Force Spectroscopy on Tetranucleosomes Using DNA Origami Nanocalipers

Force spectroscopy techniques such as optical traps and magnetic tweezers have provided useful information in chromatin studies. However, the requirement that the biomolecule of interest must be tethered to a relatively large microsphere leads to challenges. Here, we use hinge-like DNA origami nanocalipers with tunable mechanical properties to perform force spectroscopy experiment on tetranucleosomes. Using transmission electron microscopy to obtain images of single particles, we first determine an opening angle distribution of the nanocalipers. We then incorporate tetranucleosomes into the nanocalipers via Biotin-NeutrAvidin-Biotin linkage and measure the opening angle distribution of properly incorporated particles. We can then measure forces and free energies by observing how tetranucleosome incorporation changes this distribution. Our results show that the nanocalipers can apply tensile forces on tetranucleosomes in the pN range. In addition, by leveraging the advantage that we can see the structures of interest, we are able to 1) measure difference in free energies between certain tetranucleosome conformational states and 2) build up a free energy landscape as a function of tetranucleosome end-to-end distance. We hope to further use this technique to study longer arrays, different DNA linker lengths, and the effect of transcription factors.