Intra- and intermolecular translocation of the bi-domain transcription factor Oct1 characterized by liquid crystal and paramagnetic NMR

Proc Natl Acad Sci U S A. 2011 May 31;108(22):E169-76. doi: 10.1073/pnas.1100050108. Epub 2011 May 9.


The intra- and intermolecular translocation processes whereby the bi-domain transcription factor Oct1 searches for its specific DNA target site have been investigated by residual dipolar coupling (RDC) and paramagnetic relaxation enhancement (PRE) measurements. The RDC data show that the orientation of the POU(S) and POU(HD) domains of Oct1 relative to the long axis of the DNA is the same for specific and nonspecific complexes with DNA. In the context of the specific Oct1-DNA complex, sparsely-populated, spectroscopically "invisible" states reveal their footprints on the PRE profiles observed for the specific complex. Analysis of the PRE data indicates that the POU(HD) domain searches the DNA primarily by rotation-coupled sliding (intramolecular translocation), while the POU(S) domain functions as an antenna to promote intersegment transfer via intermolecular translocation. The latter involves the formation of a bridged intermediate in which the POU(HD) domain is located on the first DNA molecule and the POU(S) domain on the second. The formation of the bridge intermediate promotes the completion of intermolecular translocation of Oct1 via a first order process involving dissociation and association of the POU(HD) domain from one DNA molecule to another. Thus cross-talk between the POU(S) and POU(HD) domains, each fulfilling different and complementary components of the search process ensures efficient sampling of DNA, thereby facilitating the location of specific Oct1 target sites.

Publication types

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

MeSH terms

  • Anisotropy
  • DNA / chemistry
  • DNA / metabolism
  • DNA-Binding Proteins / chemistry
  • Escherichia coli / metabolism
  • Homeodomain Proteins / chemistry
  • Humans
  • Liquid Crystals
  • Magnetic Resonance Spectroscopy / methods*
  • Microscopy, Fluorescence / methods
  • Oligonucleotides / genetics
  • Organic Cation Transporter 1 / chemistry*
  • Organic Cation Transporter 1 / metabolism
  • Protein Binding
  • Protein Structure, Tertiary
  • Protein Transport*


  • DNA-Binding Proteins
  • Homeodomain Proteins
  • Oligonucleotides
  • Organic Cation Transporter 1
  • DNA