By means of titration viscometry a number of distinct modes could be resolved for the interaction between the antibiotic netropsin and DNA species of 50, 58, and 69 mole + (A+T) below r = 0.04 netropsin molecules bound per DNA phosphate group. The number of corresponding binding sites increases with a high power of the (A+T) content. The apparent association constants are very high (greater than 10(6) M-1, some perhaps greater than 10(6) M-1) and also rather different for most of the binding sites. It is suggested that some of these interaction modes differ in the number of hydrogen bonds formed between donors of the ligand and acceptors of the binding sites. The interaction modes were characterized quantitatively by their (species-independent) changes of DNA contour length and by the percentage of local DNA stiffening.
The titration viscometric investigation of the multi-mode interaction of netropsin (Nt) with (A.T) clusters of NaDNA12 and NH4DNA10 has been extended to different temperatures. The position of two boundaries on the r-scale (r= [Nt]bound/[DNA-P]) with increasing temperature steadily (rI/II) or more abruptly (rO/I) shifts to lower values. For the most (A.T) rich Nt-binding sites of modes (O), (I) and (II) this observation suggests the existence of an equilibrium between different DNA secondary structures with a different translation per base pair. The mode specific changes delta L1Nt of DNA contour length as induced by one Nt molecule proved to be almost independent of temperature. Concomitant stiffening effects increase with decreasing temperature, contrary to initial expectation. Conformational variability of (A.T) clusters may represent an essential feature in specific or selective DNA-protein interaction.
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