The Dynamics of DNA Electrophoresis in Lyotropic Polymer Liquid Crystals

• Other Authors: You, Seungyong (authoraut)
• Format: Others
• Language: English; English
• Published: Florida State University
• Subjects: Physics
• Online Access: http://purl.flvc.org/fsu/fd/FSU_migr_etd-0863

Electrophoresis is one of the most powerful tools used to separate biological molecules by size in a supporting medium under the influence of an electric field. Pluronic F127 gel, introduced as a new sieving medium for electrophoresis in the late 1990s, has potential promise, but the transport and separation of DNA molecules in Pluronic gel are not fully understood among scientists. This dissertation research conducts three experiments to investigate the dynamics of DNA electrophoresis in Pluronic gel. First, a direct observation study examines how DNA molecules move through the Pluronic gel on a microscopic scale using fluorescence microscopy. Evidence is presented that in some cases DNA molecules electrophorese directly through gel crystallites and in other cases along grain boundaries between gel crystallites. Next, two dimensional electrophoresis is performed in order to understand the size dependence of the mobility of DNA molecules ranging from 20 bp to 3500 bp in Pluronic gels. Small DNA molecules (<125 >bp) became slower as their molecular size decreased, while large DNA molecules (>175 bp) became exponentially slower as their molecular size increased. DNA molecules of intermediate sizes showed a sinusoidal pattern in their mobility. Based on the experimental results, we developed a phenomenological model to fit the size dependence of the DNA mobility, and discussed the separation mechanisms of the DNA molecules in the Pluronic gels. In the final experiment, DNA molecules of the same length, which moved together and formed a single band in the agarose gel, were split into two bands in the Pluronic gel. This indicates that the Pluronic gel is possibly able to separate the DNA molecules according to their sequence. We expect that this study will contribute to an enhanced understanding of the dynamics of DNA molecules in Pluronic gel and facilitation of Pluronic gel as an alternative sieving medium for electrophoresis in the fields of molecular biology and biotechnology. === A Dissertation submitted to the Department of Physics in partial fulfillment of the requirements for the degree of Doctor of Philosophy. === Fall Semester, 2009. === October 23, 2009. === Pluronic Gels, Single Molecule Imaging, Confined Macromolecules, Separation Mechanisms, Two Dimensional Electrophoresis, Fluorescence Microscopy === Includes bibliographical references. === David H. Van Winkle, Professor Directing Dissertation; Sachin Shanbhag, University Representative; James Brooks, Committee Member; Efstratios Manousakis, Committee Member; Ingo Wiedenhover, Committee Member.