DNA condensation by high-affinity interaction with avidin

J Mol Recognit. Nov-Dec 2004;17(6):558-66. doi: 10.1002/jmr.689.


Avidin, the basic biotin-binding glycoprotein from chicken egg white, is known to interact with DNA, whereas streptavidin, its neutral non-glycosylated bacterial analog, does not. In the present study we investigated the DNA-binding properties of avidin. Its affinity for DNA in the presence and absence of biotin was compared with that of other positively charged molecules, namely the protein lysozyme, the cationic polymers polylysine and polyarginine and an avidin derivative with higher isoelectric point (pI approximately 11) in which most of the lysine residues were converted to homoarginines. Gel-shift assays, transmission electron microscopy and dynamic light scattering experiments demonstrated an unexpectedly strong interaction between avidin and DNA. The most pronounced gel-shift retardation occurred with the avidin-biotin complex, followed by avidin alone and then guanidylated avidin. Furthermore, ultrastructural and light-scattering studies showed that avidin assembles on the DNA molecule in an organized manner. The assembly leads to the formation of nanoparticles that are about 50-100 nm in size (DNA approximately 5 kb) and have a rod-like or toroidal shape. In these particles the DNA is highly condensed and one avidin is bound to each 18 +/- 4 DNA base pairs. The complexes are very stable even at high dilution ([DNA] =10 pM) and are not disrupted in the presence of buffers or salt (up to 200 mM NaCl). The other positively charged molecules also condense DNA and form particles with a globular shape. However, in this case, these particles disassemble by dilution or in the presence of low salt concentration. The results indicate that the interaction of avidin with DNA may also occur under physiological conditions, further enhanced by the presence of biotin. This DNA-binding property of avidin may thus shed light on a potentially new physiological role for the protein in its natural environment.

MeSH terms

  • Avidin / chemistry*
  • Avidin / metabolism
  • Avidin / ultrastructure
  • Biotin / chemistry
  • DNA / chemistry*
  • DNA / metabolism
  • DNA / ultrastructure
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / metabolism
  • DNA-Binding Proteins / ultrastructure
  • Electrophoretic Mobility Shift Assay
  • Guanidine / chemistry
  • Microscopy, Electron, Transmission
  • Nucleic Acid Conformation
  • Salts / chemistry
  • Substrate Specificity


  • DNA-Binding Proteins
  • Salts
  • Avidin
  • Biotin
  • DNA
  • Guanidine