Seidel
In our research project, we conducted two distinct investigations. In the first part, we focused on studying structural transitions within single DNA molecules under external stress and negative supertwist. Using ethidium bromide (EtBr), we induced changes in DNA structure and observed an increase in contour length and untwisting of the helix. Through meticulous single-molecule mechanical experiments, we examined the effects of EtBr on DNA’s stretch and twist rigidity. Surprisingly, we discovered that force-induced intercalation played a dominant role in influencing the mechanical properties of the intercalator-complexed DNA. Our findings challenged existing models and pointed towards an anti-cooperative intercalation mechanism. We have submitted a manuscript detailing these exciting discoveries to The Biophysical Journal for review.
In the second part of our project, we aimed to establish mechanical experiments on single synthetic polymer chains to investigate their folding and crystallization behavior. Our objective was to bridge the gap between studies on biological and synthetic polymers by examining isolated polymer chains. To achieve this, we developed a DNA-PEO-DNA hybrid construct that allowed us to manipulate the length of the polymer chain and perform controlled experiments. However, we encountered challenges in establishing the experimental setup, particularly in achieving the desired stoichiometric attachment of PEO chains to DNA molecules. Additionally, finding suitable conditions that would keep DNA handles soluble while promoting polymer chain collapse or crystallization proved to be a complex task. Despite our efforts, we were unable to obtain publishable results in this part of the project. As a result, we decided not to extend project B13.
Throughout the research project, we collaborated with other research groups, including Prof. Jörg Kressler, Frank Cichos, and Maria Ott. These collaborations allowed us to exchange ideas, discuss challenges, and explore different experimental approaches. Their expertise in various aspects, such as coupling PEO chains to DNA and fabricating DNA constructs, greatly contributed to the project. We are grateful for their valuable insights and support.
Highlighted Publication:
J. Dikic and R. Seidel, Anticooperative Binding Governs the Mechanics of Ethidium-Complexed DNA Biophys. J. 116, 1394 (2019)
Other publications of this group:
