title: On-chip fraction collection for multiple selected ssDNA fragments using isolated extraction channels.
abstract: High efficiency and high-purity fraction collection is highly sought in analysis of fragments-of-interest from selective polymerase chain reaction (PCR) products generated by High Coverage Gene Expression Profiling (HiCEP) methods. Here we demonstrate a new electrophoretic chip device enabling automatic high-efficient fractionation of multiple ssDNA target fragments during a run of separation. We used thoroughly isolated extraction channels for each selected target to reduce the risk of cross-contamination between targets due to cross-talk of extraction channels. Fragments of 35, 108 and 138 b, were successfully isolated, then the recovery was PCR-amplified and assessed by capillary electrophoresis (CE) analysis. Total impurity level of the targets due to unwanted fragments of 0.7%, 2% and 6% respectively, was estimated. Difficulties in collecting multiple target factions are due to band diffusion and DNA adsorption to the walls for the fragments in the separation channel, which is generated by transferring the DNA target fraction from the extraction section to the target reservoir. Therefore, we have carefully measured band broadening and analyzed its influence on the separation resolution due to the delay.
authors.affiliation: Research Institute for Electronic Science, Hokkaido University, Kita-21 Nishi-10, Kita-ku, Sapporo 001-0021, Hokkaido, Japan.
authors.forename: Zheyu
authors.initials: Z
authors.lastname: Li
authors.forename: Kai
authors.initials: K
authors.lastname: Sun
authors.forename: Misato
authors.initials: M
authors.lastname: Sunayama
authors.forename: Yasutaka
authors.initials: Y
authors.lastname: Matsuo
authors.forename: Vygantas
authors.initials: V
authors.lastname: Mizeikis
authors.forename: Ryoko
authors.initials: R
authors.lastname: Araki
authors.forename: Kosei
authors.initials: K
authors.lastname: Ueno
authors.forename: Masumi
authors.initials: M
authors.lastname: Abe
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Misawa
mesh_terms: D004277:DNA, Single-Stranded / Q000032:analysis / Q000737:chemistry / Q000302:isolation & purification*; D019075:Electrophoresis, Capillary / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation* / Q000379:methods*; D016133:Polymerase Chain Reaction; D013050:Spectrometry, Fluorescence
chemical_list: D004277:DNA, Single-Stranded