Deformyldistamycin-DNA Interaction; DNA Conformational Changes as Revealed by Titration Rotational Viscometry

Abstract

The conformational changes of a natural DNA species on binding of deformyl-distamycin (dDst) have been analysed, at 22°C and 7.6 °C, in terms of changes of apparent persistence length (a) and of apparent contour length (L), by means of titration rotational viscometry with both high and low molar mass calf thymus (ct) DNA molecules. Next to ligand binding mediated alterations in DNA stiffness, changes of a are the result of helix bending and also of unbending of intrinsic helix bends. A test for the latter are viscosity measurements at different temperatures. Changes of L, on binding of non-intercalating ligands, are interpreted as the result of changes in the intrinsic solenoidal structure components of the natural eukaryotic DNA. Such tertiary-structure components do exist if base sequence dependent helix bends of (nucleosomal) DNA are phased with the helix screw [Drew & Travers, JMB 186, 773 (1985); Reinert et al., JBSD 9, 537 (1991)]. Hence, the measured very small changes of L at ligand/DNA-P ratios r < 0.02 are mainly understood as a partial abolition of intrinsic tertiary structure components and the following negative ones as a respective reinforcement of such structures by dDst binding to AT rich binding sites.

Several r-intervals with different slope of the viscosity changes could be resolved at r< 0.05. The resolution of more than four modes of dDst interaction with ctDNA at very low r values is comparable to DNA interaction of Nt and several other ligands but not of distamycin. Advanced titration rotational DNA-viscometry is again able to resolve subtle quantitative details of ligand mediated DNA conformational changes of high stereochemical relevance.