Publications

We directly measure the dynamics of the HIV trans-activation response (TAR)-DNA hairpin with multiple loops using single-molecule Förster resonance energy transfer (smFRET) methods. Multiple FRET states are identified that correspond to intermediate melting states of the hairpin. The stability of each intermediate state is calculated from the smFRET data. The results indicate that hairpin unfolding obeys a "fraying and peeling" mechanism, and evidence for the collapse of the ends of the hairpin during folding is observed. These results suggest a possible biological function for hairpin loops serving as additional fraying centers to increase unfolding rates in otherwise stable systems. The experimental and analytical approaches developed in this article provide useful tools for studying the mechanism of multistate DNA hairpin dynamics and of other general systems with multiple parallel pathways of chemical reactions.

We demonstrate the application of superlocalization microscopy to identify sequence-specific portions of single-stranded DNA (ssDNA) with sequence resolution of 50 nucleotides, corresponding to a spatial resolution of 30 nm. Super-resolution imaging was achieved using a variation of a single-molecule localization method, termed as "motion blur" point accumulation for imaging in nanoscale topography (mbPAINT). The target ssDNA molecules were immobilized on the substrate. Short, dye-labeled, and complementary ssDNA molecules stochastically bound to the target ssDNA, with repeated binding events allowing super-resolution. Sequence specificity was demonstrated via the use of a control, noncomplementary probe. The results support the possibility of employing relatively inexpensive short ssDNAs to identify gene sequence specificity with improved resolution in comparison to the existing methods.

We demonstrate the formation of molecular monolayers of π-conjugated organic molecules on nanocrystalline TiO(2) surfaces through the thermal grafting of benzyl and aryl halides. X-ray photoelectron spectroscopy and Fourier-transform infrared spectroscopy were used to characterize the reactivity of aryl and benzyl chlorides, bromides, and iodides with TiO(2) surfaces, along with controls consisting of nonhalogenated compounds. Our results show that benzyl and aryl halides follow a similar reactivity trend (I > Br > Cl >> H). While the ability to graft benzyl halides is consistent with the well-known Williamson ether synthesis, the grafting of aryl halides has no similar precedent. The unique reactivity of the TiO(2) surface is demonstrated using nuclear magnetic resonance spectroscopy to compare the surface reactions with the liquid-phase interactions of benzyl and aryl iodides with tert-butanol and -butoxide anion. While the aryl iodides show no detectable reactivity with a tert-butanol/tert-butoxide mixture, they react with TiO(2) within 2 h at 50 °C. Atomic force microscopy studies show that grafting of 4-iodo-1-(trifluoromethyl)benzene onto the rutile TiO(2)(110) surface leads to a very uniform, homogeneous molecular layer with a thickness of ∼0.45 nm, demonstrating formation of a self-terminating molecular monolayer. Thermal grafting of aryl iodides provides a facile route to link π-conjugated molecules to TiO(2) surfaces with the shortest possible linkage between the conjugated electron system and the TiO(2).

Herein we introduce a novel strategy based on capillary force lithography (CFL) to fabricate asymmetric polymeric ring structures by applying both shear and nomal forces to a poly(dimethylsiloxane) stamp. The mechanism for the formation of asymmetric rings is caused by the deflection of cylindrical PDMS pillars due to the shear load, which is therefore termed deflected CFL (dCFL). The asymmetric polymeric rings could be readily transferred to an underlying gold layer to generate split ring structures with tunable opening angles. Asymmetric structures based upon trigular and square-shaped pillars were also fabricated. These elements were formed into periodic arrays over surface areas as large as 1 cm(2) and may have optical and electromagnetic applications.

While ZnO has excellent electrical properties, it has not been widely used for dye-sensitized solar cells, in part because ZnO is chemically less stable than widely used TiO(2). The functional groups typically used for surface passivation and for attaching dye molecules either bind weakly or etch the ZnO surface. We have compared the formation of molecular layers from alkane molecules with terminal carboxylic acid, alcohol, amine, phosphonic acid, or thiol functional groups on single-crystal zinc oxide (1010) surfaces. Atomic force microscopy (AFM) images show that alkyl carboxylic acids etch the surface whereas alkyl amine and alkyl alcohols bind only weakly on the ZnO(1010) surface. Phosphonic acid-terminated molecules were found to bind to the surface in a heterogeneous manner, forming clusters of molecules. Alkanethiols were found to bind to the surface, forming highly uniform monolayers with some etching detected after long immersion times in an alkanethiol solution. Monolayers of hexadecylphosphonic acid and octadecanethiol were further analyzed by Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), and electrochemical measurements. AFM scratching shows that thiols were bound strongly to the ZnO surface, suggesting the formation of strong Zn-S covalent bonds. Surprisingly, the tridentate phosphonic acids adhered much more weakly than the monodentate thiol. The influence of organic grafting on the charge transfer to ZnO was studied by time-resolved surface photovoltage measurements and electrochemical impedance measurements. Our results show that the grafting of thiols to ZnO leads to robust surfaces and reduces the surface band bending due to midgap surface states.

Here, we present a simple platform for the use of the enhanced emission of 16-mercaptohexadecanoic acid (16-MHA) capped CdSe quantum dots (QDs) as a probe for ultrasensitive copper(II) detection. In this study, the photoluminescence (PL) of the QDs was first enhanced by Ag nanoprisms which were self-assembled on Si surfaces and then further increased by photobrightening. Using this approach, the control and different analytes could be readily probed all on a single platform using fluorescence microscopy. The enhanced PL intensity of CdSe QDs was selectively quenched in the presence of Cu(2+), accompanied by the emergence of a new red-shifted luminescence band. The quenching mechanism was found to be due to a cation exchange mechanism as confirmed by X-ray photoelectron spectroscopy (XPS) measurements. Herein, we have demonstrated that this simple methodology can offer a rapid and reliable detection of Cu(2+) with a detection limit as low as 5 nM and a dynamic range up to 100 muM in a fixed fast reaction time of 5 min. The potential applications of this technique were tested in two ways, for mixed-ion solutions and in physiological fluids, and both experiments exhibited good selectivity toward Cu(2+).

Here we present a simple platform for probing plasmon enhanced photoluminescence (PL) of quantum dots by confocal microscopy. In this study, self-assembled monolayers of silane-derivative molecules were patterned onto the oxidized GaAs surfaces to direct the attachment of Au or Ag nanoparticles onto the surface. Following the directed binding of metal nanoparticles (MNPs), a layer-by-layer deposition of oppositely charged polymers was used to create films with varying thickness by controlling the numbers of deposited layers. CdSe quantum dots (QDs) of ∼4 and 5.5 nm in diameter with 16-mercaptohexadecanoic acid as a surfactant were then adsorbed onto the outermost polymer layer via electrostatic interactions. Using confocal fluorescence microscopy, the enhanced PL from the CdSe over the Au or Ag nanoparticle patterns could be imaged directly and scaled against the regions with no Au or Ag nanoparticles, and the luminescence of the GaAs (as an internal standard) for different CdSe-metal separations. By using a pattern, PL enhancement as a function of particle-CdSe spacing can be readily probed all on a single platform, where the QDs over MNPs and not over MNPs can be directly compared in the same dielectric environment. The observed luminescence as a function of metal-QD separation can be readily fit to a combined model of metal-fluorophore fluorescence quenching and local electric field enhancement.

Herein, a simple label-free biosensor fabrication method is demonstrated based on transmission localized surface plasmon resonance (T-LSPR). The platform, which consists of a silver nanoparticle array, can be prepared in just a few minutes using benchtop chemistry. The array was made by a templating technique in conjunction with the photoreduction of Ag ions from solution. This metal surface was functionalized with biotin-linked thiol ligands for binding streptavidin molecules from solution. For an array of 19 nm diameter silver nanoparticles, a redshift in the T-LSPR spectrum of 24 nm was observed upon protein-ligand binding at saturation. The binding constant was found to be 2x10(12) M(-1). Platforms were also fabricated with silver nanoparticles of 34, 55, and 72 nm diameters. The maximum LSPR wavelength shift was nanoparticle size dependent and the maximum sensitivity was obtained with the smaller nanoparticles.

Photolithographically generated patterns have been created on immobilized CdSe QD thin films by fine-tuning their optical properties (intensity and emission wavelength) postsynthetically. These optically modified QDs show enhanced selectivity for binding of different ligands, affording the ability to fabricate optically reconfigurable surfaces for display or sensing applications. The patterns may be readily generated with any typical optical lithographic approach.

Sub-100 nm wide supported phospholipid bilayers (SLBs) were patterned on a planar borosilicate substrate by AFM-based nanoshaving lithography. First, a bovine serum albumin monolayer was coated on the glass and then selectively removed in long strips by an AFM tip. The width of vacant strips could be controlled down to 15 nm. Bilayer lines could be formed within the vacant strips by vesicle fusion. It was found that stable bilayers formed by this method had a lower size limit of approximately 55 nm in width. This size limit stems from a balance between a favorable bilayer adhesion energy and an unfavorable bilayer edge energy.