Deformyldistamycin-DNA interaction; DNA conformational changes as revealed by titration rotational viscometry

DNA multimode interaction with berenil and pentamidine; double helix stiffening, unbending and bending

The antitrypanosomal drugs berenil (Ber) and pentamidine (Pm) preferentially bind to DNA in the minor groove of A.T-rich domains. The properties of A.T clusters are essential for sequence-mediated helix bending. Groove binding drugs locally stiffen the DNA helix but may also change intrinsic helix bends or may bend straight DNA. Ligand binding to randomly distributed sites alters the apparent DNA persistence length, a. Criteria permit the distinction of the underlying mechanism(s). Helix bends, if phased with the helix screw, however, generate solenoidal superhelix components mediating an apparent change of the hydrodynamically effective DNA contour length, L. The measurement of relative changes of both, a and L, as induced by Ber or Pm is performed by titration rotational viscometry. The determination of the two quantities requires two independent measurements: the relative change of DNA intrinsic viscosity, deltay, for short (tending to rod-like) DNA molecules and for comparably long (almost coil-like) ones as a function of r, the bound drug molecules per DNA-P, and this under conditions effectively excluding intramolecular DNA-DNA crosslinking effects. At least at r< or =0.05 and < or =0.03, respectively, the two drugs virtually bind completely to a eukaryotic DNA. r ranges of different drug binding strength and, concomitantly, of different specific conformational response, could be resolved. They represent (sub)modes of different DNA sequences... Whereas the mode-specific elongation effects are fairly similar for both systems, there are pronounced quantitative differences in the relative change of DNA persistence length. The sites of highest Ber-binding strength are correlated to unbent alternating helical A.T segments followed by bent and by less bent or unbent dAn.dTn tracts straightened on Ber-binding. For Pm-DNA interaction the ligand bends the sites of highest Pm affinity. Generally, ligand induced and sequence mediated local DNA-bend removal or DNA bending, as observed for several modes of interaction with A.T rich DNA, are considered to be of gene regulatory relevance.

Synthetic DNA minor groove-binding drugs

In this review, both cationic and neutral synthetic ligands that bind in the minor groove of DNA are discussed. Certain bis-distamycins and related lexitropsins show activities against human immunodeficiency virus (HIV)-1 and HIV-2 at low nanomolar concentrations. DAPI binds strongly to AT-containing polymers and is located in the minor groove of DNA. DAPI intercalates in DNA sequences that do not contain at least three consecutive AT bp. Berenil can also exhibit intercalative, as well as minor groove binding, properties depending on sequence. Furan-containing analogues of berenil play an important role in their activities against Pneumocystis carinii and Cryptosporidium parvuam infections in vivo. Pt(II)-berenil conjugates show a good activity profile against HL60 and U-937 human leukemic cells. Pt-pentamidine shows higher antiproliferative activity against small cell lung, non-small cell lung, and melanoma cancer cell lines compared with many other tumor cell lines. trans-Butenamidine shows good anti-P. carinii activity in rats. Pentamidine is used against P. carinii pneumonia in individuals infected with HIV who are at high risk from this infection. A comparison of the cytotoxic potencies of adozelesin, bizelesin, carzelesin, cisplatin, and doxorubicin indicates that adozelesin is a potent analog of CC-1065. Naturally occurring pyrrolo[2,1-c][l,4]benzodiazepines such as anthramycin have a 2- to 3-bp sequence specificity, but a synthetic PBD dimer spans 6 bp, actively recognizing a central 5'-GATC sequence. The crosslinking efficiency of PBD dimers is much greater than that of other major groove crosslinkers, such as cisplatin, melphalan, etc. Neothramycin is used clinically for the treatment of superficial carcinoma of the bladder.

Multimode interaction of Hoechst 33258 with eukaryotic DNA; quantitative analysis of the DNA conformational changes

The interaction of the minor groove binding ligand Hoechst 33258 (Hoe) with natural DNA was investigated by high resolution titration rotational viscometry. Analysis of the concomitant DNA conformational changes was performed with two DNA samples of sufficiently different molar mass M, at 4 degrees C, 22 degrees C and 40 degrees C, for Hoe/DNA-P ratios below r = 0.02. In this narrow r range several interaction modes could be resolved. The measured conformational changes were quantified in terms of relative changes of both apparent DNA persistence length, delta a/a, and hydrodynamically operative DNA contour length, deltaL/L. Delta a/a(r) primarily is a measure of ligand-induced DNA helix stiffening, but both, delta a/a(r) and deltaL/L(r), generally depend also on ligand binding induced DNA bending or DNA unbending. The essential difference obviously is that delta a/a(r) is influenced by the randomly distributed helix bends and deltaL/L(r) by phased ones. The measurements performed at different temperatures deliver informations about existence and temperature dependent abolition of intrinsic helix curvature. Both Hoe and netropsin (Nt) prefer binding to AT rich DNA segments, which are candidates for intrinsic DNA helix bends. But our data for Hoe interaction with calf thymus DNA (ctDNA) show characteristic differences to those for Nt-ctDNA interaction. Especially for Hoe, the mode of highest affinity is saturated already at a ligand concentration of roughly 1 nM (r approximately = 0.0015 Hoe/DNA-P). It exhibits an unusually strong temperature dependence of the conformational DNA response. A Hoe-Nt competition experiment shows that Hoe binding to the sites of the very first Hoe mode is almost unaffected by bound Nt. But Hoe binding to the sites of the following Hoe modes does not occur due to the competition with Nt. Thus this mode of strongest Hoe-DNA interaction reflects a unique mechanism, possibly of high relevance for gene regulatory systems.