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Jason J Davis

Publications and source records attributed to Jason J Davis.

16 recordsLinked to original sources
PubMed2006

Spatially controlled Suzuki and Heck catalytic molecular coupling.

The initiation and control of chemical coupling has the potential to offer much within the context of "bottom up" nanofabrication. We report herein the use of a palladium-modified, catalytically active, AFM probe to initiate and spatially control surface-confined Suzuki and Heck carbon-carbon coupling reactions. These "chemically written reactions", detectable by lateral force and chemically specific optical and topographic labeling, were patterned with line widths down to 15 nm or approximately 20 molecules. Catalyzed organometallic coupling was, in this way, carried out at subzeptomolar levels. By varying the catalyst-substrate interaction times, turnover numbers of (0.6-1.2) x 10(4) and (3.0-5.0) x 10(4) molecules s(-1) were resolved for Suzuki and Heck reactions, respectively.

Journal Article↗
PubMed2006

Metalloprotein tunnel junctions: compressional modulation of barrier height and transport mechanism.

Though the incorporation of sensory or potentially-switchable biological entities into electronic devices brings with it a number of complicating issues associated with hydration, structural complexity/delicacy, and low conductance, the possibility of resolving properties of fundamental importance (such as the influence of protein fold on conductance) at a molecularly-resolved level, are exciting. Our ability to analyse charge transport through a biological macromolecule remains, though, a significant practical and theoretical challenge. Though much information can be gained by carrying out such examinations at a molecular level, there exist few methods where such controlled analyses are, in fact, feasible. Here we report on the electron transport characteristics of a blue copper metalloprotein as characterized by conductive-probe atomic force microscopy. At very low imposed force, contact resistance is high, electrical contact unstable, and the junction undergoes dielectric breakdown at 1.1-1.5 GV m(-1). At increased applied force, the current-voltage characteristics are entirely reproducible and well-described by a Simmons (non-resonant) tunnelling model. Though highly resistive, observations demonstrate the ability of the protein matrix to mediate appreciable tunnelling current. Non-resonant behaviour is consistent with observations of bias-independent tunnelling imaging. In fitting observed transport characteristics to this model, it is possible to deconvolute barrier height and length at specific experimental conditions and, specifically, to monitor the modulation of these parameters by imposed compressional force. At higher field spectroscopic features assignable to metal based density of states are reproducibly observed. These vanish in a force regime where the tunnel barrier to direct tip-sample communication decreases.

Azurin↗
PubMed2005

Interfacial sensing: surface assembled molecular receptors.

The controlled surface assembly of biological or appropriately designed synthetic host systems on optically or electrochemically-active surfaces has advanced considerably during the past decade. Recent activities, from the authors laboratory and elsewhere, and possible future directions are discussed herein.

Biomimetic Materials↗
PubMed2005

Sensing nitrite through a pseudoazurin-nitrite reductase electron transfer relay.

Nitrite is converted to nitric oxide by haem or copper-containing enzymes in denitrifying bacteria during the process of denitrification. In designing an efficient biosensor, this enzymic turnover must be quantitatively assessed. The enzyme nitrite reductase from Alcaligenes faecalis contains a redox-active blue copper centre and a nonblue enzyme-active copper centre. It can be covalently tethered to modified gold-electrode surfaces in configurations in which direct electron transfer is possible. A surface cysteine mutant of the enzyme can be similarly immobilised on bare electroactive gold substrates. Under such circumstances, however, electron transfer cannot be effectively coupled with substrate catalytic turnover. In using either the natural redox partner, pseudoazurin, or ruthenium hexammine as an "electron-shuttle" or "conduit" between enzyme and a peptide-modified electrode surface, the coupling of electron transfer to catalysis can be utilised in the development of an amperometric nitrite sensor.

Azurin↗
PubMed2005

Molecular electron transfer of protein junctions characterised by conducting atomic force microscopy.

The transport characteristics of the blue copper metalloprotein, azurin, have been characterised by conducting atomic force microscopy (C-AFM) at molecular level. Tunnel junctions have been constructed by sandwiching chemisorbed protein molecules between a conducting AFM tip and a planar conducting substrate. Asymmetric current curves with respect to the polarity of the bias (I-V) have been observed. The modulation of I-V behaviour with compressional force has been examined and is described by a modified Simmons model within which both tunnel distance (protein dimensions) and tunnel barrier are modulated. The modified Simmons formula, which considered unequal Fermi level shifts on two electrodes as being responsible for the asymmetric I-V curves, accurately describes the behaviour observed.

Azurin↗
PubMed2004

Exploring the electronic and mechanical properties of protein using conducting atomic force microscopy.

In interfacing man-made electronic components with specifically folded biomacromolecules, the perturbative effects of junction structure on any signal generated should be considered. We report herein on the electron-transfer characteristics of the blue copper metalloprotein, azurin, as characterized at a refined level by conducting atomic force microscopy (C-AFM). Specifically, the modulation of current-voltage (I-V) behavior with compressional force has been examined. In the absence of assignable resonant electron tunneling within the confined bias region, from -1 to 1 V, the I-V behavior was analyzed with a modified Simmons formula. To interpret the variation of tunneling barrier height and barrier length obtained by fitting with the modified Simmons formula, an atom packing density model associated with protein mechanical deformation was proposed and simulated by molecular dynamics. The barrier heights determined at the minimum forces necessary for stable electrical contact correlate reasonably well with those estimated from bulk biophysical (electroanalytical and photochemical) experiments previously reported. At higher forces, the tunnel barrier decreases to fall within the range observed with saturated organic systems. Molecular dynamics simulations revealed changes in secondary structure and atomic density of the protein with respect to compression. At low compression, where transport measurements are made, secondary structure is retained, and atomic packing density is observed to increase linearly with force. These predictions, and those made at higher compression, are consistent with both experimentally observed modulations of tunneling barrier height with applied force and the applicability of the atom packing density model of electron tunneling in proteins to molecular-level analyses.

Azurin↗
PubMed2003

Chemical and biochemical sensing with modified single walled carbon nanotubes.

The nano dimensions, graphitic surface chemistry and electronic properties of single walled carbon nanotubes make such a material an ideal candidate for chemical or biochemical sensing. Carbon nanotubes can be nondestructively oxidized along their sidewalls or ends and subsequently covalently functionalized with colloidal particles or polyamine dendrimers via carboxylate chemistry. Proteins adsorb individually, strongly and noncovalently along nanotube lengths. These nanotube-protein conjugates are readily characterized at the molecular level by atomic force microscopy. Several metalloproteins and enzymes have been bound on both the sidewalls and termini of single walled carbon nanotubes. Though coupling can be controlled, to a degree, through variation of tube oxidative pre-activation chemistry, careful control experiments and observations made by atomic force microscopy suggest that immobilization is strong, physical and does not require covalent bonding. Importantly, in terms of possible device applications, protein attachment appears to occur with retention of native biological structure. Nanotube electrodes exhibit useful voltammetric properties with direct electrical communication possible between a redox-active biomolecule and the delocalized pi system of its carbon nanotube support.

Biosensing Techniques↗
PubMed2003

The circularization of amyloid fibrils formed by apolipoprotein C-II.

Amyloid fibrils have historically been characterized by diagnostic dye-binding assays, their fibrillar morphology, and a "cross-beta" x-ray diffraction pattern. Whereas the latter demonstrates that amyloid fibrils have a common beta-sheet core structure, they display a substantial degree of morphological variation. One striking example is the remarkable ability of human apolipoprotein C-II amyloid fibrils to circularize and form closed rings. Here we explore in detail the structure of apoC-II amyloid fibrils using electron microscopy, atomic force microscopy, and x-ray diffraction studies. Our results suggest a model for apoC-II fibrils as ribbons approximately 2.1-nm thick and 13-nm wide with a helical repeat distance of 53 nm +/- 12 nm. We propose that the ribbons are highly flexible with a persistence length of 36 nm. We use these observed biophysical properties to model the apoC-II amyloid fibrils either as wormlike chains or using a random-walk approach, and confirm that the probability of ring formation is critically dependent on the fibril flexibility. More generally, the ability of apoC-II fibrils to form rings also highlights the degree to which the common cross-beta superstructure can, as a function of the protein constituent, give rise to great variation in the physical properties of amyloid fibrils.

Amyloid↗
PubMed2002

Bioelectrochemical single-walled carbon nanotubes.

Metalloproteins and enzymes can be immobilized on SWNTs of different surface chemistry. The combination of high surface area, robust immobilization and inherent nanotube electrochemical properties is of promising application in bioelectrochemistry.

Cytochrome c Group↗
PubMed2002

The scanning probe microscopy of metalloproteins and metalloenzymes.

In recent years, the concept of microscopy and the ability to study processes at a truly molecular level have been revolutionised by the development of a family of instruments based on acquiring data through the scanning of a proximal probe across a surface. Scanning Probe Microscopes (SPMs) enable surface-confined structures to be resolved at ångstrom-resolution, in real time, and under a variety of controllable conditions. Despite initial difficulties, much progress has been in the application of this technology to the high-resolution analysis of biological systems; these have varied from complex cellular systems to molecular biopolymers. Studying the interactions of protein with surfaces has been intrinsic to the development of our understanding of blood coagulation, fibrinolysis, thrombus formation and the synthesis of biocompatible materials. The specific interactions of metalloproteins and enzymes with electrode surfaces remains central to the understanding of the bioelectrochemical processes and to the development of biosensing devices. Though ellipsometry, Raman, microcalorimetry, surface plasmon resonance, and other spectroscopic methods, can provide much information on these interfaces, the acquired data are averaged over a large number of molecular species with a low spatial resolution. Proximal probe methods have much to offer in this regard and have revolutionized our ability to monitor such interactions.

Animals↗