Peptide-DNA Hybrid Nanomaterials for Biology and Regenerative Medicine

Peptide-DNA Hybrid Nanomaterials for Biology and Regenerative Medicine

Ronit Freeman¹, Nicholas Stephanopoulos², Samuel I. Stupp^1,3,4.5*

(* s-stupp@northwestern.edu)

1. Simpson Querrey Institute for BioNanotechnology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, United States

2. Current address: School of Molecular Sciences, Center for Molecular Design and Biomimetics, The Biodesign Institute Arizona State University, Tempe, AZ 85287, United States

3. Department of Materials Science and Engineering, Northwestern University, Evanston, IL 60208, United States

4. Department of Chemistry, Northwestern University, Evanston, IL 60208, United States

5. Department of Medicine, Northwestern University, Chicago, IL 60611, United States

Peptides and DNA represent two of the most attractive categories of molecules for the construction of nanomaterials for biology and medicine. Peptides provide a rich palette of biological functionality and self-assembly behavior, and DNA can be used to construct complex nanostructures with programmable, dynamic properties. We sought to merge the advantages of these two molecular platforms through the use of peptide-DNA (P-DNA) hybrid materials. Here we will outline recent progress in three distinct areas, each harnessing the unique potential of DNA as a novel biomaterial.

The first system used a DNA nanotube scaffold to present cell-adhesive peptides in a multivalent fashion (Figure 1A). Neural stem cells adhered to these DNA-peptide structures and differentiated selectively into neurons. Both the nanostructure and the biological signal could be independently controlled.

The second system involves the synthesis of peptide-DNA hybrid molecules that can be linked to non-bioactive substrates through Watson-Crick pairing to an immobilized complementary strand. The use of these molecular modifications on cell substrates has enabled us to manipulate different matrix functions, (Figure 1B):  (1) induce reversible biological cell adhesion over “multiple cycles” using three orthogonal mechanisms; (2) optimize at the nanometer scale the distance between two signals in the matrix for synergistic signaling of the cell; and (3) probe the individual roles of two localized signals in the matrix. This system is the first to combine all three of these matrix functions using a single molecular platform. In particular, the platform described demonstrates the possibility of dynamic features on cell matrices not possible with previous approaches, which are either not reversible or use potentially harmful stimuli to the cell such as ultraviolet light.

This system provides a fundamentally new paradigm for DNA as a functional linker to mimic diverse ECM properties, and the orthogonality and programmability of DNA makes this platform highly attractive for a wide range of biological applications. In addition, this system can be readily interfaced with other DNA nanotechnology-based constructs, which have as of yet found only limited application in regenerative medicine and related fields.

A third project appended DNA or PNA(Peptide Nucleic Acids) to peptide amphiphiles (Figure 1C). These hybrid materials merge the dynamic properties of DNA with the bioactive and self-assembly properties of peptides. The resulting constructs were tunable and reversible in both their physical and biological properties due to the functionality of the DNA, allowing for dynamic signal presentation, reversible gelation and programmable hierarchical self-assembly of peptide-based filament structures.

The formation of 3D peptide amphiphile gels using the nucleic acids as cross-linkers involved the formation of long and dense bundled fibers that are enriched with nucleic acids while the non-bundled fibers are DNA-poor. The dimensions of the fiber bundles, and as a result, the mechanical properties of the gel network can be dynamically tuned by the number of DNA crosslinks. This dynamic 3D microenvironment provides new opportunities for dynamically altering different features and testing their effect on cell behavior.