Liquid-cell scanning transmission electron microscopy and fluorescence correlation spectroscopy of DNA-directed gold nanoparticle assemblies.

In the use of solution-based 3D nanoarchitectures for optics, drug delivery, and cancer treatment, the precise nanoparticle architecture morphologies, architecture sizes, interparticle distances, and the assembly stability are all critical to their functionality. 3D nanoparticle architectures in solution are difficult to characterize, as few techniques can provide individualized information on interparticle spacing (defined by linkage molecule), nanoparticle assembly size, morphology, and identification of false aggregation. Bulk characterization techniques, including small angle x-ray scattering, can provide architecture sizes, though they are unable to precisely measure differences within interparticle spacings for individual architectures and can falsely measure assemblies caused by non-linkage grouped nanoparticles. Two solution-based characterization techniques were used to determine which assembly type and linkage length would produce the fastest assembly rate for large DNA-directed gold nanoparticle assemblies. In-situ liquid-cell scanning transmission electron microscopy (LC-STEM), measured interparticle spacings between DNA-functionalized nanoparticles, and fluorescence correlation spectroscopy provided the bulk volume fraction of large and small assemblies for nanoparticle architectures that were assembled using two different types: (1) the hybrid assemblies join two complementary single-stranded DNA linkages, and (2) the bridged assemblies are comprised of single-stranded DNA (bridging component) that is double the length of two different complementary single-stranded DNA-functionalized gold nanoparticles. Assembly times were tested at 24-hrs intervals over 3 days. Statistics derived from the in-situ LC-STEM images provided data for interparticle distance measurements, which identified the fraction of nanoparticles within the images acquired that were at the expected double-stranded DNA-binding distance of the linkages (varied in three distances for each of the two different architectures). In general, longer linkage lengths assembled in the shortest amount of time. The bridged assemblies formed fewer large architectures at 24-hrs but ultimately assembled a greater fraction of nanoparticles, which was due to the longer functionalized DNA lengths for individual nanoparticles. Fluorescence correlation spectroscopy provided a bulk average of the gold nanoparticle assembly sizes over time, which supported the conclusions drawn from the in-situ LC-STEM data. The microscopy provided sub-2 nm precision in the interparticle distances between gold nanoparticles in a solution environment. This coupled microscopy and spectroscopy characterization approach can provide more detailed information than bulk characterization methods.

Drying effect creates false assemblies in DNA-coated gold nanoparticles as determined through in situ liquid cell STEM.

The drying effect associated with utilizing transmission electron microscopy to study deoxyribonucleic acid (DNA)-coated gold nanoparticles (AuNPs) remains largely uninvestigated, though this technique is frequently utilized to characterize nanoparticle-DNA interactions. Investigation of the drying effect is essential to the progress of the many fields that utilize AuNPs, including cancer research. In this study, we compare DNA hybridization-directed nanoparticle assemblies with control samples omitting the necessary complementary DNA, effectively blocking directed assembly, in both the liquid state and the dry state, within a scanning transmission electron microscope. We show that the dry samples contain AuNPs spaced at significantly smaller intervals than identical samples measured in situ, with no dependence on the DNA bound to the AuNPs in the dry samples. A partially wet sample, with distances measured along the drying edge, provided an intermediate binding distance, strengthening the conclusion that drastic differences observed between the dry and in situ samples are due to a pronounced drying effect. This drying effect will falsely indicate certain grouping arrangements and will change the impression of the size of the groups formed, providing misinformation for the development of these controlled assemblies that could impact applications such as targeted drug vehicles for cancer treatment.

Three-dimensional modeling and simulation of DNA hybridization kinetics and mass transport as functions of temperature in a microfluidic channel.

A 3D finite element model was developed to optimize the kinetics and mass transfer characteristics of low concentration, 18 bp ssDNA targets in bulk media solution, to 18 bp complimentary oligonucleotide probes immobilized on electrochemical detection electrodes positioned along the length of a microfluidic channel. Conditions considered in the model were fluid flow rate, diffusion time, DNA melting temperature, number of matching base pairs, and temperature of the fluid in the channel. System optimization was based on maximizing the uniformity and surface concentration of the specifically bound hybridized DNA, minimizing waste volume generation and the hybridization time. With the coupled simulation method used, the total experiment time was reduced from 150 to 60 min and the simulated results were consistent with experimental results found in the literature. A stopped flow procedure was investigated as a means to improve hybridization. This procedure can not only improve uniformity and capture efficiency, and reduce waste, but can also decrease overall signal intensity relative to continuous flow operation. Finally, the use of temperature in reducing mismatched hybridization and improving duplex stability was also successfully modeled and simulated.

Surface charge dependent nanoparticle disruption and deposition of lipid bilayer assemblies.

Electrostatic interaction plays a leading role in nanoparticle interactions with membrane architectures and can lead to effects such as nanoparticle binding and membrane disruption. In this work, the effects of nanoparticles (NPs) interacting with mixed lipid systems were investigated, indicating an ability to tune both NP binding to membranes and membrane disruption. Lipid membrane assemblies (LBAs) were created using a combination of charged, neutral, and gel-phase lipids. Depending on the lipid composition, nanostructured networks could be observed using in situ atomic force microscopy representing an asymmetrical distribution of lipids that rendered varying effects on NP interaction and membrane disruption that were domain-specific. LBA charge could be localized to fluidic domains that were selectively disrupted when interacting with negatively charged Au nanoparticles or quantum dots. Disruption was observed to be related to the charge density of the membrane, with a maximum amount of disruption occurring at ∼40% positively charged lipid membrane concentration. Conversely, particle deposition was determined to begin at charged lipid concentrations greater than 40% and increased with charge density. The results demonstrate that the modulation of NP and membrane charge distribution can play a pivitol role in determining NP-induced membrane disruption and NP surface assembly.

Biocompatible microfabrication of 3D isolation chambers for targeted confinement of individual cells and their progeny.

We describe a technique to physically isolate single/individual cells from their surrounding environment by fabricating three-dimensional microchambers around selected cells under biocompatible conditions. Isolation of targeted cells is achieved via rapid fabrication of protein hydrogels from a biocompatible precursor solution using multiphoton lithography, an intrinsically 3D laser direct write microfabrication technique. Cells remain chemically accessible to environmental cues enabling their propagation into well-defined, high density populations. We demonstrate this methodology on gram negative (E. coli), gram positive (S. aureus), and eukaryotic (S. cerevisiae) cells. The opportunities to confine viable, single/individual-cells and small populations within user-defined microenvironments afforded by this approach should facilitate the study of cell behaviors across multiple generations.

High-throughput screening of transglutaminase activity using plasmonic fluorescent nanocomposites.

We describe a high-throughput screening (HTS) assay for transglutaminase (TG) enzyme activity using plasmonic fluorescent nanocomposites. We used TG to covalently crosslink 500 µM solution of 5'-biotinamidopentylamine (BP) to N,N'-dimethylcasein (DMC) which was adsorbed onto 384-well microplates. We then bound 0.2 - 2.0 × 10(11)/mL of 10 nm gold nanoparticles-streptavidin conjugate (10 nm AuNPs-SA) to BP via biotin-streptavidin interactions. Finally, J-aggregation of cyanine 1 (25 µM) or 2 (10 µM) upon the 10 nm AuNPs elicited absorption and fluorescence signaling of TG catalysis. The cyanines could be added sequentially to elicit green (590 nm) and red (700 nm) spectral responses from the same set of reactions. Catalysis was linear (r(2) > 0.98) up to 10 min within a linear dynamic range (LDR) of 0.1 - 5 µg/mL enzyme. The multi-wavelength interrogation offered fast results (< 5 min), sensitivity (limit of detection, LOD of 5 ng or 64 fmol TG) and intermediate precision (relative standard deviation, RSD of < 20% over 42 days). Plasmonic fluorescent nanocomposites offer new ways of interrogating biomolecules in HTS format.

Plasmonic fluorescent nanocomposites of cyanines self-assembled upon gold nanoparticle scaffolds.

Plasmonic fluorescent nanocomposites are difficult to prepare due to strong quenching effects on fluorophores in the vicinity of noble metal nanoparticles such as gold (AuNPs). We successfully prepared plasmonic fluorescent nanocomposites of two cyanines (1 and 2) aggregating upon 2 - 40 nm AuNPs or streptavidin-conjugated 10 nm AuNPs. We used high throughput screening (HTS) for the first time to characterize the spectral properties, aggregation kinetics, aggregation density and photostability of the nanocomposites. Fluorescence from nanocomposites declined inversely with AuNPs size: 40 nm ≥ 20 nm > 10 nm > 5 nm > 2 nm. Sensitivity (limit of detection, LOD, 10(5) - 10(11) AuNPs/mL), brightness of the nanocomposites and surface coverage of AuNPs by cyanine aggregates were all influenced by five factors: 1) AuNPs size; 2) cyanine type (1 or 2); 3) aggregate density; 4) distance between aggregates and AuNPs surface; and 5) streptavidin protein conjugation to AuNPs. We propose a model for plasmonic fluorescent nanocomposites based on these observations. Our plasmonic fluorescent nanocomposites have applications in chemical and biological assays.

Hollow microneedle-based sensor for multiplexed transdermal electrochemical sensing.

The development of a minimally invasive multiplexed monitoring system for rapid analysis of biologically-relevant molecules could offer individuals suffering from chronic medical conditions facile assessment of their immediate physiological state. Furthermore, it could serve as a research tool for analysis of complex, multifactorial medical conditions. In order for such a multianalyte sensor to be realized, it must be minimally invasive, sampling of interstitial fluid must occur without pain or harm to the user, and analysis must be rapid as well as selective. Initially developed for pain-free drug delivery, microneedles have been used to deliver vaccines and pharmacologic agents (e.g., insulin) through the skin. Since these devices access the interstitial space, microneedles that are integrated with microelectrodes can be used as transdermal electrochemical sensors. Selective detection of glucose, glutamate, lactate, hydrogen peroxide, and ascorbic acid has been demonstrated using integrated microneedle-electrode devices with carbon fibers, modified carbon pastes, and platinum-coated polymer microneedles serving as transducing elements. This microneedle sensor technology has enabled a novel and sophisticated analytical approach for in situ and simultaneous detection of multiple analytes. Multiplexing offers the possibility of monitoring complex microenvironments, which are otherwise difficult to characterize in a rapid and minimally invasive manner. For example, this technology could be utilized for simultaneous monitoring of extracellular levels of, glucose, lactate and pH, which are important metabolic indicators of disease states (e.g., cancer proliferation) and exercise-induced acidosis.

Rational redesign of glucose oxidase for improved catalytic function and stability.

Glucose oxidase (GOx) is an enzymatic workhorse used in the food and wine industries to combat microbial contamination, to produce wines with lowered alcohol content, as the recognition element in amperometric glucose sensors, and as an anodic catalyst in biofuel cells. It is naturally produced by several species of fungi, and genetic variants are known to differ considerably in both stability and activity. Two of the more widely studied glucose oxidases come from the species Aspergillus niger (A. niger) and Penicillium amagasakiense (P. amag.), which have both had their respective genes isolated and sequenced. GOx from A. niger is known to be more stable than GOx from P. amag., while GOx from P. amag. has a six-fold superior substrate affinity (K(M)) and nearly four-fold greater catalytic rate (k(cat)). Here we sought to combine genetic elements from these two varieties to produce an enzyme displaying both superior catalytic capacity and stability. A comparison of the genes from the two organisms revealed 17 residues that differ between their active sites and cofactor binding regions. Fifteen of these residues in a parental A. niger GOx were altered to either mirror the corresponding residues in P. amag. GOx, or mutated into all possible amino acids via saturation mutagenesis. Ultimately, four mutants were identified with significantly improved catalytic activity. A single point mutation from threonine to serine at amino acid 132 (mutant T132S, numbering includes leader peptide) led to a three-fold improvement in k(cat) at the expense of a 3% loss of substrate affinity (increase in apparent K(M) for glucose) resulting in a specify constant (k(cat)/K(M)) of 23.8 (mM(-1) · s(-1)) compared to 8.39 for the parental (A. niger) GOx and 170 for the P. amag. GOx. Three other mutant enzymes were also identified that had improvements in overall catalysis: V42Y, and the double mutants T132S/T56V and T132S/V42Y, with specificity constants of 31.5, 32.2, and 31.8 mM(-1) · s(-1), respectively. The thermal stability of these mutants was also measured and showed moderate improvement over the parental strain.

Orthogonal cell-based biosensing: fluorescent, electrochemical, and colorimetric detection with silica-immobilized cellular communities integrated with an ITO-glass/plastic laminate cartridge.

This is the first report of a living cell-based environmental sensing device capable of generating orthogonal fluorescent, electrochemical, and colorimetric signals in response to a single target analyte in complex media. Orthogonality is enabled by use of cellular communities that are engineered to provide distinct signals in response to the model analyte. Coupling these three signal transduction methods provides additional and/or complementary data regarding the sample which may reduce the impact of interferants and increase confidence in the sensor's output. Long-term stability of the cells was addressed via 3D entrapment within a nanostructured matrix derived from glycerated silicate, which allows the device to be sealed and stored under dry, ambient conditions for months with significant retention in cellular activity and viability (40% viability after 60 days). Furthermore, the first co-entrapment of eukaryotic and bacterial cells in a silica matrix is reported, demonstrating multianalyte biodetection by mixing disparate cell lines at intimate proximities which remain viable and responsive. These advances in cell-based biosensing open intriguing opportunities for integrating living cells with nanomaterials and macroscale systems.

Lithographically defined three-dimensional graphene structures.

A simple and facile method to fabricate 3D graphene architectures is presented. Pyrolyzed photoresist films (PPF) can easily be patterned into a variety of 2D and 3D structures. We demonstrate how prestructured PPF can be chemically converted into hollow, interconnected 3D multilayered graphene structures having pore sizes around 500 nm. Electrodes formed from these structures exhibit excellent electrochemical properties including high surface area and steady-state mass transport profiles due to a unique combination of 3D pore structure and the intrinsic advantages of electron transport in graphene, which makes this material a promising candidate for microbattery and sensing applications.

Multiplexed microneedle-based biosensor array for characterization of metabolic acidosis.

The development of a microneedle-based biosensor array for multiplexed in situ detection of exercise-induced metabolic acidosis, tumor microenvironment, and other variations in tissue chemistry is described. Simultaneous and selective amperometric detection of pH, glucose, and lactate over a range of physiologically relevant concentrations in complex media is demonstrated. Furthermore, materials modified with a cell-resistant (Lipidure(®)) coating were shown to inhibit macrophage adhesion; no signs of coating delamination were noted over a 48-h period.

Lithographically-defined 3D porous networks as active substrates for surface enhanced Raman scattering.

Interferometric lithographically fabricated porous carbon acts as active substrates for Surface Enhanced Raman Scattering (SERS) applications with enhancement factors ranging from 7 to 9 orders of magnitude.

Lipid bilayer templated gold nanoparticles nanoring formation using zirconium ion coordination chemistry.

We used positively charged lipids to prepare lipid bilayer assemblies (LBAs) upon which we assembled negatively charged gold nanoparticles (AuNPs). Treatment of the assembly with zirconium chloride resulted in the formation of nanorings of the diameters inversely related to the zirconium ion concentration. The nanorings were attributed to the zirconium ion coordinated AuNPs formed during the lipid bilayer budding process promoted by the acid effect of zirconium chloride. Nanoring organization was also dependent on the fluidity of lipid bilayers, an indication of LBA-assisted nanomaterials organization. We suggest that such bioorganic-inorganic hybrid assemblies coupled to unique topological and morphological variations might be useful as stimuli-responsive sensors or storage compartments for proteins or drugs.

Integrated carbon fiber electrodes within hollow polymer microneedles for transdermal electrochemical sensing.

In this study, carbon fiber electrodes were incorporated within a hollow microneedle array, which was fabricated using a digital micromirror device-based stereolithography instrument. Cell proliferation on the acrylate-based polymer used in microneedle fabrication was examined with human dermal fibroblasts and neonatal human epidermal keratinocytes. Studies involving full-thickness cadaveric porcine skin and trypan blue dye demonstrated that the hollow microneedles remained intact after puncturing the outermost layer of cadaveric porcine skin. The carbon fibers underwent chemical modification in order to enable detection of hydrogen peroxide and ascorbic acid; electrochemical measurements were demonstrated using integrated electrode-hollow microneedle devices.

Lithographically defined 3D nanoporous nonenzymatic glucose sensors.

Nonenzymatic glucose oxidation is demonstrated on highly faceted palladium nanowflower-modified porous carbon electrodes fabricated by interference lithography. Varying electrodeposition parameters were used to control the final shape and morphology of the deposited nanoparticles on the 3D porous carbon which showed a 12 times increase in the electrochemically active surface area over analogous planar electrodes. Extremely fast amperometric glucose responses (achieving 95% of the steady state limiting current in less than 5s) with a linear range from 1 to 10mM and a detection limit of 10 µM were demonstrated. The unusual surface properties of the pyrolyzed photoresist films produced strongly adhered palladium crystal structures that were stable for hundreds of cycles towards glucose oxidation without noticeable current decay.

A parallel microfluidic channel fixture fabricated using laser ablated plastic laminates for electrochemical and chemiluminescent biodetection of DNA.

Herein is described the fabrication and use of a plastic multilayer 3-channel microfluidic fixture. Multilayer devices were produced by laser machining of plastic polymethylmethacrylate and polyethyleneterapthalate laminates by ablation. The fixture consisted of an array of nine individually addressable gold or gold/ITO working electrodes, and a resistive platinum heating element. Laser machining of both the fluidic pathways in the plastic laminates, and the stencil masks used for thermal evaporation to form electrode regions on the plastic laminates, enabled rapid and inexpensive implementation of design changes. Electrochemiluminescence reactions in the fixture were achieved and monitored through ITO electrodes. Electroaddressable aryl diazonium chemistry was employed to selectively pattern gold electrodes for electrochemical multianalyte DNA detection from double stranded DNA (dsDNA) samples. Electrochemical detection of dsDNA was achieved by melting of dsDNA molecules in solution with the integrated heater, allowing detection of DNA sequences specific to breast and colorectal cancers with a non-specific binding control. Following detection, the array surface could be renewed via high temperature (95 °C) stripping using the integrated heating element. This versatile and simple method for prototyping devices shows potential for further development of highly integrated, multi-functional bioanalytical devices.

Increased mass transport at lithographically defined 3-D porous carbon electrodes.

Increased mass transport due to hemispherical diffusion is observed to occur in 3D porous carbon electrodes defined by interferometric lithography. Enhanced catalytic methanol oxidation, after modifying the porous carbon with palladium nanoparticles, and uncharacteristically uniform conducting polymer deposition into the structures are demonstrated. Both examples result in two regions of hierarchical porosity that can be created to maximize surface area, via nanostructuring, within the extended porous network, while taking advantage of hemispherical diffusion through the open pores.

Cell-directed integration into three-dimensional lipid-silica nanostructured matrices.

We report a unique approach in which living cells direct their integration into 3D solid-state nanostructures. Yeast cells deposited on a weakly condensed lipid/silica thin film mesophase actively reconstruct the surface to create a fully 3D bio/nano interface, composed of localized lipid bilayers enveloped by a lipid/silica mesophase, through a self-catalyzed silica condensation process. Remarkably, this integration process selects exclusively for living cells over the corresponding apoptotic cells (those undergoing programmed cell death), via the development of a pH gradient, which catalyzes silica deposition and the formation of a coherent interface between the cell and surrounding silica matrix. Added long-chain lipids or auxiliary nanocomponents are localized within the pH gradient, allowing the development of complex active and accessible bio/nano interfaces not achievable by other synthetic methods. Overall, this approach provides the first demonstration of active cell-directed integration into a nominally solid-state three-dimensional architecture. It promises a new means to integrate "bio" with "nano" into platforms useful to study and manipulate cellular behavior at the individual cell level and to interface living organisms with electronics, photonics, and fluidics.