Top-Down Algorithmic Design of Structured Nucleic Acid Assemblies

The past decade has witnessed dramatic growth in ability to "print" complex nanometer-scale structures and patterns using self-assembling nucleic acids. These structures can be used as templates to synthesize inorganic materials on the 1-100 nanometer-scale, or employed directly in applications such as DNA-based memory storage, therapeutic delivery, single-molecule structure-determination, and nanoscale excitonic materials. While various computational strategies are available to forward design these complex 3D structures manually from underlying DNA or RNA sequence and topology, the inverse problem of autonomously generating linear nucleic acid sequences from target geometry alone remains an unsolved computational challenge. In this project, fully automatic, top-down computer-aided design (CAD) algorithms are explored to generate topological sequence designs for broad classes of programmed DNA and RNA assemblies in an autonomous manner using target geometry alone. These assemblies can be "printed" via self-assembly in vitro or in vivo to form target nanoscale geometries using either synthetic or transcribed nucleic acids. The approach will offer a broadly accessible, high-level programming language to realize sequence-based programming of arbitrary 1D/2D/3D nanoscale structured materials based on nucleic acids with diverse applications in basic science and nanotechnology.

The proposed computational algorithms will be distributed freely online as open source software as well as integrated into a variety of software packages to broadly enable the top-down design of DNA and RNA assemblies. These algorithms and software will provide the broader scientific and industrial communities with easy-to-use, high-level design strategies that will accelerate the broad participation of groups in the use of nucleic acid nanotechnology for diverse applications in biomolecular and materials science and technology. The tools will open up opportunities for high school students and undergraduates to gain hands-on experience in nucleic acid nanostructure design. Curriculum developments at ASU and MIT will employ the use of this sequence design software for participation by undergraduate and graduate students in its use and application to basic questions in computer science and nanotechnology research.

Foundational aspects of the design of nanoscale structured materials using DNA and RNA will be explored. Algorithmic approaches to rendering diverse CAD-based geometric primitives using DNA and RNA will be investigated, including wireframe lattices in 2D and 3D, single-layer surfaces that may contain arbitrary curvatures, as well as 3D solid objects. Meshing algorithms will be used to discretize geometric objects in 1D, 2D, and 3D, and topological routing and sequence design will be applied to position nucleic acid strands within CAD objects. Continuous and discontinuous single stranded nucleic acids will be routed through duplexes using anti-parallel and parallel crossover configurations to exploit distinct modes of programmed self-assembly. Sequence design and routing will be validated experimentally to explore principles for obtaining optimal folding, self-assembly, and positioning of specific base pairs in 3D space. Self-assembly of nanostructures from RNA will additionally be explored, utilizing staple-free designs from single long continuous scaffold strands. Close interaction between experiment and computation will help to distill fundamental yet practical approaches to programming structured nucleic acid assemblies.