Electromechanical unzipping of individual DNA molecules using synthetic sub-2 nm pores

Nano Lett. 2008 Oct;8(10):3418-22. doi: 10.1021/nl802218f. Epub 2008 Aug 30.

Abstract

Nanopores have recently emerged as high-throughput tools for probing and manipulating nucleic acid secondary structure at the single-molecule level. While most studies to date have utilized protein pores embedded in lipid bilayers, solid-state nanopores offer many practical advantages which greatly expand the range of applications in life sciences and biotechnology. Using sub-2 nm solid-state nanopores, we show for the first time that the unzipping kinetics of individual DNA duplexes can be probed by analyzing the dwell-time distributions. We performed high-bandwidth electrical measurements of DNA duplex unzipping as a function of their length, sequence, and temperature. We find that our longer duplexes (>10 bp) follow Arrhenius dependence on temperature, suggesting that unzipping can be approximated as a single-barrier crossing, but the unzipping kinetics of shorter duplexes do not involve a barrier, due to the strong biasing electrical force. Finally, we show that mismatches in the duplex affect unzipping times in a position-sensitive manner. Our results are a crucial step toward sequence variability detection and our single-molecule nanopore sequencing technology, which rely on parallel detection from nanopore arrays.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Biotechnology / methods
  • DNA / chemistry*
  • Electrochemistry / methods*
  • Electronics
  • Kinetics
  • Lipid Bilayers / chemistry
  • Nanocomposites
  • Nanoparticles / chemistry
  • Nanotechnology / methods*
  • Nucleic Acid Conformation
  • Static Electricity
  • Stress, Mechanical
  • Temperature
  • Time Factors

Substances

  • Lipid Bilayers
  • DNA