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.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project (R01)
Project #
5R01HG001386-08
Application #
6526539
Study Section
Genome Study Section (GNM)
Program Officer
Schloss, Jeffery
Project Start
1995-09-30
Project End
2004-08-31
Budget Start
2002-09-19
Budget End
2003-08-31
Support Year
8
Fiscal Year
2002
Total Cost
$237,348
Indirect Cost
Name
State University New York Stony Brook
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
804878247
City
Stony Brook
State
NY
Country
United States
Zip Code
11794
Wan, Fen; He, Weidong; Zhang, Jun et al. (2009) Reduced matrix viscosity in DNA sequencing by CE and microchip electrophoresis using a novel thermo-responsive copolymer. Electrophoresis 30:2488-98
Wan, Fen; Zhang, Jun; Lau, Angela et al. (2008) Nanostructured copolymer gels for dsDNA separation by CE. Electrophoresis 29:4704-13
Zhang, Jun; He, Weidong; Liang, Dehai et al. (2006) Designing polymer matrix for microchip-based double-stranded DNA capillary electrophoresis. J Chromatogr A 1117:219-27
Wan, Fen; He, Weidong; Zhang, Jun et al. (2006) Scale-up development of high-performance polymer matrix for DNA sequencing analysis. Electrophoresis 27:3712-23
Zhang, Jun; Gassmann, Marcus; He, Weidong et al. (2006) Reversible thermo-responsive sieving matrix for oligonucleotide separation. Lab Chip 6:526-33
Zhang, Jun; Burger, Christian; Chu, Benjamin (2006) Nanostructured polymer matrix for oligonucleotide separation. Electrophoresis 27:3391-8
Wang, Yanmei; Liang, Dehai; Ying, Qicong et al. (2005) Quasi-interpenetrating network formed by polyacrylamide and poly(N,N-dimethylacrylamide) used in high-performance DNA sequencing analysis by capillary electrophoresis. Electrophoresis 26:126-36
Zhang, Jun; Liang, Dehai; He, Weidong et al. (2005) Fast separation of single-stranded oligonucleotides by capillary electrophoresis using OliGreen as fluorescence inducing agent. Electrophoresis 26:4449-55
Liang, Dehai; Zhang, Jun; Chu, Benjamin (2003) Study of ethidium bromide effect on dsDNA separation by capillary zone electrophoresis and laser light scattering. Electrophoresis 24:3348-55
Moritani, Tohei; Yoon, Kyunghwan; Rafailovich, Miriam et al. (2003) DNA capillary electrophoresis using poly(vinyl alcohol). I. Inner capillary coating. Electrophoresis 24:2764-71

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