title: Separation of long DNA molecules by quartz nanopillar chips under a direct current electric field.
abstract: We have established the nanofabrication technique for constructing nanopillars with high aspect ratio (100-500 nm diameter and 500-5000 nm tall) inside a microchannel on a quartz chip. The size of pillars and the spacing between pillars are designed as a DNA sieving matrix for optimal analysis of large DNA fragments over a few kilobase pairs (kbp). A chip with nanopillar channel and simple cross injector was developed based on the optimal design and applied to the separation of DNA fragments (1-38 kbp) and large DNA fragments (lambda DNA, 48.5 kbp; T4 DNA, 165.6 kbp) that are difficult to separate on conventional gel electrophoresis and capillary electrophoresis without a pulsed-field technique. DNA fragments ranging from 1 to 38 kbp were separated as clear bands, and furthermore, the mixture of lambda DNA and T4 DNA was successfully separated by a 380-microm-long nanopillar channel within only 10 s even under a direct current (dc) electric field. Theoretical plate number N of the channel (380-1450 microm long) was 1000-3000 (0.7 x 10(6)-2.1 x 10(6) plates/m). A single DNA molecule observation during electrophoresis in a nanopillar channel revealed that the optimal nanopillars induced T4 DNA to form a narrow U-shaped conformation during electrophoresis whereas lambda DNA kept a rather spherical conformation. We demonstrated that, even under a dc electric field, the optimal nanopillar dimensions depend on a gyration radius of DNA molecule that made it possible to separate large DNA fragments in a short time.
authors.affiliation: Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, The University of Tokushima, CREST, Japan. c400241002@stud.tokushima-u.ac.jp
authors.forename: Noritada
authors.initials: N
authors.lastname: Kaji
authors.forename: Yojiro
authors.initials: Y
authors.lastname: Tezuka
authors.forename: Yuzuru
authors.initials: Y
authors.lastname: Takamura
authors.forename: Masanori
authors.initials: M
authors.lastname: Ueda
authors.forename: Takahiro
authors.initials: T
authors.lastname: Nishimoto
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Nakanishi
authors.forename: Yasuhiro
authors.initials: Y
authors.lastname: Horiike
authors.forename: Yoshinobu
authors.initials: Y
authors.lastname: Baba
mesh_terms: D004247:DNA / Q000032:analysis*; D004563:Electrochemistry; D036103:Nanotechnology / Q000295:instrumentation / Q000379:methods*; D011791:Quartz / Q000032:analysis*
chemical_list: D011791:Quartz; D004247:DNA