Fluorescence studies of a single tyrosine in a type II DNA binding protein

We studied the fluorescence properties of a single tyrosine (Tyr94) located in the C-terminal tail of transcription factor 1 (TF1), a type II procaryotic DNA binding protein encoded by the Bacillus subtilis phage SPO1. The time-resolved fluorescence intensity of Tyr94 in free TF1 dimers decays as a single exponential, and this is consistent with a twofold symmetrical structure. The fluorescence is readily quenched by acrylamide, but it is less accessible to anionic quenchers (iodide and citrate), suggesting that the tyrosine is located on the protein surface in a negatively charged environment provided by neighboring Glu95 and Asp96 residues. TF1 dimers associate at moderate concentrations (greater than 0.02 mg/mL) as judged from concentration dependencies in the molar fluorescence intensity, the steady-state fluorescence polarization, and the bimolecular quenching constants. Nonspecific binding of TF1 to SPO1 and calf thymus (CT) DNA and various double-stranded polynucleotides quenches the Tyr94 fluorescence to varying extent. Fluorescence lifetimes of TF1 in the bound state correlate with spectral overlaps between TF1 emission and DNA absorption, demonstrating that excitation energy transfer to DNA bases contributes significantly to the observed quenching. From analysis of the observed quenching in the DNA complexes we conclude that Tyr94 is located within 10-14 A of the DNA helix axis and not in direct contact with the DNA bases. Equilibrium analyses based on fluorescence titrations show that the maximum binding density on DNA extrapolates to ca. 1 TF1 dimer/5 DNA base pairs. We find several differences in TF1 binding to SPO1 DNA, which contains hydroxymethyluracil instead of thymine, and CT DNA: (i) The tyrosine residue is less exposed to the solvent in the SPO1 DNA complex than in the CT DNA complex. (ii) D2O addition enhances the Tyr94 fluorescence when TF1 binds to SPO1 DNA but not when it binds to CT DNA. (iii) The TF1-SPO1 DNA complex is stable at higher NaC1 concentrations than is the TF1-CT DNA complex, and its formation involves the dissociation of more Na+ ions than does the TF1-CT DNA complex. On the basis of these observations and the fact that the Tyr94-containing tail of TF1 is essential for binding to SPO1 DNA, we discuss various models for the TF1-DNA complex.