Unraveling single-stranded DNA in a solid-state nanopore.

Solid-state nanopores are an emerging class of single-molecule sensors. Whereas most studies so far focused on double-stranded DNA (dsDNA) molecules, exploration of single-stranded DNA (ssDNA) is of great interest as well, for example to employ such a nanopore device to read out the sequence. Here, we study the translocation of long random-sequence ssDNA through nanopores. Using atomic force microscopy, we observe the ssDNA to hybridize into a random coil, forming blobs of around 100 nm in diameter for 7 kb ssDNA. These large entangled structures have to unravel, when they arrive at the pore entrance. Indeed, we observe strong blockade events with a translocation time that is exponentially dependent on voltage, tau approximately e(-V/V(0)). Interestingly, this is very different than for dsDNA, for which tau approximately 1/V. We report translocations of ssDNA but also of ssDNA-dsDNA constructs where we compare the conductance-blockade levels for ssDNA versus dsDNA as a function of voltage.

[1]  N H Dekker,et al.  Noise in solid-state nanopores , 2008, Proceedings of the National Academy of Sciences.

[2]  C. Dekker,et al.  Translocation of RecA-coated double-stranded DNA through solid-state nanopores. , 2009, Nano letters.

[3]  L. Sperling.  Introduction to physical polymer science , 1986 .

[4]  Xin Sheng Zhao,et al.  Influence of secondary structure on kinetics and reaction mechanism of DNA hybridization , 2007, Nucleic acids research.

[5]  P. Biswas,et al.  Size, shape, and flexibility of proteins and DNA. , 2009, The Journal of chemical physics.

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

[7]  C. Bustamante,et al.  Scanning force microscopy of DNA deposited onto mica: equilibration versus kinetic trapping studied by statistical polymer chain analysis. , 1996, Journal of molecular biology.

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

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

[10]  D. Branton,et al.  Voltage-driven DNA translocations through a nanopore. , 2001, Physical review letters.

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

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

[13]  S. Smith,et al.  Single-molecule studies of DNA mechanics. , 2000, Current opinion in structural biology.

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

[15]  R. Eisenberg,et al.  Computing numerically the access resistance of a pore , 2005, European Biophysics Journal.

[16]  D. Branton,et al.  Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within single RNA molecules. , 1999, Biophysical journal.

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

[18]  David Stoddart,et al.  Single-nucleotide discrimination in immobilized DNA oligonucleotides with a biological nanopore , 2009, Proceedings of the National Academy of Sciences.

[19]  H. Stanley,et al.  Statistical physics of macromolecules , 1995 .

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

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

[22]  Stefan Howorka,et al.  Nanopore Analytics: Sensing of Single Molecules , 2009 .

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

[24]  U. Bockelmann,et al.  Mechanical separation of the complementary strands of DNA. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[25]  K. Yoshikawa,et al.  Hydrodynamic radius of circular DNA is larger than that of linear DNA , 2006 .

[26]  Yeonee Seol,et al.  Elastic properties of a single-stranded charged homopolymeric ribonucleotide. , 2004, Physical review letters.

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

[28]  Simona Cocco,et al.  Force and kinetic barriers to unzipping of the DNA double helix , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[29]  Amit Meller,et al.  Progress toward ultrafast DNA sequencing using solid-state nanopores. , 2007, Clinical chemistry.

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

[31]  M. Rief,et al.  Sequence-dependent mechanics of single DNA molecules , 1999, Nature Structural Biology.

[32]  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.

[33]  G. Timp,et al.  Stretching and unzipping nucleic acid hairpins using a synthetic nanopore , 2008, Nucleic acids research.