Chromatin control of gene expression: the simplest model.
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Bacteriophage T4↗
Biomedical subjects
Stuart Lindsay
Publications and source records attributed to Stuart Lindsay.
Electrochemical origin of voltage-controlled molecular conductance switching.
We have studied electron transport in bipyridyl-dinitro oligophenylene-ethynelene dithiol (BPDN) molecules both in an inert environment and in aqueous electrolyte under potential control, using scanning tunneling microscopy. Current-voltage (IV) data obtained in an inert environment were similar to previously reported results showing conductance switching near 1.6 V. Similar measurements taken in electrolyte under potential control showed a linear dependence of the bias for switching on the electrochemical potential. Extrapolation of the potentials to zero switching bias coincided with the potentials of redox processes on these molecules. Thus switching is caused by a change in the oxidation state of the molecules.
Electrochemistry↗
Recognition imaging with a DNA aptamer.
We have used a DNA-aptamer tethered to an atomic force microscope probe to carry out recognition imaging of IgE molecules attached to a mica substrate. The recognition was efficient (approximately 90%) and specific, being blocked by injection of IgE molecules in solution, and not being interfered with by high concentrations of a second protein. The signal/noise ratio of the recognition signal was better than that obtained with antibodies, despite the fact that the average force required to break the aptamer-protein bonds was somewhat smaller.
Aluminum Silicates↗
Measuring single molecule conductance with break junctions.
Single-molecule conductance measurements made under potential control provide a critical link between chemical and molecular electronic data. These measurements are made possible by the STM break-junction method introduced recently, but questions remain about its reliability. Here we report the use of a logarithmic current-to-voltage converter to examine a wide range of currents in an STM break junction study of octanedithiol, clearly showing both the gold-quantum wire regime and the single molecule conductance regime. We find two sets of molecular currents that we tentatively ascribe to different bonding geometries of the molecules in the break junction.
Amplifiers, Electronic↗
Molecular wires and devices: advances and issues.
Substantial advances have been made in (a) our experimental and theoretical understanding of simple tunnel junctions based on molecules, (b) the role of contacts tunneling and (c) experimental studies of redox-state gated transport. In addition, a new thermally-activated transport process has been discovered in a non-redox active system. Substantial challenges remain. The engineering of molecular contacts to technologically important electronic materials will stretch the ingenuity of synthetic chemists. The theory community must rise to the challenge of describing redox-mediated transport using first-principles, parameter free approaches. These advances will enable a new generation of devices that span the silicon (electronic) and carbon (bio-organic) worlds.
Journal Article↗
Self-assembling a molecular pegboard.
This paper describes the design, construction, and application of a self-assembled, chemically addressable DNA nanogrid composed of DNA tiles of nanometer dimensions. This self-assembled structure permits precise placement of molecules at predetermined locations on a "molecular pegboard". We used the indexed DNA nanogrids to identify single molecules of DNA that hybridize at particular locations.
DNA↗
Kinetic studies of iron deposition catalyzed by recombinant human liver heavy and light ferritins and Azotobacter vinelandii bacterioferritin using O2 and H2O2 as oxidants.
The discrepancy between predicted and measured H(2)O(2) formation during iron deposition with recombinant heavy human liver ferritin (rHF) was attributed to reaction with the iron protein complex [Biochemistry 40 (2001) 10832-10838]. This proposal was examined by stopped-flow kinetic studies and analysis for H(2)O(2) production using (1) rHF, and Azotobacter vinelandii bacterial ferritin (AvBF), each containing 24 identical subunits with ferroxidase centers; (2) site-altered rHF mutants with functional and dysfunctional ferroxidase centers; and (3) recombinant human liver light ferritin (rLF), containing no ferroxidase center. For rHF, nearly identical pseudo-first-order rate constants of 0.18 s(-1) at pH 7.5 were measured for Fe(2+) oxidation by both O(2) and H(2)O(2), but for rLF, the rate with O(2) was 200-fold slower than that for H(2)O(2) (k = 0.22 s(-1)). A Fe(2+)/O(2) stoichiometry near 2.4 was measured for rHF and its site altered forms, suggesting formation of H(2)O(2). Direct measurements revealed no H(2)O(2) free in solution 0.5-10 min after all Fe(2+) was oxidized at pH 6.5 or 7.5. These results are consistent with initial H(2)O(2) formation, which rapidly reacts in a secondary reaction with unidentified solution components. Using measured rate constants for rHF, simulations showed that steady-state H(2)O(2) concentrations peaked at 14 muM at approximately 600 ms and decreased to zero at 10-30 s. rLF did not produce measurable H(2)O(2) but apparently conducted the secondary reaction with H(2)O(2). Fe(2+)/O(2) values of 4.0 were measured for AvBF. Stopped-flow measurements with AvBF showed that both H(2)O(2) and O(2) react at the same rate (k = 0.34 s(-1)), that is faster than the reactions with rHF. Simulations suggest that AvBF reduces O(2) directly to H(2)O without intermediate H(2)O(2) formation.
Azotobacter vinelandii↗
A molecular switch based on potential-induced changes of oxidation state.
We have measured the conductance of a hepta-aniline oligomer attached to gold electrodes held under potential control in electrolyte. It increases fifteen-fold (to 5.3+/-0.4 nS) on oxidation from the leucoemeraldine form to the emeraldine salt. The single-molecule current-voltage characteristic, linear in toluene, displays negative differential resistance in an acidic electrolyte. The negative differential resistance is accounted for by modification of the local surface potential by the applied bias. These results connect electrochemical data directly to molecular electronic behavior in a two-terminal device.
Aniline Compounds↗
Kinetic studies of iron deposition in horse spleen ferritin using O2 as oxidant.
An optical flow cell provided a means to conveniently measure the rate of successive Fe(2+) oxidation reactions catalyzed by horse spleen ferritin (HoSF) to determine if both ferroxidase and mineral core Fe(2+) oxidation reactions occur. The oxygen concentration and pH were held constant and multiple additions of Fe(2+)/HoSF ratios of 1, 10, 100, 150, 250 and 400 were conducted, creating core sizes ranging from 12 to 2800. During these oxidations, the absence of nonspecific Fe(OH)(3) formation and the presence (>95%) of Fe(OH)(3) deposited within the core of HoSF demonstrated the validity of monitoring iron deposition into HoSF by this procedure. Initial rates for oxidation of 5-50 Fe(2+)/HoSF established that the reaction is overall first order in Fe(2+) concentration. However, when full progress curves were analyzed at a variety of Fe(2+)/HoSF ratios, two first-order reactions (k(1) approximately 0.035 s(-1) and k(2) approximately 0.007 s(-1)) were found to contribute to the overall Fe(2+) oxidation reaction. The proportion of the fast reaction increased with increasing Fe(2+)/HoSF ratio until at approximately 400, it was the dominant reaction. For the Fe(2+)/HoSF ratios examined, the overall rate of iron deposition is independent of the size of the mineral core, a result suggesting that an increasing mineral core size does not enhance the rate of Fe(2+) oxidation. Comparison of successive additions of 1.0 Fe(2+)/HoSF showed that oxidation of the first 8-10 Fe(2+) produced a Fe(III) species with a lower molar absorptivity per Fe(III) than that of the bulk core. Measurement of the H(+)/Fe(2+) ratio confirmed this difference in behavior by giving an H(+)/Fe(2+) ratio of approximately 1.0 below and 2.0 for ratios >30 Fe(2+)/HoSF. The faster reaction was attributed to ferroxidase catalysis and the slow reaction to nonspecific ferroxidase activity of the HoSF protein shell.
Animals↗