Binding of antibiotics to DNA

The DNA molecule can serve as host to numerous guest ligands, some of which are antibiotics, and almost all of which are endowed with anticancer or antimicrobial activity. Many guest ligands are quite large and complex in structure, and an array of intermolecular contacts underlie their complementarity to their macromolecular receptor. Often the process of molecular recognition involves conformational adjustments on the part of the interacting species, but the lion's share of the adjusting is demanded of the DNA helix which commonly ends up considerably distorted. Generally the lock must bend to accommodate the key. Two fundamentally different modes of binding can be identified: intercalation and minor groove-binding. The former mode is exemplified by daunomycin or actinomycin and the latter by netropsin or distamycin. Intercalation is associated with substantial extension and unwinding of the helix whereas groove binding is characterized by replacement of the spine of hydration and by lesser effects on helix geometry such as local bending. Bifunctional (or bis-) intercalation, as seen with echinomycin, causes the most far-reaching perturbations in the structure of DNA. It might even involve altered base pairing, which has been observed in complexes between echinomycin and oligonucleotides but has not yet been detected with macromolecular DNA in solution.