Optical Mapping and Sequencing Platform for Ultra-long Single DNA Molecules
Wednesday, July 29, 2020
10:00 AM-12:00 PM
BIOMED PhD Research Proposal
Title:
Optical Mapping and Sequencing Platform for Ultra-long Single DNA Molecules
Speaker:
Dharma Varapula, PhD Candidate
School of Biomedical Engineering, Science and Health Systems
Drexel University
Advisor:
Ming Xiao, PhD
Associate Professor
School of Biomedical Engineering, Science and Health Systems
Drexel University
Details:
DNA sequencing is a technically challenging process and has become vital to interpreting human health. Short-read sequencing (SRS, Illumina sequencing), although less expensive and very accurate, still cannot detect significant amount of genetic mutations. Long-read sequencing (LRS) is increasingly being used for this but current technologies fall short in terms of read-length, throughput, and accuracy. Often, SRS and LRS are combined to detect disease-associated structural variants (SVs), making the process complex, resource-intensive, and expensive, often still missing clinically relevant large mutations. There is a need for a single molecule technology that can detect base-level information from ultra-long DNA molecules that is accurate, low-cost, and high-throughput.
Here, we propose the development of a microfabricated device that not only isolates ultra-long DNA molecules efficiently but also facilitate sequence-specific enzymatic fluorescent DNA chemistry. A glass substrate will be chemically modified to isolate and immobilize long DNA molecules. The surface modifications are designed to provide enzymatic access to the DNA, as well as minimize non-specific fluorescent dye adsorption. We will first optimize and characterize the surface modifications using fluorescence microscopy, AFM, contact angle measurements, and other surface analytical techniques. Using the optimized substrate, we will perform various enzymatic reactions (nick-labeling, CRISPR Cas9-labeling, and reversible terminator sequencing) on ultra-long DNA molecules and detect specific sequences as well as single bases, optically. To do that, we will construct and test a robust microchannel assembly and accompanying thermal incubation instrument. We will also identify and optimize other DNA sequencing chemistries to demonstrate full utility of the platform. With high DNA loading capacity and compatibility with high-speed scanning fluorescence microscopy, the device will be suitable for large-scale high-resolution single DNA molecule studies.
Contact Information
Natalia Broz
njb33@drexel.edu