Real time footage of DNA-enzyme interaction

Author:  Getz Matthew
Date:  October 2007

University of Cambridge researchers recently produced real time footage of the nanoscale interaction that occurs between a restriction enzyme and the DNA of an attacking virus. Using a revolutionary Scanning Atomic Force Microscope in Japan, the research team was able to film the mechanism by which the host restriction enzyme unravels the foreign viral DNA. This research, published online on July 23, 2007 in The Proceedings of the National Academy of Sciences (PNAS), demonstrates a new method that can be used to visualize DNA-enzyme interactions in real time. This will help improve understanding of other cellular processes, such as DNA replication and DNA repair.

Robert Henderson, who led the Cambridge research, explained, "This is the first time that such a process has been seen in real time.The microscope and new techniques give us a clear view of the molecular interactions between proteins and DNA that we could only previously interpret indirectly. The indirect methods require scientists to make assumptions to interpret their data, and video footage like this can help to provide a more direct understanding of what is really happening."

Along with researchers in Edinburgh, India, and Japan, the Cambridge team employed a state-of-the-art microscope and a method known as fast-scan atomic force microscopy (AFM). In typical AFM, several physical properties of the instrument limit the rate at which images can be generated. Though it usually takes thirty seconds to several minutes to produce one image, the modified microscope can take nanoscale images up to a rate of ten frames per second. This improved rate of image acquisition gives scientists a new technique to view how a DNA-protein interaction actually occurs. Henderson addressed this change in capability between the two methods, "Standard technology for filming on this scale can only produce one image frame every 8 minutes. However, our new work allows one frame per 500 – or fewer, milliseconds."

The footage taken was of a bacterial type III restriction enzyme attaching itself to foreign viral DNA. This enzyme is responsible for cleaving viral DNA before it has a chance to infect the bacterium. However, this method could certainly be modified in order to shed light on other DNA-protein interactions and could be used with other organisms, including humans. Of particular interest in humans would be the interactions that occur between different classes of polymerases and DNA in processes such as DNA replication, repair, mutagenesis and transcription.

Henderson suggested at the possibilities of applying these techniques in order to gain a better molecular understanding of diseases such as cancer.

"This helps us understand how enzymes recognise which bit of a DNA strand to latch onto, which is important in understanding how proteins repair damaged DNA," Henderson said. "In the long term, this could help in the search for cancer treatments, as cancer sometimes occurs where DNA is damaged but enzymes do not behave correctly in order to repair it."

The film is available to view at:

Written by Matthew Getz

Reviewed by Elizabeth Ng, Pooja Ghatalia

Published by Pooja Ghatalia