Building designer protein arrays with DNA

June 28, 2021

Scientists have organized proteins — nature’s most versatile building blocks — in desired 2-D and 3-D ordered arrays while maintaining their structural stability and biological activity. They built these designer functional protein arrays by using DNA as a programmable construction material.

The team — representing the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory, Columbia University, DOE’s Lawrence Berkeley National Laboratory, and City University of New York (CUNY) — described their approach in Nature Communications.

“For decades, scientists have dreamed about rationally assembling proteins into specific organizations with preserved protein function,” said corresponding author Oleg Gang, Leader of the Center for Functional Nanomaterials (CFN) Soft and Bio Nanomaterials Group at Brookhaven Lab and Professor of Chemical Engineering and of Applied Physics and Materials Science at Columbia Engineering. “Our DNA-based platform has enormous potential not only for structural biology but also for various bioengineering, biomedical, and bionanomaterial applications.”

The primary motivation of this work was to establish a rational way to organize proteins into designed 2-D and 3-D architectures while preserving their function. The importance of organizing proteins is well known in the field of protein crystallography. For this technique, proteins are taken from their native solution-based environments and condensed to form an orderly arrangement of atoms (crystalline structure), which can then be structurally characterized. However, because of their flexibility and aggregation properties, many proteins are difficult to crystallize, requiring trial and error. The structure and function of proteins may change during the crystallization process, and they may become nonfunctional when crystallized by traditional methods.

This new approach opens many possibilities for creating engineered biomaterials, beyond the goals of structural biology.

In this case, the scientists created octahedral-shaped DNA origami. Inside these cage-like frameworks, they placed DNA strands with a particular “color,” or coding sequence, at targeted locations (center and off center). To the surface of proteins — specifically, ferritin, which stores and releases iron, and apoferritin, its iron-free counterpart — they attached complementary DNA strands. By mixing the DNA cages and conjugated proteins and heating up the mixture to promote the reaction, the proteins went to the internal designated locations. They also created empty cages, without any protein inside.

To connect these nanoscale building blocks, or protein “voxels” (DNA cages with encapsulated proteins), in desired 2-D and 3-D arrays, second author and Columbia PhD student Brian Minevich designed different colors for the external bonds of the voxels. With this color scheme, the voxels would recognize each other in programmable, controllable ways leading to the formation of specifically prescribed types of protein lattices. To demonstrate the versatility of the platform, the team constructed single- and double-layered 2D arrays, as well as 3D arrays.

To confirm that the proteins had been encapsulated inside the cages and the lattices had been constructed as designed, the team turned to various electron- and x-ray-based imaging and scattering techniques. These techniques included electron microscopy (EM) imaging at the CFN; small-angle x-ray scattering at the National Synchrotron Light Source II (NSLS-II) Complex Materials Scattering (CMS) and Life Science X-ray Scattering (LiX) beamlines at Brookhaven; and cryogenic-EM imaging at the Molecular Foundry (MF) of Lawrence Berkeley and the CUNY Advanced Science Research Center. The CFN, NSLS-II, and MF are all DOE Office of Science User Facilities; CFN and MF are two of five DOE Nanoscale Science Research Centers.

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