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Published September 10, 2015 | Supplemental Material
Journal Article Open

Computational design of co-assembling protein–DNA nanowires


Biomolecular self-assemblies are of great interest to nanotechnologists because of their functional versatility and their biocompatibility. Over the past decade, sophisticated single-component nanostructures composed exclusively of nucleic acids, peptides and proteins have been reported, and these nanostructures have been used in a wide range of applications, from drug delivery to molecular computing. Despite these successes, the development of hybrid co-assemblies of nucleic acids and proteins has remained elusive. Here we use computational protein design to create a protein–DNA co-assembling nanomaterial whose assembly is driven via non-covalent interactions. To achieve this, a homodimerization interface is engineered onto the Drosophila Engrailed homeodomain (ENH), allowing the dimerized protein complex to bind to two double-stranded DNA (dsDNA) molecules. By varying the arrangement of protein-binding sites on the dsDNA, an irregular bulk nanoparticle or a nanowire with single-molecule width can be spontaneously formed by mixing the protein and dsDNA building blocks. We characterize the protein–DNA nanowire using fluorescence microscopy, atomic force microscopy and X-ray crystallography, confirming that the nanowire is formed via the proposed mechanism. This work lays the foundation for the development of new classes of protein–DNA hybrid materials. Further applications can be explored by incorporating DNA origami, DNA aptamers and/or peptide epitopes into the protein–DNA framework presented here.

Additional Information

© 2015 Macmillan Publishers Limited. Received 15 March 2015. Accepted 30 June 2015. Published online 2 September 2015. This study was supported by the Defense Advanced Research Projects Agency Protein Design Processes Program, a National Security Science and Engineering Faculty Fellowship (NSSEFF N00244-09-1-0011, N00244-09-1-0082), and the Gordon and Betty Moore Foundation through grant GBMF2809 to the Caltech Programmable Molecular Technology Initiative. We would like to acknowledge the Gordon and Betty Moore Foundation for support of the Molecular Observatory at Caltech, and the Department of Energy and National Institutes of Health for supporting the Stanford Synchrotron Radiation Lightsource. We thank J. Kaiser, J. Hoy and P. Nikolovski at the Caltech Molecular Observatory for assistance in crystal screening and crystallographic data collection. Y.M. thanks L.-C. Ho for her encouragement and literature research in the crystallographic work. Y.M. thanks T. J. Zwang for assistance with AFM measurements. Y.M. thanks X. Zhang and S. Yan for the useful discussion. We are grateful to J. Kostecki and M. Ary for assistance with the manuscript. Contributions: Y.M. designed and performed the experiments. Y.M. and J.-Y.Y. performed the optical microscope experiments. All authors wrote the manuscript. The authors declare no competing financial interests.

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August 20, 2023
October 23, 2023