DNA is polymorphic and exists in a variety of distinct conformations (1, 2). Duplex DNA can adopt a variety of sequence-dependent secondary structures that range from the canonical right-handed B form through the left-handed Z conformation. Multistranded triplex and tetraplex structures are now known to exist. All of these unique conformations may play important functional roles in gene expression. Consequently, there is intense current interest in the design and synthesis of small molecules that selectively target specific DNA structures, to inhibit the biological function in which these particular structures participate (3-10).Enantiomers of chiral metal complexes have attracted considerable attention as potential structural probes of DNA conformation. Norden and Tjerneld (11) first reported the preference of the ⏠enantiomer of Tris(dipyridyl)Fe(II) for right-handed B-form DNA. The Barton laboratory subsequently developed an elaborate series of chiral metal complexes, some of which were reported to recognize specific DNA conformational features (for reviews, see refs. 12-14). A comprehensive review of the interaction of chiral metal complexes with DNA (15) indicated, however, that the structural selectivity of these agents is ambiguous in many cases.We report here a dramatic and unambiguous example of structural selectivity in DNA binding for the naturally occurring anticancer agent (Ï©)-daunorubicin and its novel (ÏȘ)-enantiomer, WP900 (Fig. 1). The synthesis of WP900 proved to be demanding and required some 37 steps. We find that the daunorubicinÍWP900 enantiomeric pair can discriminate between right-and left-handed DNA, and that each compound can act as an allosteric effector to convert DNA to a conformation that binds each ligand with higher affinity. The structural selectivities of daunorubicin and WP900 appear to be far greater than those reported to date for any chiral metal compound. To the best of our knowledge, there have been no other reports of a detailed investigation of DNA binding for an enantiomeric pair that does not involve a chiral metal complex.
Materials and MethodsMaterials. Daunorubicin was obtained from Sigma and was used without further purification. The concentrations of daunorubicin solutions were determined by optical absorption at 480 nm by using 480 Ï 11,500 M ÏȘ1 â
cm ÏȘ1