Steven A. Soper

The major focus of our group is to generate new tools for discovery and medical diagnostics through the analysis of biological macromolecules including DNAs, RNAs and proteins. These tools cover a diverse range of activities, such as the generation of new reagents, novel assays and methodologies, and hardware innovations across various length scales (millimeter to nanometer). What is particularly compelling with our major research goal is that these tools are being integrated into operating systems that can be used for a variety of applications, such as the diagnosis and prognosis of many forms of cancers, stroke and infectious diseases. In order to build systems specifically designed for macro-molecular analyses, our research spans many sub-areas, such as polymer-based micro- and nanomachining, fluorescent probe development, construction of ultrasensitive detection apparati and nano-biology (performing molecular biological reactions in ultra-small volumes). In addition, we are currently working with collaborators in several areas, such as mechanical engineering, molecular biology, surface science, materials, organic chemistry and mass spectrometry. Provided below is a short description of a few of our many projects. To facilitate these multi-disciplinary efforts, our group is part of the Center for BioModular Multi-Scale Systems, which is a multi-institutional research center with access to state-of-the-art equipment and expertise in many disciplines in the sciences and engineering as well.

In the area of reagent development, we have been working on the generation of new instruments that utilize fluorescence-based single-molecule detection. Because the ability to detect single fluorescent molecules depends on low levels of background and fluorescent reporters with high extinction coefficients, quantum yields and favorable photochemical stability, we have synthesized new water-soluble metal phthalocyanines that absorb and emit radiation in the infrared region of the electromagnetic spectrum. Studies are being pursued to understand the photophysical behavior of these metal phthalocyanines, such as why the fluorescent properties of these dyes are highly dependent on the identity of the metal center. The phthalocyanines are being used for labeling oligonucleotides employed to recognize unique reporter sequences within nucleic acid biomarkers to transduce the presence of these markers in real clinical samples.

Novel assays are being developed to facilitate the near real-time reporting of biomarkers unique to a particular disease type. For example, one of our projects is focused on designing and building a Point-of-Care molecular diagnostic test for stroke, which is currently unavailable. We are using fluorescence single-molecule detection to determine the presence of certain messenger RNAs in whole blood that are highly expressed when a patient experiences brain tissue damage. Following isolation of the total RNA from a particular class of cells found in whole blood, the messenger RNAs are subjected to a ligation-based reaction, which allows the formation of so-called molecular beacons. These molecular beacons contain a pair of fluorescent molecules, such as the phthalocyaines described above, and following their formation, allow the dye-pair to undergo a fluorescence resonance energy transfer (FRET) process that generates a unique color signature only if the target messenger RNA is present. We are also developing new assays for collecting tumor cells from circulation, analyzing point mutations in the DNA of these tumor cells and looking at the membrane protein composition of tumor cells that have been shed into circulation and can spawn metastatic disease.

Finally, our hardware developments are primarily focused on designing, fabricating and evaluating microfluidic and nanofluidic chips for cellular and molecular analyses. While many research groups worldwide are engaged in developing lab-on-a-chip systems for biomedical applications, our approach is unique in that conventional polymers, such as Plexiglas and polycarbonate, are being used as the substrate. We are using a variety of new tools to build the prerequisite chips that consist of fluidic channels, which range in size from 10 nm up to 100 µm in size. These tools include hot embossing, optical lithography, laser machining, focused ion beam milling, electron beam lithography, and an assortment of metrology tools (scanning electron microscopy, atomic force microscopy, scanning profilometry, ATR-FTIR, X-ray photoelectron microscopy, and Raman spectroscopy to name a few). The interesting aspect of these chips is that a plethora of surface modification protocols are undertaken on the polymer chips to allow the attachment of biological entities to their surfaces. For example, UV expose of many polymer surfaces creates a functional scaffold composed of carboxylic acids that can be used to covalently attach recognition elements, such as antibodies, directly to their surfaces. These strategies are being employed to generate systems appropriate for the immuno-selection of circulating tumor cells from whole blood for diagnosing a variety of cancers. We are now employing nanofabrication techniques to generate structures in polymer substrates that have dimensions on the order of 10 nm to allow the identification of single-molecules through their unique transport behavior through these nano-confined environments.

Research Interests

• Development of micro-/nanofabricated biochemical analysis systems for clinical diagnostic applications including the analysis of circulating tumor cells and cell free DNA
• Novel fabrication methods for personalized medicine
• Single-molecule fluorescence