Intercalation, DNA kinking, and the control of transcription

Science. 1996 Feb 9;271(5250):778-84. doi: 10.1126/science.271.5250.778.


Biological processes involved in the control and regulation of transcription are dependent on protein-induced distortions in DNA structure that enhance the recruitment of proteins to their specific DNA targets. This function is often accomplished by accessory factors that bind sequence specifically and locally bend or kink the DNA. The recent determination of the three-dimensional structures of several protein-DNA complexes, involving proteins that perform such architectural tasks, brings to light a common theme of side chain intercalation as a mechanism capable of driving the deformation of the DNA helix. The protein scaffolds orienting the intercalating side chain (or side chains) are structurally diverse, presently comprising four distinct topologies that can accomplish the same task. The intercalating side chain (or side chains), however, is exclusively hydrophobic. Intercalation can either kink or bend the DNA, unstacking one or more adjacent base pairs and locally unwinding the DNA over as much as a full turn of helix. Despite these distortions, the return to B-DNA helical parameters generally occurs within the adjacent half-turns of DNA.

Publication types

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

MeSH terms

  • Base Composition
  • Base Sequence
  • DNA / chemistry*
  • DNA / metabolism
  • DNA Helicases / chemistry
  • DNA Helicases / metabolism
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / metabolism*
  • Hydrogen Bonding
  • Intercalating Agents / chemistry
  • Intercalating Agents / metabolism*
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleic Acid Conformation*
  • Transcription Factors / chemistry
  • Transcription Factors / metabolism*
  • Transcription, Genetic*


  • DNA-Binding Proteins
  • Intercalating Agents
  • Transcription Factors
  • DNA
  • DNA Helicases