DNA is the central storage molecule of genetic information in humans and almost all other organisms. Analyzing the genetic information along the DNA molecule is of great importance in life science and biomedical engineering. Recently, nanofluidics has been recognized as an efficient approach to study the behavior of DNA at the single-molecular level, which can unravel the phenomena that remain hidden in conventional bulk experiments. When confined in nanochannels, the coiled DNA molecules naturally stretch out as a combined result of the elastic properties and the excluded volume effects. Therefore, a reliable nanofluidic platform is the prerequisite for single-molecule DNA studies. This thesis focuses on the development of sub-100 nm disposable nanofluidic devices and the expe...[ Read more ]

DNA is the central storage molecule of genetic information in humans and almost all other organisms. Analyzing the genetic information along the DNA molecule is of great importance in life science and biomedical engineering. Recently, nanofluidics has been recognized as an efficient approach to study the behavior of DNA at the single-molecular level, which can unravel the phenomena that remain hidden in conventional bulk experiments. When confined in nanochannels, the coiled DNA molecules naturally stretch out as a combined result of the elastic properties and the excluded volume effects. Therefore, a reliable nanofluidic platform is the prerequisite for single-molecule DNA studies. This thesis focuses on the development of sub-100 nm disposable nanofluidic devices and the experimental demonstration of such devices for biomolecular detection and analysis.

We first investigated various techniques for fabricating low-cost nanochannels on different substrates. We showed that the lithography-free nanocracking on a polystyrene substrate is a promising approach for lab-on-chip nano-manufacturing. Based on such nanocracking technology, an on-demand nanofluidic pre-concentrator was developed, which leveraged isolated droplets to avoid the sample diffusion and dispersion issues as compared to conventional devices. To prevent concentration decay during the sample ejection, a pressure-assisted strategy was introduced in the system for precisely positioning the concentrated sample plug at the ejecting nozzle. By integrating the ion concentration polarization with on-demand droplet generation, our system can adaptively encapsulate the highly concentrated sample and effectively enhance the long-term stability. We experimentally demonstrated the pre-concentration of a fluorescently labelled biomolecule, bovine serum albumin (BSA), by an amplification factor of 10,000. By adjusting the applied voltage, accumulation time, and pulsed pressure imposed on the control microchannel, our system can generate a droplet of desired volume with a target sample concentration at a prescribed time.

Second, we developed a novel nanofluidic device to confine and align single-molecule DNA in dynamically formed nanochannels for optical analysis. By judiciously harnessing the microvalve control and the deformation of nanoslits made in the PDMS, we dynamically generated submillimeter-long uniform nanochannels with an effective confining dimension down to 20 nm based on low-cost soft lithography. Using such devices, we investigated DNA stretching and attained 80% of the contour length for DNA elongation. The curved edge of the microvalve smoothly bridges the different depths between the stretching nanochannels and the adjoining microchannels by more than 3 orders of magnitude, which greatly facilitates the introduction of DNA into the nanochannels without the need for high pressure or electric fields. Unlike traditional direct-bonded nanochannels, the sample nanochannels in our device recover in microscale when the pressure is released, eliminating clogging of the nanochannels and allowing surface passivation for preventing non-specific interactions. We further performed DNA denaturation mapping in the device and showed that the experimental denaturation barcode agreed well with the theoretical data.

This thesis presents improved techniques for the development of low-cost nanofluidic devices and their practical implementation for on-demand sample pre-concentration and single-molecule DNA analysis. We believe our work based on nanofluidics has shed new light on the enhanced biomolecular detection and analysis.