Research

I am interested in applying molecular biology and chemistry techniques towards developing better drug delivery methods, better ways to understand biological processes, and improved diagnostic tools. Recently, I have been developing improved methods for the production of DNA nanostructures based on the DNA origami method, which is a powerful tool for the development of many biological applications. I have a little over two years of research experience at the undergraduate level at UCLA. After completing  one year of lab rotations at the UC Berkeley-UCSF Graduate Program in Bioengineering, in the summer of 2013, I joined the Douglas Lab at UCSF. I recently completed my dissertation research on the development of novel phage-based strategies for the production of highly custom single-stranded DNA scaffolds for DNA origami applications.

Graduate Research -- UC Berkeley-UCSF

Thesis Lab (June 2013-May 2018)
  • Lab PI: Prof. Shawn Douglas
  • Institution: UCSF
  • Thesis Project: Developing of novel phage-based strategies for the production of highly custom single-stranded DNA scaffolds for DNA origami applications.
  • Project Details: DNA origami is a powerful tool for the production of self-assembled nanostructures and has shown promising applications in a wide range of fields. These structures are typically assembled through a reaction between one long single-stranded DNA (ssDNA) scaffold and many short oligonucleotide staples. In our efforts towards developing applications of DNA origami, we determined that two important properties for scaffold production include the ability to customize its size and sequence, and the ability to produce scaffolds cost effectively at scale. Several in vitro methods exist for producing custom scaffolds. However, because they rely on enzymatic processes, these methods are unreliable at large scale. On the other hand, scalable production of scaffolds based on the M13 bacteriophage genome has been demonstrated. However, the M13 genome will only accommodate insertions up to 2.5 kilobases (kb) reliably, limiting customizability. Likewise, phagemid vectors allow for the production of phage-based scaffolds with larger custom regions, but they still require 2.9 kb of fixed sequence. To overcome these issues, we developed a modified expression system using a novel phagemid, which we call pScaf. pScaf includes a standard M13 origin of replication (M13 ori) as well as a modified M13 ori which behaves as a terminator of ssDNA synthesis, allowing for packaging and export of the intervening sequence as a custom phage particle, while reducing the fixed-sequence region to only 381 bases. In order to develop these vector, we first characterized the effects of various mutations to the M13ori in order to obtain a variant displaying the desired behavior. We then developed cloning strategies for the reliable insertion of custom sequences of arbitrary size into the pScaf backbone. Finally, we demonstrated the efficacy of the platform by producing a series of custom ssDNA scaffolds ranging in size from 1.5 to 10 kilobases in length, providing a significant improvement over current techniques. We further showed that these scaffolds are suitable for DNA origami by folding them into various DNA nanostructures. For more information, a preprint of our manuscript may be found here.

First Rotation (September-December 2012)
Second Rotation (January-March 2013)
  • Lab PI: Prof. Amy Herr
  • Rotation Mentor:  Dr. Robert Lin
  • Institution: UC Berkeley
  • Project: Evaluating the detection limits of HRP substrates for protein detection in polyacrylamide microchannels.

Third Rotation (March-May 2013)
  • Lab PI: Prof. Tejal Desai
  • Rotation Mentor: Dr. Hari Chirra
  • Institution: UCSF
  • Project: Developing a microfabricated device for targeted and controlled drug delivery to the colon.

Undergraduate Research -- UCLA

From March 2010 through my graduation in June 2012, I worked in the laboratory of Dr. Daniel T. Kamei at UCLA, where I worked in the areas of improved point-of-care diagnostics and oral drug delivery.
  • Improved Point-of-Care Diagnostics: There is great need for the rapid detection of biomolecules, such as viruses and proteins at the point of care. One commonly used detection method is the lateral-flow immunoassay (LFA) which utilizes a test strip that takes up a sample through lateral-flow and detects the presence of a target biomolecule through specific antibodies bound to a colorimetric indicator. LFA requires little-to-now training or power to operate and has a rapid time-to-result, making it useful for the point of care. However, it also lacks sensitivity compared to its lab-based counterparts, such as the ELISA. Therefore, our lab set out to find a way to improve the detection limit of the LFA. One approach to doing so is to combine it with a pre-concentration method using aqueous two-phase systems (ATPS). Specifically, we first looked at aqueous two-phase micellar systems (ATPMS), which when heated form two distinct macroscopic phases, a micelle-poor top phase and a micelle-rich bottom phase. Biomolecules will then partition, or distribute themselves, between the two phases based on their physicochemical properties, such as size and hydrophobicity. For example, viruses face many steric, excluded-volume interactions with micelles in the micelle-rich bottom phase, and therefore partition extermeley into the micelle-poor top phase. Therefore, by controlling the temperature and surfactant concentration to shrink the volume of this phase, we can effectively concentrate the virus there, followed by subsequent extraction and application to LFA. In a proof-of-concept study, we were able to use this method to improve the detection limit of LFA for a model virus by a factor of ten. Next, we attempted to apply the technique to concentration of proteins. However, proteins are typically smaller in size then viruses and face fewer steric, excluded-volume interactions, resulting in less extreme partitioning (and thus incomplete concentration). To address this issue, we introduced the use of "gold probes", colloidal gold nanoparticles conjugated to antibody for our target protein, within the ATPMS. These probes are able to bind to the target protein, increasing its effective size, thus aiding partitioning into the micelle-poor phase, where the protein was concentrated and applied to LFA. Again, in a proof-of-concept study, we were able to show ten-fold improvement in the detection limit of LFA for a model protein.
  • Oral Drug Delivery: As part of a senior design project, we developed a novel enteric coating method for drug-loaded PLGA nanoparticles using alternating layers of chitosan and alginate. In vitro release studies showed that drug release from these coated particles was very slow in acidic environments, representing the stomach, whereas release was much more rapid in basic environments, representing the colon. This platform could be used for oral delivery of many different drugs to the colon for treatment of diseases such as cancer and ulcerative colitis.