New DNA binding ligands as a model of chromomycin A3

Small molecules with DNA-binding affinity within the minor groove have become of great interest. In this study, new DNA-binding ligands were designed to mimic Chromomycin A3 (CRA3), which contains a hydroxylated tetrahydroanthracene chromophore substituted with di and trisaccharides. The trisaccharide part of CRA3 that is supposed to contribute to form the Mg2+-coordinated dimer was expected to be mimicked by a simple alkyl group attached to the chromophore part as new model compounds. The present study has successfully demonstrated that the new ligands form Mg2+-coordinated dimer complexes to exhibit DNA-binding affinity