In recent years there has been an increased drive towards point of care testing (POCT), in which assays are performed at the site of the patient. This has many benefits, critically; the time for a result to be obtained will be significantly reduced, allowing for greater and more effective decision making. Many currently used bioassay methods are not affordable in resource poor areas where infectious disease is most prevalent, in order to combat this issue many research groups are attempting to miniaturise equipment for portability and make assays more affordable and therefore more accessible. With the aims of generating a new assay platform which is highly portable and affordable, the work in this thesis presents the development of several generic methods utilising nano- and micro-scale beads coated with aptamer which are then monitored interacting with target proteins with Tunable Resistive Pulse Sensing (TRPS). Aptamers are short oligonucleotide sequences which are capable of binding to a wide range of targets with high selectivity and comparable affinity to antibodies while possessing greater stability and have begun to challenge the role of antibodies. When aptamers bind a target, they often undergo a conformational change. In the assays described herein, this conformational change is key to the observed signal changes. TRPS is a pore-based system in which beads moving through a pore cause a measurable increase in resistance which can be used to derive particle size, concentration, and mobility. During the course of this thesis several template TRPS aptasensors have been developed. TRPS was successfully used to confirm the successful coating of nano- and micro-scale beads with DNA aptamers by monitoring an increase in electrophoretic mobility when the negatively charged DNA is added to the surface. Following on from this, TRPS was used to monitor the interaction of aptamer tagged beads with thrombin protein enabling thrombin detection down to 1.4 nM and the comparison of several thrombin-aptamers with results comparable to previously published SPR data. Thrombin was postulated to shield the negative DNA, resulting in a decrease in mobility, and the magnitude of this charge shielding was found to depend upon the binding mechanism of the aptamer used. This effect is not thought to be specific to our system nor to thrombin, the principles outlined here may be applied to other RPS technologies, or by interchanging of the aptamer, different proteins. In later chapters, this method is expanded to include multiplexed detection of growth factors and a significant improvement in signal. vi Following on from this, the controlled aggregation of avidin coated beads in the presence of biotinylated-BSA was explored. Factors impacting upon this assay were discussed including magnetic separation, particle size and particle concentration, and different methods of data interpretation were presented. This aggregation study identified several key parameters in the use of TRPS in aggregation assays. Using the methods outlined by the study of aggregates, a dispersion assay was then designed in which the interaction of thrombin proteins with clusters of particles brought about the release of many small particles by the disruption of double stranded DNA linkages. This dispersion assay incorporated magnetic separation to simplify the read-out and relied on measuring particle concentration rather than mobility, enabling the use of additional pressure to increase speed and ease of use. Using this method, thrombin was able to be detected down to 100 fM, a significant advancement in TRPS aptasensors.

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Much of recent progress in medical research and diagnostics has been enabled through the advances in molecular analysis technologies, which now permit the detection and analysis of single molecules with high sensitivity and specificity. Assay sensitivity is fundamentally limited by the efficiency of the detection method used for read-out. Inefficient detection systems are usually compensated for by molecular amplification at the cost of elevated assay complexity. This thesis presents microfluidic automation and digital quantification of targeted nucleic acid detection methods based on padlock and selector probes and rolling circle amplification (RCA). In paper I, the highly sensitive, yet complex circle-to-circle amplification assay was automated on a digital microfluidic chip. In paper II, a new RCA product (RCP) sensing principle was developed based on resistive pulse sensing that allows label free digital RCP quantification. In paper III, a microfluidic chip for spatial RCP enrichment was developed, which enables the detection of RCPs with an unprecedented efficiency and allows for deeper analysis of enriched RCPs through next generation sequencing chemistry. In paper IV, a smart phone was converted into a multiplex fluorescent imaging device that enables imaging and quantification of RCPs on slides as well as within cells and tissues. KRAS point mutations were detected (i) in situ, directly in tumor tissue, and (ii) by targeted sequencing of extracted tumor DNA, imaged with the smart phone RCP imager. This thesis describes the building blocks required for the development of highly sensitive low-cost RCA-based nucleic acid analysis devices for utilization in research and diagnostics.

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