High-efficiency fluorescence quenching of conjugated polymers by proteins

The fluorescence of the water-soluble anionic conjugated polymer, poly[lithium 5-methoxy-2-(4-sulfobutoxy)-1,4-phenylenevinylene] (MBL-PPV), is quenched in dilute aqueous solution by cytochrome c, a small, naturally occurring electron-transfer protein. The large value obtained for the Stern-Volmer constant (K(sv) = 3.2 x 10(8) at pH 7.4, and approximately 10(9) in acidic solutions) is attributed to a combination of two factors: (1) facile ET between the luminescent semiconducting polymer and the protein and (2) the Columb attraction between the oppositely charged polyelectrolytes. This system shows significant potential for biosensor applications.     

Comparison of microbial receptor assay and liquid chromatography for determination of penicillin G and amoxicillin in milk powder

A microbial receptor assay (Charm II Tablet Beta-Lactam Test) and liquid chromatography (LC) were compared for determination of penicillin G (PG) and amoxicillin (AMOX) in reconstituted milk powder. Nonfat dry milk and whole dry milk were reconstituted (10%, w/v) to concentrations of 0, 2.5, 5, 7.5, and 10 ppb PG; nonfat dry milk was reconstituted (10%, w/v) to 0, 7.5, 10, and 15 ppb AMOX. Reconstituted samples were analyzed blindly by each method. Concentrations determined by both methods demonstrated good agreement. A significant difference between methods (p < or = 0.05) was observed only for 7.5 ppb PG in defatted dry milk. Significant differences were not observed between known concentrations and concentrations determined by the Charm II assay for PG or AMOX in defatted dry milk and PG in whole dry milk. Results by LC showed significant differences (p < 0.05) between known and measured concentrations at 10 ppb PG in both milks and 0 ppb AMOX in defatted dry milk. These results suggest that both the microbial receptor assay and LC may be useful for determination of PG and AMOX near safe level and tolerance, respectively, in reconstituted milk powder.     

Rearrangement of epoxynitriles: a convenient homologation of acyclic and cyclic ketones to carboxylic acids

A convenient two-step homologation of both aliphatic and aromatic ketones to the corresponding carboxylic acid has been developed. First ketones were converted to epoxynitriles with the Darzens reaction. Second, a Lewis acid mediated rearrangement of these epoxynitriles with lithium bromide was achieved to give homologated secondary alkanoic acids (as well as aryl-alkanoic) in good yields. The mechanism and the scope of the rearrangement reaction were investigated. This strategy constitutes a two-step homologation of ketones to secondary carboxylic acids.     

A novel interface for variable flow nanoscale LC/MS/MS for improved proteome coverage

A variable flow "peak trapping" liquid chromatography (LC) interface has been developed for the coupling of nanoscale LC to electrospray ionization mass spectrometry (ESI-MS). The presented peak trapping LC interface allows for the extended analysis time of co-eluting compounds and has been employed for the identification of proteins via tandem mass spectrometry (MS/MS). The variable flow process can be controlled either manually or in a completely automated manner where the mass spectrometer status determines the status of the variable flow interface. When the mass spectrometer operates in MS survey mode, the interface is operated in a so-called "high-flow" mode. Alternatively, the interface is operated in a "low-flow" mode during MS/MS analysis. In the "high-flow" mode of the variable flow process the column flow rate is typically around 200 nL/min, whereas in the "low-flow" mode the column effluent is introduced into the source of the mass spectrometer at 25 nL/min. In addition to the flow reduction during MS/MS analysis, the gradient is paused to preserve the peptide separation on the analytical nanoscale LC column. The performance of the variable flow nanoscale LC/MS/MS interface is demonstrated by the automated analysis of standard peptide mixtures and protein digests utilizing variable flow, data-dependent scanning MS/MS techniques, and automated database searching.     

Fermentation of “Quick Fiber” produced from a modified corn-milling process into ethanol and recovery of corn fiber oil

Approximately 9% of the 9.7 billion bushels of corn harvested in the United States was used for fuel ethanol production in 2002, half of which was prepared for fermentation by dry grinding. The University of Illinois has developed a modified dry grind process that allows recovery of the fiber fractions prior to fermentation. We report here on conversion of this fiber (Quick Fiber [QF]) to ethanol. QF was analyzed and found to contain 32%wt glucans and 65%wt total carbohydrates. QF was pretreated with dilute acid and converted into ethanol using either ethanologenic Escherichia coli strain FBR5 or Saccharomyces cerevisiae. For the bacterial fermentation the liquid fraction was fermented, and for the yeast fermentation both liquid and solids were fermented. For the bacterial fermentation, the final ethanol concentration was 30 g/L, a yield of 0.44 g ethanol/g of sugar(s) initially present in the hydrolysate, which is 85% of the theoretical yield. The ethanol yield with yeast was 0.096 gal/bu of processed corn assuming a QF yield of 3.04 lb/bu. The residuals from the fermentations were also evaluated as a source of corn fiber oil, which has value as a nutraceutical. Corn fiber oil yields were 8.28%wt for solids recovered following prtetreatment.     

Electrochemistry and Spectroscopy of Sulfate Complexes of (Tetraphenylporphyrinato)manganese

The electrochemical and spectroscopic properties of [Mn₂(tpp)₂(SO₄)] (H₂tpp=tetraphenylporphyrin=5,10,15,20‐tetraphenyl‐21H,23H‐porphine) were studied to characterize the stability of this compound as a function of solvent, redox state, and sulfate concentration. In non‐coordinating solvents such as 1,2‐dichloroethane, the dimer was stable, and two cyclic voltammetric waves were observed in the region for Mn^III reduction. These waves correspond to reduction of the dimer to [Mn^II(tpp)] and [Mn^III(tpp)(OSO₃)]^?, and reduction of [Mn^III(tpp)(OSO₃)]^? to [Mn^II(tpp)(OSO₃)]^2?, respectively. In the coordinating solvent DMSO, [Mn₂(tpp)₂(SO₄)] was unstable and dissociated to form [Mn^III(tpp)(DMSO)₂]⁺. A single voltammetric wave was observed for Mn^III reduction in this solvent, corresponding to formation of [Mn^II(tpp)(DMSO)]. In non‐coordinating solvent systems, addition of sulfate (as the bis(triphenylphosphoranylidene)ammonium (PPN⁺) salt) resulted in dimer dissociation, yielding [Mn^III(tpp)(OSO₃)]^?. Reduction of this monomer produced [Mn^II(tpp)(OSO₃)]^2?. In DMSO, addition of SO led to displacement of solvent molecules forming [Mn^III(tpp)(OSO₃)]^?. Reduction of this species in DMSO led to [Mn^II(tpp)(DMSO)].     

An experimental study of chromatographic dynamics in open and packed non-cylindrical conduits

A systematic investigation of the influence of the perimeter shape of open and particle packed fused silica capillaries on chromatographic properties such as resistance to flow and dispersion of solutes propelled through these channels has been conducted. Verifications of these uncommon experiments with existing theoretical treatments are presented and the insights transferred to a novel polymer chip design with integrated facilities for complex separations. A comparison of the chromatographic performance of a real life proteomics sample on this chip with a capillary column of "similar" dimensions is presented.     

Two-, three-, and four-coordinate Ag(I) coordination polymers formed by the novel phosphinite PPh2(3-OCH2C5H4N)

The novel phosphinite PPh(2)(3-OCH(2)C(5)H(4)N) (1) has been synthesized, and its coordination properties to Ag(I) have been studied. When reacted in a 1:1 ratio with Ag(I), coordination polymers with different coordination numbers about the Ag are found depending on the anion. For PPh(2)(3-OCH(2)C(5)H(4)N)AgBF(4) (2), a two-coordinate Ag is observed with a P-Ag-N angle of 167 degrees. Mixed three and four coordination about Ag is observed for PPh(2)(3-OCH(2)C(5)H(4)N)AgOTf (3), and for the trifluoroacetate derivative, PPh(2)(3-OCH(2)C(5)H(4)N)Agtfa (4), only a four-coordinate Ag is produced. X-ray crystal-structure determinations for compounds 2-4 have been carried out. The X-ray structures show a wide range of Ag-Ag distances in the polymers, which are dependent on the conformation of the bridging ligand.     

NMR and UV studies of 3'-S-phosphorothiolate modified DNA in a DNA : RNA hybrid dodecamer duplex; implications for antisense drug design

High-resolution NMR spectroscopy has been used to establish the conformational consequences of the introduction of a single 3[prime or minute]-S-phosphorothiolate link in the DNA strand of a DNA : RNA hybrid. These systems are of interest as potential antisense therapeutic agents. Previous studies on similarly modified dinucleotides have shown that the conformation of the sugar to which the sulfur is attached shifts to the north (C(3[prime or minute])-endo/C(2[prime or minute])-exo). Comparisons made between NOESY cross-peak intensities, and coupling constants from PE-COSY spectra, for both non-modified and modified duplexes confirm that this conformational shift is also present in the double helical oligonucleotide system. In addition it is noted that in both the dinucleotides and the modified duplex, the conformation of the sugar ring 3[prime or minute] to the site of modification is also shifted to the north. That this pattern is observed in the small monomeric system as well as the larger double helix is suggestive of some pre-ordering of the sequences. The conclusion is supported by consideration of the (1)H chemical shifts of the heterocyclic bases near the site of the modification. The enhanced stability that these conformational changes should bring was confirmed by UV thermal melting studies. Subsequently a series of singly and doubly 3[prime or minute]-S-phosphorothiolate-modified duplexes were investigated by UV. The results are indicative of an additive effect of the modification with thermodynamic benefit being derived from alternate spacing of two modified linkers.     

Targeting apoptosis via chemical design: inhibition of bid-induced cell death by small organic molecules

Bid is a key member of the Bcl-2 family proteins involved in the control of the apoptotic cascade in cells, leading to cell death. Uncontrolled cell death is associated with several human pathologies, such as neurodegenerative diseases and ischemic injuries. Therefore, Bid represents a potential yet unexplored and challenging target for strategies aimed at the development of therapeutic agents. Here we show that a multidisciplinary NMR-based approach that we named SAR by ILOEs (structure activity relationships by interligand nuclear Overhauser effect) allowed us to rationally design a series of 4-phenylsulfanyl-phenylamine derivatives that are capable of occupying a deep hydrophobic crevice on the surface of Bid. These compounds represent the first antiapoptotic small molecules targeting a Bcl-2 protein as shown by their ability to inhibit tBid-induced SMAC release, caspase-3 activation, and cell death.