Partial sequencing of a single DNA molecule with a scanning tunnelling microscope

Nat Nanotechnol. 2009 Aug;4(8):518-22. doi: 10.1038/nnano.2009.155. Epub 2009 Jul 5.


The scanning tunnelling microscope is capable of the real-space imaging and spectroscopy of molecules on an atomic scale. Numerous attempts have been made to use the scanning tunnelling microscope to sequence single DNA molecules, but difficulties in preparing samples of long-chain DNA molecules on surfaces, and problems in reproducing results have limited these experiments. Here, we report single-molecule DNA sequencing with a scanning tunnelling microscope by using an oblique pulse-injection method to deposit the molecules onto a copper surface. First, we show that guanine bases have a distinct electronic state that allows them to be distinguished from the other nucleic acid bases. Then, by comparing data on M13mp18, a single-stranded phage DNA, with a known base sequence, the 'electronic fingerprint' of guanine bases in the DNA molecule is identified. These results show that it is possible to sequence individual guanine bases in real long-chain DNA molecules with high-resolution scanning tunnelling microscope imaging and spectroscopy.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • DNA, Single-Stranded / chemistry*
  • DNA, Single-Stranded / ultrastructure
  • Guanine / chemistry
  • Microscopy, Scanning Tunneling / methods*
  • Molecular Sequence Data
  • Peptide Nucleic Acids / chemistry
  • Peptide Nucleic Acids / ultrastructure
  • Sequence Analysis, DNA / methods*


  • DNA, Single-Stranded
  • Peptide Nucleic Acids
  • Guanine