Jenny Vi Le

My Story:

The organization of eukaryotic DNA into nucleosomes and chromatin undergoes dynamic structural changes to regulate genome processing, including transcription and DNA repair. Critical chromatin rearrangements occur over a wide range of distances, including the mesoscopic length scale of tens of nanometers. However, there is a lack of methodologies that probe changes over this mesoscopic length scale within chromatin. We have designed, constructed, and implemented a DNA-based nanocaliper that probes this mesoscopic length scale based. This DNA-based nanocaliper was created through DNA origami, a method that uses DNA as building blocks to assemble complex and 3D nanostructures. We developed an approach of integrating nucleosomes into our nanocaliper at two attachment points with over 50% efficiency. Here, we focused on attaching the two DNA ends of the nucleosome to the ends of the two nanocaliper arms, so the hinge angle acts as a readout of the nucleosome end-to-end distance. We found that the nanocaliper angle is a sensitive measure of nucleosome disassembly and can read out transcription factor (TF) binding to its target site within the nucleosome. This includes the unwrapping of the nucleosome with transcription activator Gal4-VP16. We are currently expanding the nanocaliper function to study the compaction and remodeling of nucleosome arrays via histone linker proteins and chromatin remodelers. These studies demonstrate the feasibility of using DNA nanotechnology to both detect and manipulate nucleosome structure, providing a foundation of future mesoscale studies of nucleosome and chromatin structural dynamics.