title: Separation of DNA with different configurations on flat and nanopatterned surfaces.
abstract: We demonstrate that electrophoresis on a flat Si substrate is an effective method in separation of DNA with different configurations, e.g., linear, supercoiled, and relaxed or DNA of different length, e.g., supercoiled DNA ladder. The surface separation arises from the different number of contacts due to the conformational differences between adsorbed DNA chains. Imposing a Au nanopattern on the Si surface further improves the separation effect. The simulation of electric field on this patterned surface by the finite element method shows that Au nanodots act as local pinning points for DNA segments due to dielectrophoretic force. The results of molecular dynamics simulation showed that the conformational differences between adsorbed polymer chains were amplified on the patterned surface and enhanced separations were achieved, which are consistent with the experimental results.
authors.affiliation: Department of Materials Science and Engineering, SUNY at Stony Brook, New York 11794, USA. binli@ic.sunysb.edu
authors.forename: Bingquan
authors.initials: B
authors.lastname: Li
authors.forename: Xiaohua
authors.initials: X
authors.lastname: Fang
authors.forename: Haobin
authors.initials: H
authors.lastname: Luo
authors.forename: Young-Soo
authors.initials: YS
authors.lastname: Seo
authors.forename: Eric
authors.initials: E
authors.lastname: Petersen
authors.forename: Yuan
authors.initials: Y
authors.lastname: Ji
authors.forename: Miriam
authors.initials: M
authors.lastname: Rafailovich
authors.forename: Jonathan
authors.initials: J
authors.lastname: Sokolov
authors.forename: Dilip
authors.initials: D
authors.lastname: Gersappe
authors.forename: Benjamin
authors.initials: B
authors.lastname: Chu
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000302:isolation & purification*; D004278:DNA, Superhelical / Q000737:chemistry / Q000302:isolation & purification; D004583:Electrons; D006046:Gold / Q000737:chemistry; D008855:Microscopy, Electron, Scanning; D049329:Nanostructures / Q000737:chemistry* / Q000648:ultrastructure; D010957:Plasmids / Q000737:chemistry / Q000302:isolation & purification; D013499:Surface Properties
chemical_list: D004278:DNA, Superhelical; D006046:Gold; D004247:DNA