Molecule of the Month: Actinomycin
Some antibiotics attack cells by intercalating between the bases in a DNA double helix
Intercalating into DNA
Intercalators in Action
Exploring the Structure
Actinomycin and DNA (PDB entry 173d)
Many intercalating molecules have no preference for a particular sequence of DNA, but actinomycin binds most strongly to GC steps. The structure of actinomycin with a short piece of DNA (PDB entry 173d ) revealed the reason for this: the cyclic peptide portion of the molecule forms specific hydrogen bonds with the edges of the guanine bases. To take a closer look at this interaction, click on the image for an interactive Jmol.
Topics for Further Discussion
- Structures for many other DNA intercalating drugs are available in the PDB. You can start by searching for "anthracycline", the name of a large class of anticancer drugs.
April 2013, David Goodsellhttp://doi.org/10.2210/rcsb_pdb/mom_2013_4