10.1016/j.bmcl.2004.07.043
The research focuses on developing new DNA-binding ligands modeled after Chromomycin A3 (CRA3), a potent antitumor antibiotic known for binding in the minor groove of GC-rich regions of duplex DNA. The new ligands were designed to mimic CRA3's structure, particularly its trisaccharide part, using a simple alkyl group attached to the chromophore. The study successfully demonstrated that these new ligands form Mg2+-coordinated dimer complexes, exhibiting DNA-binding affinity. The synthesis involved several steps, including [4+2] cycloaddition, aldol reaction, deprotection, dehydroxylation, and hydrogenation. The ligands' Mg2+-binding properties were investigated using UV spectra, and their DNA-binding affinity was evaluated through a competitive displacement assay with ethidium bromide (ETBr) and self-complementary DNA duplexes. The experiments showed that the alkyl chain in the new ligands contributes significantly to the formation of dimer complexes and DNA binding, with the 3(S) isomer showing high affinity to DNA in the presence of MgCl2. The study concluded that the simple alkyl chain can mimic some roles of the trisaccharide part for Mg2+-dimer complex formation and Mg2+-mediated DNA binding, and further efforts are underway to develop stronger DNA-binding ligands based on this model.