Hydrodynamics of diamond-shaped gradient nanopillar arrays for effective DNA translocation into nanochannels

Chao Wang, Robert L. Bruce, Elizabeth A. Duch, Jyotica V. Patel, Joshua T. Smith, Yann Astier, Benjamin H. Wunsch, Siddharth Meshram, Armand Galan, Chris Scerbo, Michael A. Pereira, Deqiang Wang, Evan G. Colgan, Qinghuang Lin, Gustavo Stolovitzky

Research output: Contribution to journalArticle

14 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)1206-1218
Number of pages13
JournalACS Nano
Volume9
Issue number2
DOIs
StatePublished - Feb 24 2015

Fingerprint

Diamond
Hydrodynamics
Oligonucleotide Array Sequence Analysis
Diamonds
DNA
deoxyribonucleic acid
diamonds
hydrodynamics
gradients
Chromosome Mapping
Optical Imaging
plugging
Molecules
sequencing
genome
DNA Sequence Analysis
Photolithography
photolithography
Stretching
molecules

Keywords

  • DNA stretching
  • genome mapping
  • gradient nanopillars
  • hydrodynamics
  • nanochannels
  • single-molecule fluorescent imaging
  • translocation

ASJC Scopus subject areas

  • Engineering(all)
  • Materials Science(all)
  • Physics and Astronomy(all)
  • Medicine(all)

Cite this

Wang, C., Bruce, R. L., Duch, E. A., Patel, J. V., Smith, J. T., Astier, Y., ... Stolovitzky, G. (2015). Hydrodynamics of diamond-shaped gradient nanopillar arrays for effective DNA translocation into nanochannels. ACS Nano, 9(2), 1206-1218. https://doi.org/10.1021/nn507350e

Hydrodynamics of diamond-shaped gradient nanopillar arrays for effective DNA translocation into nanochannels. / Wang, Chao; Bruce, Robert L.; Duch, Elizabeth A.; Patel, Jyotica V.; Smith, Joshua T.; Astier, Yann; Wunsch, Benjamin H.; Meshram, Siddharth; Galan, Armand; Scerbo, Chris; Pereira, Michael A.; Wang, Deqiang; Colgan, Evan G.; Lin, Qinghuang; Stolovitzky, Gustavo.

In: ACS Nano, Vol. 9, No. 2, 24.02.2015, p. 1206-1218.

Research output: Contribution to journalArticle

Wang, C, Bruce, RL, Duch, EA, Patel, JV, Smith, JT, Astier, Y, Wunsch, BH, Meshram, S, Galan, A, Scerbo, C, Pereira, MA, Wang, D, Colgan, EG, Lin, Q & Stolovitzky, G 2015, 'Hydrodynamics of diamond-shaped gradient nanopillar arrays for effective DNA translocation into nanochannels', ACS Nano, vol. 9, no. 2, pp. 1206-1218. https://doi.org/10.1021/nn507350e
Wang, Chao ; Bruce, Robert L. ; Duch, Elizabeth A. ; Patel, Jyotica V. ; Smith, Joshua T. ; Astier, Yann ; Wunsch, Benjamin H. ; Meshram, Siddharth ; Galan, Armand ; Scerbo, Chris ; Pereira, Michael A. ; Wang, Deqiang ; Colgan, Evan G. ; Lin, Qinghuang ; Stolovitzky, Gustavo. / Hydrodynamics of diamond-shaped gradient nanopillar arrays for effective DNA translocation into nanochannels. In: ACS Nano. 2015 ; Vol. 9, No. 2. pp. 1206-1218.
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