BME PhD Prospectus Defense - Joseph Hersey

1:30 pm on Thursday, March 7, 2013
3:30 pm on Thursday, March 7, 2013
44 Cummington St, Room 203
Research Advisor:
Professor Mark Grinstaff

Thesis Committee Members:
Professor Amit Meller
Professor Richard H. Myers
Professor Xue Han

Title: "Tunable Nanofiber mesh coated SiN nanopore for the detection of genetic materials"

Solid-state nanopores show promise as single-molecule sensors for biomedical applications, but to improve their resolution and efficiency DNA molecules must remain longer in the nanopore sensing volume. We propose a novel, simple, and versatile method to improve nanopore sensitivity and temporal resolution by slowing DNA translocation via interactions outside the nanopore, while still leaving the nanopore itself available for further functionalization. Current nanopore technologies do not have the temporal resolution to accurately detect small changes in DNA or RNA length limiting their diagnostic applications. This enhanced resolution will be achieved by electrospinning a chemically tunable nanofiber mesh (NFM) directly to a solid-state nanopore chip, where its fibers (hydrophobic, UV-activated cationic, or UV-activated anionic) may interact with DNA molecules during sensing from outside the nanopore slowing their movement through it. The NFM is composed of a network of fibers (100-1000 nm diameter) formed from poly(ε-caprolactone) (PCL) doped with poly(glycerol-co-ε-caprolactone) (PGC), deposited onto a surface by electrospinning. The PGC component of this polymer may be functionalized to include a range of side chain moieties which confer tunable hydrophobicity and surface charge. We will first construct nanopore-nanofiber mesh (NP-NFM) hybrid devices with different charge and mesh characteristics, then screen these devices to determine which combinations might be suitable for nanopore sensing by characterizing the conductance and noise associated with each NP-NFM. Candidate devices will be tested using a range of double stranded DNA lengths to create a calibration curve for each type of NFM to relate the average translocation time to analyte length. These calibration curves will be fine-tuned using an ultraviolet light (UV) activated polymer that transitions from hydrophobic to hydrophilic by deprotecting either anionic or cationic charges along the PGC backbone when exposed to UV light (365 nm). Many neurological disorders are studied through microarray technologies and RNA sequencing techniques, this modified NP-NFM system has the potential to be used in combination with these methods to further profile the population of mRNA’s associated with diseased and healthy samples. Knowledge of ultimately which proteins are over or under expressed by a Parkinson’s, Alzheimer’s, or Huntington’s disease patient will lead to the identification of novel targets for pharmaceutical interventions.