DNA-protein noncovalent cross-linking: ruthenium dipyridophenazine biotin complex for the assembly of proteins and gold nanoparticles on DNA templates

Chembiochem. 2007 May 7;8(7):804-12. doi: 10.1002/cbic.200600550.


We report the first example of a small molecule that can noncovalently cross-link DNA with streptavidin and streptavidin-labeled materials. Molecule 1 possesses a ruthenium dipyridophenazine DNA-intercalating moiety and a biotin unit; these two units are adequately separated to ensure efficient cross-linking of DNA with protein. Complex 1 is essentially nonemissive in aqueous solution and when bound to streptavidin, however, its luminescence is turned "on" when it binds to DNA. We have used these properties to establish that this complex can simultaneously bind to DNA and streptavidin, and can thus bring these two biomolecules together. We also synthesized a related molecule, 3, in which the biotin and DNA-intercalating moieties are covalently bound. While complex 3 can intercalate into DNA through a threading mechanism, luminescence experiments show that it cannot simultaneously bind DNA and streptavidin, most likely due to the proximity of its two molecular-recognition units. The cross-linking ability of molecule 1 was used to template the assembly of streptavidin molecules on circular plasmid DNA, as visualized by atomic force microscopy. In addition, using 1, we show the organization of discrete groups of gold nanoparticles labeled with streptavidin on a linear DNA template of finite size, with transmission electron microscopy. In these experiments the DNA template acted as a "molecular ruler" that dictated the number of particles in the assembly.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biotin / chemistry*
  • DNA / chemistry*
  • Gold / chemistry*
  • Metal Nanoparticles*
  • Microscopy, Atomic Force
  • Microscopy, Electron, Transmission
  • Nuclear Magnetic Resonance, Biomolecular
  • Organometallic Compounds / chemistry*
  • Proteins / chemistry*
  • Spectrometry, Mass, Electrospray Ionization


  • Organometallic Compounds
  • Proteins
  • ruthenium dipyridophenazine
  • Biotin
  • Gold
  • DNA