DNA linking number change induced by sequence-specific DNA-binding proteins

Nucleic Acids Res. 2010 Jun;38(11):3643-54. doi: 10.1093/nar/gkq078. Epub 2010 Feb 25.


Sequence-specific DNA-binding proteins play a key role in many fundamental biological processes, such as transcription, DNA replication and recombination. Very often, these DNA-binding proteins introduce structural changes to the target DNA-binding sites including DNA bending, twisting or untwisting and wrapping, which in many cases induce a linking number change (Delta Lk) to the DNA-binding site. Due to the lack of a feasible approach, Delta Lk induced by sequence-specific DNA-binding proteins has not been fully explored. In this paper we successfully constructed a series of DNA plasmids that carry many tandem copies of a DNA-binding site for one sequence-specific DNA-binding protein, such as lambda O, LacI, GalR, CRP and AraC. In this case, the protein-induced Delta Lk was greatly amplified and can be measured experimentally. Indeed, not only were we able to simultaneously determine the protein-induced Delta Lk and the DNA-binding constant for lambda O and GalR, but also we demonstrated that the protein-induced Delta Lk is an intrinsic property for these sequence-specific DNA-binding proteins. Our results also showed that protein-mediated DNA looping by AraC and LacI can induce a Delta Lk to the plasmid DNA templates. Furthermore, we demonstrated that the protein-induced Delta Lk does not correlate with the protein-induced DNA bending by the DNA-binding proteins.

Publication types

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

MeSH terms

  • AraC Transcription Factor / metabolism
  • Base Sequence
  • Binding Sites
  • Cyclic AMP Receptor Protein / metabolism
  • DNA, Circular / chemistry*
  • DNA, Circular / metabolism
  • DNA-Binding Proteins / metabolism*
  • Escherichia coli Proteins / metabolism
  • Lac Repressors / metabolism
  • Nucleic Acid Conformation
  • Plasmids / genetics
  • Protein Binding
  • Repressor Proteins / metabolism
  • Viral Proteins / metabolism


  • AraC Transcription Factor
  • Cyclic AMP Receptor Protein
  • DNA, Circular
  • DNA-Binding Proteins
  • Escherichia coli Proteins
  • Galactose repressor proteins
  • Lac Repressors
  • O protein, Bacteriophage lambda
  • Repressor Proteins
  • Viral Proteins