A portable device for time-resolved fluorescence based on an array of CMOS SPADs with integrated microfluidics

[eng] Traditionally, molecular analysis is performed in laboratories equipped with desktop instruments operated by specialized technicians. This paradigm has been changing in recent decades, as biosensor technology has become as accurate as desktop instruments, providing results in much shorter periods and miniaturizing the instrumentation, moving the diagnostic tests gradually out of the central laboratory. However, despite the inherent advantages of time-resolved fluorescence spectroscopy applied to molecular diagnosis, it is only in the last decade that POC (Point Of Care) devices have begun to be developed based on the detection of fluorescence, due to the challenge of developing high-performance, portable and low-cost spectroscopic sensors. This thesis presents the development of a compact, robust and low-cost system for molecular diagnosis based on time-resolved fluorescence spectroscopy, which serves as a general-purpose platform for the optical detection of a variety of biomarkers, bridging the gap between the laboratory and the POC of the fluorescence lifetime based bioassays. In particular, two systems with different levels of integration have been developed that combine a one-dimensional array of SPAD (Single-Photon Avalanch Diode) pixels capable of detecting a single photon, with an interchangeable microfluidic cartridge used to insert the sample and a laser diode Pulsed low-cost UV as a source of excitation. The contact-oriented design of the binomial formed by the sensor and the microfluidic, together with the timed operation of the sensors, makes it possible to dispense with the use of lenses and filters. In turn, custom packaging of the sensor chip allows the microfluidic cartridge to be positioned directly on the sensor array without any alignment procedure. Both systems have been validated, determining the decomposition time of quantum dots in 20 nl of solution for different concentrations, emulating a molecular test in a POC device.[cat] Tradicionalment, l'anàlisi molecular es realitza en laboratoris equipats amb instruments de sobretaula operats per tècnics especialitzats. Aquest paradigma ha anat canviant en les últimes dècades, a mesura que la tecnologia de biosensor s'ha tornat tan precisa com els instruments de sobretaula, proporcionant resultats en períodes molt més curts de temps i miniaturitzant la instrumentació, permetent així, traslladar gradualment les proves de diagnòstic fora de laboratori central. No obstant això i malgrat els avantatges inherents de l'espectroscòpia de fluorescència resolta en el temps aplicada a la diagnosi molecular, no ha estat fins a l'última dècada que s'han començat a desenvolupar dispositius POC (Point Of Care) basats en la detecció de la fluorescència, degut al desafiament que suposa el desenvolupament de sensors espectroscòpics d'alt rendiment, portàtils i de baix cost. Aquesta tesi presenta el desenvolupament d'un sistema compacte, robust i de baix cost per al diagnòstic molecular basat en l'espectroscòpia de fluorescència resolta en el temps, que serveixi com a plataforma d'ús general per a la detecció òptica d'una varietat de biomarcadors, tancant la bretxa entre el laboratori i el POC dels bioassaigs basats en l'anàlisi de la pèrdua de la fluorescència. En particular, s'han desenvolupat dos sistemes amb diferents nivells d'integració que combinen una matriu unidimensional de píxels SPAD (Single-Photon Avalanch Diode) capaços de detectar un sol fotó, amb un cartutx microfluídic intercanviable emprat per inserir la mostra, així com un díode làser UV premut de baix cost com a font d'excitació. El disseny orientat a la detecció per contacte de l'binomi format pel sensor i la microfluídica, juntament amb l'operació temporitzada dels sensors, permet prescindir de l'ús de lents i filtres. Al seu torn, l'empaquetat a mida de l'xip sensor permet posicionar el cartutx microfluídic directament sobre la matriu de sensors sense cap procediment d'alineament. Tots dos sistemes han estat validats determinant el temps de descomposició de "quantum dots" en 20 nl de solució per a diferents concentracions, emulant així un assaig molecular en un dispositiu POC

The Design and Construction of Novel Near -Infrared Time -Correlated Single Photon Counting Devices for the Identification of Analytes in Multiplexed Applications.

This manuscript details the design, construction, and application of novel near infrared time correlated single photon counting devices to the identification of analytes in analytical separations. The thrust of this research is to provide a simple, low cost technique for the high-speed identification of DNA sequencing bases that are labeled with a series of unique near infrared fluorophores. These fluorophores are unique because they possess the same emission and absorption maxima, but different fluorescence lifetimes. Consequently, they allow analytes to be discriminated by fluorescence lifetime as opposed to color. The first goal of this dissertation research was to implement a time correlated single photon counting system with the use of single mode fiber optics. Utilizing a passively mode locked Ti: Sapphire Laser, a single photon avalanche diode, single mode fiber optics and a mechanical switch a fiber optic based time correlated single photon counting device with subnanosecond resolution was constructed. The experimental results showed that group velocity dispersion was low and that it was possible to perform multiple time correlated single photon counting experiments with a limited number of excitation sources and detectors. It was determined that the average instrumental response of each channel was 181 picoseconds. The fluorescence lifetime of a near infrared dye, aluminum tetrasulfonated naphthalocyanine was determined to be 3.08 nanoseconds. The second phase of this doctoral research involved the construction and characterization of a near infrared time correlated single photon counting scanning device. This integrated device consisted of a pulsed diode laser, single photon avalanche diode, and a time correlated single photon counting board. The instrument response function of this system was determined to be less than 300 ps. The sensitivity and ability to discriminate between various fluorophores was determined. In addition to its application for scanning solid surfaces such as DNA microarrays, the device was utilized to detect analytes in a micro-capillary electrophoresis separation. The fluorescence lifetimes of these analytes were determined on-line

Capillary and microchip gel electrophoresis using multiplexed fluorescence detection with both time-resolved and spectral-discrimination capabilities: applications in DNA sequencing using near-infrared fluorescence

Increasing the information content obtainable from a single assay and system miniaturization has continued to be important research areas in analytical chemistry. The research presented in this dissertation involves the development of a two-color, time-resolved fluorescence microscope for the acquisition of both steady-state and time-resolved data during capillary and microchip electrophoresis. The utility of this hybrid fluorescence detector has been demonstrated by applying it to DNA sequencing applications. Coupling color discrimination with time-resolved fluorescence offers increased multiplexing capabilities because the lifetime data adds another layer of information. An optical fiber-based fluorescence microscope was constructed, which utilized fluorescence in near-IR region, greatly simplifying the hardware and allowing superior system sensitivity. Time-resolved data was processed using electronics configured in a time-correlated single photon counting format. Cross-talk between color channels was successfully eliminated by utilizing the intrinsic time-resolved capability associated with the detector. The two-color, time-resolved microscope was first coupled to a single capillary and carried out two-color, two-lifetime sequencing of an M13 template, achieving a read length of 650 bps at a calling accuracy of 95.1%. The feasibility of using this microscope with microchips (glass-based chips) for sequencing was then demonstrated. Results from capillaries and microchips were compared, with the microchips providing faster analysis and adequate electrophoretic performance. Lifetimes of a set of fluorescent dyes were determined with favorable precision, in spite of the low loading levels associated with the microchips. The sequencing products were required to be purified and concentrated prior to electrophoretic sorting to improve data quality. PMMA-based microchips for DNA sequencing application were evaluated. The microchips were produced from thermo plastics, which allowed rapid and inexpensive production of microstructures with high aspect ratios. It was concluded that surface coating was needed on the polymer chips in order to achieve single-base resolution required for DNA sequencing. The capability of the two-color time-resolved microscope operated in a scanning mode was further explored. The successful construction of the scanner allows scanning of multi-channel microchips for high throughput processing

Microchip imaging cytometer: making healthcare available, accessible, and affordable

The Microchip Imaging Cytometer (MIC) is a class of integrated point-of-care detection systems based on the combination of optical microscopy and flow cytometry. MIC devices have the attributes of portability, cost-effectiveness, and adaptability while providing quantitative measurements to meet the needs of laboratory testing in a variety of healthcare settings. Based on the use of microfluidic chips, MIC requires less sample and can complete sample preparation automatically. Therefore, they can provide quantitative testing results simply using a finger prick specimen. The decreased reagent consumption and reduced form factor also help improve the accessibility and affordability of healthcare services in remote and resource-limited settings. In this article, we review recent developments of the Microchip Imaging Cytometer from the following aspects: clinical applications, microfluidic chip integration, imaging optics, and image acquisition. Following, we provide an outlook of the field and remark on promising technologies that may enable significant progress in the near future

Summer 2009 Research Symposium Abstract Book

Summer 2009 volume of abstracts for science research projects conducted by Trinity College students

Pseudo-Random Single Photon Counting for Time-Resolved Optical Measurements

Ph.DDOCTOR OF PHILOSOPH

Microfluidic paper-based analytical devices with instrument-free detection and miniaturized portable detectors

icrofluidic paper-based analytical devices (mu PADs) have attracted much attention over the past decade because they offer clinicians the ability to deliver point-of-care testing and onsite analysis. Many of the advantages of mu PADs, however, are limited to work in a laboratory setting due to the difficulties of processing data when using electronic devices in the field. This review focuses on the use of mu PADs that have the potential to work without batteries or with only small and portable devices such as smartphones, timers, or miniaturized detectors. The mu PADs that can be operated without batteries are, in general, those that allow the visual judgment of analyte concentrations via readouts that are measured in time, distance, count, or text. Conversely, a smartphone works as a camera to permit the capture and processing of an image that digitizes the color intensity produced by the reaction of an analyte with a colorimetric reagent. Miniaturized detectors for electrochemical, fluorometric, chemiluminescence, and electrochemiluminescence methods are also discussed, although some of them require the use of a laptop computer for operation and data processing

Droplet microactuator system

The present invention relates to a droplet microactuator system. According to one embodiment, the droplet microactuator system includes: (a) a droplet microactuator configured to conduct droplet operations; (b) a magnetic field source arranged to immobilize magnetically responsive beads in a droplet during droplet operations; (c) a sensor configured in a sensing relationship with the droplet microactuator, such that the sensor is capable of sensing a signal from and/or a property of one or more droplets on the droplet microactuator; and (d) one or more processors electronically coupled to the droplet microactuator and programmed to control electrowetting-mediated droplet operations on the droplet actuator and process electronic signals from the sensor