title: Reduced DNA flexibility in complexes with a type II DNA binding protein.
abstract: 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.
authors.affiliation: Department of Chemistry, University of California, San Diego, La Jolla 92093-0342.
authors.forename: T
authors.initials: T
authors.lastname: Härd
authors.forename: D R
authors.initials: DR
authors.lastname: Kearns
mesh_terms: D001435:Bacteriophages; D004279:DNA, Viral / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D004996:Ethidium / Q000378:metabolism; D005454:Fluorescence Polarization / Q000379:methods; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D010432:Pentoxyl / Q000031:analogs & derivatives / Q000378:metabolism; D014764:Viral Proteins
chemical_list: D004279:DNA, Viral; D004268:DNA-Binding Proteins; C059361:TF1 DNA-binding protein, Bacteriophage SPO1; D014764:Viral Proteins; C008055:5-hydroxymethyluracil; D010432:Pentoxyl; D004996:Ethidium