• WABLOG: From the desk of Matthias Wabl

DNA Origamis to the Rescue in Lupus Research

DNA Origamis
A tantalizing question in lupus research has been how anti-dsDNA antibodies bind DNA, and whether there are physiological mimetopes by which B cells expressing these antibodies might be selected. Because no crystals could be generated, there is no available X-ray structure of anti-dsDNA antibodies or Fab fragments bound to DNA. With cryo-electron microscopy, we now have a tool comparable—and potentially superior—to traditional X-ray crystallography techniques. In this way, we compare the structure of antibodies that differ by a single or a few amino acids and are dsDNA-binding and nonbinding, respectively. However, to obtain structures of antibodies bound to DNA fragments, we have to constrain the flexibility of DNA—the part of it that is not bound to antibody. In vivo, DNA is constrained in complexes such as chromatin or retroviral pre-integration complex. Similarly, for our structural study we constrain the dsDNA in synthetic nucleosome or DNA origami structures.

During the last decade, DNA origami has progressed past an art form and is being tried for a number of applications. The specificity of the interactions between complementary base pairs makes DNA an exciting construction material for molecular origamis—creating scaffolds that hold other molecules in place or structures all on its own. For our research, we use two examples of antibody complexes with constrained dsDNA. In one example, synthetic DNA is folded into a 6-helix honeycomb structure, which forms a tube. In the other example, the antibodies are complexed with synthetic nucleosomes.

The figure shows electron micrographs (EM) of DNA-antibody complexes. In the upper panel, an antibody is bound to a 6-helical honeycomb tubular structure made of DNA. To the left of the panel is an inter­pretation of the first EM picture; antibody is in blue, DNA in grey. It appears that antibodies mostly bind to the ends of the origami structure, where the full DNA double helices are more accessible. In the lower panel, an anti­body is bound to a synthetic nucleosome. To the left, interpretation of the first EM picture. To the right, enlarged schematic of the nucleosome structure; DNA (gray) in a ring outside, and histones (blue) in the center. (In collaboration with Eugene Palovcak, Yifan Cheng, Lea Tröster, Maryam Shansab and Shawn Douglas).

Ecotropic virus in mice that are modifiers of autoimmunity

The fairly recent realization that endogenous elements play an important role in the immune system has revived a great interest in them. We now know that endogenous retroelements are adjuvants in the immune response to T cell-independent type 2 antigens; and retroelements are implicated in monogenic and polygenic (“spontaneous”) autoimmune disease. Read More »

Proof, Facts, and Alternative Medicine

Philosophers of science are a bit like Catholic priests as marriage counselors: They entertain ideas that are different from those of the practitioners. The foolhardy assumption that a hypothesis cannot be proved, but only disproved, is irrelevant to the workings of modern science, which is based on experiments. (In fact, strictly speaking, a hypothesis can neither be proven nor disproved). Experiments restrict the range of discussion on a subject. While it is axiomatic that, for a limited number of experiments there is an unlimited number of explanations, or hypotheses, the hypotheses have to be reasonable. When reasonable explanations are tested and excluded, the remaining explanation becomes the basis of the next experiment. It is this next experiment that theoreticians forget about: It is the accumulation of positive outcomes from successive experiments that establishes a fact, such as that DNA is the hereditary material. “Alternative” medicine is, at best, based on “experience,” not on experiments. While experiences no doubt constitute facts as well and, indeed, greatly outnumber facts established by experiments, experiences tend to be tied to various ad hoc explanations that fit the day. The therapy prescription to “throw enough cards (or remedies), and eventually some odds will go your way,” is questionable, as there are too many possibilities.