The specific aim of the renewal proposal deals with the development and the optimization of better separation media for DNA capillary/microchip (array) electrophoresis. A conceptual model based on the DNA chain dynamics and fundamental principles of polymer physics, together with the aid of polymer synthesis, has been developed and is being tested. We propose to complete the tests, to design new separation media based on the model, and to put our separation media into practice. The essence of the conceptual model on polymer separation medium has been developed and tested out extremely well. Based on this model, the separation medium should be neutral, hydrophilic, and stable. It should also have surface-active properties. More importantly, in order to achieve a faster run time, the polymer chains should be more extended so that the same obstacles can be created with lesser amounts of polymers, implying that a lesser amount of polymers will be needed to create the same effective mesh size. Furthermore, in order to separate larger size fragments (e.g., DNAs; though not limited to DNAs alone), the polymer chain entanglement times should be as long as possible (so as to simulate a chemically cross-linked gel). What we have done and shall do is to demonstrate definitively the concepts of this model by using a set of test experiments since there are synthetic limitations to create an ideal separation medium. Furthermore, no quantitative theoretical treatment exists at this complex level, and in practice, most polymers do not mix well. Thus, with this new conceptual model, we hope to be able to provide the appropriate means to improve any existing and future separation media for capillary electrophoresis. Preliminary tests by Applied Biosystems on one of our more readily accessible separation media have already shown that it is better than the commercial separation medium currently being used by ABI.
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