Research

Biology is continuously advanced by improvements in measurement technologies, experiencing paradigm shifts due to the deeper levels to which scientists can peer into a system. Armed with the fruits of the genomic and proteomic revolutions, biomedicine is now primed for technologies that integrate multiparameter gene and protein profiling and are applicable within the clinical setting. By combining traditional chemical and biological insight with cutting-edge concepts from materials science, physics, and engineering, our group brings an interdisciplinary approach to developing new tools to tackle longstanding, refractory problems in the biomolecular sciences—technologies that will enable fundamental biological discovery, and in some applications, expedite the transfer of biomolecular insight to the hands of the physician where it can directly impact patient care.

Motivated by practical challenges associated with performing multiparameter biological analysis, our group is developing several powerful analysis tools that will be applicable in clinical settings and beyond. Our goal is to facilitate personalized diagnosis and individualized treatment by providing a more detailed picture of the biomolecular signatures of disease from a single patient. On account of their simplicity, scalability, and molecular generality, these tools also have broad applicability to many aspects of clinical and pharmaceutical research as well as fundamental biological studies.

Platform Overview

Representation of Sandwich Immunoassay on a Single Microring Sensor

Representation of Sandwich Immunoassay on a Single Microring Sensor

Silicon photonic microring resonators are intrinsically multiplexable sensor arrays capable of bulk refractive index detection as well as specific molecular recognition monitoring. Our group has applied this technology to diverse applications ranging from clinical diagnostics to polymer growth kinetics. The platform leverages existing capabilities in the microelectronics industry to fabricate sensors chips at effective scales. We have applied the technology to protein, DNA, mRNA, miRNA, biotoxin, and virus detection, and we use both label and label-free formats for detection. Commercial applications of the technology to date have been primarily focused on the pharmaceutical space, including immunogenicity, autoimmunity, and cancer biomarker applications. Aside from biological applications, we are currently exploring novel surface modification strategies to expand the utility of the platform.

Recent review from our lab covering optical resonator sensors and biomolecule detection:

  • Applications of Optical Microcavity Resonators in Analytical Chemistry, J.H. Wade, R.C. Bailey, Annual Reviews in Analytical Chemistry20169, 1-25.
    DOI: 10.1146/annurev-anchem-071015-041742
  • Emerging Biosensing Approaches for microRNA Analysis, R.M. Graybill, R.C. Bailey, Analytical Chemistry201688, 431-450.
    DOI: 10.1021/acs.analchem.5b04679

Nanodiscs as a Model Membrane System

Physisorption of Nanodiscs to a Microring Sensor

Physisorption of Nanodiscs to a Microring Sensor

Interfacing nanodiscs with the silicon photonic microring resonators is an ongoing collaboration between the Bailey, Sligar, and Morrissey labs at the University of Illinois. Nanodiscs are lipid membrane mimics held together by two membrane scaffold proteins. Through the development of different attachment mechanisms, it has been possible to multiplex the nanodiscs on the rings. This multiplexing allows for high throughput analysis of lipid-protein and protein-membrane protein interactions. In particular, the group has worked to characterize the binding interactions involved in the blood coagulation cascade. Most of the enzymatic reactions that lead to blood clot formation occur at the membrane surface and the activity and binding of the proteins are in part influenced by the local lipid composition and salt concentrations. With the combined technologies of nanodiscs and microring resonators it is possible to obtain protein binding constants for 31 different lipid compositions simultaneously. Furthermore, by using salt gradients, it is possible to observe binding in real-time, over a variety of conditions. These technologies allow for in-depth exploration of blood coagulation.

 

Applied Microfluidics

In the Bailey Lab, we are developing low cost, robust, and simple-to-use microfluidic tools for miniaturized chemical and biochemical analysis. For instance, we are engineering a microfluidic platform for epigenetic profiling. Post-translational modifications to epigenetic DNA-histone protein associations regulate the accessibility of histone-bound DNA to transcription factors. This process influences gene expression, leading to heritable genetic differences in individuals with otherwise identical DNA, and has even been implicated in cancer progression. Our platform compartmentalizes each step of the analysis into ~200 pL volume droplets surrounded by an immiscible oil phase. Using each droplet as its own unique reaction vessel, droplet microfluidics can enable high throughput (500 droplets/second) processing of small samples down to the single cell level. For automation of epigenetic profiling, we have developed droplet microfluidic systems for encapsulating cells, injecting reagents, incubating reactions, and more. Additional work continues to interface microfluidic devices with other analytical approaches such as membrane protein analysis, surface functionalization and characterization, and immunoassays.

 

Functionalized Magnetic Bead Encapsulation

Functionalized Magnetic Bead Encapsulation

Picoinjection into Droplets

Picoinjection into Droplets

Investigation of Transport through a Nanoporous Gold Substrate

Nanoporous materials have found numerous applications in DNA sequencing, tunable transport, and nanoparticle characterization. Nanopores generally operate on either size-exclusion or charge-selective principles, whereby the pore is fabricated to certain dimensions in order to permit only molecules of specific sizes through or the surface charge is adjusted by altering the pH of the solution. Coating the nanopores with a conductive metal further simplifies surface charge tuning as it allows for modifying the surface charge electrochemically, rather than changing the solution composition. While most studies have focused on either a single pore or a small array of cylindrical pores, such geometries severely limit throughput and practical applications for lab-on-a-chip separations. As an alternative, we have explored nanoporous Au (NPG) in order to benefit from its high pore density and random, bicontinuous structure. Furthermore, the inherent conductivity and ease of Au surface modification create a highly tunable pore surface for dynamically modifying the separations process without requiring a new device for every unique separation.

The intricate geometry and tunable surface charge of NPG effectively unites size- and charge-based separation techniques into a single platform capable of integration with microfluidic devices. Dynamic control over the separations process with an applied electric potential allows for selectively gating the transport of specific molecules. Our group is currently working on separating proteins, DNA, and quantum dots.