Sieving properties of end group‐halogenated Pluronic polymer matrix in DNA separation under nondenaturing CE analysis |
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| Authors: | Hee Sung Hwang Gi Won Shin Aaron Cohen Chang Yeol Ryu Gyoo Yeol Jung |
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| Affiliation: | 1. School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea;2. Institute of Environmental and Energy Technology, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea;3. Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, USA;4. Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea |
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| Abstract: | CE‐SSCP analysis is a well‐established DNA separation method that is based on variations in mobility caused by sequence‐induced differences in the conformation of single‐stranded DNA. The resolution of CE‐SSCP analysis was improved by using a Pluronic polymer matrix, and it has been successfully applied in various genetic analyses. Because the Pluronic polymer forms a micellar cubic structure in the capillary, it provides a stable internal structure for high‐resolution CE‐SSCP analysis. We hypothesized that formation of micellar cubic structure is influenced by the end hydroxyl group of the Pluronic polymer, which affords structural stability through hydrogen bonding. To test this hypothesis, the hydroxyl group was halogenated to eliminate the hydrogen bonding without disturbing the polarity of polymer matrix. CE‐SSCP resolution of two DNA fragments with a single base difference was significantly worse in the halogenated polymer matrices due to band broadening. The viscoelastic properties of control (which has hydroxyl group), chlorinated, and brominated F108 solution upon heating were also investigated by rheological experiments, and we found that gelation was significantly associated with resolution. In this series of experiments, the effect of the hydroxyl group in Pluronic polymer matrix on separation resolution of CE‐SSCP analysis was demonstrated. |
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| Keywords: | CE‐SSCP Halogenation Pluronic polymer Polymer matrix |
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