DNA interaction of the imidazole-containing lexitropsin ImPy: titration viscometric study in comparison to netropsin.

The imidazole (Im) containing lexitropsin ImPy related to netropsin (Nt) is a sequence reading DNA ligand which, in contrast to Nt, permits binding to a GC base pair. The ImPy induced DNA conformational changes differ significantly from those induced by Nt as monitored by titration viscometry, although interaction modes have also been resolved with boundaries at the same ligand to DNA phosphate ratio, r. Evidently ImPy covers similar binding sites (in the same sequence) as Nt for natural calf thymus DNA at r < 0.023. This result suggests that the preferred binding sites of ImPy are A tracts (cf. K.E.R. JBSD 9(1993) 973), in agreement with previous data. The respective DNA coil expansion, most probably caused by unbending (l.c.), is similar but smaller compared to the Nt-DNA interaction. These results again suggest that, at low r values, the van der Waals interaction in the narrowed minor groove of AT clusters provides a dominating energy contribution to ImPy binding. At r > 0.03 the DNA coil expansion increases to extremely high values in that r range where Nt binding (to mixed AT/GC sequences) induces no effect at all owing to steric hindrance with the amino group of guanine. On the basis of many quantitative results for the Nt-DNA systems these effects can be understood in terms of an unbending of intrinsic helix bends (l.c.). They are of considerable interest in connection with the ability of such compounds to influence the direction of the local regulatory relevant DNA curvature.

Interaction of anthracycline antibiotics with biopolymers: comparative studies of DNA binding and antimicrobial activity of rhodomycin-type anthracycline antibiotics.

The binding of the anthracyclines beta-rhodomycin-I and beta-rhodomycin-II to calf thymus DNA was investigated by both equilibrium and kinetic methods taking into account ligand dimerization (ionic strength I = 0.2 M, pH 6.0). The analysis was based upon a cooperative single-step binding mechanism with overlapping of potential binding sites on a linear homogeneous lattice. Equilibrium binding parameters were estimated from spectrophotometric titration experiments by means of a nonlinear fitting program. The results were compared with those obtained previously for the related antibiotic iremycin and were complemented by kinetic parameters determined from temperature-jump experiments at high binding ratio. The binding constants and the mean attachment times of the drugs were found to increase in the serial order iremycin, beta-rhodomycin-I and beta-rhodomycin-II, which is in line with their increasing antimicrobial activity on Bacillus subtilis ATCC 6633.

Interaction of anthracycline antibiotics with biopolymers. VIII. Binding parameters of aclacinomycin A to DNA.

The binding of aclacinomycin A to DNA was investigated spectrophotometrically under equilibrium conditions. The self-association behaviour of aclacinomycin A was identified as dimerization. Based on a model of overlapping potential binding sites the subsequent results were obtained: equilibrium constant of cooperative binding K = (7.58 +/- 2.15) X 10(6) M(-1), size of a binding site alpha = 3.98 +/- 0.14 base pairs, cooperativity parameter sigma = 0.12 +/- 0.10. These parameters were compared with those of adriamycin, daunomycin, and iremycin to draw some conclusions regarding the structural specialities of aclacinomycin A.

Temperature mediated variation of DNA secondary structure in (A.T) clusters; evidence by use of the oligopeptide netropsin as a structural probe.

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.

Aspects of specific protein-DNA interaction; multi-mode binding of the oligopeptide antibiotic netropsin to (A.T)-rich DNA segments.

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.