Assembly of Protein-DNA Framework Nanostructures: Structurally Defining Protein-DNA Interfaces With Aptamer

DNA and proteins have been extensively explored for self-assembly of nanostructures. Each has its own advantages and limitations. By integrating them together, protein-DNA frameworks (PDFs) could potentially combine their advantages while overcoming the limitations associated with each component; thus, providing a huge diversity in terms of structures, functionalities, assembly versatilities, and responsiveness. Though each has been demonstrated to self-assemble into large structures, it remains a great challenge to engineer well-structured protein-DNA interfaces for PDF assembly. Herein, we report a robust and versatile approach to this problem. Specific and high-affinity protein-aptamer binding can nicely interface protein and DNA with structural control. A series of bivalent thrombin aptamers were designed to co-assemble with thrombin into a range of PDFs including discrete triangles and 3D prisms, linear and circular oligomers, 1D chains/ladders, and 2D arrays. The versatility of such a strategy was further demonstrated by the self-assembly of Plasmodium falciparum lactate dehydrogenase (PfLDH)-containing PDFs. In this work, AlphaFold 3, a universal modeling program, dramatically facilitates structural modeling and helps the designs. We believe that such a rational PDF design will find wide applications as multimodal biomaterials integrating the diverse functionalities of proteins and the ease of assembly programmability of DNA.