Determination of Electrophoretic Forces in a Gel Matrix in Different Ionic Strength Conditions

Abstract

Nanocoding, a genome analysis platform, relies on very low ionic strength conditions to elongate DNA molecules up to 1.06 (fully stretched DNA molecule = 1)1, which is the largest stretch reported in the literature. Understanding how electroosmotic and electrophoretic forces vary, as ionic strength decreases, will enable better Nanocoding devices to be developed. Using two different gel assays to determine electroosmotic and overall mobility (includes contributions from electrophoretic forces and electroosmotic forces), we were able to determine electrophoretic mobility in different ionic strength solutions. Our first gel assay relied on electrophoresising linear DNA molecules [pUC19 (2.7 kb), pBR322 (4.4 kb), φX174 (5.4 kb), and PSNAPf-H2B (6.2 kb)] in varying gel concentrations (1.5%, 1.25%, 1%, 0.75%, 0.5%) to determine the free solution mobility (overall mobility) of these molecules in dilutions of TE buffer. As the buffer concentration decreases from 2X (Ionic strength = 13.8 mM) to 1X (Ionic strength = 7.3 mM), the overall mobility increased. As we further diluted TE (< 1X TE), the overall mobility drastically decreased as the ionic strength decreased.1. Kounovsky-Shafer, K.L., Hernandez-Ortiz, J.P., Jo, K., Odijk, T., de Pablo, J.J., and David C. Schwartz, D.C. Presentation of large DNA molecules for analysis as nanoconfined dumbbells, Macromolecules, 2013, 46 (20), 8356-8368.