Chemical recognition and binding kinetics in a functionalized tunnel junction

Nanotechnology. 2012 Jun 15;23(23):235101. doi: 10.1088/0957-4484/23/23/235101.

Abstract

4(5)-(2-mercaptoethyl)-1H-imidazole-2-carboxamide is a molecule that has multiple hydrogen bonding sites and a short flexible linker. When tethered to a pair of electrodes, it traps target molecules in a tunnel junction. Surprisingly large recognition-tunneling signals are generated for all naturally occurring DNA bases A, C, G, T and 5-methyl-cytosine. Tunnel current spikes are stochastic and broadly distributed, but characteristic enough so that individual bases can be identified as a tunneling probe is scanned over DNA oligomers. Each base yields a recognizable burst of signal, the duration of which is controlled entirely by the probe speed, down to speeds of 1 nm s -1, implying a maximum off-rate of 3 s -1 for the recognition complex. The same measurements yield a lower bound on the on-rate of 1 M -1 s -1. Despite the stochastic nature of the signals, an optimized multiparameter fit allows base calling from a single signal peak with an accuracy that can exceed 80% when a single type of nucleotide is present in the junction, meaning that recognition-tunneling is capable of true single-molecule analysis. The accuracy increases to 95% when multiple spikes in a signal cluster are analyzed.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Binding Sites
  • Conductometry / instrumentation*
  • Equipment Design
  • Equipment Failure Analysis
  • Kinetics
  • Nanostructures / chemistry*
  • Nanostructures / ultrastructure*
  • Nucleotides / analysis*
  • Oligonucleotide Array Sequence Analysis / instrumentation*
  • Particle Size
  • Semiconductors*

Substances

  • Nucleotides