Automated fabrication of 2-nm solid-state nanopores for nucleic acid analysis.

We demonstrate the automated and reproducible fabrication of sub-2-nm nanopores in 10-nm thick silicon nitride membranes, through controlled dielectric breakdown in solution. Our results reveal that under the appropriate conditions, nanopores can be fabricated with a size no larger than 2.0 ± 0.5-nm in diameter for a sample of N = 23 nanopores, with an average and standard deviation of 1.3 ± 0.6-nm. The dimensions of these nanopores are confirmed by using individual translocating DNA molecules as molecular rulers. We show that a 2.0-nm and a 2.1-nm diameter nanopore are capable of distinguishing single-stranded DNA versus double-stranded DNA, and that a 2.4-nm diameter nanopore can be used to investigate the overstretching transition in short dsDNA fragments. These results highlight the reliability and precision of the automated fabrication of nanopores via controlled dielectric breakdown, showing great promise for the manufacturing of future nanopore-based technologies.

[1]  R. Dutton,et al.  Descreening of field effect in electrically gated nanopores , 2010, 1005.5187.

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

[3]  C. Dekker,et al.  Fabrication of solid-state nanopores with single-nanometre precision , 2003, Nature materials.

[4]  M. Wanunu.  Nanopores: A journey towards DNA sequencing. , 2012, Physics of Life Reviews.

[5]  H. Bayley,et al.  Continuous base identification for single-molecule nanopore DNA sequencing. , 2009, Nature nanotechnology.

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

[7]  Jie Yan,et al.  Transition dynamics and selection of the distinct S-DNA and strand unpeeling modes of double helix overstretching , 2010, Nucleic acids research.

[8]  M. Niederweis,et al.  Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase , 2012, Nature Biotechnology.

[9]  U. Keyser,et al.  Salt dependence of ion transport and DNA translocation through solid-state nanopores. , 2006, Nano letters.

[10]  Min Jun Kim,et al.  SEM-induced shrinking of solid-state nanopores for single molecule detection. , 2011, Nanotechnology.

[11]  Cees Dekker,et al.  Controlling nanopore size, shape and stability , 2010, Nanotechnology.

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

[13]  Stijn van Dorp,et al.  Origin of the electrophoretic force on DNA in solid-state nanopores , 2009 .

[14]  W. Webb,et al.  Ionic strength-dependent persistence lengths of single-stranded RNA and DNA , 2011, Proceedings of the National Academy of Sciences.

[15]  J. Reiner,et al.  Nanoscopic porous sensors. , 2008, Annual review of analytical chemistry.

[16]  M. Niederweis,et al.  Nanopore DNA sequencing with MspA , 2010, Proceedings of the National Academy of Sciences.

[17]  Cees Dekker,et al.  Modeling the conductance and DNA blockade of solid-state nanopores , 2011, Nanotechnology.

[18]  Jie Yan,et al.  Two distinct overstretched DNA structures revealed by single-molecule thermodynamics measurements , 2012, Proceedings of the National Academy of Sciences.

[19]  Meni Wanunu,et al.  Electromechanical unzipping of individual DNA molecules using synthetic sub-2 nm pores. , 2008, Nano letters.

[20]  A. Balan,et al.  Differentiation of short, single-stranded DNA homopolymers in solid-state nanopores. , 2013, ACS nano.

[21]  C. Dekker,et al.  Translocation of double-strand DNA through a silicon oxide nanopore. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

[22]  A. Meller,et al.  Detection of urea-induced internal denaturation of dsDNA using solid-state nanopores , 2010, Journal of physics. Condensed matter : an Institute of Physics journal.

[23]  A. Meller,et al.  DNA profiling using solid-state nanopores: detection of DNA-binding molecules. , 2009, Nano letters.

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

[25]  B. Shklovskii,et al.  Effective charge and free energy of DNA inside an ion channel. , 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

[26]  Michael J. Aziz,et al.  Ion-beam sculpting at nanometre length scales , 2001, Nature.

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

[28]  Jacob K Rosenstein,et al.  Slow DNA transport through nanopores in hafnium oxide membranes. , 2013, ACS nano.

[29]  Gregory Timp,et al.  Direct visualization of single-molecule translocations through synthetic nanopores comparable in size to a molecule. , 2013, ACS nano.

[30]  C. Bustamante,et al.  Overstretching B-DNA: The Elastic Response of Individual Double-Stranded and Single-Stranded DNA Molecules , 1996, Science.

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

[32]  B. Luan,et al.  Control and reversal of the electrophoretic force on DNA in a charged nanopore , 2010, Journal of physics. Condensed matter : an Institute of Physics journal.

[33]  Cees Dekker,et al.  Distinguishing single- and double-stranded nucleic acid molecules using solid-state nanopores. , 2009, Nano letters.

[34]  Aleksei Aksimentiev,et al.  Electro-osmotic screening of the DNA charge in a nanopore. , 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.

[35]  U. Rant,et al.  Electrically facilitated translocations of proteins through silicon nitride nanopores: conjoint and competitive action of diffusion, electrophoresis, and electroosmosis. , 2010, Nano letters.

[36]  E. Yusko,et al.  Electroosmotic flow can generate ion current rectification in nano- and micropores. , 2010, ACS nano.

[37]  I. Rouzina,et al.  Effect of pH on the overstretching transition of double-stranded DNA: evidence of force-induced DNA melting. , 2001, Biophysical journal.

[38]  H. W. Zandbergen,et al.  Electron-beam-induced deformations of SiO2 nanostructures , 2005 .

[39]  R. Bashir,et al.  Nanopore sensors for nucleic acid analysis. , 2011, Nature nanotechnology.

[40]  M. Godin,et al.  Precise control of the size and noise of solid-state nanopores using high electric fields , 2012, Nanotechnology.

[41]  D. Branton,et al.  The potential and challenges of nanopore sequencing , 2008, Nature Biotechnology.