Article

Fast DNA sequencing with a graphene-based nanochannel device

Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, Hyojadong, Namgu, Pohang 790-784, Korea.
Nature Nanotechnology (Impact Factor: 33.27). 02/2011; 6(3):162-5. DOI: 10.1038/nnano.2010.283
Source: PubMed

ABSTRACT Devices in which a single strand of DNA is threaded through a nanopore could be used to efficiently sequence DNA. However, various issues will have to be resolved to make this approach practical, including controlling the DNA translocation rate, suppressing stochastic nucleobase motions, and resolving the signal overlap between different nucleobases. Here, we demonstrate theoretically the feasibility of DNA sequencing using a fluidic nanochannel functionalized with a graphene nanoribbon. This approach involves deciphering the changes that occur in the conductance of the nanoribbon as a result of its interactions with the nucleobases via π-π stacking. We show that as a DNA strand passes through the nanochannel, the distinct conductance characteristics of the nanoribbon (calculated using a method based on density functional theory coupled to non-equilibrium Green function theory) allow the different nucleobases to be distinguished using a data-mining technique and a two-dimensional transient autocorrelation analysis. This fast and reliable DNA sequencing device should be experimentally feasible in the near future.

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Available from: Kwang S. Kim, Aug 20, 2015
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    • "Recently, graphene[6] with the atomic thinness, stability and electrical sensitivity, has been the hotspot of intense research with the potential to characterize single nucleotides of DNA[1] [7] [8] [9] [10]. Since molecular dynamics (MD) simulations can be used to investigate the entire translocation process, the opportunity for molecular modeling arises to play a major role in this Copyright © 2013 by ASME research area[11] [12] [13] [14]. "
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    ABSTRACT: Molecular dynamics simulations are performed to provide valuable information about the translocation of four single-stranded DNAs with ten identical bases through graphene nanopore with diameter of 2 nm. The monolayer graphene nanopore is highly sensitive to ssDNA translocation events and the 10-base resolution detection can be realized by electrophoreticly threading ssDNA through graphene nanopore. Due to the similar sizes of the four nucleotides, the blockage current is unlikely to provide a distinguishable signal. However, by simply monitoring and analyzing the translocation time of poly(dA)10, poly(dC)10, poly(dG)10 and poly(dT)10 though graphene pore, each ssDNA can be identified and characterized.
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    • "Already, theoretical calculations for DNA nano-sequencers has been demonstrated and the possibility of integrating this with other nano-scale read-out technologies (e.g. RFIDs or OPIDs) could allow sequencing without the DNA needing to leave the system [140]. Further, this would also improve the false-negative rate as DNA can be degraded or altered during transport out of the body. "
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    • "The largest promise for high-resolution molecular sensor is held by the graphene films, nanoporous or otherwise, as being conductive and sensing ones at the same time and remaining robust enough for repeated sensing. Several theoretical designs of graphene sequencing devices with graphene nanopore and nanoribbon covered nanochannel [5] were proposed. Orientation fluctuations of nucleotides during translocation through nanopore and corresponding overlaps of current distribution in experiment and simulation demonstrated the necessity of further development of single-based resolution methods. "
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    ABSTRACT: Use of solid film nanopore in which DNA is threaded through for efficient DNA sequencing devices has various practical issues concerned with nucleobase motion that should be controlled. Translocation rate and different orientation of nucleobases, stochastic motion of single-strand DNA through a nanopore introduce definite amount of noise into the signal defining interaction of nucleobase and nanopore. We propose to consider the single layer graphene nanopore as a two-way interaction scanning device.The interaction forces between pore and base are structure dependent, even within orientation and noise average over a base, and can be evaluated. The appropriate translocation rate of the base molecule provide a time-dependent function of interaction change inside of interaction interval of each individual base with graphene nanopore. In such case transient characteristics of the individual bases can be used for identification of the bases. The forces between bases and graphene nanopore of 1.5nm diameter are calculated as interaction characteristics of bases. Molecular dynamics method is used for the DNA base and graphene nanopore calculations with the MM2/MM3 potentials for the base and REBO graphene potential. Interaction potential between the bases and graphene are of the MM2/MM3 type although the possibility of the Van der Waals interaction only can also be considered. The noise of the force signal due to orientation of the bases in the pore is evaluated and base-dependent interaction recognition is considered relative to the magnitude of the AFM signal in the non-contact mode. The time-dependent in-plane for graphene transient force signal resolution for different bases is probed. Possibility of base identification by combination of transient in-plane force taken as orientation averaged signal is studied. Obtained results can simultaneously give additional information for the electronic transport calculations with possible transient base orientations relative to the edge of pore in graphene.
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