title: Hydrodynamics of diamond-shaped gradient nanopillar arrays for effective DNA translocation into nanochannels.
abstract: Effective DNA translocation into nanochannels is critical for advancing genome mapping and future single-molecule DNA sequencing technologies. We present the design and hydrodynamic study of a diamond-shaped gradient pillar array connected to nanochannels for enhancing the success of DNA translocation events. Single-molecule fluorescence imaging is utilized to interrogate the hydrodynamic interactions of the DNA with this unique structure, evaluate key DNA translocation parameters, including speed, extension, and translocation time, and provide a detailed mapping of the translocation events in nanopillar arrays coupled with 10 and 50 μm long channels. Our analysis reveals the important roles of diamond-shaped nanopillars in guiding DNA into as small as 30 nm channels with minimized clogging, stretching DNA to nearly 100% of their dyed contour length, inducing location-specific straddling of DNA at nanopillar interfaces, and modulating DNA speeds by pillar geometries. Importantly, all critical features down to 30 nm wide nanochannels are defined using standard photolithography and fabrication processes, a feat aligned with the requirement of high-volume, low-cost production.
authors.affiliation: IBM T. J. Watson Research Center , Yorktown Heights, New York 10598, United States.
authors.forename: Chao
authors.initials: C
authors.lastname: Wang
authors.forename: Robert L
authors.initials: RL
authors.lastname: Bruce
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Duch
authors.forename: Jyotica V
authors.initials: JV
authors.lastname: Patel
authors.forename: Joshua T
authors.initials: JT
authors.lastname: Smith
authors.forename: Yann
authors.initials: Y
authors.lastname: Astier
authors.forename: Benjamin H
authors.initials: BH
authors.lastname: Wunsch
authors.forename: Siddharth
authors.initials: S
authors.lastname: Meshram
authors.forename: Armand
authors.initials: A
authors.lastname: Galan
authors.forename: Chris
authors.initials: C
authors.lastname: Scerbo
authors.forename: Michael A
authors.initials: MA
authors.lastname: Pereira
authors.forename: Deqiang
authors.initials: D
authors.lastname: Wang
authors.forename: Evan G
authors.initials: EG
authors.lastname: Colgan
authors.forename: Qinghuang
authors.initials: Q
authors.lastname: Lin
authors.forename: Gustavo
authors.initials: G
authors.lastname: Stolovitzky
mesh_terms: D010582:Bacteriophage lambda; D004247:DNA / Q000235:genetics; D004867:Equipment Design; D057446:Hydrodynamics; D009038:Motion; D036103:Nanotechnology / Q000295:instrumentation*; D017422:Sequence Analysis, DNA
chemical_list: D004247:DNA
keywords: DNA stretching; genome mapping; gradient nanopillars; hydrodynamics; nanochannels; single-molecule fluorescent imaging; translocation