Development of the Silicon Photonic Microring Resonator Platform with Applications for the Detection of Nucleic Acids and Other Biopolymers

Abstract

Progress in the development of biosensors has dramatically improved analytical techniques. Biosensors have advantages over more conventional analytical techniques arising from attributes such as straightforward analyses, higher throughput, miniaturization, smaller sample input, and lower cost. Specifically, silicon-based biosensors including microring resonators have led to major advances in diverse applications because they produce sensors that can be arrayed in planar substrates for multiplexed detection and can be produced at large scales. This dissertation presents how microring resonators have been used for the detection of ribonucleic acids, RNA, and other inorganic biopolymers. The first chapter describes the basics of biosensors and the factors that affect their operation. This chapter is also dedicated to the sensing mechanism of whispering gallery mode biosensors, in the form of microring resonators. In addition, it summarizes the most recent applications of microrings in environmental and clinical analysis, highlighting the research in RNA detection. The next two chapters describes an approach for RNA detection utilizing the microring resonators. This methodology is based on the coupling of a nucleic acid amplification technique, asymmetric Polymer Chain Reaction, aPCR, with the microring resonator platform. Promising results are shown in the detection and quantification of RNA, where our approach offers the sensitivity and selectivity required for the use of transcripts in clinical analysis. Compared to other biosensing strategies, we are able to perform a higher multiplexity of the measurements, use nanogram sample input, and adapt the protocol to the detection of short (microRNAs) and long transcripts (long non-coding RNAs). The fourth chapter presents how the aPCR-microring combination can be applied to the profiling of a miRNA biomarker panel. The investigation consists of an analysis of the dynamic miRNA signatures of two glioblastoma cell lines upon various treatments. Furthermore, I utilized the normalized expression of the miRNAs to construct heatmaps and performed multivariate statistical analysis. The results indicated that this technology makes it possible to carry out functional screening of targets for diagnostic and therapeutic evaluation. The fifth chapter features an innovative application of microrings in the quantitative analysis of polyphosphate, also known as polyP. PolyP is a ubiquitous molecule, interest in which has increased over the last decade because of the discovery of its important biological roles in mammals and microorganisms. However, methodologies for its analysis still fall short in identifying ways to quantifying polyP directly in complex matrices. To detect polyP in complex matrices, molecules are captured in the surface via high-affinity binding to cationic polymers. Then, we integrated a selective recognition of the molecules via a polyphosphate binding protein domain. This strategy enabled the detection of nanomolar concentrations and the measurement of the molecule directly in the matrix with no purification and thus, it opens up a variety of potential applications. The final chapter summarizes all the research carried out during my thesis. The possibilities that microring resonators have to offer as biosensors, and the diverse approaches that can be combined to enhance the characterization of molecules. In the field of RNA, future directions will include the combination of RNA expression panels with the profiling of other biomarkers to understand better the signatures of patient samples under therapeutic treatments. In the field of polyP, future directions in the analysis of polyP are the size characterization of these polymers using other separation instruments such as capillary electrophoresis (CE).