Design of Nucleic Acid-Templated Ordered Protein Assemblies

Introduction

Here I propose to create a new class of designed nanomaterials that will combine the advantageous features of protein design and DNA nanotechnology: nucleic acid-templated protein assemblies. I propose three different approaches that all utilize the addressability of nucleic acids on the nanometer to micrometer length scale to control size, shape, and composition of designed protein assemblies.

Approach One

In the first approach, the structural and mechanical properties of the assembly will be defined by the protein components, while the nucleic acid component serves merely to define the dimensions of the assembly and to introduce addressability to an otherwise symmetric, repetitive assembly.

All components, including the nucleic acid template, can be genetically encoded, potentially enabling assembly of entire nanoparticles inside living cells.

Approach Two

The second approach uses more complex nucleic acid templates, such as DNA or RNA nanostructures, to control size, shape, and addressability of two- or three-dimensional protein assemblies.

• The shape of the final protein assembly reflects the shape of the templating nucleic acid nanostructure.
• The protein assembly can be viewed as a coating that adds rigidity, stability, and, crucially, biological functionality to the template nanostructure.

Both approaches one and two are amenable to library-scale screening by coupling size and shape of the particles as well as patterning of functional domains (“phenotype”) to the sequence of the nucleic acid template (“genotype”).

Approach Three

In a third approach, the nucleic acid is not incorporated into the final assembly, but merely serves as a “mold” to define size and composition of a protein assembly.

A single DNA origami mold could thus “catalyze” the assembly of many nanoparticles, circumventing potential scalability bottlenecks from approach two.

Conclusion

These assemblies use the synergy between DNA nanotechnology and protein design to achieve properties that would not be accessible to either technology alone.