Reduced DNA flexibility in complexes with a type II DNA binding protein

Biochemistry. 1990 Jan 30;29(4):959-65. doi: 10.1021/bi00456a017.


We studied internal molecular motions in Bacillus subtilis phage SPO1 DNA using the time-resolved fluorescence polarization anisotropy (FPA) of intercalated ethidium. The torsional flexibility of this (hydroxymethyl)uracil-containing DNA is very similar to that of naturally occurring thymine-containing DNAs, as judged from fits of the time-resolved FPA decay to an elastic DNA model. Binding of transcription factor 1 (TF1), a type II procaryotic DNA binding protein encoded by the phage SPO1, enhances the FPA, indicating a substantial decrease in the average DNA torsional flexibility in the DNA-TF1 complex. The FPA increase is correlated with a reduced ethidium binding affinity. The effects can be noticed at TF1 binding ratios less than 1 TF1 dimer/500 DNA base pairs, and the measured torsional rigidity at high TF1 binding ratios (1 TF1 dimer/15-20 DNA base pairs) is about 7 times greater than in the absence of TF1. On the basis of a discussion of various mechanisms for the observed effect we argue that it is due to protein-induced DNA bending at low binding densities although other explanations are also possible. This interpretation might have implications for understanding the biological function of TF1.

Publication types

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

MeSH terms

  • Bacteriophages
  • DNA, Viral / metabolism*
  • DNA-Binding Proteins / metabolism*
  • Ethidium / metabolism
  • Fluorescence Polarization / methods
  • Molecular Structure
  • Nucleic Acid Conformation
  • Pentoxyl / analogs & derivatives
  • Pentoxyl / metabolism
  • Viral Proteins*


  • DNA, Viral
  • DNA-Binding Proteins
  • TF1 DNA-binding protein, Bacteriophage SPO1
  • Viral Proteins
  • 5-hydroxymethyluracil
  • Pentoxyl
  • Ethidium