This thesis presents microfluidic devices for selection and amplification of nucleic acids (aptamers) that bind to specific targets. Aptamers are very attractive molecules in many biological applications due to their interesting properties including high target binding affinities and stability. Using conventional platforms for aptamer generation (SELEX, systematic evolution of ligands by exponential enrichment) is labor-intensive and time consuming. Microfluidic devices have been developed to improve the aptamer enrichment efficiency. However, aptamer generation using these devices is still inefficient because they require complicated flow control components for sample and reagent handling and additional off-chip processes. We developed microfluidic SELEX platforms for rapid isolation of aptamers that possess greatly simplified designs which enable easy chip fabrication and operation. The simplicity of the devices is achieved by utilizing a combination of bead-based selection and amplification of target binding nucleic acids, and gel-based electrokinetic transfer of nucleic acids.

In the devices, nucleic acids that bind to targets are isolated on target-functionalized microbeads or target cells in a microchamber and electrokinetically transported to another chamber through a gel-filled microchannel by an electric field. The strands are then hybridized onto reverse primers immobilized on microbeads and amplified via polymerase chain reaction (PCR) using on-chip temperature control. The amplified strands are separated from the beads and electrophoretically transferred back into the selection chamber for subsequent SELEX rounds. Using the devices, we demonstrated enrichment of target-binding nucleic acids against human immunoglobulin E (IgE), the glucose-boronic acid complex, and MCF-7 cancer cells. With the physical and functional integration allowed by the monolithic design realized in our devices, the total process time for selection of aptamers was drastically reduced compared with that required by conventional aptamer selection platforms. Moreover, the binding affinities of the selected strands using our devices are comparable to those of aptamers obtained using the conventional platforms.