[Spatial structure of DNA complex with the oligopeptide dansyl hydrazide trivaline]

The structure of complexes between double-stranded DNA and oligopeptide dansyl hydrazide trivaline was studied by linear dichroism, electron microscopy and hydrodynamical methods. The results show that the binding of the oligopeptide to DNA is a cooperative process that leads to the formation of particles significantly differing in the structure from free DNA. The linear dichroism studies were carried out in a wide range of flow-speed gradients. From the theoretical analysis of these data a conclusion can be drawn that the DNA-oligopeptide complexes possesses a higher rigidity as compared with that of free DNA. The hydrodynamical behaviour of these particles is consistent with the rigid rod-like structure of the particles with a long axis nearly parallel to the DNA helix axis in the complexes. The sedimentation patterns of the complexes suggest the existence of the fast and slow sedimenting species. The sedimentation coefficient measured for a fast sedimenting species is about 3 times higher than that of free DNA. The linear dichroism spectra obtained for the floworiented DNA-oligopeptide complexes correlate with the existence of a superhelical organization of DNA in the complex. This offers a possibility for the determining of the angle of the DNA local axis inclination with respect to the superhelix axis. On electron micrographs the DNA-oligopeptide complexes look like rod-shaped structures with the thickness of about 180 A and 80 A on the rotatory-shadowed preparations and on the uranylacetate stained preparations, respectively. The rod-shaped structures are formed by two interwound DNA molecules. The superhelix has a pitch of about 150 A with an angle of twist inclination of about 40 degrees. These values are in good agreement with the optical anisotropic data. It is suggested that the complex structure is stabilized by periodically spaced hydrophobic contacts between the dimeric oligopeptide species bound to the DNA molecules.