Orientation of the bases of single-stranded DNA and polynucleotides in complexes formed with the gene 32 protein of bacteriophage T4. A linear dichroism study.
Linear dichroism measurements were performed in the wavelength region 250 to 350 nm on complexes between the single-stranded DNA binding protein of bacteriophage T4 (gp32) and single-stranded DNA and a variety of homopolynucleotides in compressed polyacrylamide gels. The complexes appeared to orient well, giving rise to linear dichroism spectra that showed contributions from both the protein aromatic residues and the bases of the polynucleotides. In most cases the protein contribution appeared to be very similar, and the linear dichroism of the bases could be explained by similar orientations of the bases for most of the complexes. Assuming a similar, regular structure for most of the polynucleotides in complex, only a limited set of combinations of tilt and twist angles can explain the linear dichroism spectra. These values of tilt and twist are close to (-40 degrees, 30 degrees), (-40 degrees, 150 degrees), (40 degrees, -30 degrees) or (40 degrees, -150 degrees), with an uncertainty in both angles of about 15 degrees. Although the linear dichroism results do not allow a choice between these possible orientations, the latter two combinations are not in agreement with earlier circular dichroism calculations. For the complexes formed with poly(rC) and poly(rA), the linear dichroism spectra could not be explained by the same base orientations. In these two cases also the protein contribution to the linear dichroism appeared to be different, indicating that for some aromatic residues the orientations are not the same as those in the other complexes. The different structures of these complexes are possibly related to the relatively low binding affinity of gp32 to poly(rC), and to a lesser extent to poly(rA).
van Amerongen
H
H
Department of Biophysics, Free University, Amsterdam, The Netherlands.
van Grondelle
R
R
D000818:Animals; D004277:DNA, Single-Stranded / Q000235:genetics*; D004279:DNA, Viral / Q000235:genetics; D004591:Electrophoresis, Polyacrylamide Gel; D046911:Macromolecular Substances; D011061:Poly A / Q000235:genetics; D011066:Poly C / Q000235:genetics; D011071:Poly T / Q000235:genetics; D011072:Poly U / Q000235:genetics; D011119:Polynucleotides / Q000235:genetics*; D011995:Recombination, Genetic; D013057:Spectrum Analysis; D013604:T-Phages / Q000235:genetics*; D014764:Viral Proteins / Q000235:genetics*
D004277:DNA, Single-Stranded; D004279:DNA, Viral; D046911:Macromolecular Substances; D011119:Polynucleotides; D014764:Viral Proteins; D011061:Poly A; D011071:Poly T; C015465:poly(dA); D011072:Poly U; D011066:Poly C