Slow DNA transport through nanopores in hafnium oxide membranes.

We present a study of double- and single-stranded DNA transport through nanopores fabricated in ultrathin (2-7 nm thick) freestanding hafnium oxide (HfO2) membranes. The high chemical stability of ultrathin HfO2 enables long-lived experiments with <2 nm diameter pores that last several hours, in which we observe >50 000 DNA translocations with no detectable pore expansion. Mean DNA velocities are slower than velocities through comparable silicon nitride pores, providing evidence that HfO2 nanopores have favorable physicochemical interactions with nucleic acids that can be leveraged to slow down DNA in a nanopore.

[1]  G. Humphrey.  Heats of Formation of Hafnium Oxide and Hafnium Nitride , 1953 .

[2]  Nicholas N. Watkins,et al.  Highly Sensitive, Mechanically Stable Nanopore Sensors for DNA Analysis , 2009, Advanced materials.

[3]  Marcus Textor,et al.  Alkyl Phosphate Monolayers, Self-Assembled from Aqueous Solution onto Metal Oxide Surfaces , 2001 .

[4]  Esther Kim,et al.  Atomic Layer Deposition of Hafnium and Zirconium Oxides Using Metal Amide Precursors , 2002 .

[5]  D. Reinhoudt,et al.  Electrochemical stability of self-assembled alkylphosphate monolayers on conducting metal oxides. , 2011, Langmuir : the ACS journal of surfaces and colloids.

[6]  Jiajun Gu,et al.  PROBING SINGLE DNA MOLECULE TRANSPORT USING FABRICATED NANOPORES. , 2004, Nano letters.

[7]  Alexander Y. Grosberg,et al.  Electrostatic Focusing of Unlabeled DNA into Nanoscale Pores using a Salt Gradient , 2009, Nature nanotechnology.

[8]  Nicholas M. Fahrenkopf,et al.  Immobilization mechanisms of deoxyribonucleic acid (DNA) to hafnium dioxide (HfO2) surfaces for biosensing applications. , 2012, ACS applied materials & interfaces.

[9]  David W. McComb,et al.  DNA Tunneling Detector Embedded in a Nanopore , 2010, Nano letters.

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

[11]  R. Ghodssi,et al.  Mechanical property characterization of LPCVD silicon nitride thin films at cryogenic temperatures , 2004, Journal of Microelectromechanical Systems.

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

[13]  K. Schulten,et al.  Imaging alpha-hemolysin with molecular dynamics: ionic conductance, osmotic permeability, and the electrostatic potential map. , 2005, Biophysical journal.

[14]  M. Kosmulski.  Attempt to determine pristine points of zero charge of Nb2O5, Ta2O5, and HfO2 , 1997 .

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

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

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

[18]  C. M. Beck,et al.  Thermodynamics of silicon nitride. I. Standard molar enthalpies of formation ΔfHmoat the temperature 298.15 K of α-Si3N4and β-Si3N4☆ , 1999 .

[19]  Z. Siwy,et al.  Nanopore analytics: sensing of single molecules. , 2009, Chemical Society reviews.

[20]  DNA Translocation through Graphene Nanopores , 2011 .

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

[22]  K. Shepard,et al.  Integrated nanopore sensing platform with sub-microsecond temporal resolution , 2012, Nature Methods.

[23]  A. Meller,et al.  pH tuning of DNA translocation time through organically functionalized nanopores. , 2013, ACS nano.

[24]  C Raillon,et al.  Fast and automatic processing of multi-level events in nanopore translocation experiments. , 2012, Nanoscale.

[25]  C. Tropini,et al.  Multi-nanopore force spectroscopy for DNA analysis. , 2007, Biophysical journal.

[26]  T. Ala‐Nissila,et al.  Translocation dynamics with attractive nanopore-polymer interactions. , 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.

[27]  Gustavo Stolovitzky,et al.  Characterizing and controlling the motion of ssDNA in a solid-state nanopore. , 2011, Biophysical journal.

[29]  D. Ly,et al.  Electronic barcoding of a viral gene at the single-molecule level. , 2012, Nano letters.

[30]  Peixuan Guo,et al.  Solid-State and Biological Nanopore for Real-Time Sensing of Single Chemical and Sequencing of DNA , 2014 .

[31]  L. Qin,et al.  Rapid and precise scanning helium ion microscope milling of solid-state nanopores for biomolecule detection , 2011, Nanotechnology.

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

[33]  Nicholas A W Bell,et al.  DNA origami nanopores. , 2012, Nano letters.

[34]  P. Batson,et al.  Formation of nanopores in a SiN/SiO2 membrane with an electron beam , 2005 .

[35]  D. Lubensky,et al.  Driven polymer translocation through a narrow pore. , 1999, Biophysical journal.

[36]  Makusu Tsutsui,et al.  Electrical detection of single methylcytosines in a DNA oligomer. , 2011, Journal of the American Chemical Society.

[37]  C. Dekker,et al.  DNA sequencing with nanopores , 2012, Nature Biotechnology.

[38]  Mark Akeson,et al.  Automated Forward and Reverse Ratcheting of DNA in a Nanopore at Five Angstrom Precision1 , 2012, Nature Biotechnology.

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

[40]  Andre Marziali,et al.  Noise analysis and reduction in solid-state nanopores , 2007 .

[41]  T. G. Martin,et al.  DNA origami gatekeepers for solid-state nanopores. , 2012, Angewandte Chemie.

[42]  P. Carr,et al.  Mixed-mode retention of peptides on phosphate-modified polybutadiene-coated zirconia. , 1995, Analytical chemistry.

[43]  Aaron T. Kuan,et al.  Nanometer-thin solid-state nanopores by cold ion beam sculpting. , 2012, Applied physics letters.

[44]  Ruoshan Wei,et al.  Stochastic sensing of proteins with receptor-modified solid-state nanopores. , 2012, Nature nanotechnology.

[45]  P. Borer,et al.  Sampling a biomarker of the human immunodeficiency virus across a synthetic nanopore. , 2013, ACS nano.

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

[47]  Amit Meller,et al.  Single molecule measurements of DNA transport through a nanopore , 2002, Electrophoresis.

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

[49]  Cees Dekker,et al.  Detection of local protein structures along DNA using solid-state nanopores. , 2010, Nano letters.

[50]  J. Alarie,et al.  A device for performing lateral conductance measurements on individual double-stranded DNA molecules. , 2012, ACS nano.

[51]  Gerhard Hummer,et al.  Extracting kinetics from single-molecule force spectroscopy: nanopore unzipping of DNA hairpins. , 2007, Biophysical journal.

[52]  Claudia Felser,et al.  Hard x-ray photoelectron spectroscopy of chalcopyrite solar cell components , 2012 .

[53]  Helmut Baumgart,et al.  Nanoindentation Investigation of HfO2 and Al2O3 Films Grown by Atomic Layer Deposition , 2008 .

[54]  H. Hiller.  In: Ullmann''''s Encyclopedia of Industrial Chemistry , 1989 .

[55]  In-Ho Lee,et al.  Nanopore sensor for fast label-free detection of short double-stranded DNAs. , 2007, Biosensors & bioelectronics.

[56]  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.

[57]  Nahid N. Jetha,et al.  Single-molecule bonds characterized by solid-state nanopore force spectroscopy. , 2009, ACS nano.

[58]  K. Schulten,et al.  Microscopic Kinetics of DNA Translocation through synthetic nanopores. , 2004, Biophysical journal.

[59]  Klaus Schulten,et al.  Detection and Quantification of Methylation in DNA using Solid-State Nanopores , 2013, Scientific Reports.

[60]  D. Branton,et al.  Molecule-hugging graphene nanopores , 2013, Proceedings of the National Academy of Sciences.

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

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

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

[64]  R. Bashir,et al.  Electron beam induced local crystallization of HfO2 nanopores for biosensing applications. , 2013, Nanoscale.

[65]  M Misakian,et al.  Driven DNA transport into an asymmetric nanometer-scale pore. , 2000, Physical review letters.

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

[67]  E. Pop,et al.  Stacked graphene-Al2O3 nanopore sensors for sensitive detection of DNA and DNA-protein complexes. , 2012, ACS nano.

[68]  M. Ventra,et al.  Colloquium: Physical approaches to DNA sequencing and detection , 2007, 0708.2724.

[69]  N. Ashkenasy,et al.  Effects of electrons on the shape of nanopores prepared by focused electron beam induced etching , 2011, Nanotechnology.

[70]  C. Dekker,et al.  Detection of nucleosomal substructures using solid-state nanopores. , 2012, Nano letters.

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

[72]  T. G. Martin,et al.  Synthetic Lipid Membrane Channels Formed by Designed DNA Nanostructures , 2012, Science.

[73]  Mark Bates,et al.  Dynamics of DNA molecules in a membrane channel probed by active control techniques. , 2003, Biophysical journal.

[74]  Qing Zhao,et al.  Boron Nitride Nanopores: Highly Sensitive DNA Single‐Molecule Detectors , 2013, Advanced materials.