A fundamental discovery of a new property of DNA was reported in the Science magazine on Feb. 15th, 2013. The research article, entitled “Probing Allostery through DNA”, reveals the existence of DNA allostery using single molecule biophysical techniques, which exhibits not only interesting physics but also physiological relevance. This work was accomplished through a collaboration of the Xie group at Harvard University as well as Sun/Xie lab and Su lab at BIOPIC, PKU.

 

Allostery has been extensively studied for enzymes or proteins, in which binding of a molecule on one part of a macromolecule affects the binding of another molecule at a distal site of the macromolecule. DNA encodes genetic information as a string of base sequences in a double-helical structure. The base sequence encodes not only genes whose expression determine cell functions, but also provides specific binding sites for multiple DNA binding proteins, such as transcription factors and histones, which often bind close to each other on genomic DNA to carry out their cellular functions. Whether there is allostery through DNA affecting protein binding affinity to DNA and how it may regulate gene expression have not been characterized.

 

A single molecule study in this work provides a solution to this puzzle. In the experiments, dsDNA sequences were designed such that there are two protein-binding sites with varying separation. One binding site was for the fluorescently labeled protein and the other binding site was for a different type of DNA-binding protein that is not labeled. By conducting single-molecule fluorescence microscopy, the researchers could monitor individual protein dissociation events from a few hundreds of DNA templates simultaneously, thus obtain the mean residence time of the protein. It is found that the mean residence time of one protein (fluorescently labeled) is significantly altered by the other (unlabeled) protein bound nearby and exhibits an oscillatory behavior, with the magic 10 base period, dictated by the famous double helix structure of DNA.

 

Using various control experiments as well as MD simulation, the researchers confirmed that such a change truly comes from DNA allostery rather than direct protein-protein interaction or electrostatic interaction. In other words, the long-range effect results from a conformational change of DNA double helix induced by protein binding.

 

It is exciting to note that DNA allostery is a rather large effect (factor of 5 change) that was previously hidden in conventional ensemble experiments. In addition, it is discovered that the allosteric property of DNA is general, true for any protein pair. This is significant as multiple proteins, such as transcription factors and RNA polymerase, often bind close to each other on genomic DNA to carry out their cellular functions in concert. We now must consider this new effect in order to understand gene regulation. It is also proved that DNA allostery indeed affects gene expression inside live cells, so it is physiologically important, hence future studies must take this into account. As pointed out in the accompanying perspective published in the same issue of Science, this kind of allosteric effect through dsDNA has profound implication for gene regulation.