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.

京都大学 / 新制・課程博士 / 博士(農学) / 甲第23520号 / 農博第2467号 / 新制||農||1086(附属図書館) / 学位論文||R3||N5351(農学部図書室) / 京都大学大学院農学研究科食品生物科学専攻 / (主査)教授 谷 史人, 教授 保川 清, 准教授 中川 究也 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

No description available.

No description available.

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.

Es besteht enormes Interesse den Stofftransport in nanoskaligen Systemen zu verstehen und selektiv zu steuern, um analytische und synthetische Anwendungen zu entwickeln, aber auch um die physiologischen Prozesse lebender Zellen zu entschlüsseln. Im Rahmen dieser Arbeit wurde der Einfluss der elektrochemischen Doppelschicht an ausgewählten nanoskaligen Elektrolytsystemen untersucht. Die Gleichrichtung von Ionenströmen (engl. Ionic Current Rectification ICR) in Nanoporen mit einer Oberflächenladung äußert sich in einer gekrümmten Strom-Spannungs-Kurve. Die Überlappung von innerem und äußerem Potential ist dabei hinsichtlich der Ionenverteilung und somit der Porenleitfähigkeit einander verstärkend oder gegenläufig. Auf Grundlage dieses Mechanismus wurde die Gleichrichtung bei einem sehr großen Verhältnis von Porenöffnung zu Debye-Länge erklärt. Ferner wurde mittels der eingeführten relativen Leitfähigkeit κ´ die verschiedenen Leitfähigkeitszustände in Abhängigkeit der Elektrolytkonzentration und Temperatur sichtbar gemacht und Implikationen für Sensoranwendungen wie z.B. dem resistiven Pulszähler zur Partikelanalyse abgeleitet. Es wurde ein numerisches Modell basierend auf dem Poisson-Nernst-Planck-Gleichungssystem entwickelt, um die Translokation eines Nanopartikels durch eine konische Nanopore bei einer geringen Leitsalzkonzentration zu beschreiben. Neben dem klassischen Volumenausschluss-Effekt tritt zusätzlich ein Gleichrichtungseffekt (ICR-Effekt) in der Pore auf. Eine Analyse zur Entflechtung von Partikelgröße und Partikelladung aus der Pulshöhe und Pulsform wurde erfolgreich durchgeführt. Wie der Stofftransport durch eine Oberflächenladung auf dem umgebenden Material einer Nanoelektrode beeinflusst wird, wurde anhand des voltammetrischen Verhaltens diskutiert. An sehr kleinen Elektroden (< 10 nm) ist demnach der Einfluss der elektrochemischen Doppelschicht auf die Strom-Spannungs-Kurve besonders groß und kann auch bei Vorliegen eines hohen Leitsalzüberschusses nicht vernachlässigt werden. In leitsalzfreien Elektrolyten sind die gefundenen Effekte so deutlich, dass sie auch an größeren Elektroden experimentell zweifelsfrei festgestellt worden sind. / There is an enormous interest in understanding and selectively controlling the material transport in nanoscale systems to develop analytical and synthetic applications, but also to decipher the physiological processes of living cells. Within this thesis, the influence of the electrochemical double layer on selected nanoscale electrolyte systems was studied. Ionic Current Rectification (ICR) in nanopores carrying a surface charge manifests itself in a non-linear current-voltage-curve. The overlap of interior and exterior potential is cumulative or opposing with regard to the ion distribution and therefore the pore conductivity. Based on this mechanism, ICR for very large ratios of pore size and Debye length was explained. Furthermore, the different conducting states as a function of electrolyte concentration and temperature were visualized by introducing the relative conductivity κ´ and hence implications for sensor applications such as the resistive pulse sensor have been deduced. A numerical model based on the Poisson-Nernst-Planck-equations was developed to describe the translocation of a nanoparticle through a conical nanopore at a low electrolyte concentration. An additional rectification effect (ICR effect) occurs in the pore beside the conventional volume exclusion effect. An analysis was successfully performed to deconstruct the particle size and particle charge from the pulse height and shape. The material transport is affected by a surface charge on the shrouding material of nanoelectrodes as it was discussed by means of the voltammetric behaviour. The influence of the electrochemical double layer on the current-voltage-curve is particularly large at very small electrodes (< 10 nm) and cannot be neglected even at a high excess of supporting electrolyte. The observed effects were pronounced in unsupported electrolytes, so that they could be clearly detected experimentally at even larger electrodes.

Es besteht enormes Interesse den Stofftransport in nanoskaligen Systemen zu verstehen und selektiv zu steuern, um analytische und synthetische Anwendungen zu entwickeln, aber auch um die physiologischen Prozesse lebender Zellen zu entschlüsseln. Im Rahmen dieser Arbeit wurde der Einfluss der elektrochemischen Doppelschicht an ausgewählten nanoskaligen Elektrolytsystemen untersucht. Die Gleichrichtung von Ionenströmen (engl. Ionic Current Rectification ICR) in Nanoporen mit einer Oberflächenladung äußert sich in einer gekrümmten Strom-Spannungs-Kurve. Die Überlappung von innerem und äußerem Potential ist dabei hinsichtlich der Ionenverteilung und somit der Porenleitfähigkeit einander verstärkend oder gegenläufig. Auf Grundlage dieses Mechanismus wurde die Gleichrichtung bei einem sehr großen Verhältnis von Porenöffnung zu Debye-Länge erklärt. Ferner wurde mittels der eingeführten relativen Leitfähigkeit κ´ die verschiedenen Leitfähigkeitszustände in Abhängigkeit der Elektrolytkonzentration und Temperatur sichtbar gemacht und Implikationen für Sensoranwendungen wie z.B. dem resistiven Pulszähler zur Partikelanalyse abgeleitet. Es wurde ein numerisches Modell basierend auf dem Poisson-Nernst-Planck-Gleichungssystem entwickelt, um die Translokation eines Nanopartikels durch eine konische Nanopore bei einer geringen Leitsalzkonzentration zu beschreiben. Neben dem klassischen Volumenausschluss-Effekt tritt zusätzlich ein Gleichrichtungseffekt (ICR-Effekt) in der Pore auf. Eine Analyse zur Entflechtung von Partikelgröße und Partikelladung aus der Pulshöhe und Pulsform wurde erfolgreich durchgeführt. Wie der Stofftransport durch eine Oberflächenladung auf dem umgebenden Material einer Nanoelektrode beeinflusst wird, wurde anhand des voltammetrischen Verhaltens diskutiert. An sehr kleinen Elektroden (< 10 nm) ist demnach der Einfluss der elektrochemischen Doppelschicht auf die Strom-Spannungs-Kurve besonders groß und kann auch bei Vorliegen eines hohen Leitsalzüberschusses nicht vernachlässigt werden. In leitsalzfreien Elektrolyten sind die gefundenen Effekte so deutlich, dass sie auch an größeren Elektroden experimentell zweifelsfrei festgestellt worden sind. / There is an enormous interest in understanding and selectively controlling the material transport in nanoscale systems to develop analytical and synthetic applications, but also to decipher the physiological processes of living cells. Within this thesis, the influence of the electrochemical double layer on selected nanoscale electrolyte systems was studied. Ionic Current Rectification (ICR) in nanopores carrying a surface charge manifests itself in a non-linear current-voltage-curve. The overlap of interior and exterior potential is cumulative or opposing with regard to the ion distribution and therefore the pore conductivity. Based on this mechanism, ICR for very large ratios of pore size and Debye length was explained. Furthermore, the different conducting states as a function of electrolyte concentration and temperature were visualized by introducing the relative conductivity κ´ and hence implications for sensor applications such as the resistive pulse sensor have been deduced. A numerical model based on the Poisson-Nernst-Planck-equations was developed to describe the translocation of a nanoparticle through a conical nanopore at a low electrolyte concentration. An additional rectification effect (ICR effect) occurs in the pore beside the conventional volume exclusion effect. An analysis was successfully performed to deconstruct the particle size and particle charge from the pulse height and shape. The material transport is affected by a surface charge on the shrouding material of nanoelectrodes as it was discussed by means of the voltammetric behaviour. The influence of the electrochemical double layer on the current-voltage-curve is particularly large at very small electrodes (< 10 nm) and cannot be neglected even at a high excess of supporting electrolyte. The observed effects were pronounced in unsupported electrolytes, so that they could be clearly detected experimentally at even larger electrodes.

No description available.