| Single DNA molecule approaches have played important roles in genomic science due to their ability to provide individual information from a large number of DNA molecules. Nevertheless, a principal challenge in contemporary single DNA molecule approaches is how to effectively immobilize and manipulate DNA molecules for the generation of large biologically relevant datasets. Towards this goal, this thesis introduces micro- and nanofabricated devices for manipulation of elongated DNA molecules within nanoscale geometries and examines DNA dynamics in microchannels. Ideally, large DNA coils stretch via nanoconfinement when channel dimensions are within tens of nanometers. Such small dimensions make these devices impractical due to the requirements of exotic technology, costly materials, and poor operational efficiencies. In this thesis, such problems have been overcome through reduction of ionic strength that stiffens DNA molecules allowing their presentation using easily fabricated devices. As an example of genomic applications, DNA mapping in nanofluidic device has been demonstrated using elongated DNA barcoded with a novel sequence specific labeling biochemistry. The observation of DNA elongation at different ionic strength is compared with a newly developed polymer physics theory. In addition, DNA dynamic behavior in microchannel is investigated, specifically DNA migration toward the centerline in microchannels under shear induced flow. This observation is correlated with recently a developed Brownian dynamics simulation. These studies will lead to a new high-throughput genomic analysis platforms as well as the elucidation of unexplored DNA polymer phenomena within nano- and microfluidic confinement. |
