Detection of long and short DNA using nanopores with graphitic polyhedral edges.

Graphene is a unique material with a thickness as low as a single atom, high in-plane conductivity and a robust lattice that is self-supporting over large length scales. Schematically, graphene is an ideal solid-state material for tuning the properties of a nanopore because self-supported sheets, ranging from single to multiple atomic layers, can create pores with near-arbitrary dimensions which can provide exquisite control of the electric field drop within the pore. In this study, we characterize the drilling kinetics of nanopores using a thermionic electron source and various electron beam fluxes to minimize secondary hole formation. Once established, we investigated the use of multilayer graphene to create highly tailored nanostructures including nanopores with graphite polyhedral crystals formed around the nanopore edge. Finally, we report on the translocation of double stranded and single stranded DNA through such graphene pores and show that the single stranded DNA translocates much slower allowing detection of extremely short fragments (25 nucleotides in length). Our findings suggest that the kinetic and controllable properties of graphene nanopores under sculpting conditions can be used to further enhance the detection of DNA analytes.

[1]  Grégory Pandraud,et al.  Atomic-scale electron-beam sculpting of near-defect-free graphene nanostructures. , 2011, Nano letters.

[2]  J. Giérak,et al.  Dynamics of completely unfolded and native proteins through solid-state nanopores as a function of electric driving force. , 2011, ACS nano.

[3]  Rashid Bashir,et al.  Solid-state nanopore channels with DNA selectivity. , 2007, Nature nanotechnology.

[4]  Alan Gelperin,et al.  DNA-decorated carbon nanotubes for chemical sensing. , 2005 .

[5]  S. Grimme,et al.  Structures and interaction energies of stacked graphene-nucleobase complexes. , 2008, Physical chemistry chemical physics : PCCP.

[6]  A. Reina,et al.  Graphene as a sub-nanometer trans-electrode membrane , 2010, Nature.

[7]  J. Charlier,et al.  Synthesis of graphite polyhedral crystals using a combustion flame method , 2005 .

[8]  Y. Gogotsi,et al.  Analysis of non-planar graphitic structures: from arched edge planes of graphite crystals to nanotubes , 2002 .

[9]  F. Banhart.  The Formation of a Connection between Carbon Nanotubes in an Electron Beam , 2001 .

[10]  C. Berger,et al.  Highly ordered graphene for two dimensional electronics , 2006 .

[11]  Klaus Schulten,et al.  Computational investigation of DNA detection using graphene nanopores. , 2011, ACS nano.

[12]  Meni Wanunu,et al.  DNA translocation governed by interactions with solid-state nanopores. , 2008, Biophysical journal.

[13]  M. J. Kim,et al.  Chemical, Thermal, and Electric Field Induced Unfolding of Single Protein Molecules Studied Using Nanopores , 2022 .

[14]  Yury Gogotsi,et al.  Conical crystals of graphite , 2002 .

[15]  Shibing Long,et al.  Enhanced DNA Sequencing Performance Through Edge‐Hydrogenation of Graphene Electrodes , 2010, 1012.0031.

[16]  Johan Nilsson,et al.  Electronic properties of graphene multilayers. , 2006, Physical review letters.

[17]  A. Meller,et al.  Rapid Fabrication of Uniformly Sized Nanopores and Nanopore Arrays for Parallel DNA Analysis , 2006 .

[18]  F. Banhart,et al.  Graphitization Mechanism during the Carbon-Nanotube Formation Based on the In-Situ HRTEM Observation , 2002 .

[19]  Cees Dekker,et al.  Unraveling single-stranded DNA in a solid-state nanopore. , 2010, Nano letters.

[20]  Neil Peterman,et al.  DNA translocation through graphene nanopores. , 2010, Nano letters.

[21]  Marc Gershow,et al.  DNA molecules and configurations in a solid-state nanopore microscope , 2003, Nature materials.

[22]  C. Dekker.  Solid-state nanopores. , 2007, Nature nanotechnology.

[23]  Aleksei Aksimentiev,et al.  Assessing graphene nanopores for sequencing DNA. , 2012, Nano letters.

[24]  H. Duan,et al.  Turning PMMA Nanofibers into Graphene Nanoribbons by In Situ Electron Beam Irradiation , 2008 .

[25]  Cees Dekker,et al.  Direct force measurements on DNA in a solid-state nanopore , 2006 .

[26]  K. Schulten,et al.  Sizing DNA using a nanometer-diameter pore. , 2004, Biophysical journal.

[27]  D. Branton,et al.  Characterization of individual polynucleotide molecules using a membrane channel. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[28]  Aleksei Aksimentiev,et al.  Slowing down DNA translocation through a nanopore in lithium chloride. , 2012, Nano letters.

[29]  D. Ugarte.  Curling and closure of graphitic networks under electron-beam irradiation , 1992, Nature.

[30]  M. Yoshikawa,et al.  Structure and electronic properties of graphite nanoparticles , 1998 .

[31]  Jingmin Jin,et al.  Rapid electronic detection of probe-specific microRNAs using thin nanopore sensors. , 2010, Nature nanotechnology.

[32]  Steven G. Louie,et al.  Graphene at the Edge: Stability and Dynamics , 2009, Science.

[33]  D. Talaga,et al.  Single-molecule protein unfolding in solid state nanopores. , 2009, Journal of the American Chemical Society.

[34]  Robert M Shelby,et al.  Sequence-independent helical wrapping of single-walled carbon nanotubes by long genomic DNA. , 2006, Nano letters.

[35]  M F Crommie,et al.  Direct imaging of lattice atoms and topological defects in graphene membranes. , 2008, Nano letters.

[36]  Jeremy S. Lee,et al.  Nanopore detection of antibody prion interactions. , 2010, Analytical biochemistry.

[37]  D. Branton,et al.  Voltage-driven DNA translocations through a nanopore. , 2001, Physical review letters.

[38]  Andre K. Geim,et al.  Raman spectrum of graphene and graphene layers. , 2006, Physical review letters.

[39]  H. Postma,et al.  Rapid sequencing of individual DNA molecules in graphene nanogaps. , 2008, Nano letters.

[40]  Mark Akeson,et al.  Single-molecule analysis of DNA-protein complexes using nanopores , 2007, Nature Methods.

[41]  E. Kaxiras,et al.  DNA nucleoside interaction and identification with carbon nanotubes. , 2007, Nano letters.

[42]  Aleksei Aksimentiev,et al.  Slowing the translocation of double-stranded DNA using a nanopore smaller than the double helix , 2010, Nanotechnology.

[43]  D. Teweldebrhan,et al.  Modification of graphene properties due to electron-beam irradiation , 2008, 0812.0571.

[44]  J. Joanny,et al.  Fast DNA translocation through a solid-state nanopore. , 2004, Nano letters.

[45]  R. Ahuja,et al.  Physisorption of nucleobases on graphene : Density-functional calculations , 2007, 0704.1316.

[46]  D. Branton,et al.  Unzipping kinetics of double-stranded DNA in a nanopore. , 2002, Physical review letters.

[47]  Bo Zhang,et al.  Detection of nucleic acids with graphene nanopores: ab initio characterization of a novel sequencing device. , 2010, Nano letters.

[48]  Alan Gelperin,et al.  DNA-decorated carbon nanotubes for chemical sensing , 2005, Nano letters.

[49]  A. I. Zad,et al.  Mechanical properties of graphene cantilever from atomic force microscopy and density functional theory , 2010, Nanotechnology.

[50]  Y. Gogotsi,et al.  Graphite polyhedral crystals. , 2000, Science.

[51]  Lianmao Peng,et al.  Fabrication and Electrical and Mechanical Properties of Carbon Nanotube Interconnections , 2005 .

[52]  D. McNabb,et al.  Slowing DNA translocation in a solid-state nanopore. , 2005, Nano letters.

[53]  Marija Drndic,et al.  Electron beam nanosculpting of suspended graphene sheets , 2008 .