Nanopore-based resistive pulse sensing represents an important class of single-molecule measurements. It provides information about many molecules of interest (i.e. DNA, proteins, peptides, clusters, polymers, etc.) without the need for labeling. Two experiments that are especially well suited for studying with nanopore sensors are DNA sequencing and DNA-protein force measurements. This thesis will describe progress that has been made in both areas. DNA sequencing has become an active area of research for stochastic single-molecule sensing, with many researchers striving for the ultimate goal of single-molecule de novo DNA sequencing. One intriguing method towards that goal involves the use of a DNA exonuclease or polymerase enzyme, which when attached close to the mouth of a pore, leads to cleavage of individual DNA nucleotide bases for loading into the pore for sensing. Though this method seems promising, the end goal has been elusive because the nucleotide motion is dominated by diffusion over the relevant length scales. This limits the likelihood of the cleaved nucleotide entering the pore to be characterized. The first part of this thesis will describe a method for addressing this problem, where it is shown that increasing the nucleotide capture probability can be achieved by lowering the bulk diffusion coefficient relative to the pore diffusion coefficient. The second part of this thesis will describe the design and implementation of a new type of sensor that combines a biological nanopore experimental apparatus with optical tweezers. The goal of this apparatus is to develop a means to independently measure the force on a charged molecule inside of the pore. The setup will be thoroughly described, and preliminary results showing that it is possible to optically trap a micron sized bead within a few microns of an isolated biological nanopore while simultaneously making current measurements through that pore will be presented. This will enable force measurements on DNA molecules tethered to the bead, which opens the door for the study of molecular force interactions between DNA and biological nanopores, DNA-bound protein interactions that cause diseased states, and controlled translocation of DNA through biological nanopores.

Arthur Ashkin's Nobel Prize-winning single-beam gradient force optical tweezers have revolutionized research in many fields of science. The invention has enabled various atomic and single molecular studies, proving to be an essential tool for observing and understanding nature at the nanoscale. This thesis showcases the uniqueness of single-beam gradient force traps and the advances necessary to overcome the limitations inherent in conventional techniques of optical trapping. With decreasing particle sizes, the power required for a stable trap increases and could potentially damage a particle. This is a significant limitation for studying biomolecules using conventional optical traps. Plasmonic nanoaperture optical trapping using double-nanohole apertures is introduced as a solution to overcoming these limitations. Achievements in double-nanohole optical trapping made possible by the pioneering work of Gordon et. al are highlighted as well. This thesis focuses on the advances in nanoaperture fabrication methods and improvements to experimental techniques adopted in single molecular optical trapping studies. The technique of colloidal lithography is discussed as a cost-effective high-throughput alternative method for nanofabrication. The limitation in using this technique for producing double-nanohole apertures with feature sizes essential for optical trapping is analyzed. Improvements to enable tuning of aperture diameter and cusp separation is one of the main achievements of the work detailed in this thesis. Furthermore, the thesis explains the modified fabrication process tailor-made for designing double-nanohole apertures optimized for optical trapping. Transmission characterization of various apertures fabricated using colloidal lithography is carried out experimentally and estimated by computational electrodynamics simulations using the finite-difference time-domain (FDTD) method. Optical trapping with double-nanohole apertures fabricated using colloidal lithography is demonstrated with distinct results revealing trapping of a single polystyrene molecule, a rubisco enzyme and a bovine serum albumin (BSA) protein. / Graduate

There are a growing variety of research fields requiring non-contact micro- manipulation. An increasing number of these fields are turning to optical tweezers as a solution, owing to their high spatial and temporal resolution. Optical tweezers have the ability to quantitively exert and measure forces on the piconewton scale, a convenient force scale for soft biological materials, and are hugely versatile due to the wide assortment of beam shaping techniques that can be employed. The work in this thesis can be broadly divided into two main themes: that quantifying the optical trapping forces in shaped beams; and bringing control and simplification of complex systems to non-expert users who may utilise optical tweezers as part of interdisciplinary collaborations. Static beam shaping is used to generate a conically refracted optical trap and the trapping properties are characterised. It is shown that trapping in the lower Raman spot gives full, 3D gradient trapping, while the upper Raman spot allows for particle guiding due to its levitation properties. Particles in the Lloyd/Poggendorff rings experience a lower trap stiffness than particles in the lower Raman spot but benefit from rotational control. Dynamic beam shaping techniques are exploited for the simplification of complex systems through the development and testing of the HoloHands program. This software allows a holographic optical tweezers experiment to be controlled by gestures that are detected by a Microsoft Kinect. Multiple particle manipulation is demonstrated, as well as a calibration of the tweezers system. Application of trapping forces is demonstrated through an examination of integrin – ligand bond strength. Both wild type effector T cells and those with a kindlin-3 binding site mutation similar to that found in neutrophils from Leukocyte Adhesion Deficiency sufferers are investigated. Through the use of back focal plane interferometry, a bond rupture force of (17.9 ± 0.6) pN at a force loading rate of (30 ± 4) pN/s, was measured for single integrins expressed on wild type cells. As expected, a significant drop in rupture force of bonds was found for mutated cells, with a measured rupture force of (10.1 ± 0.9) pN at the same pulling rate. Therefore, kindlin-3 binding to the cytoplasmic tail of the β2-tail directly affects bond strength of single integrin-ligand bonds. An experimental system for studying these cells under more physiologically relevant conditions is also presented. Additionally, a low-cost optical micromanipulation system that makes use of simple microfabricated components coupled to a smartphone camera for imaging is proposed and demonstrated. Through the layering of hanging droplets of polydimethylsiloxane (PDMS) on microscope coverslips, lenses capable of optical trapping are created. Combination of PDMS with Sudan II dye led to the fabrication of long pass filters. An extension of this low-cost system into the life sciences is proposed through the adaptive use of bubble wrap, which allows for the culturing of cells in a chamber compatible with optical trapping.

This dissertation describes the development of a device capable of suspending a microscale object in a controlled flow. The uPIVOT is a system integrating two laser-based techniques: micron particle image velocimetry (uPIV) and optical tweezers (OT). The OT allows the suspension and manipulation of micron-sized objects such as microspheres or biological cells. uPIV provides imaging of the suspended object and velocity measurements from which fluid induced stresses can be determined. Using this device, we measured fluid velocities around an optically suspended polystyrene microsphere (an experimental first) and studied the interaction between two particles suspended in a uniform flow. The results were consistent with theoretical low Reynolds number, Newtonian flow predictions. Additionally, we analyzed a single cell's mechanical response to a controlled and measurable multiaxial external force (fluid flow) without the cell being physically attached to a surface. The cell's mechanical response was monitored by observing its morphology and measuring its deformation. The results show significant deformations of optically suspended cells at substantially smaller stresses than previously reported and demonstrate the opportunity to optically distinguish a cell by its trapping efficiency. These initial applications of the uPIVOT demonstrate the potential of this unique device as a research tool for novel studies in the fields of fluid/particle(s) interactions, non-Newtonian fluid mechanics, and single cell biomechanics.

Studies of light-matter interactions in organic semiconductors and in optical tweezer trapping of nanoparticles are presented. In the research related to organic semiconductor materials, a variety of novel materials and their composites have been characterized, and physical mechanisms behind their optoelectronic properties have been established. Three novel functionalized hexacene derivatives were deemed sufficiently stable to enable characterization of these materials in devices. From dark current and photocurrent measurements of the hexacene thin-films, it was determined that all three derivatives are photoconductive in the near-infrared, and space charge limited mobility values were obtained. In addition, physical mechanisms behind charge transfer, charge carrier photogeneration, and charge transport in small-molecule donor/acceptor composite films have been systematically studied. In these studies, it was determined that the charge transfer from the donor to the acceptor molecule can result in either an emissive charge transfer exciton (exciplex) or a non-emissive charge transfer exciton formation, depending on the energy difference between LUMO of the donor and the acceptor. However, the most dramatic trends in photoluminescent and photoconductive properties of the donor/acceptor composites were correlated with the separation between the donor and acceptor molecules at the donor/acceptor interface. In particular, composite films with larger separations exhibited electric field-assisted charge transfer exciton dissociation, which contributed to nanosecond time-scale photocurrents under a 500 ps pulsed photoexciation. Large donor/acceptor separation also resulted in reduced charge carrier recombination, which led to a factor of 5-10 increase in continuous wave photocurrents in certain donor/acceptor composites, as compared to those in pristine donor films. In the optical tweezer based studies, work towards the development of high spatial resolution optical tweezer controlled nanoprobes is presented. In particular, the possibility of exploiting the optical resonance of a particle to increase the optical tweezer forces acting on it within the trap has been investigated. Such an increase in the force would improve the potential spatial resolution of an optical tweezer controlled probe. Experimental results and numerical simulations on micron sized resonant dielectric particles showed a small increase in the optical forces that confine such particles within the trap, when tweezer trapping is conducted at wavelengths on the red-side of the optical resonance. Preliminary work on optical tweezer controlled ion/pH sensitive probes and on surface charge measurements is also reported. / Graduation date: 2012

Riboswitches are gene regulatory elements found in messenger RNA that function by changing structure upon the binding of a ligand to an aptamer domain. Single adenine-binding pbuE riboswitch aptamer RNAs were unfolded and refolded co-transcriptionally using optical tweezers for single molecule force spectroscopy. The kinetic and energetic properties of distinct folding intermediates were characterised with and without the binding of adenine. These observed intermediates were related to structural elements of the aptamer, which were found to fold sequentially, in a transcriptionally independent manner. The mechanical switch underlying the regulatory action of the riboswitch was observed directly (adenine stabilisation of the weakest helix), and the energy landscape for the folding was reconstructed. The construction of a dual-beam optical trap with separate detection and trapping laser beams manipulated and focused into a rigid, modified inverted microscope is also described. This instrument aims to achieve ngstrm-level resolution through careful design to reduce noise.

Mechanical unfolding of -1 frameshift signals such as RNA pseudoknots have aimed to test the hypothesis that the stability of the pseudoknot is directly correlated to the frameshifting efficiency. Here we report unfolding of the Beet Western Yellow Virus (BWYV) pseudoknot by optical tweezers experiments complemented by computer simulations using steered molecular dynamics (SMD). Seven pseudoknot scenarios were studied: the wild-type pseudoknot in the presence and absence of Mg<super>2+</super>, the wild-type pseudoknot at high pH (deprotonated C8), and C8U, C8A, A24G, G19U, and G19UC mutant constructs. The mutants were selected to probe three key structural features of the BWYV pseudoknot, a triple-stranded helix at the base of stem 1, the stem junction region of stem 1 and stem 2, and a unique quadruple base-pair interaction involving a protonated cytosine in position 8 (C8). These regions are thought to control ribosomal frameshifting by different strategies such as thermodynamic stability, kinetic influences, and dynamics involving contacts with the ribosome. In addition, the mutants have been shown to either abolish frameshifting ability of the pseudoknot (C8 mutant cases and A24G), or actually increase the frameshifting efficiency (as seen with G19U and G19UC). We find three major conclusions from the stretching of the pseudoknot constructs with optical tweezers. First, stretching in the absence of Mg<super>2+</super> results in no observed unfolding transitions. We interpret this to mean that magnesium is indispensible for the stable folding of the pseudoknot. Second, we found that frameshifting efficiency is not correlated with the force required to unfold the pseudoknots. However, we observe the unfolding of stem 1 in all of the pseudoknots stretched, where stem 2 unfolding is below our noise level. For this reason, we cannot rule out the possibility that an estimate of the thermodynamic stability of the entire pseudoknot would correlate with frameshifting efficiency. And third, we found that each pseudoknot mutant that resulted in reduced frameshifting efficiency also exhibited more off-equilibrium unfolding transitions that the wild-type pseudoknot under comparable loading rates. We conclude from these studies that the resistance of a pseudoknot to unfolding is controlled by both thermodynamic and kinetic parameters. We then suggest new technologies that would allow for greater resolution in order to correlate pseudoknot unfolding behavior with -1 programmed ribosomal frameshifting events.

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Optical tweezers have allowed us to harness the momentum of light to trap, move, and manipulate microscopic particles with Angstrom-level precision. Position and force feedback systems grant us the ability to feel the microscopic world. As a tool, optical tweezers have allowed us to study a variety of biological systems, from the mechanical properties of red blood cells to the quantised motion of motor-molecules such as kinesin. They have been applied, with similar impact, to the manipulation of gases, atoms, and Bose-Einstein condensates. There are, however, limits to their applicability. Historically speaking, optical tweezers have only been used to trap relatively simple structures such as spheres or cylinders. This thesis is concerned with the development of a fabricational and optical manipulation protocol that allows holographical optical tweezers to trap photonic membranes. Photonic membranes are thin, flexible membranes, that are capable of supporting nanoplasmonic features. These features can be patterned to function as metamaterials, granting the photonic membrane the ability to function as almost any optical device. It is highly desirable to take advantage of these tools in a microfluidic environment, however, their extreme aspect ratios mean that they are not traditionally compatible with the primary technology of microfluidic manipulation: optical tweezers. In line with recent developments in optical manipulation, an holistic approach to optical trapping is used to overcome these limitations. Full six-degree-of-freedom control over a photonic membrane is demonstrated through the use of holographical optical tweezers. Furthermore, a photonic membrane (PM)-based surface-enhanced Raman spectroscopy sensor is presented which is capable of detecting rhodamine dye from a topologically undulating sample. This work moves towards marrying these technologies such that photonic membranes, designed for bespoke applications, can be readily deployed into a microfluidic environment. Extending the range of tools available in the microfluidic setting helps pave the way toward the next set of advances in the field of optical manipulation.