Noise analysis and reduction in solid-state nanopores

The electrical noise characteristics of ionic current through organic and synthetic nanopores have been investigated. Comparison to proteinaceous alpha-Hemolysin pores reveals two dominant noise sources in silicon nitride nanometre-scale pores: a high-frequency noise associated with the capacitance of the silicon support chip (dielectric noise), and a low-frequency current fluctuation with 1/ f α characteristics (flicker noise). We present a technique for reducing the dielectric noise by curing polydimethylsiloxane (PDMS) on the nanopore support chip. This greatly improves the performance of solid-state nanopore devices, yielding an unprecedented signal-to-noise ratio when observing dsDNA translocation events and ssDNA probe capture for force spectroscopy applications. (Some figures in this article are in colour only in the electronic version)

[1]  Nahid N. Jetha,et al.  Nonexponential kinetics of DNA escape from alpha-hemolysin nanopores. , 2008, Biophysical journal.

[2]  Z. Siwy,et al.  Origin of 1/f(alpha) noise in membrane channel currents. , 2002, Physical review letters.

[3]  J. Brugger,et al.  Fabrication and functionalization of nanochannels by electron-beam-induced silicon oxide deposition. , 2006, Langmuir : the ACS journal of surfaces and colloids.

[4]  Cees Dekker,et al.  Fabrication and characterization of nanopore-based electrodes with radii down to 2 nm. , 2006, Nano letters.

[5]  F. Hooge.  1/f noise sources , 1994 .

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

[7]  Peng Chen,et al.  Atomic Layer Deposition to Fine-Tune the Surface Properties and Diameters of Fabricated Nanopores. , 2004, Nano letters.

[8]  Meni Wanunu,et al.  Chemically modified solid-state nanopores. , 2007, Nano letters.

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

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

[11]  I. Kosinska.  How the asymmetry of internal potential influences the shape of I-V characteristic of nanochannels. , 2006, The Journal of chemical physics.

[12]  D. Branton,et al.  Rapid nanopore discrimination between single polynucleotide molecules. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[13]  Qun Cai,et al.  Nanopore sculpting with noble gas ions. , 2006, Journal of applied physics.

[14]  S. Bezrukov,et al.  Examining noise sources at the single-molecule level: 1/f noise of an open maltoporin channel. , 2000, Physical review letters.

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

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

[17]  A. Broers,et al.  Characterization of electron beam induced modification of thermally grown SiO2 , 1995 .

[18]  Philip G. Collins,et al.  1/f noise in carbon nanotubes , 2000 .

[19]  A. L. McWhorter,et al.  1/f noise and related surface effects in germanium , 1955 .

[20]  Charles G. Sodini,et al.  A 1/f noise technique to extract the oxide trap density near the conduction band edge of silicon , 1989 .

[21]  P. M. Horn,et al.  Low-frequency fluctuations in solids: 1/f noise , 1981 .

[22]  M. Burns,et al.  Nanopore sequencing technology: research trends and applications. , 2006, Trends in biotechnology.

[23]  H. Tong,et al.  Silicon nitride nanosieve membrane , 2004 .

[24]  Z. Siwy,et al.  Ion‐Current Rectification in Nanopores and Nanotubes with Broken Symmetry , 2006 .

[25]  U. Keyser,et al.  Nanobubbles in solid-state nanopores. , 2006, Physical review letters.

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

[27]  Min Jun Kim,et al.  Characteristics of solid-state nanometre pores fabricated using a transmission electron microscope , 2007 .

[28]  C. Hu,et al.  A unified model for the flicker noise in metal-oxide-semiconductor field-effect transistors , 1990 .

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

[30]  Subhendu Ghosh,et al.  Self-organised criticality and 1/f noise in single-channel current of voltage-dependent anion channel , 2006 .

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

[32]  M. Akeson,et al.  New DNA sequencing methods. , 2001, Annual review of biomedical engineering.

[33]  A. Marziali,et al.  A nanosensor for transmembrane capture and identification of single nucleic Acid molecules. , 2004, Biophysical journal.

[34]  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.

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

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

[37]  M. Burns,et al.  Nanopore sequencing technology: nanopore preparations. , 2007, Trends in biotechnology.

[38]  Tang,et al.  Self-Organized Criticality: An Explanation of 1/f Noise , 2011 .

[39]  M. Akeson,et al.  Nanopore sensors for nucleic acid analysis , 2003 .

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

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

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

[43]  Marc Gershow,et al.  Detecting single stranded DNA with a solid state nanopore. , 2005, Nano letters.

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

[45]  Cees Dekker,et al.  Optical tweezers for force measurements on DNA in nanopores , 2006 .

[46]  Jonathan R. I. Lee,et al.  Localized Functionalization of Single Nanopores , 2006 .

[47]  F. Hooge.  1/ƒ noise is no surface effect , 1969 .

[48]  C. Klampfl,et al.  Simple test system for single molecule recognition force microscopy , 2003 .

[49]  R A Levis,et al.  The use of quartz patch pipettes for low noise single channel recording. , 1993, Biophysical journal.

[50]  Sean Conlan,et al.  Stochastic sensing of organic analytes by a pore-forming protein containing a molecular adapter , 1999, Nature.

[51]  G. Luke,et al.  Electric and magnetic properties of the stage-2 FeBr2 graphite intercalation compound , 2003 .

[52]  D. Deamer,et al.  Nanopores and nucleic acids: prospects for ultrarapid sequencing. , 2000, Trends in biotechnology.