DPG Spring Meeting Poster: Measuring DNA Translocation through Nanopores in Graphene and Carbon Nanomembranes with Optical Tweezers

31 Mar 2014   | 2014

Sebastian Knust¹, Andreas Meyer², André Spiering¹, Christoph Pelargus¹, Andy Sischka¹, Peter Reimann², and Dario Anselmetti¹

¹ Experimental Biophysics and Applied Nanoscience, Faculty of Physics, Bielefeld University
² Theoretical Physics and Soft Matter Theory, Faculty of Physics, Bielefeld University

Abstract

We measured forces acting on DNA during translocation through a nanopore with Optical Tweezers. A video-based force detection and analysis system was developed, allowing for virtually interference-free axial force measurements with an overall force resolution of ±0.5 pN at a sample rate of 123 Hz [1].

We previously measured the translocation of dsDNA through 20 nm thick Si3N4 membranes (0.1 pN/mV for pores ≥ 30 nm) [2, 3]. Lipid coating as well as carbon nanomembranes and graphene with a thickness of 3 nm and 0.3 nm respectively allow for even more sensitive measurements.

Experimental Setup

Optical Tweezers Setup

  • Video-based force detection → reduced interference
  • Calibration via Stokes friction and Allan variance
  • Force sensitivity better than 0.5 pN at 123 Hz sample rate

Translocation Theory

Translocation theory with slip length

  • Dynamics dominated by electrohydrodynamic effects (electro-osmotic flow)
  • Modeling with combination of Poisson, Nernst-Planck and Stokes equations
  • Mere zero surface charge on coated membrane does not explain high forces
  • → Introduction of slip length at the DNA-solution-interface
  • Supported by theoretical treatment of DNA nanostructure [3] and recent MD simulations [4]

Results:

Slip length \(\)
Surface charge for Si3N4 \(\)

Nanomembrane Preparation

Graphene

Graphene Exfoliation Process

  • Mechanical exfoliation with nitto tape
  • Automated searching routine for graphene flakes
  • Transfer on chip with cellulose polymer

Carbon nanomembranes

Fabrication of Carbon Nanomembranes

Resulting thickness of 1-3 nm

Nanopore Preparation

Fabrication of Nanopores

  • Zeiss Orion Plus HIM
  • 0.35 nm imaging resolution
  • Pore sizes as small as 5-6 nm

Graphene

Strongly localised heating phenomena (plasmon?)
→ Melts polystyrene beads
→ Dissipates biotin-streptavidin bond between bead and DNA

Carbon Nanomembranes

DNA translocation through CNM nanopore

  • 3 nm membrane thickness
  • 70 nm NP size
  • 50 mV
  • 20 mM KCl
  • Interference caused by silicon chip geometry

References

[1] S. Knust et al., Video-based and interference-free axial force detection and analysis for optical tweezers. Rev. Sci. Instr. 83, 103704 (2012)
[2] A. Spiering et al., Nanopore translocation dynamics of a single DNA-bound protein. Nano Lett. 11, 2978 (2011)
[3] A. Sischka et al., in preparation
[4] S. Kesselheim, W. Müller, C. Holm, Origin of Current Blockades in Nanopore Translocation Experiments. Phys. Rev. Lett. 112, 018101 (2014)

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