title: The application of capillary electrophoresis for assisting whole-cell aptamers selection by characterizing complete ssDNA distribution.
abstract: Whole-cell SELEX faces more difficulties than SELEX against purified molecules target. In this work, we demonstrate the application of capillary electrophoresis for assisting whole-cell aptamers selection by characterizing complete ssDNA distribution. We chose three cancer cell lines U251, Hela and PC3 as target, FAM labeled Sgc8c (a 41mer aptamer) and FAM labeled 41mer random ssDNA library as ssDNA model. CE conditions of running buffer and capillary length and inner diameter as well as UV and LIF detection were optimized. The distribution percentage of Sgc8c and ssDNA library against U251, Hela and PC3 was demonstrated, the relative peak area of their complex is 8.94%, 1.05% and 0.44% for Sgc8c and 9.03%, 1.04% and 0.12% for ssDNA library respectively. Under the chosen experimental conditions, binding ability comparison of three cell lines was U251>Hela>PC3, which was validated by laser confocol microscope. For each cell, distribution percentage of ssDNA library was compared with that of Sgc8c. Finally, whole-cell complex of U251-Sgc8c was confirmed by increase incubation time and fraction CE analysis.
authors.affiliation: School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
authors.forename: Beilei
authors.initials: B
authors.lastname: Lou
authors.affiliation: School of Life Science, Beijing Institute of Technology, Beijing 100081, China; Beijing Centre for Physical and Chemical Analysis, Beijing 100089, China.
authors.forename: Erning
authors.initials: E
authors.lastname: Chen
authors.affiliation: Beijing Centre for Physical and Chemical Analysis, Beijing 100089, China.
authors.forename: Xinying
authors.initials: X
authors.lastname: Zhao
authors.affiliation: School of Life Science, Beijing Institute of Technology, Beijing 100081, China. Electronic address: qufengqu@bit.edu.cn.
authors.forename: Feng
authors.initials: F
authors.lastname: Qu
authors.affiliation: School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
authors.forename: Jieying
authors.initials: J
authors.lastname: Yan
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry / Q000302:isolation & purification*; D045744:Cell Line, Tumor; D002623:Chemistry Techniques, Analytical / Q000379:methods*; D004277:DNA, Single-Stranded / Q000737:chemistry*; D019075:Electrophoresis, Capillary; D015723:Gene Library; D006367:HeLa Cells; D006801:Humans; D015203:Reproducibility of Results; D052156:SELEX Aptamer Technique
chemical_list: D052157:Aptamers, Nucleotide; D004277:DNA, Single-Stranded
keywords: Aptamers selection; Capillary electrophoresis; Whole-cell; ssDNA distribution