Nanofluidic devices have emerged as new powerful tools for biomolecule analysis. Their utility in probing single DNA molecules is of particular interest because of both the biological importance and the ideal polymer physical properties of DNA. Such applications often involve an initial step of capturing the large, globule-shaped molecules from bulk solution and linearizing them in the nanoscale confining structures. The entropic barrier inherent to this process is typically overcome by pulling DNA into a nanoconduit using a large electric field. The resulting high velocity of molecular transport, coupled with the finite temporal resolution of detection, can make single-molecule characterizations difficult. In this dissertation, novel three-dimensional nanofunnels are described that address this problem. Focused ion beam milling is developed to fabricate complex nanostructures. The nanofunnels facilitate the capture process, enabling the introduction of DNA molecules into fluidic nanochannels with significantly lower electric fields. The gradual confinement change of the nanofunnel produces an entropy gradient for DNA molecules transitioning from bulk solution to a nanochannel. Tuning the electric field results in the stable trapping of a single DNA molecule in the nanofunnel. The precisely defined geometry enables an accurate force analysis on the molecule. For confined molecules placed in an electric field, electro-hydrodynamic interactions are discovered that differ from those present in freely diffusing or anchored molecules. Concentration polarization, a phenomenon unique to nanofluidics, is also described for devices containing a nanochannel-nanofunnel structure. The phenomenon is found to correlate with the ionic current rectification, an effect which was previously studied primarily in conical pores. Both phenomena are found to evolve over several minutes in the nanochannel-nanofunnel devices. Moreover, the electro-osmotic flow is found to greatly affect the concentration polarization and ionic current rectification. The discoveries presented in this dissertation have both theoretical and practical importance. A better understanding of the entropic and electrohydrodynamic forces on a large polyion (DNA) was achieved. The nanofunnels developed here have potential applications in nanofluidics-based DNA mapping and sequencing technologies and in the pre-concentration of biomolecules for subsequent on-chip separations or analyses.Doctor of Philosoph
