Structural changes induced by binding of the high-mobility group I protein to a mouse satellite DNA sequence

Biophys J. 2000 May;78(5):2543-59. doi: 10.1016/S0006-3495(00)76799-3.


Using spectroscopic methods, we have studied the structural changes induced in both protein and DNA upon binding of the High-Mobility Group I (HMG-I) protein to a 21-bp sequence derived from mouse satellite DNA. We show that these structural changes depend on the stoichiometry of the protein/DNA complexes formed, as determined by Job plots derived from experiments using pyrene-labeled duplexes. Circular dichroism and melting temperature experiments extended in the far ultraviolet range show that while native HMG-I is mainly random coiled in solution, it adopts a beta-turn conformation upon forming a 1:1 complex in which the protein first binds to one of two dA.dT stretches present in the duplex. HMG-I structure in the 1:1 complex is dependent on the sequence of its DNA target. A 3:1 HMG-I/DNA complex can also form and is characterized by a small increase in the DNA natural bend and/or compaction coupled to a change in the protein conformation, as determined from fluorescence resonance energy transfer (FRET) experiments. In addition, a peptide corresponding to an extended DNA-binding domain of HMG-I induces an ordered condensation of DNA duplexes. Based on the constraints derived from pyrene excimer measurements, we present a model of these nucleated structures. Our results illustrate an extreme case of protein structure induced by DNA conformation that may bear on the evolutionary conservation of the DNA-binding motifs of HMG-I. We discuss the functional relevance of the structural flexibility of HMG-I associated with the nature of its DNA targets and the implications of the binding stoichiometry for several aspects of chromatin structure and gene regulation.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Base Sequence
  • Binding Sites
  • Biophysical Phenomena
  • Biophysics
  • Circular Dichroism
  • DNA, Satellite / chemistry*
  • DNA, Satellite / genetics
  • DNA, Satellite / metabolism*
  • High Mobility Group Proteins / chemistry*
  • High Mobility Group Proteins / metabolism*
  • In Vitro Techniques
  • Macromolecular Substances
  • Mice
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Nucleic Acid Denaturation
  • Peptides / chemistry
  • Protein Binding
  • Protein Conformation
  • Spectrometry, Fluorescence


  • DNA, Satellite
  • High Mobility Group Proteins
  • Macromolecular Substances
  • Peptides