Structural DNA nanotechnology is an emerging field with exciting potential for applications such as single molecule sensing, drug delivery, and manipulating molecular components. Realizing the functional potential of DNA nanomachines and nanorobots requires the ability to design dynamic mechanical behavior such as complex motion, conformational dynamics, and force generation. Our lab has developed approaches to design and construct DNA nanostructures with programmable 1D, 2D, and 3D motion as well as dynamic nanostructures with programmed, responsive, or externally controlled conformational dynamics. While these DNA nanorobotic platforms have a range of applications, challenges with the design process remain a major hurdle to broader implementation.
Currently, design of DNA devices is carried out through a bottom up process that requires manually routing the underlying DNA architecture, which relies on prior expertise. I will present a new design approach with an accompanying software tool we developed that leverages a hybrid top-down geometric modeling approach with bottom-up fine tuning of component level designs. This approach simplifies the design process and reduces design times from hours to minutes.
Furthermore, our software tool enables a significant advance in 3D design complexity, especially for multi-component dynamic devices. Moving forward, we aim to develop devices where nanoscale mechanical and dynamic properties can be exploited to probe physical properties or molecular interactions in real time. I will highlight ongoing work in our lab developing DNA nanodevices to probe the structure and dynamics of biomolecular complexes with an initial focus on studying nucleosomes, which are the fundamental packing unit of DNA in chromosomes.