New tools for studying DNA-protein interactions

The genetic material of most organisms is carried by DNA, a complex organic molecule. DNA is very long for humans, and the length of the molecule is estimated to be about 2 meters. In cells, DNA appears in a dense form and molecular chains are coiled together in a complex but efficient manner. Histones are structural support proteins, and a part of DNA molecules can be wrapped around histones, which play a key role in the compaction process of DNA. The wrapping process of DNA–histones is reversible—these two molecules can unfold and rewrap—but we know little about the mechanisms involved. Now, by applying high-speed atomic force microscopy (HS-AFM), Richard Wong and colleagues from Kanazawa University (NanoLSI WPI) provide valuable insights into the spatiotemporal dynamics of DNA—histone interactions.

The researchers looked at the interaction between DNA and a histone called H2A (one of the five major histones). To test the applicability of HS-AFM as a feasible tool for imaging DNA–histone interactions, they first focused on the native state of H2A. Wong and colleagues were able to delineate the topology of the molecule and how it changed over time. Importantly, they show that a tapping force is constantly applied to the molecule during HS-AFM and does not lead to conformational changes or actual damage.

To observe the interaction between DNA-h2a and HS-AFM in real time, scientists prepared DNA samples of different lengths and forms: plasmid (long and round), long linear and short linear DNA, of which short linear DNA has the highest motility. Experiments have shown that the choice of DNA carrier in atomic force microscopy imaging is essential; it has been found that a special lipid layer works better because it does not strongly absorb DNA strands.

The most significant results were obtained by observing the interaction of H2A with short linearized DNA (called"geometrical DNA"by researchers). Specifically, four different interaction situations can be distinguished: touch, slide, pinch, and wrap, and the associated motion does resemble the motion of the geometrid.

Wong and coworkers also studied the effect of ionic strength on DNA–histones binding affinity by varying the salt concentration of the fluid containing DNA–histones aggregates. When increasing the salinity of the liquid, the aggregates were found to dissolve. The aggregate shifts when the liquid is diluted again, thereby reducing the salt content. The results show that changing the ionic strength (i.e., salt concentration) of the DNA-H2A complex environment provides a method to simulate changes in the strength of DNA–histones interactions because they occur in living organisms.

The report by Wong and colleagues is the first to look at DNA–histones interactions in real time and convincingly suggests the applicability of HS-AFM in studying this biological process, equally applicable to disease.

Finally, it is worth highlighting the contribution of Nishide Goro, the first author of the paper, who is a PhD student in the Department of Nanobiology at the Graduate School of Frontier Science Initiative, Kanazawa University. Under the guidance of Professor Wang and Dr. Lin, Mr. Nishide played a key role in the research reported, he performed the experiments, co-designed the research, and co-wrote the paper. Mr. Nishide also participates in the WISE program of Nanoprecision Medicine, Science, and Technology at Kanazawa University, which aims to take advantage of our growing understanding of nanoscale biological and other processes to innovate in disease prevention, diagnosis, and treatment approaches.

Collected by Profacgen, a biotech company that has a professional team for studying DNA-protein interactions.

Collected by Profacgen, an insect cell protein production provider.