Measurement of the position-dependent electrophoretic force on DNA in a glass nanocapillary.

The electrophoretic force on a single DNA molecule inside a glass nanocapillary depends on the opening size and varies with the distance along the symmetrical axis of the nanocapillary. Using optical tweezers and DNA-coated beads, we measured the stalling forces and mapped the position-dependent force profiles acting on DNA inside nanocapillaries of different sizes. We showed that the stalling force is higher in nanocapillaries of smaller diameters. The position-dependent force profiles strongly depend on the size of the nanocapillary opening, and for openings smaller than 20 nm, the profiles resemble the behavior observed in solid-state nanopores. To characterize the position-dependent force profiles in nanocapillaries of different sizes, we used a model that combines information from both analytical approximations and numerical calculations.

[1]  Cees Dekker,et al.  Electrophoretic force on a protein-coated DNA molecule in a solid-state nanopore. , 2009, Nano letters.

[2]  O. Otto,et al.  Probing DNA with micro- and nanocapillaries and optical tweezers , 2010, Journal of physics. Condensed matter : an Institute of Physics journal.

[3]  David A. Sivak,et al.  Controlling DNA capture and propagation through artificial nanopores. , 2007, Nano letters.

[4]  Andy Sischka,et al.  Dynamic translocation of ligand-complexed DNA through solid-state nanopores with optical tweezers , 2010, Journal of physics. Condensed matter : an Institute of Physics journal.

[5]  L. Steinbock,et al.  Controllable shrinking and shaping of glass nanocapillaries under electron irradiation. , 2013, Nano letters.

[6]  Ulrich F Keyser,et al.  Detecting DNA folding with nanocapillaries. , 2010, Nano letters.

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

[8]  Thomas T. Perkins,et al.  Dynamical scaling of DNA diffusion coefficients , 1996 .

[9]  M. G. Lorenz,et al.  Adsorption of DNA to sand and variable degradation rates of adsorbed DNA , 1987, Applied and environmental microbiology.

[10]  S. Ghosal,et al.  DNA interactions in crowded nanopores. , 2013, Nano letters.

[11]  N. Dekker,et al.  Direct force measurements on double-stranded RNA in solid-state nanopores. , 2010, Nano letters.

[12]  O. Otto,et al.  Rapid internal contraction boosts DNA friction , 2013, Nature Communications.

[13]  P. Reimann,et al.  Nanopore translocation dynamics of a single DNA-bound protein. , 2011, Nano letters.

[14]  U. Keyser,et al.  Tether forces in DNA electrophoresis. , 2010, Chemical Society reviews.

[15]  R. Rosenfeld.  Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

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

[17]  Electrophoresis of a polyelectrolyte through a nanopore. , 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

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

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

[20]  Urs Staufer,et al.  Sensing protein molecules using nanofabricated pores , 2006 .

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

[22]  I. Yang,et al.  Flow cytometric investigation on degradation of macro-DNA by common laboratory manipulations , 2011 .

[23]  P. Reimann,et al.  Hydrodynamic slip on DNA observed by optical tweezers-controlled translocation experiments with solid-state and lipid-coated nanopores. , 2014, Nano letters.

[24]  Nadanai Laohakunakorn,et al.  A Landau-Squire nanojet. , 2013, Nano letters.

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

[26]  O. Otto,et al.  Note: Direct force and ionic-current measurements on DNA in a nanocapillary. , 2011, The Review of scientific instruments.

[27]  C. Tanford.  Macromolecules , 1994, Nature.

[28]  Aleksandra Radenovic,et al.  DNA translocation through low-noise glass nanopores. , 2013, ACS nano.

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

[30]  U. Keyser.  Optical tweezers for mechanical control over DNA in a nanopore. , 2012, Methods in molecular biology.

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

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

[33]  Silvia Hernández-Ainsa,et al.  Single protein molecule detection by glass nanopores. , 2013, ACS nano.

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

[35]  W Wackernagel,et al.  Adsorption of plasmid DNA to mineral surfaces and protection against DNase I , 1991, Applied and environmental microbiology.

[36]  Vivek V. Thacker,et al.  Studying DNA translocation in nanocapillaries using single molecule fluorescence. , 2012, Applied physics letters.