Temperature dependence of DNA translocations through solid-state nanopores

In order to gain a better physical understanding of DNA translocations through solid-state nanopores, we study the temperature dependence of λ-DNA translocations through 10 nm diameter silicon nitride nanopores, both experimentally and theoretically. The measured ionic conductance G, the DNA-induced ionic-conductance blockades [Formula: see text] and the event frequency Γ all increase with increasing temperature while the DNA translocation time τ decreases. G and [Formula: see text] are accurately described when bulk and surface conductances of the nanopore are considered and access resistance is incorporated appropriately. Viscous drag on the untranslocated part of the DNA coil is found to dominate the temperature dependence of the translocation times and the event rate is well described by a balance between diffusion and electrophoretic motion. The good fit between modeled and measured properties of DNA translocations through solid-state nanopores in this first comprehensive temperature study, suggest that our model captures the relevant physics of the process.

[1]  S. Turner,et al.  Reversible Positioning of Single Molecules inside Zero-Mode Waveguides , 2014, Nano letters.

[2]  M. Afzal,et al.  Temperature and concentration dependence of viscosity of aqueous electrolytes from 20.degree.C to 50.degree.C chlorides of (sodium(1+), potassium(1+), magnesium(2+), calcium(2+), barium(2+), strontium(2+), cobalt(2+), nickel(2+), copper(2+) and chromium(3+) , 1989 .

[3]  Study of the silicon nitride/aqueous electrolyte interface on colloidal aqueous suspensions and on electrolyte/insulator/semiconductor structures , 1989 .

[4]  S. Ghosal Electrokinetic-flow-induced viscous drag on a tethered DNA inside a nanopore. , 2007, Physical review. E, Statistical, nonlinear, and soft matter physics.

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

[6]  Xing‐dong Zhang,et al.  Computer simulation of biomolecule–biomaterial interactions at surfaces and interfaces , 2015, Biomedical materials.

[7]  C. Dekker,et al.  DNA Translocations through Solid-State Plasmonic Nanopores , 2014, Nano letters.

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

[9]  David G. Grier,et al.  The charge of glass and silica surfaces , 2001 .

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

[11]  A. Grosberg,et al.  Force-driven polymer translocation through a nanopore: an old problem revisited. , 2011, The journal of physical chemistry. B.

[12]  C. Dekker,et al.  Rapid manufacturing of low-noise membranes for nanopore sensors by trans-chip illumination lithography , 2012, Nanotechnology.

[13]  P. Glover,et al.  Streaming potential in porous media: 1. Theory of the zeta potential , 1999 .

[14]  Luke P. Lee,et al.  Graphene nanopore with a self-integrated optical antenna. , 2014, Nano letters.

[15]  J. Hall Access resistance of a small circular pore , 1975, The Journal of general physiology.

[16]  A. Hall,et al.  Detecting DNA Depurination with Solid-State Nanopores , 2014, PloS one.

[17]  P. Nuttall,et al.  Ion Transport in Nanopores , 2013 .

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

[19]  Wei Li,et al.  Probing and controlling photothermal heat generation in plasmonic nanostructures. , 2013, Nano letters.

[20]  A. Hall,et al.  Interpreting the conductance blockades of DNA translocations through solid-state nanopores. , 2014, ACS nano.

[21]  U. Keyser,et al.  Nanopore tomography of a laser focus. , 2005, Nano letters.

[22]  C. Dekker,et al.  Streaming currents in a single nanofluidic channel. , 2005, Physical review letters.

[23]  A. Vologodskii,et al.  Temperature dependence of DNA persistence length , 2010, Nucleic acids research.

[24]  J. Edel,et al.  SSB binding to single-stranded DNA probed using solid-state nanopore sensors. , 2014, The journal of physical chemistry. B.

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

[26]  Cees Dekker,et al.  Fast translocation of proteins through solid state nanopores. , 2013, Nano letters.

[27]  A. Radenović,et al.  Nanopore detection of single molecule RNAP-DNA transcription complex. , 2012, Nano letters.

[28]  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.

[29]  G. S. Manning The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides , 1978, Quarterly Reviews of Biophysics.

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

[31]  Joseph B. Herzog,et al.  Thermoplasmonics: quantifying plasmonic heating in single nanowires. , 2014, Nano letters.

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

[33]  Cees Dekker,et al.  Measurement of the docking time of a DNA molecule onto a solid-state nanopore. , 2012, Nano letters.

[34]  C. Dekker,et al.  Non-equilibrium folding of individual DNA molecules recaptured up to 1000 times in a solid state nanopore , 2013, Nanotechnology.

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

[36]  A. Conlisk,et al.  Forces affecting double-stranded DNA translocation through synthetic nanopores , 2011, Biomedical microdevices.

[37]  Sheereen Majd,et al.  Controlling protein translocation through nanopores with bio-inspired fluid walls , 2011 .

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

[39]  Yunfei Chen,et al.  Temperature effect on translocation speed and capture rate of nanopore-based DNA detection , 2015 .

[40]  Michael J Ford,et al.  Optimization of plasmonic heating by gold nanospheres and nanoshells. , 2006, The journal of physical chemistry. B.

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

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

[43]  A. Grosberg,et al.  Electrophoresis of a DNA coil near a nanopore. , 2013, Physical review. E, Statistical, nonlinear, and soft matter physics.

[44]  Milica Radisic,et al.  Biomaterial based cardiac tissue engineering and its applications , 2015, Biomedical materials.

[45]  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.

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

[47]  C. Dekker,et al.  Plasmonic nanopore for electrical profiling of optical intensity landscapes. , 2013, Nano letters.

[48]  A. A. Maryott,et al.  Dielectric constant of water from 0 to 100 C , 1956 .

[49]  Theodore D. Moustakas,et al.  Optoelectronic control of surface charge and translocation dynamics in solid-state nanopores , 2013, Nature nanotechnology.

[50]  D. Stein,et al.  Statistics of DNA capture by a solid-state nanopore. , 2012, Physical review letters.

[51]  C. Dekker,et al.  Data analysis methods for solid-state nanopores , 2015, Nanotechnology.

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

[53]  S. Maier,et al.  Rapid ultrasensitive single particle surface-enhanced Raman spectroscopy using metallic nanopores. , 2013, Nano letters.

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

[55]  P. Renaud,et al.  Transport phenomena in nanofluidics , 2008 .

[56]  M. Muthukumar,et al.  Polymer capture by electro-osmotic flow of oppositely charged nanopores. , 2007, The Journal of chemical physics.

[57]  G. Groeseneken,et al.  Harnessing plasmon-induced ionic noise in metallic nanopores. , 2013, Nano letters.

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

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

[60]  Alexander Y. Grosberg,et al.  DNA capture into a nanopore: interplay of diffusion and electrohydrodynamics. , 2010, The Journal of chemical physics.