Steve Soper

Area of Interest

Our work is focused on developing new tools for analyzing biological macro­molecules, including DNA and proteins. Specifically, we are interested in fabricating miniaturized systems for mutation analysis (diagnostics), isolating cells from mixed populations, developing systems for high throughput protein analyses and evolving new technologies for DNA sequencing as part of the Human Genome Initiative. In order to build devices specifically for 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 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 on the campus of LSU, which is focused on building enabling tools for discovery in the life sciences and clinical applications in medicine.

Mutations (wrong order of the DNA building blocks) in coding regions of genes can serve as important markers for the early diagnosis of genetically related diseases, such as breast cancer, cystic fibrosis and sickle cell anemia. One of our projects involves developing novel tools for the efficient detection of mutations in K-ras genes associated with colorectal cancer. In addition, we have a project focused on capturing cancer cells in circulating blood which carry cell surface markers associated with breast cancer. These projects (funded by the National Cancer Institute) involve collab­or­ations with our Center forAdvanced Micro­structures and Devices (CAMD) to fabricate high-aspect-ratio molding tools to hot-emboss devices in various polymers, such as poly (methyl­methacrylate) or polycarbonate. These devices are used to prepare the DNA sample (isolate DNA from various body fluids), amplify the number of DNA molecules to be analyzed via PCR, discriminate the normal DNAs from mutant DNAs using mutation screening reactions, sort the DNA by size in an electric field and detection using miniaturized laser-induced fluorescence fiber optic detectors of DNA tagged with colored dyes possessing unique photophysical properties. Figure 1 shows some of the devices we have fabricated using our established micro- and nano-manufacturing techniques.

Another example of our research is focused on developing tools for the capture of low abundant cells from mixed populations in clinical samples. For example, devices are being constructed to collect rare circulating tumor cells from whole blood using microfluidics. Circulating tumor cells can be present at a level of 1-10 cells per milliliter of blood with the level of normal cells (red blood cells and white blood cells) being substantially higher (10 million per milliliter of blood). Therefore, we have developed a device to capture these rare cells using an affinity capture method that can pre-select the tumor cells with high efficiency and clear the red and white blood cells. The tumor cells are then quantitatively counted using a non-labeling process, which consists of running the cells through a pair of electrodes and measuring the solution conductance. Figure 2 details the system and shows micrographs of tumor cells captured and counted from whole blood using this system.

Our research is also directed toward improving the process of identifying proteins comprising the proteome. We are developing an integrated system that can pre-select a certain sub-population of proteins from the proteome and then efficiently identify those proteins using mass spectrometry interfaced to a fluidic system. The system consists of the following processing steps: (1) Solid-phase capture using an affinity bed of the protein sub-population to be analyzed; (2) two-dimensional electrophoresis platform for isolation of the constituent proteins; (3)solid-phase bioreactors to digest the isolated proteins into peptide fragments; (4) capillary electrochromatography unit for the high-resolution separation of the generated peptides and (5) interface to a mass spectrometer for identifying the peptides and consequently, the proteins. An example of our system and the results generated for protein fingerprinting is shown in Figure 3.

Another interesting project involves developing single molecule detection methods for the real time molecular screening of mutated DNAs. We have developed an assay that can provide molecular signatures of disease states in < 5 min using single molecule detection. The assays utilize a ligation reaction, which forms a molecular beacon that contains two fluorescent dyes at their ends. Using a microfluidic device and confocal fluorescence detection, we can obtain information on the presence of point mutations in genomic DNA in less than 5 minutes, nearly 20 times faster than what can be done with conventional instrumentation. In Figure 4 is shown data accumulated using this assay format.

 

Awards & Honors

William L. and Patricia Senn, Jr. Professor

Director, Center for BioModular Multi-Scale Systems

A. Benedetti-Pichler Award in Microchemistry

Charles E. Coates Award for Outstanding Contributions to Chemical/Engineering Research in Louisiana, 2001

Editorial Board, The Analyst, 2000-present

Editorial Board, Single Molecules, 1999-present

Whitaker Research Fellow, 1996

Phi Kappa Phi Research Award, 1996

College of Basic Sciences Research Award, 1995

R&D 100 Award, Single Molecule Detection, 1992

 

Selected Publications

Chen, H. Wang and S.A. Soper.  Continuous Flow Thermal Cycler Microchip for Cycle Sequencing.  Analytical Chemistry, 2006, 78, 6223-6231 

Shadpour and S.A. Soper.  Two-Dimensional Separation of Proteins using Poly(methyl methacrylate) Microchips.  Analytical Chemistry, 2006, 78, 3519-3527

Yang, S.A. Soper and W. Wang.  Microfabrication of Pre-aligned Fiber Bundle Couplers using Ultraviolet Lithography of SU-8.  Sensors and Actuators, A, 2006, 127, 123-130

Hashimoto, F. Barany and S.A. Soper.  Polymerase Chain Reaction / Ligase Detection Reaction / Hybridization Assays using Flow-Through Microfluidic Devices for the Detection of Low Abundant DNA Point Mutations.  Biosensors and Bioelectronics, 2006, 21, 1915-1923

Perry, M. Witek, R. Sinville, and S.A. Soper.  SPRI for Isolating Genomic DNA from Whole Cell Lysates.  Nucleic Acids Research, 2006, 34, e74

Kong, H. Chen and S.A. Soper.  Fabrication of Gold Microelectrodes for Amperometric Detection on a Polcarbonate Chip by Photo-directed Electroless Plating.  Electrophoresis, 2006, 27, 2940-2950

Shadpour, H. Musyimi, J. Chen and S.A. Soper.  Investigation of the Physio-Chemical Properties of Various Polymers for Microchip Electrophoresis Applications.  Journal of Chromatography, A, 2006, 1111, 238-251

Zhu and S.A. Soper.  Fluorescence Lifetime Identification Methods for High Throughput DNA Sequencing in Plastic Chips.  Analytical Biochemistry,2004, 330, 206-218

Witek, S. Wei, A. Adams, R. L. McCarley and S.A. Soper.  Cell Transport and Lysis in Plastic Microfluidic Chips.  Lab on a Chip, 2004, 4, 464-472

H.K. Musyimi, D. Narcisse, X. Xhang, S.A. Soper and K.K. Murray.  Online CE MALDI-TOF-MS using a Rotating Ball Interface.  Analytical Chemistry,2004, 76, 5968-5973

G.A. Thomas, R. Sinville, S. Sutton, H.D. Farquar, Y. Wei, F. Barany, R.P. Hammer and S.A. Soper.  Detecting Low Abundant Point Mutations in K-ras Genes using Micro-electrophoresis in Plastic Chips.  Electrophoresis, 2004, 25, 1668-1677

Hashimoto, P. Chen, M.W. Mitchell, D.E. Nikitopoulos, S.A. Soper and M.C. Murphy.  Rapid PCR in a Continuous Flow Device.  Lab on a Chip,2004, 4, 638-645

Wang, B. Vaidya, H.D. Farquar, W. Stryjewski, R.P. Hammer, R.L. McCarley, S.A. Soper, Y-W. Cheng, F. Barany.  Microarrays Assembled in Microfluidic Chips Fabricated from Poly(methyl methacrylate) for the Detection of Low-abundant DNA Mutations.  Anal. Chem., 2003, 75, 1130-1140

Lassiter and S.A. Soper.  Optimization of Sequencing Conditions for Time-Resolved Multiplexed Detection in DNA Sequencing Applications using Near-IR Fluorescence Detection.  Electrophoresis, 2002, 23, 1480-1489

Qi, S. Ford, X. Liu, J. Barrows, G. Thomas, K. Kelly, A. McCandless, K. Lian, J. Goettert, S.A. Soper.  Hot Embossing High-Aspect-Ratio Microstructures in Poly(Methylmethacrylate) for Constructing Microfluidic Devices with Integrated Components.  Lab-on-a-Chip, 2002, 2, 88-95

Galloway, W. Stryjewski, D. Patterson, A. Henry, R.L. McCarley and S.A. Soper.  Contact Conductivity Detection in PMMA-Based Microfluidic Devices for the Transduction of Mono- and Polyionic Molecules.  Analytical Chemistry, 2002, 74, 2407-2415

Thomas, L. Spring, V. Williams and S.A. Soper.  Heteroduplex Analysis of Mycobacterium Tuberculosis using High-Resolution Capillary Electrophoresis.  Clin. Chem., 2001, 47, 1195

Wabuyele and S.A. Soper.  Single Molecule Analysis of dsDNA Molecules in Polymer Microfluidic Chips.  Electrophoresis, 2001, 22, 3939

Meng, S. Qi, S.A. Soper and P.A. Limbach.  Interfacing a Polymer-based Micromachined Device to a Nonoelectrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometer.  Anal. Chem., 2001, 73, 1286

Wabuyele and S.A. Soper.  Amplification of Single DNA Molecules Using the Polymerase Chain Reaction.  Single Molecules, 2001, 2, 13

Y.Y. Davidson, S.A. Soper, S. Margolis and L.C. Sander.  Immobilization of Restriction Enzymes on Porous Silica Particles via a Glutaraldehyde Linkage for the Micro-Digestion of dsDNAs with Analysis by Capillary Electrophoresis.  J. High Resol. Chromatogr. & Rel. Techn., 2001,

McWhorter and S.A. Soper.  Conductivity Detection of PCR Products Separated by Open Tubular Liquid Chromatography.  J. Chromatogr., 2000, 883, 1

Xu and S.A. Soper.  Micro-Capillary Reactors for Direct Sample Introduction into Slab Gels for Solid-Phase DNA Sequencing.  BioTechniques,2000, 28, 904

Waddell, S. Lassiter and S.A. Soper.  Time-Resolved Near-IR Fluorescence Detection in Capillary Electrophoresis.  J. Liq. Chrom. & Rel. Technol.,2000, 23, 1139

Waddell, Y. Wang, W. Stryjewski, S. McWhorter, A. Henry, D. Evans, R.L. McCarley and S.A. Soper.  High Resolution Near-IR Imaging of DNA Micro-arrays with Time-Resolved Acquisition of Fluorescence Lifetimes.  Anal. Chem., 2000, 72, 5907

A.C. Henry, T.J. Tutt, C.S. McWhorter, Y. Davidson, S.A. Soper and R.L. McCarley.  Chemical Modification of Poly(methyl methacrylate) Used in the Construction of Microanalytical Devices.  Anal. Chem., 2000, 72, 5331-5337

S.A. Soper, S.M. Ford, S. Qi, R.L. McCarley, K. Kelley and M.C. Murphy.  Microelectromechanical Systems Fabricated in Polymeric Materials: Applications in Chemistry and Life Sciences.  Anal. Chem., 2000, 72, 643A-651A

McWhorter and S.A. Soper.  Near-Infrared Fluorescence Detection in Capillary Electrophoresis.  Electrophoresis, 2000, 21, 1267

S.J. Lassiter, W. Stryjewski, B.L. Legendre, R. Erdmann, M. Wahl, J. Wurm, R. Peterson, L. Middendorf and S.A. Soper.  Time-Resolved Fluorescence Imaging of Slab Gels for Lifetime Base-Calling in DNA Sequencing Applications.  Anal. Chem., 2000, 72, 5373

A.C. Henry, T.T. Tutt, C.S. McWhorter, Y.Y. Davidson, M. Galloway, S.A. Soper and R.L. McCarley.  Surface Modification of Plastics Used in the Fabrication of Microanalytical Devices.  Anal. Chem., 2000, 72, 5331

S.A. Soper, S.M. Ford, S. Qi, R.L. McCarley, K. Kelly and M.C. Murphy.  Microelectromechanical Systems (MEMS) Fabricated in Polymeric Materials: Applications in Chemistry and Life Sciences.  Anal. Chem., 2000, 72, 642A

S.M. Ford, J. Davies, B. Kar, C.V. Owens, S.A. Soper, M. Klopf, G. Calderon and V. Saile.  High-Aspect Ratio Micormachining in Polymethylmethacrylate (PMMA) using X-ray Lithography for the Fabrication of Micro-Electrophoresis Devices.  J. Biomech. Eng., 1999, 121, 13

 

Former Ph.D. Students

Suzanne Lassiter, Ph.D.,12/02, Department of Agriculture
Michelle Galloway, Ph.D., 08/04, Post-Doctoral Fellow
James Flanagan, Ph.D.,05/98, Scientist
Yun Wang, Ph.D., 05/04, Post-Doctoral Fellow
Yichuan Xu, Ph.D., 05/03, Post-Doctoral Fellow
Musundi Wabuyele, Ph.D., 05/03, Post-Doctoral Fellow
Sean Ford, PhD, 05/02, MEZZO Systems
Gloria Thomas, Ph.D., Assistant Professor
Ben Legendre, PhD, TransGenomics
Daryl Williamsm PhD, General Electric
Yolanda Davidson, PhD, NIST
Cylde Owens, PhD, Oak Ridge National Lab
Emanuel Waddell, PhD, Assistant Professor
Scott McWhorter, PhD, DOE Savannah River