HS-AFM Shows Promise for Studying DNA-Histone Interactions

Researchers from Kanazawa University used high-speed atomic force microscopy to obtain valuable insights into the spatiotemporal dynamics of DNA-histone interactions.

The team specifically looked at the interaction between DNA and a histone called H2A, one of the five main histones. To check the applicability of HS-AFM as a viable tool for imaging the DNA-histone interaction, they first focused on H2A in its native state. Richard Wong, senior author of the study published in The Journal of Physical Chemistry Letters recently, and colleagues were able to image the topology of the molecule, and how it changes over time. Importantly, they showed that the HS-AFM process, during which a tapping force is constantly exerted on the molecule, does not lead to conformational changes or actual damage.

For real-time observation of the DNA-H2A interaction with HS-AFM, the scientists prepared DNA samples with different lengths and forms: plasmid (long and circular), long-linearized and short-linearized DNA, with the latter having the highest motility. The experiments showed that the choice of substrate on which to put the DNA for AFM imaging is crucial; a particular type of lipid layer was found to be good as it does not strongly absorb DNA strands.

The observations of the interaction of H2A with short-linearized DNA, which the researchers nicknamed 'inchworm DNA', led to the most notable results. Specifically, four different interaction situations could be distinguished: touching, sliding, sandwiching and wrapping, with the associated motions indeed resembling the movements of inchworms.

Wong and colleagues also investigated the effect of ionic strength on the DNA-histone binding affinity, by changing the salt concentration of the liquid containing the DNA-histone aggregate. When increasing the liquid's salinity, the aggregate was found to dissolve. When diluting the liquid again, and so reducing the salt content, the aggregate reformed. This result shows that varying the ionic strength (i.e., the salt concentration) of the environment of the DNA-H2A complex provides a way to mimic the variations in the strength of DNA-histone interactions as they happen in living organisms.