CAREER: Hybrid protein-DNA nanostructures and devices

Arizona State University, Scottsdale AZ

Investigators

Abstract

Non-technical Summary: One of the greatest challenges for science is to create materials that can interact with, and influence, biological systems in order to treat disease, regrow damaged tissues, or elucidate fundamental scientific mechanisms. This proposal aims to develop new methods for building these materials, relying on the smart, programmable assembly of molecules like proteins or DNA. In particular, the PI aims to develop: (1) nanofibers (similar to those in tissue) composed of DNA elements linked by proteins; (2) three-dimensional cages mimicking viruses from both protein building blocks and DNA scaffolds; (3) mechanical elements like hinges or boxes with latches that are activated by proteins. The use of proteins will allow for stability, control over structure, and interaction with cells that is not possible with DNA alone, whereas the DNA components will permit for complex designs that are difficult to make with proteins alone. The final materials will be useful as gels for stimulating cell repair, cages that can selectively target therapeutics to diseased cells, and nano-machines that can probe fundamental biological processes. The materials developed will also serve as a modular toolkit that can be used by scientists in a range of disciplines to create new materials for applications beyond biology and medicine, such as energy applications or nano-scale factories that mimic cells. In addition, the PI will develop an integrated training program for undergraduate and graduate students to introduce them to cutting-edge research in bio-nanotechnology, as well as outreach programs to middle and high school students to help demonstrate the beauty of nanotechnology and its great potential to make a difference to human health. Technical Summary: The goal of this proposal is to develop functional nanomaterials that combine the structural programmability of DNA nanotechnology with the functional diversity of proteins. DNA is unparalleled as a building block for complex, self-assembled structures, but these assemblies are limited to the physical and chemical properties of oligonucleotides. The PI proposes to build DNA nanostructures that incorporate proteins in controlled locations and orientations on DNA scaffolds, to serve as both structural components and functional elements, with a particular emphasis on dynamic responsiveness to stimuli such as light or temperature. Two key Research Directions will be explored, each with several synthetic targets: 1) The first Research Direction involves creating hybrid nanostructures integrating DNA and protein self-assembly, specifically one-dimensional nanofibers and three-dimensional cages. The nanofibers will be constructed using protein-protein interactions such as that between a nanobody and its target. The protein interaction will drive hierarchical assembly of rigid DNA elements, which can be tuned in geometry and valence to obtain branched fibers or even hydrogels. The cages will be constructed using a trimeric protein building block modified with DNA, which will be integrated with programmable DNA components to create three-dimensional polyhedra with various geometries. 2) The second Research Direction aims to create dynamic DNA nanostructures driven by light or heat, using stimulus-responsive proteins, specifically latches for 3D cages and hinge elements for rigid tweezers. For this purpose, photoswitchable proteins that can reversibly associate with light and thermally responsive proteins that reversibly aggregate with heat will be used as actuation elements. Both projects will require integrating proteins in controlled orientations on DNA scaffolds through site-specific bioconjugation chemistry of multiple oligonucleotide handles. For this purpose, the PI will develop novel strategies for synthesizing seamless protein-DNA hybrid materials. The final materials will enable nano-devices with applications in drug delivery, sensing, catalysis, molecular robotics, and biomaterials for regenerative medicine and tissue engineering. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.