Improving multiplexed RNA detection assays by interfacing enzymatic amplification strategies with silicon photonic microring resonators

The ability to make multiplexed measurements has significantly improved our understanding of disease onset and progression. This newfound understanding has the potential to transform clinical diagnostics. Also known as personalized medicine, diagnostic decisions are improved by relying on a detailed knowledge of an individual’s biochemical signature. While routine clinical tests detect one biomarker at a time, new technologies are needed that enable the analysis of multiple targets per clinical sample. This doctoral dissertation presents a platform that can complete these goals by developing assays that combing enzymatic processing steps with silicon photonic microring resonators, a technology pioneered by the Bailey Research Laboratory. While other efforts in lab have been geared to other classes of biomolecules, the developed assays discussed in this dissertation are designed to profile nucleic acid biomarkers in a host of clinically relevant samples. The results from these studies are confirmed using clinical gold standard techniques and compared with findings in the literature to validate the platform. Chapter 1 discusses how silicon photonic microring resonators fit into the landscape of next-generation multiplexed biomolecular detection platforms while also developing the motivation to use enzymatic processing of nucleic acids to produce ultra-sensitive detection platforms. Chapter 2 gives an exhaustive review of current microRNA (miRNA) detection platforms, both clinical gold standards and emerging technologies. Given the unique detection challenges of microRNAs, this class of RNA molecule was used to develop a detection platform which could then be translated to other RNA molecules. Chapter 3 describes the use of enzymatic processing of miRNA sequences and subsequent on-chip enzymatic signal enhancement strategy to lower the required input of RNA material to a clinically relevant amount. Chapter 4 outlines further improvements to enzymatic pre-processing of miRNA molecules by interfacing an adapted polymerase chain reaction process with the microring platform to study miRNA expression in glioblastoma patients. It also eliminates the need for on-chip signal amplification. Chapter 5 adapts this workflow and uses it for the detection of long-noncoding RNA (lncRNA) molecules in a previously uncharacterized glioblastoma cell line. Chapter 6 outlines additional research efforts and future directions, which include efforts to build a platform combining enzymatic pre-processing with microring resonator detection and efforts to push into an expanded set of clinical and research applications where low sample inputs and short analysis times are needed.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Chemistry

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2017

Author dc:creator

• Graybill, Richard Martin

Contributors dc:contributor

• Bailey, Ryan C.
• Sweedler, Jonathan V.
• Mitchell, Douglas A.
• Fan, Timothy M.

• Biosensor
• Silicon photonic microring resonators
• Enzymatic amplification

Statement dc:rights

• Copyright 2017 Richard Martin Graybill

Language dc:language

en

Handle dc:identifier

http://hdl.handle.net/2142/97741

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/97741