FFATA: Noise-Synchronized Electrophoretic Manipulation in Nanoporous Hydrogels
The proposed work aims to show how the same dynamics governing phenomena as diverse as global climate change and sensory perception can be exploited to direct macromolecular transport through nanoporous surroundings. The researchers aim to demonstrate this in the context of gel electrophoresis by establishing a resonance condition in an entropic trapping transport regime that synchronizes the otherwise noisy uncorrelated motion of DNA between pores in the matrix. Surprising consequences of exploiting this unique effect include simultaneous transport of different-sized molecules in opposite directions, and a counterintuitive inverted size dependence of separation efficiency. This resonance effect can be precisely manipulated by adjusting the driving electric field and pore size distribution of the surrounding gel matrix. Building on the foundation of promising preliminary studies, new fundamental research will be performed aimed at understanding how the nanoscale pore morphology of hydrogels can be tailored to fully harness the unique features of entropic trapping-based macromolecular transport. This information, currently lacking, is a key to fully exploiting the benefits of this resonance effect in practical settings. First, a predictive transport model based on input generated will be developed by applying a combination of mechanical, calorimetric, and TEM-based studies to quantify the nanoscale pore size distribution across a broad range of matrix formulations. These results will allow us to rationally tailor gel compositions and polymerization conditions to achieve optimal resonance synchronization targeting macromolecular analytes of specific size. Second, the results will be extended to a broader range of analytes by applying new photoinitiator and gel compositions to obtain larger average pore sizes, and by incorporating additional activation modes into the transport model with input from single molecule visualization studies. Third, the fundamental insights gained in Objectives 1 and 2 will be adapted toward realistic separations involving analysis of STR/SNP products, long DNA, and proteins. The ability to access the same dynamics that explain global climate change events and apply them to describe macromolecular transport at the nanoscale is intellectually intriguing, with few parallels in published literature. The ubiquity of gel electrophoresis casts a relatable backdrop for the practical use of resonance phenomenon to achieve vastly improved fractionation by simply applying a periodic electric field in a gel with a specific pore size distribution. Timely far-reaching implications include establishing design rules to construct matrix architectures optimally tailored to exploit these effects, and enabling new manipulation and sorting functionalities in other emerging adaptations of nanoscale potential well traps. This resonant synchronization effect, previously thought possible only in idealized nanomachined topologies, can be readily accessed in widely used polymeric hydrogels despite their heterogeneous nanopore arrangement. The proposed research will establish rules for design of matrix architectures optimally tailored to exploit this unique transport mode. By providing a new avenue to access these phenomena in ordinary hydrogels (as opposed to idealized planar nanomachined topologies), an unprecedentedly pathway exists for the results of this research to be directly implemented in virtually any molecular biology lab. These effects are also likely to significantly broaden the possibilities to execute synchronized manipulation of macromolecules and particles in 3-D nanoenvironments This technology has enormous potential to impact molecular biology by enabling significant improvements in electrophoretic separation efficiency. We propose to incorporate this instrumentation into simple devices that allow the DNA separation process to be viewed and studied in the classroom. The researchers plan to harness the portability and ease of operation of this system to develop numerous adaptations aimed at students ranging from K-12 through college, as well as additional outreach opportunities (workshops for high school students and teachers, minority outreach, graduate school recruiting, etc.). This research will be integrated into curriculum at both the undergraduate and graduate levels, leveraging the PI''s involvement in multiple REU efforts and as chair of a biotechnology-focused professional science master''s program.