for more than 5 h at room temperature in the folded ReAzM(II) structure. The absorption spectrum of ReAz(W108*)M(II) exhibits maxima at 512 and 536 nm. Oxidation of K4[Mo(CN)8] by ReAz(W108*)Zn(II) places the W108*/W108 reduction potential in the protein above 0.8 V vs NHE.     

Steric mode of enzymic hydroxylation at primary carbon atoms: Hydroxylation of (1R)- and (1S)-[1-3H, 2H, 1H][1-14C]-octanes by Pseudomonas Oleovorans

(1R)- and (1S) [1-³H, ²H, ¹H]-octanes and mixed with [1-¹⁴C]-octane, were synthesized. The mixed samples were incubated with homogenats of P. oleovorans strain TF4-1L and the biosynthesized mixtures of octanols isolated. It was shown that mainly the achiral termini [-C¹H₃] were hydroxylated and that chiral methyls were oxygenated to the extent of 20–30%. In all instances the products derived from hydroxylation at the chiral methyls [-C-³H, ²H, ¹H] were mixtures of (1R)- and (1S)-octanols, the major component of which was the alcohol obtained by displacement of ¹H. The results indicate that hydroxylation proceeded with a normal isotope effect k_h>k_d>k_t. The amount of (1R)-octanol in the mixtures of octanols derived from (1R)- and (1S)-octane was determined. It was found that the C-1 hydroxylation of octane proceeded with retention, i.e. the incoming hydroxyl assumed the orientation of the displaced hydrogen (or isotopic hydrogen) atom.     

Affinity NMR: decoding DNA binding

We have shown that affinity NMR can be used to edit a NMR spectrum so that ligands that have affinity to DNA can be observed in the presence of other nonbinding molecules. Diffusion encoded spectroscopy (DECODES) can be used to identify the binding ligands. We were able to identify Hoechst 33342 as binding to the Drew-Dickerson dodecamer d(CGCGAATTCGCG)2 in the presence of the nonbinding molecules adenine, adenosine, and thiamine. Affinity NMR appears to be readily applicable to DNA systems for the following reasons. (1) The relaxation rate of the DNA oligonucleotides is favorable, thus the signal intensity loss due to relaxation is not severe. (2) A comparison of the patterns of the DNA cross-peaks upon binding in the two-dimensional total correlation spectroscopy and correlation spectroscopy spectrum are easily performed, and the ligand signals in the two-dimensional DECODES spectrum can be readily identified. (3) The aromatic part of the DNA spectrum is devoid of 2D cross-peaks in these correlation spectra, greatly facilitating the interpretation of the bound ligand in the DECODES spectrum.     

Quantitative analysis of small pharmaceutical drugs using a high repetition rate laser matrix-assisted laser/desorption ionization source

In this work, a high repetition rate laser matrix-assisted laser desorption/ionization (MALDI) source is studied on a quadrupole-time-of-flight (QqTOF) and a triple quadrupole (QqQ) mass spectrometer for rapid quantification of small pharmaceutical drugs. The high repetition rate laser allows an up to 100-fold higher pulse frequency as compared with regular MALDI lasers, resulting in much larger sample throughput and number of accumulated spectra. This increases the reproducibility of signal intensities considerably, with average values being around 5% relative standard deviation after taking into account the area ratio of the analyte to an internal standard. Experiments were conducted in MS/MS mode to circumvent the large chemical background due to MALDI matrix ions in the low mass range. The dynamic range of calibration curves on the QqTOF mass spectrometer extended over at least two orders of magnitude, whereas on the QqQ it extended over at least three orders of magnitude. Detection limits ranged from 60-400 pg/microL on the QqTOF and from 6-70 pg/microL on the QqQ for a series of benzodiazepines. The benzodiazepine content of commercial pill formulations was quantified, and less than 5% error was obtained between the present method and the manufacturer's certified values. Furthermore, a high sample throughput was achieved with this method, so that a single MALDI spot could be quantitatively scanned in as little as 15 s, and an entire 96-well MALDI plate in 24 min.     

Dissociative electron transfer on ionic surfaces

A theory of electron transfer between adsorbed ions and electrically charged ionic surfaces is developed. Electron transfer from a charged AgBr surface to an Ag⁺ ion, as well as from Br^? ion to AgBr surface holes is studied. The Ag and Br atoms resulting from the process are shown to be dissociated from the surface.     

Activation volume measurement for C[bond]H activation. Evidence for associative benzene substitution at a platinum(II) center

The reaction of the platinum(II) methyl cation [(N-N)Pt(CH(3))(solv)](+) (N-N = ArN[double bond]C(Me)C(Me)[double bond]NAr, Ar = 2,6-(CH(3))(2)C(6)H(3), solv = H(2)O (1a) or TFE = CF(3)CH(2)OH (1b)) with benzene in TFE/H(2)O solutions cleanly affords the platinum(II) phenyl cation [(N-N)Pt(C(6)H(5))(solv)](+) (2). High-pressure kinetic studies were performed to resolve the mechanism for the entrance of benzene into the coordination sphere. The pressure dependence of the overall second-order rate constant for the reaction resulted in Delta V(++) = -(14.3 +/- 0.6) cm(3) mol(-1). Since the overall second order rate constant k = K(eq)k(2), Delta V(++) = Delta V degrees (K(eq)) + Delta V(++)(k(2)). The thermodynamic parameters for the equilibrium constant between 1a and 1b, K(eq) = [1b][H(2)O]/[1a][TFE] = 8.4 x 10(-4) at 25 degrees C, were found to be Delta H degrees = 13.6 +/- 0.5 kJ mol(-1), Delta S degrees = -10.4 +/- 1.4 J K(-1) mol(-1), and Delta V degrees = -4.8 +/- 0.7 cm(3) mol(-1). Thus DeltaV(++)(k(2)) for the activation of benzene by the TFE solvento complex equals -9.5 +/- 1.3 cm(3) mol(-1). This significantly negative activation volume, along with the negative activation entropy for the coordination of benzene, clearly supports the operation of an associative mechanism.