Modeling-driven design and assembly of 3D DNA nanomaterials
Abstract
The central goal of this proposal is to develop integrated methods that combine theoretical modeling and high-performance computer simulations with experiments for realization of complex self-assembled DNA nanomaterials. We will apply these novel methods to design and experimentally realize complex 3D nanolattices, including tetrastack lattice, which has not been successfully assembled with cavity size comparable to the wavelength of visible-light. Such a structure can be used to create optical metamaterial that would open new possibilities in manipulating light for information processing with applications in optical computing. DNA has emerged as a promising material for nanostructure design due to the ease of manipulation in laboratory settings as well as the high degree of programmability. Furthermore, DNA can be functionalized with organic and inorganic compounds, allowing nanoscale-precision placement of these compounds in a prescribed 3D lattice. However, kinetics of the assembly is complex due to kinetic traps and competing phases that hinder the successful assembly of the desired lattice geometry. Often, the final experimental design is achieved by trial-and-error, which is costly and tedious. In order to achieve more complex structure assembly, a new modeling framework is needed to design DNA nanoparticles that assemble with high yield into the desired 3D arrangement. However, modeling of the self-assembly of DNA materials has been particularly difficult due to the long time-scales and system sizes involved. To address these challenges, we will develop a new universal DNA-3D-patchy-particle platform, where each DNA building block is functionalized by a ~patch~, a single-stranded DNA (or kissing loop) that binds to its complementary patch on a different particle. We will use DNA nanostructures (either DNA origamis or 3D single-stranded DNA) as basic building blocks that are then self-assembled into 3D lattices through designed interactions between the patches. We will develop a computational simulation and design platform that builds upon existing state-of- the-art computational modeling tools for DNA nanotechnology, which can scale up simulations to systems consisting of up to a few million nucleotides. To overcome the challenge of long time- scales, we will use multiscale modeling to study the kinetics of complex lattice. We will also establish a new theoretical method based on Boolean satisfiability problems for the design of interactions between DNA nanoparticles that will automatically avoid kinetic traps and alternative assemblies. To validate the theory and simulations experimentally, we will use SAXS, TEM and SEM to characterize the assembled lattices. We will further develop a new experimental approach, based on superresolution microscopy, to characterize lattice geometry. Besides the tetrastack lattice, we will also use these tools to design other DNA crystal systems. First, we will design multifarious crystal systems based on tetrahedral coordinated particles, which can assemble into multiple different lattices such as diamond cubic or clathrate. We will also design a DNA-based seed structure that will seed the assembly of lattice crystallization at normally sub-critical conditions. Finally, we will use the set of developed tools to design and experimentally realize three-dimensional quasicrystal nanostructures (dodecagonal and icosahedral). APPROVED FOR PUBLIC RELEASE.
Document Details
- Document Type
- DoD Grant Award
- Publication Date
- Feb 17, 2020
- Source ID
- N000142012094
Entities
People
- Petr Šulc
Organizations
- Arizona State University
- Office of Naval Research
- United States Navy