Integration of Biomolecular Recognition Elements with Solid-State Devices

Continued advances in stand-alone chemical sensors requires the introduction of new materials and transducers, and the seamless integration of the two. Electronic sensors represent one of the most efficient and versatile sensing transducers that offer advantages of high sensitivity, compatibility with multiple types of materials, network connectivity, and capability of miniaturization. With respect to materials to be used on this platform, many classes and subclasses of materials, including polymers, oxides, semiconductors, and composites have been investigated for various sensing environments. Despite numerous commercial products, major challenges remain. These include enhancing materials for selectivity/specificity, and low cost integration/ miniaturization of devices. Breakthroughs in either area would signify a transformative innovation. In this thesis, a combined materials and devices approach has been explored to address the above challenges. Biomolecular recognition elements, exemplified by aptamers, are the most recent addition to the library of tunable materials for specific detection of analytes. At the same time, nanoscale electrical devices based on tunnel junctions offer the potential for simple design, large scale integration, field deployment, network connectivity, and importantly, miniaturization to the molecular scale. To first establish a framework for studying sorption properties of solid oligonucleotides, custom designed aptamers sequences were studied to determine equilibrium partition coefficients. Linear-solvation-energy-relationship (LSER) analysis provides quantifications of non-covalent bonding properties and reveals the dominance of hydrogen bonding basicity in oligonucleotides. We find that DNA-analyte interactions have selective sorption properties similar to synthetic polymers. LSER analysis provides a chemical basis for material-analyte interactions. Oligonucleotide sequences were integrated with gold nanoparticle chemiresistors to transfer the selective sorption properties to microfabricated electrical devices. Responses generated by oligonucleotides under dry conditions were similar to standard organic mediums used as capping agents and suggests that DNA-based chemiresistor sensors operate with a similar mechanism based on sorption induced swelling. The equilibrium mass-sorption behavior of bulk DNA films could be translated to the chemiresistor sensitivity profiles. Our work establishes oligonucleotides, including aptamers, as a class of sorptive materials that can be systematically studied, engineered, and integrated with nanoscale electronic sensor devices. Experiments to investigate secondary structure effects were inconclusive and we conclude that further work should investigate DNA aptamers in buffered, aqueous environments to unequivocally establish the ability of chemiresitors to signal molecular recognition. Concurrent with the above studies, device integration and miniaturization was investigated to combine many sensing materials into a single, compact design. Arrays of nanoscale chemiresistors with critical features on the order of 10 – 100 nm were developed, using dielectrophoretic assembly of gold nanoparticles to control placement of the sensing material with nanometer accuracy. The nanoscale chemiresistors achieved the smallest known gold nanoparticle chemiresistors relying on just 2 – 3 layers of nanoparticles within 50 nm gaps, and were found to be more robust and less dependent on film thickness than previously published designs. Due to shorter diffusion paths, the sensors are also faster in response and recovery. A proof-of-concept, integrated single-chip sensor array was created and it showed similar response patterns as non-integrated sensor arrays. Dielectrophoresis is established as a key enabler for nanoscale, integrated devices. Based on the major findings of the thesis work, additional investigations were initiated to investigate the potential for nanoscale chemiresitor sensors to operate in buffered, aqueous (liquid) flow cells. Preliminary experiments show that chemiresistor sensing is transferable to liquid environments where analyte molecules are observed to partition from the bulk liquid to the sensing materials, leading to a detectable change of the device electrical properties. Comparing micron- and nano-scale devices fabricated using aqueous oligonucleotide-functionalized gold nanoparticles, it was found that nanoscale chemiresistors are more resistant to solvent damage than 5 µm chemiresistors. We conclude that future experiments to investigate aptamer sensing in aqueous solutions is a promising direction. Overall, this thesis is a significant contribution to materials development and device design to attain improved sensor selectivity and higher levels of device integration. First, it offers a scheme for design, selection, and validation of materials that confer analyte-specific interactions. Second, it paves the way for large scale sensor integration and parallel operation on a single chip. Lastly, it offers an approach to combine biomolecular recognition elements with electronic devices into robust, nanoscale detection systems. Based on the major findings of the thesis work, additional investigations were initiated to investigate the potential for nanoscale chemiresitor sensors to operate in buffered, aqueous (liquid) flow cells. Preliminary experiments show that chemiresistor sensing is transferable to liquid environments where analyte molecules are observed to partition from the bulk liquid to the sensing materials, leading to a detectable change of the device electrical properties. Comparing micron- and nano-scale devices fabricated using aqueous oligonucleotide-functionalized gold nanoparticles, it was found that nanoscale chemiresistors are more resistant to solvent damage than 5 µm chemiresistors. We conclude that future experiments to investigate aptamer sensing in aqueous solutions is a promising direction. Overall, this thesis is a significant contribution to materials development and device design to attain improved sensor selectivity and higher levels of device integration. First, it offers a scheme for design, selection, and validation of materials that confer analyte-specific interactions. Second, it paves the way for large scale sensor integration and parallel operation on a single chip. Lastly, it offers an approach to combine biomolecular recognition elements with electronic devices into robust, nanoscale detection systems.