Publications

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When attempting to integrate single-molecule fluorescence microscopy with microfabricated devices such as microfluidic channels, fabrication constraints may prevent using traditional coverslips. Instead, the fabricated devices may require imaging through material with a different thickness or index of refraction. Altering either can easily reduce the quality of the image formation (measured by the Strehl ratio) by a factor of 2 or more, reducing the signal-to-noise ratio accordingly. In such cases, successful detection of single-molecule fluorescence may prove difficult or impossible. Here we provide software to calculate the effect of non-design materials upon the Strehl ratio or ensquared energy and explore the impact of common materials used in microfabrication.

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Dermal interstitial fluid (ISF) is an underutilized information-rich biofluid potentially useful in health status monitoring applications whose contents remain challenging to characterize. Here, we present a facile microneedle approach for dermal ISF extraction with minimal pain and no blistering for human subjects and rats. Extracted ISF volumes were sufficient for determining transcriptome, and proteome signatures. We noted similar profiles in ISF, serum, and plasma samples, suggesting that ISF can be a proxy for direct blood sampling. Dynamic changes in RNA-seq were recorded in ISF from induced hypoxia conditions. Finally, we report the first isolation and characterization, to our knowledge, of exosomes from dermal ISF. The ISF exosome concentration is 12–13 times more enriched when compared to plasma and serum and represents a previously unexplored biofluid for exosome isolation. This minimally invasive extraction approach can enable mechanistic studies of ISF and demonstrates the potential of ISF for real-time health monitoring applications.

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The purpose of this project was to gain a fundamental understanding of molecular diffusion in nanogap electrodes and the diffusive behavior of single molecules undergoing electron transfer. Electrochemical methods for single molecule detection have remained elusive due to the vanishingly small currents involved in single molecule electron transfer. Electrochemical detection of single molecules undergoing redox cycling would enable detection of single enzymes, proteins, and DNA strands resulting in new and improved ultrasensitive sensing devices impacting Detection At The Limits research challenge (DATL), supporting needs in DHS and DoD. We attempted to integrate orthogonal validation techniques, Total Internal Reflection Fluorescence Microscopy (TIRF), and molecular simulation to clarify (1) the mechanism leading to current build up due to redox cycling and (2) diffusion and adsorption of single molecules undergoing redox reactions. While creation of nanogap electrodes with transparent windows was ultimately successful in this project (along with TIRF demonstration of single molecule imaging), time and methods constraints did not allow final electrochemical measurements to be coupled for simultaneous interrogation.

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Sandia National Laboratories will provide technical assistance, within time and budget, to Requester on testing and analyzing a microneedle-based electrolyte sensing platform. Hollow microneedles will be fabricated at Sandia and integrated with a fluidic chip using plastic laminate prototyping technology available at Sandia. In connection with commercial ion selective electrodes the sensing platform will be tested for detection of electrolytes (sodium and/or potassium) within physiological relevant concent ration ranges.

Optical fluorescence-based DNA assays are commonly used for pathogen detection and consist of an optical substrate containing DNA capture molecules, binding of target RNA or DNA sequences, followed by detection of the hybridization event with a fluorescent probe. Though fluorescence detection can offer exquisite signal-to-background ratios, with high specificity, vast opportunities exist to improve current optical-based genomic sensing approaches. For these reasons, there is a clear need to explore alternative optical sensing paradigms to alleviate these restrictions. Bio-templated nanomaterial synthesis has become a powerful concept for developing new platforms for bio-sensing, as the biomolecule of interest can act as part of the sensing transducer mechanism. We explored the use of DNA origami structures to immobilize gold nanoparticles in very precise localized arrangements producing unique optical absorption properties with implications in novel DNA sensing schemes. We also explored the use of in-situ TEM as a novel characterization method for DNA-nanoparticle assemblies.

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We report here the characteristics of photoelectrochemical (PEC) etching of epitaxial InGaN semiconductor thin films using a narrowband laser with a linewidth less than ∼1 nm. In the initial stages of PEC etching, when the thin film is flat, characteristic voltammogram shapes are observed. At low photo-excitation rates, voltammograms are S-shaped, indicating the onset of a voltage-independent rate-limiting process associated with electron-hole-pair creation and/or annihilation. At high photo-excitation rates, voltammograms are superlinear in shape, indicating, for the voltage ranges studied here, a voltage-dependent rate-limiting process associated with surface electrochemical oxidation. As PEC etching proceeds, the thin film becomes rough at the nanoscale, and ultimately the self-limiting etch kinetics lead to an ensemble of nanoparticles. This change in InGaN film volume and morphology leads to a characteristic dependence of PEC etch rate on time: an incubation time, followed by a rise, then a peak, then a slow decay.

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Bioweapons and emerging infectious diseases pose growing threats to our national security. Both natural disease outbreak and outbreaks due to a bioterrorist attack are a challenge to detect, taking days after the outbreak to identify since most outbreaks are only recognized through reportable diseases by health departments and reports of unusual diseases by clinicians. In recent decades, arthropod-borne viruses (arboviruses) have emerged as some of the most significant threats to human health. They emerge, often unexpectedly, from cryptic transmission foci causing localized outbreaks that can rapidly spread to multiple continents due to increased human travel and trade. Currently, diagnosis of acute infections requires amplification of viral nucleic acids, which can be costly, highly specific, technically challenging and time consuming. No diagnostic devices suitable for use at the bedside or in an outbreak setting currently exist. The original goals of this project were to 1) develop two highly sensitive and specific diagnostic assays for detecting RNA from a wide range of arboviruses; one based on an electrochemical approach and the other a fluorescent based assay and 2) develop prototype microfluidic diagnostic platforms for preclinical and field testing that utilize the assays developed in goal 1. We generated and characterized suitable primers for West Nile Virus RNA detection. Both optical and electrochemical transduction technologies were developed for DNA-RNA hybridization detection and were implemented in microfluidic diagnostic sensing platforms that were developed in this project.

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Formation of complex nanomaterials would ideally involve single-pot reaction conditions with one reactive site per nanoparticle, resulting in a high yield of incrementally modified or oriented structures. Many studies in nanoparticle functionalization have sought to generate highly uniform nanoparticles with tailorable surface chemistry necessary to produce such conjugates, with limited success. In order to overcome these limitations, we have modified commercially available nanoparticles with multiple potential reaction sites for conjugation with single ssDNAs, proteins, and small unilamellar vesicles. These approaches combined heterobifunctional and biochemical template chemistries with single molecule optical methods for improved control of nanomaterial functionalization. Several interesting analytical results have been achieved by leveraging techniques unique to SNL, and provide multiple paths for future improvements for multiplex nanoparticle synthesis and characterization. Hyperspectral imaging has proven especially useful for assaying substrate immobilized fluorescent particles. In dynamic environments, temporal correlation spectroscopies have been employed for tracking changes in diffusion/hydrodynamic radii, particle size distributions, and identifying mobile versus immobile sample fractions at unbounded dilution. Finally, Raman fingerprinting of biological conjugates has been enabled by resonant signal enhancement provided by intimate interactions with nanoparticles and composite nanoshells.