Short-range spectroscopic ruler based on a single-molecule optical switch

Phys Rev Lett. 2005 Mar 18;94(10):108101. doi: 10.1103/PhysRevLett.94.108101. Epub 2005 Mar 15.


We demonstrate a novel all-optical switch consisting of two molecules: a primary fluorophore (Cy5) that can be switched between a fluorescent and a dark state by light of different wavelengths, and a secondary chromophore (Cy3) that facilitates switching. The interaction between the two molecules exhibits a distance dependence much steeper than that of conventional Fo rster resonance energy transfer. This enables the switch to act as a ruler with the capability to probe distances difficult to access by other spectroscopic methods, thus presenting a new tool for the study of biomolecules at the single-molecule level.

Publication types

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

MeSH terms

  • Bacterial Proteins / chemistry
  • Biotin / analogs & derivatives*
  • Biotin / chemistry
  • Carbocyanines / chemistry*
  • DNA / chemistry*
  • DNA Damage
  • Fluorescence Resonance Energy Transfer / methods*
  • Models, Molecular
  • Optics and Photonics
  • RNA, Catalytic / chemistry
  • Serum Albumin, Bovine / chemistry


  • Bacterial Proteins
  • Carbocyanines
  • RNA, Catalytic
  • biotin-streptavidin complex
  • cyanine dye 3
  • cyanine dye 5
  • Serum Albumin, Bovine
  • Biotin
  • DNA