Nanoscale holes in solid-state membranes, so-called nanopores, furnish nanosensors for probing biological molecules such as DNA and protein. Under electric fields, charged molecules like DNA are pushed through these pores and the flow of ions surrounding the translocating DNA can be recorded to recognize individual DNA bases, and in turn, the sequence of DNA. Traditional nanopore sensors often use solid-state membranes, which are too thick to recognize single bases on a DNA strand. This limitation can be overcome by using two-dimensional materials such as graphene or MoS$_2$. Only a single base pair of DNA fits into the thin two-dimensional material nanopores at any time, such that these nanopores can potentially provide single-base resolution for DNA sensing. In addition, graphene and MoS$_2$ are both lectrically conductive, thereby allowing the use of electric current in the layer to detect and characterize the DNA in the pore. Instead of actually building and testing the device experimentally, molecular dynamics simulations can assist and enable a bottom-up design of two-dimensional material nanopore devices by unveiling the atomic-level processes occurring during nanopore sensing.

Spotlight: DNA Through Graphene Pore (Dec 2011)

DNA translocation through graphene nanopore

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Threading DNA electrically through nanometer-sized pores, so-called nanopores, holds promise for detecting and sequencing DNA (see Nov 2005 and Oct 2004 highlights). Nanopore measurements tend to be the more sensitive the smaller the pores are. The material graphene, which is just one atom thick and looks like a two-dimensional ``honeycomb" made up of carbon atoms, offers the ultimate physical resolution for measuring DNA (the stacking distance between base-pairs in DNA is about 0.35 nm). As reported recently, molecular dynamics simulations using NAMD revealed the motion of DNA being threaded through graphene nanopores at atomic level resolution. Simulations not only agree qualitatively with previous experiments on DNA translocation through graphene nanopores, but go one step further than the experiments and suggest how individual base pairs can be discriminated. The recent computational study is one further example for the guidance that molecular dynamics simulations provide in nanosensor development (see a recent review). More information can be found on our graphene nanopore website.

Related Spotlights

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Publications Database
  • Electrically tunable quenching of DNA fluctuations in biased solid-state nanopores. Hu Qiu, Anuj Girdhar, Klaus Schulten, and Jean-Pierre Leburton. ACS Nano, 10:4482-4488, 2016.
  • Intrinsic stepwise translocation of stretched ssDNA in graphene nanopores. Hu Qiu, Aditya Sarathy, Jean-Pierre Leburton, and Klaus Schulten. Nano Letters, 15:8322-8330, 2015.
  • Tunable graphene quantum point contact transistor for DNA detection and characterization. Anuj Girdhar, Chaitanya Sathe, Klaus Schulten, and Jean-Pierre Leburton. Nanotechnology, 26:134005, 2015. (10 pages).
  • Electronic detection of dsDNA transition from helical to zipper conformation using graphene nanopores. Chaitanya Sathe, Anuj Girdhar, Jean-Pierre Leburton, and Klaus Schulten. Nanotechnology, 25:445105, 2014. (9 pages).
  • Graphene quantum point contact transistor for DNA sensing. Anuj Girdhar, Chaitanya Sathe, Klaus Schulten, and Jean-Pierre Leburton. Proceedings of the National Academy of Sciences, USA, 110:16748-16753, 2013.
  • Computational investigation of DNA detection using graphene nanopores. Chaitanya Sathe, Xueqing Zou, Jean-Pierre Leburton, and Klaus Schulten. ACS Nano, 5:8842-8851, 2011.
  • Computational microscopy of the role of protonable surface residues in nanoprecipitation oscillations. Eduardo R. Cruz-Chu and Klaus Schulten. ACS Nano, 4:4463-4474, 2010.
  • Ionic current rectification through silica nanopores. Eduardo R. Cruz-Chu, Aleksei Aksimentiev, and Klaus Schulten. Journal of Physical Chemistry C, 113:1850-1862, 2009.
  • Molecular control of ionic conduction in polymer nanopores. Eduardo R. Cruz-Chu, Thorsten Ritz, Zuzanna S. Siwy, and Klaus Schulten. Faraday Discussion, 143:47-62, 2009.
  • Modeling transport through synthetic nanopores. Aleksei Aksimentiev, Robert K. Brunner, Eduardo Cruz-Chu, Jeffrey Comer, and Klaus Schulten. IEEE Nanotechnology, 3:20-28, 2009.
  • Computer modeling in biotechnology, a partner in development. Aleksei Aksimentiev, Robert Brunner, Jordi Cohen, Jeffrey Comer, Eduardo Cruz-Chu, David Hardy, Aruna Rajan, Amy Shih, Grigori Sigalov, Ying Yin, and Klaus Schulten. In Protocols in Nanostructure Design, Methods in Molecular Biology, pp. 181-234. Humana Press, 2008.
  • Water-silica force field for simulating nanodevices. Eduardo R. Cruz-Chu, Aleksei Aksimentiev, and Klaus Schulten. Journal of Physical Chemistry B, 110:21497-21508, 2006.
  • The role of molecular modeling in bionanotechnology. Deyu Lu, Aleksei Aksimentiev, Amy Y. Shih, Eduardo Cruz-Chu, Peter L. Freddolino, Anton Arkhipov, and Klaus Schulten. Physical Biology, 3:S40-S53, 2006.
  • The electromechanics of DNA in a synthetic nanopore. J. B. Heng, A. Aksimentiev, C. Ho, P. Marks, Y. V. Grinkova, S. Sligar, K. Schulten, and G. Timp. Biophysical Journal, 90:1098-1106, 2006.
  • Stretching DNA using an electric field in a synthetic nanopore. J. B Heng, A. Aksimentiev, C. Ho, P. Marks, Y. V. Grinkova, S. Sligar, K. Schulten, and G. Timp. Nano Letters, 5:1883-1888, 2005.
  • Imaging alpha-hemolysin with molecular dynamics: Ionic conductance, osmotic permeability and the electrostatic potential map. Aleksij Aksimentiev and Klaus Schulten. Biophysical Journal, 88:3745-3761, 2005.
  • Orientation discrimination of single stranded DNA inside the a-hemolysin membrane channel. Jerome Mathé, Aleksei Aksimentiev, David R. Nelson, Klaus Schulten, and Amit Meller. Proceedings of the National Academy of Sciences, USA, 102:12377-12382, 2005.
  • Beyond the gene chip. J. B. Heng, A. Aksimentiev, C. Ho, V. Dimitrov, T. Sorsch, J. Miner, W. Mansfield, K. Schulten, and G. Timp. Bell Labs Technical Journal, 10:5-22, 2005.
  • Sizing DNA using a nanometer-diameter pore. J. B. Heng, C. Ho, T. Kim, R. Timp, A. Aksimentiev, Y. V. Grinkova, S. Sligar, K. Schulten, and G. Timp. Biophysical Journal, 87:2905-2911, 2004.
  • Microscopic kinetics of DNA translocation through synthetic nanopores. Aleksij Aksimentiev, Jiunn Benjamin Heng, Gregory Timp, and Klaus Schulten. Biophysical Journal, 87:2086-2097, 2004.
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