Nano-grids of Yeast Cytochrome C

One innovative thought in biomolecular electronics is the exploitation of electron transfer proteins. Using nature's self assembly techniques, proteins can build highly organized edifices with retained functional activity, and they can serve as platforms for biosensors. In this research work, Yeast Cytochrome C (YCC) is immobilized with a help of a linker molecule, 3-Mercaptopropyltrimethoxysilane (3-MPTS) on a hydroxylated surface of a silicon substrate. Atomic Force Microscopy (AFM) is used for characterization. AFM data shows immobilization of one YCC molecule in between eight grids that are formed by the linker molecules. 3-MPTS monolayers are organized in grids that are 1.2 nm apart. Immobilization of 3-MPTS was optimized using a concentration of 5 mM in a completely dehydrated state for 30 minutes. The functionally active grids of YCC can now be incorporated with Cytochrome C oxidase on a Platinum electrode surface for transfer of electrons in development of biosensors, such as nitrate sensor, that are small in size, cheaper, and easier to manufacture than the top-down approach of fabrication of molecular biodevices

Multimode Analysis of Nanoscale Biomolecular Interactions

Biomolecular interactions, including protein-protein, protein-DNA, and protein-ligand interactions, are of special importance in all biological systems. These interactions may occer during the loading of biomolecules to interfaces, the translocation of biomolecules through transmembrane protein pores, and the movement of biomolecules in a crowded intracellular environment. The molecular interaction of a protein with its binding partners is crucial in fundamental biological processes such as electron transfer, intracellular signal transmission and regulation, neuroprotective mechanisms, and regulation of DNA topology. In this dissertation, a customized surface plasmon resonance (SPR) has been optimized and new theoretical and label free experimental methods with related analytical calculations have been developed for the analysis of biomolecular interactions. Human neuroglobin (hNgb) and cytochrome c from equine heart (Cyt c) proteins have been used to optimize the customized SPR instrument. The obtained Kd value (~13 µM), from SPR results, for Cyt c-hNgb molecular interactions is in general agreement with a previously published result. The SPR results also confirmed no significant impact of the internal disulfide bridge between Cys 46 and Cys 55 on hNgb binding to Cyt c. Using SPR, E. coli topoisomerase I enzyme turnover during plasmid DNA relaxation was found to be enhanced in the presence of Mg2+. In addition, a new theoretical approach of analyzing biphasic SPR data has been introduced based on analytical solutions of the biphasic rate equations. In order to develop a new label free method to quantitatively study protein-protein interactions, quartz nanopipettes were chemically modified. The derived Kd (~20 µM) value for the Cyt c-hNgb complex formations matched very well with SPR measurements (Kd ~16 µM). The finite element numerical simulation results were similar to the nanopipette experimental results. These results demonstrate that nanopipettes can potentially be used as a new class of a label-free analytical method to quantitatively characterize protein-protein interactions in attoliter sensing volumes, based on a charge sensing mechanism. Moreover, the molecule-based selective nature of hydrophobic and nanometer sized carbon nanotube (CNT) pores was observed. This result might be helpful to understand the selective nature of cellular transport through transmembrane protein pores.

Mechanical and electrical properties of single-walled carbon nanotubes synthesized by chemical vapor deposition

Despite the tremendous application potentials of carbon nanotubes (CNTs) proposed by researchers in the last two decades, efficient experimental techniques and methods are still in need for controllable production of CNTs in large scale, and for conclusive characterizations of their properties in order to apply CNTs in high accuracy engineering. In this dissertation, horizontally well-aligned high quality single-walled carbon nanotubes (SWCNTs) have been successfully synthesized on St-cut quartz substrate by chemical vapor deposition (CVD). Effective radial moduli (Eradial) of these straight SWCNTs have been measured by using well-calibrated tapping mode and contact mode atomic force microscopy (AFM). It was found that the measured Eradial decreased from 57 to 9 GPa as the diameter of the SWCNTs increased from 0.92 to 1.91 nm. The experimental results were consistent with the recently reported theoretical simulation data. The method used in this mechanical property test can be easily applied to measure the mechanical properties of other low-dimension nanostructures, such as nanowires and nanodots. The characterized sample is also an ideal platform for electrochemical tests. The electrochemical activities of redox probes Fe(CN)63-/4-, Ru(NH3) 63+, Ru(bpy)32+ and protein cytochrome c have been studied on these pristine thin films by using aligned SWCNTs as working electrodes. A simple and high performance electrochemical sensor was fabricated. Flow sensing capability of the device has been tested for detecting neurotransmitter dopamine at physiological conditions with the presence of Bovine serum albumin. Good sensitivity, fast response, high stability and anti-fouling capability were observed. Therefore, the fabricated sensor showed great potential for sensing applications in complicated solution.^

AFM and SPR studies of protein adsorption at solid/liquid interface

Membrane-like structure formed by surfactant molecules of didodecyldimethylammonium bromide (DDAB) on both HOPG and gold electrodes were studied with AFM and SPR techniques. The study shows that the thickness of the adsorbed layer of DDAB is strongly dependent on the concentration of the vesicle solution. We have also investigated the adsorption of redox protein, Cytochrome c, on graphite electrode with in situ tapping mode AFM. The protein adsorbs spontaneously onto the electrode covered with an adsorbed phosphate layer and forms a uniform monolayer. The adsorbed protein exhibits a reversible electron transfer at 0.17 V (Ag/AgCI) once the electrode potential has been increased to 0.75V. Using surface plasmon resonance spectroscopy we have measured subtle conformational change in protein, Cyt c, due to electron transfer of a single electron on MPA-coated gold electrode. The electron transfer induced change in the resonant angle is about 0.006 deg., which corresponds to ~ 0.2 A decreases in the thickness. This is consistent with that reduced state is more compact than the oxidized state.

Mechanical and Electrical Properties of Single-walled Carbon Nanotubes Synthesized by Chemical Vapor Deposition

Despite the tremendous application potentials of carbon nanotubes (CNTs) proposed by researchers in the last two decades, efficient experimental techniques and methods are still in need for controllable production of CNTs in large scale, and for conclusive characterizations of their properties in order to apply CNTs in high accuracy engineering. In this dissertation, horizontally well-aligned high quality single-walled carbon nanotubes (SWCNTs) have been successfully synthesized on St-cut quartz substrate by chemical vapor deposition (CVD). Effective radial moduli (Eradial) of these straight SWCNTs have been measured by using well-calibrated tapping mode and contact mode atomic force microscopy (AFM). It was found that the measured Eradial decreased from 57 to 9 GPa as the diameter of the SWCNTs increased from 0.92 to 1.91 nm. The experimental results were consistent with the recently reported theoretical simulation data. The method used in this mechanical property test can be easily applied to measure the mechanical properties of other low-dimension nanostructures, such as nanowires and nanodots. The characterized sample is also an ideal platform for electrochemical tests. The electrochemical activities of redox probes Fe(CN)63-/4-, Ru(NH3)63+, Ru(bpy)32+ and protein cytochrome c have been studied on these pristine thin films by using aligned SWCNTs as working electrodes. A simple and high performance electrochemical sensor was fabricated. Flow sensing capability of the device has been tested for detecting neurotransmitter dopamine at physiological conditions with the presence of Bovine serum albumin. Good sensitivity, fast response, high stability and anti-fouling capability were observed. Therefore, the fabricated sensor showed great potential for sensing applications in complicated solution.