Topotecan, a cancer inhibitor, interacts with an important protein (TopoIB), causing a (cancer) cell to malfunction. The TopoIB protein is responsible for the removal of loops from DNA, which arise amongst other things during cell division.

The TopoIB protein binds to the DNA molecule, clamps around it and cuts one of the two DNA strands, after which it allows it to unwind and finally joins the broken ends together.

Until now it has been supposed that topotecan only causes the TopoIB protein to reside longer than normal on the DNA molecule, disturbing the cell division and damaging the (cancer) cell. But the researchers at the University of Delft have now discovered that adding topotecan also dramatically impedes the unwinding and that DNA loops accumulate as a result. The accumulation of these DNA loops forms the basis for an alternative mechanism, and could help in the development of better cancer medicine.

A TopoisomeraseIB protein (green) is hindered in unwinding DNA loops by the cancer inhibitor topotecan (red). The DNA polymerase protein (grey), a protein which duplicates DNA, is hindered by the DNA loops (TU Delft/Tremani)

PhD candidate Daniel Koster, Master’s student Elisa Bot and researcher Nynke Dekker of the Molecular Biophysics group of the Kavli Institute of Nanoscience Delft have managed to unravel this mechanism in an extremely direct manner.

In the laboratory they fixed a single DNA molecule between a glass plate and a magnetic sphere. With the help of two magnets they could both pull and twist the DNA molecule. When they added TopoIB to a twisted piece of DNA, they saw that the loops were slowly removed.

What is exceptional is that the action of one TopoIB enzyme on one DNA molecule could be observed live. In collaboration with St. Jude Children’s Research Hospital Memphis (USA) the mechanism could also be observed in living yeast cells.

Source: Antitumour drugs impede DNA uncoiling by topoisomerase I - Daniel A. Koster, Komaraiah Palle, Elisa S. M. Bot, Mary-Ann Bjornsti & Nynke H. Dekker. Nature advance online publication 24 June 2007, doi:10.1038/nature05938