Stephanopoulos Lab

We work on the design, synthesis, and application of functional nanomaterials using self-assembling molecules from biology.

Contact Us

727 E. Tyler St., Tempe, AZ 85287

The Biodesign Institute, Room A120B

nstepha1@asu.edu 

480-727-3443

RESEARCH

The common theme that underlies all our research is self-assembling hybrid protein- and peptide-DNA nanomaterials. We seek to merge the functionality and chemical/structural diversity of proteins with the programmability of DNA nanotechnology. This goal requires integration of nucleic acids and polypeptides in a site-specific manner to create hybrid biomolecules. Three broad areas of interest include:

Structural Peptide/Protein-DNA nanotechnology

Biological systems like cells are a marvel of self-assembling protein nanostructures, which carry out functions like signaling, mechanical support, ligand binding, or intracellular transport. Despite the great chemical diversity of proteins, however, it is still challenging to rationally design nanostructures from scratch. DNA nanotechnology, by contrast, has the advantage of programmability thanks to the specificity of Watson-Crick pairing, but at the expense of chemical and functional diversity.

We aim to merge protein and DNA nanotechnology, by integrating self-assembling protein motifs such as coiled-coils, oligomeric assemblies, or protein-protein interactions with DNA nanostructures. This in turn requires the use of multiple, site-specific bioconjugation reactions to attach oligonucleotide handles to the polypeptide molecule.

We aim to create both symmetric structures like fibers, sheets, or 3D cages, and highly anisotropic materials that approach the complexity of DNA origami. We envision these hybrid materials as nanoscaffolds for targeted cargo delivery (“artificial viruses”), development of antibody mimics, structural biology, regenerative medicine, or as components in cell-mimetic molecular factories.

Functional Protein-DNA Nanotechnology

In addition to their fascinating structural properties, proteins have a wealth of promising functional attributes for nanotechnology. We are especially interested in their stimulus-responsive properties, such as conformational changes or reversible binding with triggers such as light, pH, or ligands. As such, we aim to design and synthesize DNA nanostructures that can be actuated by proteins—in a highly reversible and programmable manner—with the ultimate goal of functional nano-machines that can perform complex functions both inside and outside of cells.

These materials in turn require the control of protein orientation on a DNA scaffold, so much of our effort is geared towards developing chemical methods for synthesizing these hybrid nanostructures, especially proteins with multiple site-specific oligonucleotide handles. In this way, we hope to seamlessly integrate the protein surface with the oligonucleotide nanostructure, and begin to construct nano-robots with DNA “skeletons” and protein “muscles.”

Multi-scale Tissue Engineering

Regenerative medicine aims to repair or rebuild tissue lost to injury or disease. Tissues, however, are complex 3D assemblies of cells and their extracellular matrix (ECM), with hierarchical order spanning multiple length scales. We are developing extracellular matrix mimetic materials from protein-DNA hybrids, using the DNA as a common platform to transition between length scales ranging from a few nanometers to many centimeters. Three key length scales include:
1.  5-100 nm: We use DNA nanoscaffolds to position extracellular matrix proteins to create functional receptor clusters for enhancing and instructing cell signaling
2.  20-1000 nm: We are synthesizing protein-DNA nanofibers that mimic extracellular proteins like collagen but with greater control over nanoscale morphology and dynamic behavior, as structural and mechanical support for cells

3.  1 um-1cm: We are developing methods to pattern DNA-modified cells along with their extracellular matrix (through DNA-protein conjugates), for assembly of 3D tissues with sub-cellular precision

 

In all these approaches, we take advantage of the unique properties of DNA to create functional biomaterials, including the orthogonal, dynamic control over multiple ligand presentation. For all these projects, we collaborate extensively with biologists, engineers, and doctors (at ASU, the Mayo Clinic, or other universities) to validate our materials in vitro, and eventually transition them to in vivo applications in tissue engineering and regenerative medicine.