Complexes of the minor groove of DNA.

An increasing number of high-resolution structures suggest that both the minor and major grooves of DNA can function as receptors for proteins and small molecules. In this review, we try to illustrate the diversity of small molecule ligands that are capable of specifically recognizing the minor groove of DNA. Complex formation results in varying degrees of conformational changes in both DNA and ligands. The discussion focuses on intermolecular interactions that contribute to binding affinity and specificity. There probably is no simple general recognition code that explains the binding specificity of minor-groove ligands. To understand DNA recognition by small molecules, characterization of the binding mode at near-atomic resolution must be combined with thermodynamic data on the energetics of ligand binding to short oligonucleotides.