In 1986, O'Donnell started his own lab at Cornell University Medical College. In 1996, he moved his lab to Rockefeller University. The goal of his research focuses on elucidating the mechanism of the proteins involved in DNA replication. His approach involves studying both the biochemical activities of these proteins as well as their physical structures. Most notably, O'Donnell discovered the first known ring-shaped protein that encircles DNA for function referred to as a DNA-sliding clamp. The DNA clamp tethers the DNA polymerase to its DNA template thereby allowing the polymerase to efficiently synthesize long genomes without letting go. In collaboration with John Kuriyan, they determined the structures of the bacterial beta clamp and human PCNA clamp showing that they form rings that are nearly superimposable and thus they likely share a common ancestor. His work on the many enzymes involved in duplicating DNA has spanned from bacterial to eukaryotic systems.