Tao Ye

A Mechanical Actuator Driven Electrochemically by Artificial Molecular Muscles

A microcantilever, coated with a monolayer of redox-controllable, bistable [3]rotaxane molecules (artificial molecular muscles), undergoes reversible deflections when subjected to alternating oxidizing and reducing electrochemical potentials. The microcantilever devices were prepared by precoating one surface with a gold film and allowing the palindromic [3]rotaxane molecules to adsorb selectively onto one side of the microcantilevers, utilizing thiol-gold chemistry. An electrochemical cell was employed in the experiments, and deflections were monitored both as a function of (i) the scan rate (< or =20 mV s(-1)) and (ii) the time for potential step experiments at oxidizing (>+0.4 V) and reducing (<+0.2 V) potentials. The different directions and magnitudes of the deflections for the microcantilevers, which were coated with artificial molecular muscles, were compared with (i) data from nominally bare microcantilevers precoated with gold and (ii) those coated with two types of control compounds, namely, dumbbell molecules to simulate the redox activity of the palindromic bistable [3]rotaxane molecules and inactive 1-dodecanethiol molecules. The comparisons demonstrate that the artificial molecular muscles are responsible for the deflections, which can be repeated over many cycles. The microcantilevers deflect in one direction following oxidation and in the opposite direction upon reduction. The approximately 550 nm deflections were calculated to be commensurate with forces per molecule of approximately 650 pN. The thermal relaxation that characterizes the devices deflection is consistent with the double bistability associated with the palindromic [3]rotaxane and reflects a metastable contracted state. The use of the cooperative forces generated by these self-assembled, nanometer-scale artificial molecular muscles that are electrically wired to an external power supply constitutes a seminal step toward molecular-machine-based nanoelectromechanical systems (NEMS).

Changing Stations in Single Bistable Rotaxane Molecules under Electrochemical Control

We have directly observed electrochemically driven single-molecule station changes within bistable rotaxane molecules anchored laterally on gold surfaces. These observations were achieved by employing molecular designs that significantly reduced the mobility and enhanced the assembly of molecules in orientations conducive to direct measurement using scanning tunneling microscopy. The results reveal molecular-level details of the station changes of surface-bound bistable rotaxane molecules, correlated with their different redox states. The mechanical motions within these mechanically interlocked molecules are influenced by their interactions with the surface and with neighboring molecules, as well as by the conformations of the dumbbell component.

A single-molecule view of conformational switching of DNA tethered to a gold electrode.

Surfaces that can actively regulate binding affinities or catalytic properties in response to external stimuli are a powerful means to probe and control the dynamic interactions between the cell and its microenvironment. Active surfaces also enable novel functionalities in biosensors and biomolecular separation technologies. Although electrical stimuli are often appealing due to their speed and localization, the operation of these electrically activated surfaces has mostly been characterized with techniques averaging over many molecules. Without a molecular-scale understanding of how biomolecules respond to electric fields, achieving the ultimate detection sensitivity or localized biological perturbation with the ultimate resolution would be difficult. Using electrochemical atomic force microscopy, we are able to follow the conformational changes of individual, short DNA molecules tethered to a gold electrode in response to an applied potential. Our study reveals conformations and dynamics that are difficult to infer from ensemble measurements: defects in the self-assembled monolayer (SAM) significantly perturb conformations and adsorption/desorption kinetics of surface-tethered DNA; on the other hand, the SAM may be actively molded by the DNA at different potentials. These results underscore the importance of characterizing the systems at the relevant length scale in the development of electrically switchable biofunctional surfaces.

Nanoscale Positioning of Individual DNA Molecules by an Atomic Force Microscope

Here we report a method to assemble nanoscale DNA structures with single-molecule precision. This assembly is accomplished by performing nanografting in the presence of short, thiolated DNA strands that have been diluted by a positively charged alkanethiol. The expected number of DNA molecules per patch can be modulated by the application of an electric potential to the surface during patterning. Our ability to position individual DNA within a controlled nanoscale environment and observe these molecules in situ will allow us to understand and potentially decouple the heterogeneity caused by the local environment from the intrinsic properties in single-molecule biophysical measurements. Additionally, our approach can potentially be extended to the molecule-by-molecule assembly of larger artificial test structures of nucleic acids or proteins.

Measuring and Suppressing the Oxidative Damage to DNA During Cu(I)-Catalyzed Azide–Alkyne Cycloaddition

We have used the quantitative polymerase chain reaction (qPCR) to measure the extent of oxidative DNA damage under varying reaction conditions used for copper(I)-catalyzed click chemistry. We systematically studied how the damage depends on a number of key reaction parameters, including the amounts of copper, ascorbate, and ligand used, and found that the damage is significant under nearly all conditions tested, including those commonly used for bioconjugation. Furthermore, we discovered that the addition of dimethyl sulfoxide, a known radical scavenger, into the aqueous mixture dramatically suppresses DNA damage during the reaction. We also measured the efficiency of cross-linking two short synthetic oligonucleotides via click chemistry, and found that the reaction could proceed reasonably efficiently even with DMSO present. This approach for screening both DNA damage and reactivity under a range of reaction conditions will be valuable for improving the biocompatibility of click chemistry, and should help to extend this powerful synthetic tool for both in vitro and in vivo applications.

A switchable surface enables visualization of single DNA hybridization events with atomic force microscopy.

Here we describe a novel surface that enables direct visualization of the hybridization of single DNA molecules with an unprecedented resolution using atomic force microscopy. The surface consists of single-stranded DNA probes that are covalently anchored to a self-assembled monolayer. The surface satisfies the contradictory requirements for high-resolution imaging and hybridization by switching the DNA-surface interaction between a strong state and a weak state. Our approach opens up unique opportunities in elucidating hybridization at the molecular scale.

Second harmonic generation investigations of charge transfer at chemically-modified semiconductor interfaces

Charge transfer and accumulation at semiconductor devices can lead to device degradation. Understanding and controlling such a process is therefore important. Second harmonic generation has been shown to be a sensitive probe of charging of semiconductor interfaces, with the added advantages of high spatial and temporal resolution. We have investigated the use of self assembled monolayers (SAMs) as a means to control charging. Our results suggest that octadecylsiloxane SAMs, bound to the native oxide, significantly reduce charge accumulation at oxide interfaces.

Electrochemical Etching of Gold within Nanoshaved Self-Assembled Monolayers

Wet etching of metal substrates with patterned self-assembled monolayers (SAMs) is an inexpensive and convenient method to produce metal nanostructures. For this method to be relevant to the fabrication of high precision plasmonic structures, the kinetics of nanoscale etching process, particularly in the lateral direction, must be elucidated and controlled. We herein describe an in situ atomic force microscopy (AFM) study to characterize the etching process within patterned SAMs with nanometer resolution and in real time. The in situ study was enabled by several unique elements, including single crystalline substrates to minimize the variability of facet-dependent etch rate, high-resolution nanoshaved SAM patterns, electrochemical-potential-controlled etching, and AFM kymographs to improve temporal resolution. Our approach has successfully quantified the extent of both lateral etching and vertical etching at different potentials. Our study reveals the presence of an induction period prior to the onset of significant lateral etching, which would be difficult to observe with the limited time resolution and sample-to-sample variation of ex situ studies. By increasing the vertical etch rate during this induction period with higher potentials, gold was etched up to 40 nm in the vertical direction with minimal lateral etching. High-resolution etching was also demonstrated on single crystal gold microplates, which are high quality gold thin films suitable for plasmonics studies.

Electrodeposition of Metal Wires onto a Molecular Scale Template: An In Situ Investigation

We have demonstrated that the intrinsic nanometer length scales of two-dimensional molecular assemblies can be exploited to electrodeposit metal nanostructures with regular spacing and orientation. We observed evidence for preferential deposition of metals into parallel lines on Au(111) surface with a periodicity of 4.5 nm as determined by the hemimicelles formed by sodium dodecylsulfate. The preferential deposition of metals in molecular templates was achieved under optimal electrode potentials and ionic concentrations. The observed metal structures provide insight into the interactions between metal atoms, organic functional groups as well as the aqueous environment. Understanding and tailoring these interactions will lead to more precise control and new strategies for nanoscale placement and for connecting organic molecules to metal nanostructures.

Electrochemical Nanoscale Templating: Laterally Self-Aligned Growth of Organic−Metal Nanostructures

The electrodeposition of Ag into organized surfactant templates adsorbed onto (22 × √3) reconstructed Au(111) is investigated by in situ electrochemical scanning tunneling microscopy. Ag(+) concentrations of as low as 2.5 × 10(-6) M allow the visualization of the electrochemical molecular templating effect of a sodium dodecyl sulfate (SDS) adlayer. The SDS hemicylindrical stripes determine the adsorption sites of the Ag(+) ions and the directionality of Ag nanodeposition. The SDS-Ag nanostructures grow along the long axis of SDS hemicylindrical stripes, and an interaction of Ag with the Au(111) substrate leads to a structural change in the SDS stripe pattern. The SDS-Ag nanostructures undergo dynamic rearrangement in response to changes in the applied electrode potential. At negative potentials, the orientations of SDS-Ag nanostructures are pinned by the (22 × √3) reconstructed pattern. Furthermore, observed differences in Ag nanostructuring on Au(111) without molecular templates (i.e., on a bare Au(111) surface) confirm the role of self-assembled organic templates in producing metal-organic nanostructures under control of the surface potential, which can determine the feature size, shape, and period of the metal nanostructure arrays.