Characterization of a single molecule DNA switch in free solution

We have studied a donor-acceptor fluorophore-labeled DNA switch where the acceptor is Alexa-647, a carbocyanine dye, in solution at the single molecule level to elucidate the fluorescence switching mechanism. The acceptor, which is in an initial high fluorescence trans state, undergoes a photoisomerization reaction resulting in two additional states during its sub-millisecond transit across the probe volume. These two states are assigned to a nonfluorescent triplet trans state that strongly quenches the donor emission and a singlet cis state that blocks the fluorescence resonance energy transfer (FRET) pathway and gives rise to donor-only fluorescence. The formation of these states is faster than the transit time, so that all three states are approximately equally populated under our experimental conditions. The acceptor dye can stick to the DNA in all these states, with the rate of unsticking determining the rate of isomerization into the other states. Measurement of the rate of change of the FRET signal therefore provides information about the fluorophore-DNA intramolecular dynamics. These results explain the large zero peak in the proximity ratio, often seen in single molecule FRET experiments, and suggest that photoinduced effects may be important in single molecule FRET experiments using carbocyanine dyes. They also suggest that for fast photoinduced switching the interactions of the acceptor dye with the DNA and other surfaces should be prevented.     

Template-directed synthesis of mechanically interlocked molecular bundles using dynamic covalent chemistry

Mixing the dipyrido[24]crown-8 derivatives carrying one or two formyl group(s) on the 4 position(s) of their pyridine ring(s) with a 3-fold symmetrical trisammonium ion template in a 3:1 ratio in CD3NO2 results in the formation of thermodynamically stable [4]pseudorotaxanes which, upon addition of a 1,3,5-trisaminobenzene cap, form mechanically interlocked molecular bundles with one and two caps, respectively, by virtue of dynamic imine bond formation.     

Radiolysis of Aqueous Solutions of Benzoate Ion: A Radiation Chemistry Experiment for Undergraduates

This investigation describes the chemical effects of ionizing radiation on dilute aqueous solutions of benzoate ion. We have composed an experimental procedure that allows undergraduate chemistry students to identify and to quantitatively determine the amount of the products that are produced. The student investigators determine the absorbed dose that a sample receives when exposed to a ⁶⁰Co source, irradiate dilute aqueous solutions of benzoate ion, and analyze the resulting mixture of hydroxybenzoate ions using high-performance liquid chromatography. The radiolysis of dilute solutions of benzoate ion results in the formation of a mixture of ortho-, meta-, and para-hydroxybenzoate ions that are readily separated on a C₁₈ -Bondapak column. By the use of appropriate calibration curves, the yield (G values) of each of the isomers may be determined and compared.This paper was presented at the 15th Biennial Conference on Chemical Education, Waterloo, Ontario, Canada, August 1998 by N. Zevos and at the 26th Northeast Regional Meeting of the American Chemical Society by Evon Powell.     

Inert site in a protein zinc cluster: isotope exchange by high resolution mass spectrometry

Using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry, we show that one Zn2+ ion in the Zn4 cluster of cyanobacterial metallothionein is inert to exchange with 67Zn2+. We suggest that this is zinc in site A, which together with the surrounding alpha and beta secondary structure forms a zinc-finger fold.     

The Extraction of Polycyclic Aromatic Hydrocarbons from Atmospheric Particulate Matter Samples by Accelerated Solvent Extraction (ASE)

Abstract

The Accelerated solvent extraction (ASE) of PAHs (23 2- to 6-ring species) spiked onto glass fibre filters (GFFs) was studied as a function of variable extraction solvents, pressure, temperature and extraction times. Acceptable recoveries (85% ± 15%) were obtained for certain combinations of conditions and a tentative method (1500 psi, 150°C, 70:30 hexane:acetone mixture, 7 min heat-up time, 5 min static extraction time, 60% flush volume, 2 static cycles was selected for further testing. However, this method did not prove as effective as the traditional Soxhlet method of extraction when these parameters were used to extract native PAHs from ambient atmospheric particulate matter collected on a GFF by Integrated Atmospheric Deposition Network (IADN) sampling protocols. The extraction recovery study for spiked GFFs was repeated using slightly different extraction conditions: 2000 psi, 100°C, 70:30 hexane:acetone, 5 min heat-up time, 5 min static extraction time, 150% flush volume, 3 static cycles. When this method was applied to the extraction of native PAHs from ambient atmospheric particulate matter collected on GFFs, the results showed equivalent or better recoveries to that of the Soxhlet method. The total time of extraction was 25 min requiring only 30 mL of solvent. This ASE method is presently used to quantitatively determine PAHs in IADN particle-phase samples.     

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.     

Prototype reflectivity analyses of hydrogen storage levels in single-walled carbon nanotubes

A prototype case study is presented that examines the level of hydrogen content in H-SWNTs using the Surface Plasmon Resonance technique. The damping effect and the angular shift in the resonance minimum of an SWNT-gold interface due to the presence of hydrogen is analyzed using a parametric model, which is based on the concept of an effective permittivity. The new approach provides for a non-invasive analysis of the level of hydrogen content in H-SWNTs and is potentially extendable to other carbon-based hydrogen storage materials.     

The use of comet assay data with a simple reaction mechanism to evaluate the relative effectiveness of free radical scavenging by quercetin, epigallocatechin gallate and N-acetylcysteine in UV-irradiated MRC5 lung fibroblasts

Comet assay data (tail DNA %) have been gathered for the concentration dependent role of three antioxidants (AOs); quercetin (Q), epigallocatechin gallate (EGCG) and N-acetylcysteine (NAC) in reducing UV-induced damage to DNA in normal fetal lung fibroblasts (MRC5). All three compounds demonstrate a concentration dependent reduction maximum with a pro-oxidant effect at higher (though not cytotoxic) concentrations. Manipulation of a simple 4-step reaction mechanism for free radical (FR) scavenging by AOs produced rate constant ratios which allowed the relative effectiveness (Q > EGCG > NAC) of the AOs to be evaluated.     

Headgroup effect on silane structures at buried polymer/silane and polymer/polymer interfaces and their relations to adhesion

Sum frequency generation (SFG) vibrational spectroscopy was used to study the effect of silane headgroups on the molecular interactions that occur between poly(ethylene terephthalate) (PET) and various epoxy silanes at the PET/silane and PET/silicone interfaces. Three different silanes were investigated: (3-glycidoxypropyl) trimethoxysilane (γ-GPS), (3-glycidoxypropyl) methyl-dimethoxysilane (γ-GPMS), and (3-glycidoxypropyl) dimethyl-methoxysilane (γ-GPDMS). These silanes share the same backbone and epoxy end group but have different headgroups. SFG was used to examine the interfaces between PET and each of these silanes, as well as silanes mixed with methylvinylsiloxanol (MVS). We also examined the interfaces between PET and uncured or cured silicone with silanes or silane-MVS mixtures. Silanes with different headgroups were found to exhibit a variety of methoxy group interfacial segregation and ordering behaviors at various interfaces. The effect of MVS was also dependent upon silane headgroup choice, and the interfacial molecular structures of silane methoxy headgroups were found to differ at PET/silane and PET/silicone interfaces. Epoxy silanes have been widely used as adhesion promoters for polymer adhesives; therefore, the molecular structures probed using SFG were correlated to adhesion testing results to understand the molecular mechanisms of silicone-polymer adhesion. Our results demonstrated that silane methoxy headgroups play important roles in adhesion at the PET/silicone interfaces. The presence of MVS can change interfacial methoxy segregation and ordering, leading to different adhesion strengths.