Philip S. Waggoner

Tribological Effects on DNA Translocation in a Nanochannel Coated with a Self-Assembled Monolayer

A biomimetic nanochannel coated with a self-assembled monolayer (SAM) can be used for sensing and analyzing biomolecules. The interaction between a transported biomolecule and a SAM governs the mechanically or electrically driven motion of the molecule. To investigate the translocation dynamics of a biomolecule, we performed all-atom molecular dynamics simulations on a single-stranded DNA in a solid-state nanochannel coated with a SAM that consists of octane or octanol polymers. Simulation results demonstrate that the interaction between DNA and a hydrophobic or a hydrophilic SAM is effectively repulsive or adhesive, respectively, resulting in different translocation dynamics of DNA. Therefore, with proper designs of SAMs coated on a channel surface, it is possible to control the translocation dynamics of a biomolecule. This work also demonstrates that traditional tribology methods can be deployed to study a biological or biomimetic transport process.

Electrochemical Protection of Thin Film Electrodes in Solid State Nanopores

Solid state nanopores are a core element of next-generation single molecule tools in the field of nano-biotechnology. Thin film electrodes integrated into a pore can interact with charges and fields within the pore. In order to keep the nanopore open and thus functional electrochemically induced surface alteration of electrode surfaces and bubble formation inside the pore have to be eliminated. This paper provides electrochemical analyses of nanopores drilled into TiN membranes which in turn were employed as thin film electrodes. We studied physical pore integrity and the occurrence of water decomposition yielding bubble formation inside pores by applying voltages between -4.5 and +4.5 V to membranes in various protection stages continuously for up to 24 h. During potential application pores were exposed to selected electrolyte-solvent systems. We have investigated and successfully eliminated electrochemical pore oxidation and reduction as well as water decomposition inside nanopores of various diameters ranging from 3.5 to 25 nm in 50 nm thick TiN membranes by passivating the nanopores with a plasma-oxidized layer and using a 90% solution of glycerol in water as KCl solvent. Nanopore ionic conductances were measured before and after voltage application in order to test for changes in pore diameter due to electrochemical oxidation or reduction. TEM imaging was used to confirm these observations. While non-passivated pores were electrochemically oxidized, neither electrochemical oxidation nor reduction was observed for passivated pores. Bubble formation through water decomposition could be detected in non-passivated pores in KCl/water solutions but was not observed in 90% glycerol solutions. The use of a protective self-assembled monolayer of hexadecylphosphonic acid (HDPA) was also investigated.

Electrochemical Characterization of Thin Film Electrodes Toward Developing a DNA Transistor

The DNA-Transistor is a device designed to control the translocation of single-stranded DNA through a solid-state nanopore. Functionality of the device is enabled by three electrodes exposed to the DNA-containing electrolyte solution within the pore and the application of a dynamic electrostatic potential well between the electrodes to temporarily trap a DNA molecule. Optimizing the surface chemistry and electrochemical behavior of the device is a necessary (but by no means sufficient) step toward the development of a functional device. In particular, effects to be eliminated are (i) electrochemically induced surface alteration through corrosion or reduction of the electrode surface and (ii) formation of hydrogen or oxygen bubbles inside the pore through water decomposition. Even though our motivation is to solve problems encountered in DNA transistor technology, in this paper we report on generic surface chemistry results. We investigated a variety of electrode-electrolyte-solvent systems with respect to their capability of suppressing water decomposition and maintaining surface integrity. We employed cyclic voltammetry and long-term amperometry as electrochemical test schemes, X-ray photoelectron spectroscopy, atomic force microscopy, and scanning, as well as transmission electron microscopy as analytical tools. Characterized electrode materials include thin films of Ru, Pt, nonstoichiometric TiN, and nonstoichiometric TiN carrying a custom-developed titanium oxide layer, as well as custom-oxidized nonstoichiometric TiN coated with a monolayer of hexadecylphosphonic acid (HDPA). We used distilled water as well as aqueous solutions of poly(ethylene glycol) (PEG-300) and glycerol as solvents. One millimolar KCl was employed as electrolyte in all solutions. Our results show that the HDPA-coated custom-developed titanium oxide layer effectively passivates the underlying TiN layer, eliminating any surface alterations through corrosion or reduction within a voltage window from -2 V to +2 V. Furthermore, we demonstrated that, by coating the custom-oxidized TiN samples with HDPA and increasing the concentration of PEG-300 or glycerol in aqueous 1 mM KCl solutions, water decomposition was suppressed within the same voltage window. Water dissociation was not detected when combining custom-oxidized HDPA-coated TiN electrodes with an aqueous 1 mM KCl-glycerol solution at a glycerol concentration of at least 90%. These results are applicable to any system that requires nanoelectrodes placed in aqueous solution at voltages that can activate electrochemical processes.

Increasing the speed of solid-state nanopores

In this work, the authors studied the time response of solid-state nanopores to the applied potentials and the corresponding capacitances. They primarily examined the effect of the doping of the silicon substrates as well as the addition of dielectrics above and below the device membrane. For simple silicon nitride membranes on a moderately doped Si, the measured RC time constants in 1M KCl are on the order of hundreds of microseconds or larger. The authors found that the silicon substrate’s doping level has a significant effect on the equivalent circuit of the device and the use of a more lightly doped Si significantly speeds up the device response. They attributed this effect to the reduction of depletion layer capacitance at the Si-electrolyte interfaces. In the best device structure tested, time constants of ∼425 ns were observed in 1M KCl, which is much faster than most DNA translocation times and on the same order of magnitude as the transit time of each base through typical nanopores.