Kathryn R. Williams

An Autonomous and Controllable Light‐Driven DNA Walking Device

The development of nanotechnology has been largely inspired by the biological world. The complex, but well-organized, living system hosts an array of molecular-sized machines responsible for information processing, structure building and, sometimes, movement. We present here a novel light-powered DNA mechanical device, which is reminiscent of cellular protein motors in nature, especially those of green plants. This walking device, which is based on pyrene- assisted photolysis of disulfide bonds, is capable of autonomous locomotion, with light control of initiation, termination and velocity. Based on DNA sequence design and such physical conditions as temperature and ionic strength, this photon-fueled DNA walker exhibits the type of operational freedom and mechanical speed that may rival protein motors in the future.

Self-Assembly of a Bifunctional DNA Carrier for Drug Delivery

NIH; National Key Scientific Program of China[2011CB911000]; China National Grand Program on Key Infectious Disease[2009ZX10004-312]; China National Scientific Foundation of China[20805038, 20620130427]; National Basic Research Program of China[2007CB935603, 2010CB732402]

A Logical Molecular Circuit for Programmable and Autonomous Regulation of Protein Activity Using DNA Aptamer-Protein Interactions

Researchers increasingly envision an important role for artificial biochemical circuits in biological engineering, much like electrical circuits in electrical engineering. Similar to electrical circuits, which control electromechanical devices, biochemical circuits could be utilized as a type of servomechanism to control nanodevices in vitro, monitor chemical reactions in situ, or regulate gene expressions in vivo. (1) As a consequence of their relative robustness and potential applicability for controlling a wide range of in vitro chemistries, synthetic cell-free biochemical circuits promise to be useful in manipulating the functions of biological molecules. Here, we describe the first logical circuit based on DNA-protein interactions with accurate threshold control, enabling autonomous, self-sustained and programmable manipulation of protein activity in vitro. Similar circuits made previously were based primarily on DNA hybridization and strand displacement reactions. This new design uses the diverse nucleic acid interactions with proteins. The circuit can precisely sense the local enzymatic environment, such as the concentration of thrombin, and when it is excessively high, a coagulation inhibitor is automatically released by a concentration-adjusted circuit module. To demonstrate the programmable and autonomous modulation, a molecular circuit with different threshold concentrations of thrombin was tested as a proof of principle. In the future, owing to tunable regulation, design modularity and target specificity, this prototype could lead to the development of novel DNA biochemical circuits to control the delivery of aptamer-based drugs in smart and personalized medicine, providing a more efficient and safer therapeutic strategy.

INFRARED MULTIPHOTON DISSOCIATION OF ELECTROSPRAYED CROWN ETHER COMPLEXES

Complexes of 18-crown-6, 15-crown-5, and 12-crown-4 with Na+, K+, Rb+, Cs+ and H3O+ were observed and characterized using infrared multiphoton dissociation (IRMPD) in conjunction with Fourier transform ion cyclotron resonance mass spectrometry. The complexes were formed in methanol-water solution and were subsequently transported into the gas phase using two different electrospray ionization sources. Trapped complexes were dissociated utilizing IRMPD to obtain fragmentation and binding information on selected crown ether complexes. Dissociation of crown ether-alkali metal complexes proceeded via the loss of the alkali metal ion at low laser fluences; dissociation of the crown was not observed. For all of the alkali metal-crown ether complexes investigated, it was found that Na+ binds to the crown ether more strongly than any of the larger alkali metal ions. In contrast to the alkali metal complexes, IRMPD of (18-crown-6)H3O+ proceeded via loss of H2O to produce protonated 18-crown-6 ions. At higher laser fluences, (15-crown-5)H3O+ and (12-crown-4)H3O+ lost water and then fragmented by sequential loss of C2H4O units.

Engineering Molecular Beacons for Intracellular Imaging

Molecular beacons (MBs) represent a class of nucleic acid probes with unique DNA hairpin structures that specifically target complementary DNA or RNA. The inherent “OFF” to “ON” signal transduction mechanism of MBs makes them promising molecular probes for real-time imaging of DNA/RNA in living cells. However, conventional MBs have been challenged with such issues as false-positive signals and poor biostability in complex cellular matrices. This paper describes the novel engineering steps used to improve the fluorescence signal and reduce to background fluorescence, as well as the incorporation of unnatural nucleotide bases to increase the resistance of MBs to nuclease degradation for application in such fields as chemical analysis, biotechnology, and clinical medicine. The applications of these de novo MBs for single-cell imaging will be also discussed.

Quantitation of ion abundances in fourier transform ion cyclotron resonance mass spectrometry

To improve the analytical usefulness of Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), an extensive survey of various methods for quantitation of peak magnitudes has been undertaken using a series of simulated transient response signals with varying signal-to-noise ratio. Both peak height (five methods) and peak area (four methods) were explored for a range of conditions to determine the optimum methodology for quantitation. Variables included dataset size, apodization function, damping constant, and zero filling. Based on the results obtained, recommended procedures for optimal quantitation include: apodization using a function appropriate for the peak height ratios observed in the spectrum (i.e., Hanning for ratios of about 1:10, three-term Blackman-Harris for ratios of ∼1:100, or Kaiser-Bessel for ratios of ∼1:1000); zero filling until the peaks of interest are represented by 10–15 points (generally obtained with one order of zero filling); and use of the polynomial y=(ax2+bx+c)n and the three data points of highest intensity of the peak to locate the peak maximum, Ymax=(−b2/4a+c)n. In this peak fitting procedure, which we have termed the “Comisarow method,” n is 5.5, 9.5, and 12.5 for the Hanning, three-term Blackman-Harris, and Kaiser-Bessel apodization functions, respectively. Accuracy of quantitation using an optimal peak height determination is about equal to that for peak area measurements. These recommendations were found to be valid when tested with real FTICR-MS spectra of xenon isotopes.

Thermal decomposition of poly(α,α,α′,α′-tetrafluoro-p-xylylene) in nitrogen and oxygen

The thermal decomposition of poly(α,α,α′,α′-tetrafluoro-p-xylylene) (parylene AF-4) films with thicknesses of ca. 7.5 and 10 μm has been studied by both dynamic (10°C min−1) and isothermal TG in either nitrogen or oxygen atmospheres.In dynamic studies with nitrogen, gross decomposition occurs between 546.7±1.4 and 589.0±2.6°C, with 26.8±4.4% of the initial mass remaining at 700°C. With oxygen as the purge gas, the onset of decomposition shifts slightly to 530.8±4.2°C. The end of the transition at 587.4±2.6°C is within experimental error of the nitrogen value, but no polymer remains above 600°C.Isothermal data were obtained at 10°C intervals from 420 to 490°C in nitrogen, and from 390 to 450°C in oxygen. Plots of log(Δ%wt/Δt)vs. T−1 are linear throughout the specified range for oxygen and from 420 to 470°C for nitrogen. The calculated activation energies of (147±16) kJ mol−1 and (150±12) kJ mol−1 in N2 and O2, respectively, are equal within experimental error.

X-RAY PHOTOELECTRON SPECTROSCOPY OF ALUMINUM OXALATE TETRAHYDRATE

Abstract The X-ray photoelectron spectra of aluminum oxalate tetrahydrate have been determined starting at a temperature of −25°C and as a function of elapsed time as the sample warms from −25 to 37°C. At −25°C, two of the oxalate groups are rapidly decomposed by the X-rays. As the sample warms, the third oxalate group decomposes and aluminum oxide is produced. In contrast, aluminum oxalate tetrahydrate is thermally stable to 60°C, where it begins to lose water. Oxalate does not thermally decompose until a temperature of 150°C is reached.

Lyotropic Phase From Hybrid Organic-Inorganic Layered Copper Hydroxides

Lyotropic liquid crystalline suspensions have been observed for organic/inorganic layered copper(II) hydroxycarboxylates dispersed in organic solvents such as toluene. Polycrystalline powders of the lamellar phases Cu 2 (OH) 4-x (C n H 2n+1 COO) x were prepared for the octanoate (n=7), stearate (n=17), eicosanoate, (n=19), and docosanoate (n=21), and dispersions of each show lyotropic phase behavior when viewed under cross polarized microscopy. The dispersions form a birefringent gel at higher weight percent. The birefringence results from the lyotropic liquid crystals alignment of submicron flattened needles of the organic/inorganic layered solid. Similar behavior is observed for Ni(II) and Co(II)hydroxycarboxylates. The gel phases can be cast onto solid supports, and after solvent evaporation, oriented films of the starting powder are formed. In the case of the nickel film, magnetic order, characteristic of the starting powder, is retained in the oriented film.

Neutron activation analysis of zeolite catalysts

A new method for the determination of aluminum and silicon has been developed for zeolite catalysts. In contrast to previous methods, thermal neutrons are used for the analysis of both elements, and cadmium absorbers are not needed. The silicon determination utilizes a one-hour irradiation to observe the31Si produced by the (n, γ) reaction of30Si. A 15-second irradiation is used for the27Al(n, γ)28Al reaction. The28Al activity is corrected for the contribution from the28Si(n,p)28Al reaction by using the analyzed weight of silicon in the sample and the data for a silicon standard irradiated simultaneously with the zeolite and the aluminum standard. The quantitation limits are 0.012 g for silicon and 3.3×10−5 g for aluminum. Sodium presents a significant interference, but this element can be removed by taking advantage of the ion exchange properties of these materials.