Research

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.

GRADUATE RESEARCH

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 large number of vibrational spectra paired with a novel statistical method for quantification provides a framework for the development of a novel, cheap and fast sub-nM biodetection device. (April 2012 – December 2013)

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 SequencingJu/Turro Laboratory – Department of Chemical Engineering

Developed a third-generation sequencing technology combining novel synthetic biochemistry with plasmonic nanostructures of sub-wavelength dimensions. Surface enhanced Raman scattering (SERS) active substrates coupled with innovative Raman tag selection in DNA sequencing are highly desirable and will open the door to routine, reliable, and continuous high-throughput, personalized genome analysis possibly coupled with microfluidic technology. (July 2011 – December 2013) > associated software

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 the microfluidic device is a low-cost tool that enhances sample cleanup prior to MS for single nucleotide polymorphism (SNP) genotyping. (March 2010 – December 2013) > associated software

6. Molecular Dynamics Simulation Liao Laboratory – Department of Mechanical Engineering

Investigated the behavior of the ATP active site of hepatitis C virus (HCV) NS3 helicase during polynucleotide unwinding. Used molecular dynamics (MD) simulation to examine the mutational effect of T324, a hinge residue connecting domains 1 and 2, on the dynamics of the ATP binding site. Found that the ATP binding cleft flexibility is controlled by a long-range atomic network, affecting residues located in domain 1. These results call for a future evaluation to elucidate the exact relationship between ATPase activity decrease and 3D structural changes, and fuel new therapeutic development of HCV. (February 2010 – November 2011)

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)

UNDERGRADUATE RESEARCH

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: “Genetomic Promototypes: High-throughput, Computational Design of Synthetic Promoter Regions”. Implemented a user-friendly, advanced software package called BASHER for the high-throughput design of synthetic promoter regions of Saccharomyces cerevisiae. Built a powerful and flexible tool for hypothesis testing of regulatory logic in the eukaryotic yeast cell. Beside site-directed mutagenesis, structural analysis, and investigation of transcription regulation, incorporated combinational and spatial effects of cis-binding sites into the package. (September – May 2007)

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 genomic promoter sequence design. Analyzed unique, large-scale genomic datasets using state of the art bioinformatics tools, and developed novel algorithms and software tools. Gained strong computer programming skills in Perl and MATLAB. (May – August 2005, January – August 2006)

SUNY Research Foundation, SUNY Potsdam – Potsdam, NY

Participated in faculty-undergraduate summer research program designing a computer simulation of the transmission of DNA through multiple generations of isolated populations. Investigated the Hardy-Weinberg Principle through the statistical analysis of the ratio of recessive to dominant genes within a population. Modeled the reproduction and growth of populations with mating behavior and genetic composition according to Mendelian genetic principles. Work involved population genetics, probabilistic computational biology, statistical analysis, software development, the theory of random walks, complexity theory. (May – August 2004)

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)