Small: Collaborative Research: Programmed Cyclic Molecular Dancing on 2D Origami Lattices

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Molecular interactions can be seen as molecular communications and exchanges of information. In recent years the understanding of molecular information processing has been explored through DNA-based bottom-up self-assembly. These studies explore algorithmic, programmable molecular interactions including molecular devices. In this work, two PIs with complementary expertise, a chemist and a mathematician, join together to further the possibilities for programmed molecular interactions. The goal of this highly interdisciplinary project is to introduce environmental control within the DNA self-assembly process that will direct molecular interactions in a preprogrammed manner. It introduces a "clock" (an essential part of computation) that controls programmed oscillating attachments/detachments of different molecular species on a predesigned platform. The proposed project will enable self-assembly of a variety of preprogrammed molecular shapes from the same set of building blocks. These shapes could serve as scaffolds for nanoelectronic components, which if achieved, will allow for smaller, denser and faster computer hardware. Furthermore, programmed dynamical molecular interactions would be the first incarnation of nucleic acid robots (nubots) acting on a platform. Several undergraduates and at least two PhD graduate students (one in each institution) will receive training through this award. This project will prepare these individuals as unique interdisciplinary research scientists able to pursue studies that require broad scientific knowledge.The goal of this project is to introduce environmental control for periodic dynamical, molecular arrangements in molecular programming, to develop a method for molecular signal communication between different molecular species, and to use this method to obtain molecular arrangements that cycle in time. In particular the project will (1) develop molecular conditions for environmental control through laser illumination that will allow oscillating platform attachments/detachments between two different molecular floating tile species and (2) introduce algorithmic molecular interactions with oscillating dynamics between two molecular species by simulating a two-dimensional Game-of-Life-like dynamics on a two dimensional DNA origami array. The system has a platform consisting of a 2D DNA origami array whose tiles have signaling strands, and free floating tiles able to attach to their respective "identity" counterparts on the platform and to transmit signals to neighboring locations. The array tiles are arranged in a checker-board fashion such that in an alternate manner, at each cycle, one of the colors receives the floating tiles and computes the identity of the next cycle tiles of the other color tiles. The floating tiles are equipped with nano-particles whose exposure to appropriate laser wave length increases the local temperature and thereby can disassociate those floating tiles from the platform.