Today we stand on the verge of a revolution within the biomedical sciences, brought forth by the explosion of transformative technologies that enable avenues of discoveries previously thought to be unreachable. Understanding the ability of technology to drive innovation, I have spent the past several years generating new methods for third-generation DNA sequencing, ultra-sensitive biomolecule detection and quantification, and nanopore-based single-molecule screening. These works generated four first-author publications, all within high-impact journals, as well as an additional manuscript currently in revision. As a junior faculty, I will apply my passion for creating DNA technology toward the goal of high-throughput sensing and actuating of enzymes with single-molecule resolution, while enabling discoveries using these tools for comprehensive biological system studies in a collaborative setting. My laboratory will pioneer methods for nanopore-based multiplex enzymatic screening, develop an information-encoding platform to write DNA, and create new plasmon-based techniques for DNA sequencing. As an independent investigator, I will spend my next 5 years creating, validating, and with collaborators, pursuing discoveries focused on three areas:
Multiplex screening tools for single-molecule enzyme activity studies
High-throughput enzyme assays are fundamental tools in the medical and biological sciences. Advances in screening technology, have fueled great interest in the recent development of enzyme evolution and discovery, as well as in high-throughput screening for drug discovery. In a typical assay, a host of experimental conditions are optimized to ultimately achieve the desired enzymatic screen with suitable sensitivity and robustness. To address these challenges, my laboratory will work to develop scalable, nanopore-based multiplex screening methods for DNA processing enzymes, in which single enzyme activities will be monitored in real-time with current changes in a nanopore.
Design of high-throughput methods to write DNA
The information revolution is generating large amounts of complex digital media. This has introduced multiple challenges dealing with archiving, maintenance, and retrieval of information. DNA is an attractive candidate for long-term information storage because of its high-density encoding capability, optimal archiving conditions, and already established techniques to decode its stored content. By capitalizing on these special physical and chemical properties, my laboratory will develop scalable, nanopore-based information-encoding methods using an enzymatic approach to write DNA.
Plasmon-based applications for DNA sequencing
DNA sequencing is a fundamental tool in biological and medical research. It enabled the mapping of the entire “human genome”, although it remains incomplete due to the major challenge of resolving the highly repetitive centromeric regions. Currently, sequencing by synthesis (SBS), which uses fluorescently labeled nucleotides, has emerged as one of the most widely used high-throughput technologies developed so far. Nevertheless, its short-read length and low accuracy is still a limiting factor to meet the requirements of personalized medicine. With further improvements in detection techniques to probe nucleotide incorporation, SBS could be an engine that drives third-generation platforms leading to the true realization of the “$1,000 Genome”. Towards this goal, my lab will develop a platform for measuring SERS signals resulting from the polymerase extension of nucleotides in SBS reactions.
By taking advantage of several of my previously created technologies, together with the development of a novel set of high-throughput and multiplex tools, I hope to greatly expedite new insights into a wide variety of biological system studies based on single-molecule enzyme activity screens and create foundationally disruptive technologies for DNA reading and writing.
1. Click Chemistry Monitoring – Ju Laboratory – Department of Chemical Engineering
Developed a versatile validation method to monitor copper-free click reaction efficiency for small molecule conjugation. The monitoring principle is based on loss of the Raman signals of alkyne and azido moieties on the partnering molecules caused by non-Raman active triazole formation as a function of time. Since these universal Raman reporter groups are specific for click reactions, this method may facilitate a broad range of applications for monitoring the conjugation efficiency of molecules in diverse areas such as bioconjugation, material science or drug discovery. (July 2013 – December 2013) > associated software
2. SERS Nanosensor – Ju/Lin/Boisen Laboratory – Department of Chemical/Mechanical Engineering/Micro- and Nanotechnology
Developed a nanosensor device consisting of aptamer-functionalized metallic nanopillars for sensitive surface-enhanced Raman spectroscopy (SERS) quantification of biomolecules. The device utilizes surface plasmon resonance with ultra-high sensitivity properties and provides excellent signal reproducibility and uniformity. The automated collection of
3. Intensity Distribution Model – Ju/Lin/Boisen Laboratory – Department of Chemical/Mechanical Engineering/Micro- and Nanotechnology
Developed an analytical model to predict experimental hotspot intensity distribution on the aptamer functionalized nanopillar substrates for biomolecular quantification. The statistical model may be generally used for biomolecular quantification on any SERS substrates with planar geometries, in which the hotspots can be approximated as the electromagnetic enhancement fields generated by closely spaced dimers. The potential for single molecule detection was also shown by estimating the number of vasopressin molecules probed by SERS during biomolecular quantification, thus opening up an exciting new chapter in the field of SERS quantification. (April 2012 – December 2013)
4. Raman Sequencing – Ju/Turro Laboratory – Department of Chemical Engineering
Developed a third-generation sequencing technology combining novel synthetic biochemistry with plasmonic nanostructures of sub-wavelength dimensions.
5. Microfluidic Genotyping – Ju/Lin Laboratory – Department of Chemical/Mechanical Engineering
Developed a microfluidic device for genotyping based on the single-base extension and solid-phase capture methods previously developed in our lab. The device reduces processing time and allows for rapid analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI–TOF MS). In addition, it allows simultaneous processing of multiple samples and can be reused after regeneration of beads with no carryover effects. These results indicate that
6. Molecular Dynamics Simulation – Liao Laboratory – Department of Mechanical Engineering
Investigated the behavior of the ATP active site of
7. Walkameter – Ju Laboratory – Department of Chemical Engineering
Designed and tested a microfluidic automation system composed of PDMS chamber, temperature, and fluidics control sub-units. Implemented a modular LINUX software for fluidic and temperature control in Python. Demonstrated the feasibility of a novel biochemistry technique to extend the read-length of human DNA sequencing on a high-throughput manner, and its applicability to serve as a supplementary biochemistry step for current next-next generation sequencing instruments. (September 2008 – February 2010)
Harvard Medical School, Department of Genetics – Church Laboratory – Boston, MA
Employed as an R&D Engineer to develop a next-generation, cost-effective, open-source DNA sequencing instrument (“Polonator”) in the Church Lab. Conducted, both independently and in a team environment, optical and heat transfer experiments to optimize the fluidics subsystem of the biomedical device. Gained theoretical knowledge and practical experience in mechanical, electrical, computer and biological engineering. Learned fundamental principles of genomic DNA preparation, amplification and analysis, as well as automated sequencing data generation/storage. (August 2007 – September 2008)
Honors Program, Clarkson University – Potsdam, NY
Honors Thesis: “
Harvard Medical School, Department of Genetics – Church Laboratory – Boston, MA
Conducted research in the Church Lab with an interdisciplinary group of experimental and computational biologists focusing on the development of a wide range of new technologies in the field of genomics/systems biology. Developed interactive software for
SUNY Research Foundation, SUNY Potsdam – Potsdam, NY
State University of New York College at Potsdam – Potsdam, NY
Explored bioinformatics and computer-aided drug design through the Presidential Scholar Program, which provides recognition and additional financial resources for independent research projects. Visited universities and pharmaceutical research laboratories targeting genomics development. Attended bioinformatics workshops at the Ninth Annual Consortium for Computing Sciences Northeastern Conference at Union College. (August 2004 – January 2005)