Understanding DNA Electrophoresis in Colloidal Crystals

Abstract

The electrophoretic separation of DNA (deoxyribose nucleic acid) has been a target of engineering and optimization since its inception. In the following pages, I describe an engineering investigation into the physics of DNA separation in colloidal crystals. Colloidal crystals are formed through self-assembly of micron-sized spheres, suspended as a colloidal suspension. In this work, we follow the pioneering separation work of Zeng and Harrison, seeking to better understand the properties that allow for the observed enhanced separations of small, <1 kilo base-pair (kbp) DNA and large (>10 kbp) DNA. I demonstrate some key insights required to fabricate these devices, then move on to evaluating their performance. In the first section I tackle the quality of the crystal and its potential effects on separation performance. In the second section, I attempt to explain the order of magnitude better separation behavior between agarose gels and colloidal crystals by evaluating the mobility regimes for large DNA. At the end of this work, I have included a discussion on the future place of colloidal crystals as a separation medium.