Slowing the translocation of double-stranded DNA using a nanopore smaller than the double helix

Utkur Mirsaidov, Jeffrey Comer, Valentin Dimitrov, Aleksei Aksimentiev, Gregory Timp

Research output: Contribution to journalArticlepeer-review


It is now possible to slow and trap a single molecule of double-stranded DNA (dsDNA), by stretching it using a nanopore, smaller in diameter than the double helix, in a solid-state membrane. By applying an electric force larger than the threshold for stretching, dsDNA can be impelled through the pore. Once a current blockade associated with a translocating molecule is detected, the electric field in the pore is switched in an interval less than the translocation time to a value below the threshold for stretching. According to molecular dynamics (MD) simulations, this leaves the dsDNA stretched in the pore constriction with the base-pairs tilted, while the B-form canonical structure is preserved outside the pore. In this configuration, the translocation velocity is substantially reduced from 1 bp/10 ns to ∼1 bp/2 ms in the extreme, potentially facilitating high fidelity reads for sequencing, precise sorting, and high resolution (force) spectroscopy.

Original languageEnglish (US)
Article number395501
Issue number39
StatePublished - Oct 1 2010

ASJC Scopus subject areas

  • Bioengineering
  • General Chemistry
  • General Materials Science
  • Mechanics of Materials
  • Mechanical Engineering
  • Electrical and Electronic Engineering


Dive into the research topics of 'Slowing the translocation of double-stranded DNA using a nanopore smaller than the double helix'. Together they form a unique fingerprint.

Cite this