title: Sieving properties of end group-halogenated Pluronic polymer matrix in DNA separation under nondenaturing CE analysis.
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.
authors.affiliation: School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea.
authors.forename: Hee Sung
authors.initials: HS
authors.lastname: Hwang
authors.forename: Gi Won
authors.initials: GW
authors.lastname: Shin
authors.forename: Aaron
authors.initials: A
authors.lastname: Cohen
authors.forename: Chang Yeol
authors.initials: CY
authors.lastname: Ryu
authors.forename: Gyoo Yeol
authors.initials: GY
authors.lastname: Jung
mesh_terms: D004247:DNA / Q000032:analysis / Q000737:chemistry / Q000302:isolation & purification*; D019075:Electrophoresis, Capillary / Q000379:methods; D054879:Halogenation; D006801:Humans; D008297:Male; D020442:Poloxamer / Q000737:chemistry*; D016133:Polymerase Chain Reaction; D018807:Polymorphism, Single-Stranded Conformational; D013696:Temperature
chemical_list: D020442:Poloxamer; D004247:DNA
keywords: CE-SSCP; Halogenation; Pluronic polymer; Polymer matrix