CONFINING INDIVIDUAL DNA MOLECULES IN A NANOSCALE CONE

Abstract

<p>This thesis details our progress toward developing an experimental method that will study conical confinement effects on deoxyribonucleic acid (DNA). Using micropipettes with tip diameters on the order of ~ 1 μm, we study T4 bacteriophage DNA in the small radii of the micropipette tips to build upon our understanding of the entropic force due to confinement. Using two separate methods, evaporative flow and applied electric field, we are able to force the DNA molecules into confinement at<br />the micropipette tip. Labeling the DNA chains with a YOYO-1® fluorescent dye, we image the motion of the chains after the applied force is removed. We observe that the DNA molecules move away from the tip of the micropipettes and the dynamics are well parametrized by our theoretical model for a polymer in conical confinement. However, when our experimental protocol is performed using 1 μm polystyrene beads instead of DNA, we still see motion of the beads away from the tip after stopping the applied force. Studying polystyrene beads in various solvent conditions, we determine that due to the strict boundary conditions of our current experimental setups, ions in the DNA solvent cause the majority of particle motion seen in our DNA experiments, not polymer entropic effects. Using evaporative flow as our confining force, these dynamics are caused by a diffusion of concentrated ions at the tip. When the applied electric field was used to induce confinement, the excess dynamics occur due to a polarization of ions in the micropipette solution. Regardless of cause, these solvent ion dynamics mask the polymer entropic confinement effects in our current micropipette experiments. Using the knowledge we have gained through this study, we propose modifications which build upon our current experimental procedure, eliminating the effects due to evaporation or polarization of solvent ions. We hope that<br />these proposed changes will allow us to successfully measure the entropic force in axisymmetric, continuously changing confinement.</p>