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Computational design of co-assembling protein–DNA nanowires

Mou, Yun and Yu, Jiun-Yann and Wannier, Timothy M. and Guo, Chin-Lin and Mayo, Stephen L. (2015) Computational design of co-assembling protein–DNA nanowires. Nature, 525 (7568). pp. 230-233. ISSN 0028-0836. http://resolver.caltech.edu/CaltechAUTHORS:20150528-195712684

[img] Image (JPEG) (Extended Data Figure 1: Design model of irregular bulk protein–DNA nanoparticle) - Supplemental Material
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[img] Image (JPEG) (Extended Data Figure 2: Circular dichroism spectroscopy of dualENH) - Supplemental Material
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[img] Image (JPEG) (Extended Data Figure 3: Biophysical characterization of dualENH) - Supplemental Material
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[img] Image (JPEG) (Extended Data Figure 4: Fluorescence polarization experiments with dualENH and wild-type ENH) - Supplemental Material
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[img] Image (JPEG) (Extended Data Figure 5: Microscope imaging experiments) - Supplemental Material
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[img] Image (JPEG) (Extended Data Figure 6: Co-crystal structure of the protein–DNA complex) - Supplemental Material
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[img] Image (JPEG) (Extended Data Figure 7: dualENH–DNA binding and nanostructure formation are inhibited at high salt concentrations) - Supplemental Material
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[img] Image (JPEG) (Extended Data Table 1: Sequences of wild-type ENH and dualENH) - Supplemental Material
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[img] Image (JPEG) (Extended Data Table 2: Co-crystal structure statistics for dualENH complexed with dsDNA containing motif 11 (PDB accession 4QTR)) - Supplemental Material
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[img] PDF (Supplementary Discussion) - Supplemental Material
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Abstract

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.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1038/nature14874DOIArticle
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14874.htmlPublisherArticle
http://rdcu.be/dS98PublisherFree ReadCube access
http://www.pdb.org/pdb/search/structidSearch.do?structureId=4QTROrganizationProtein Data Bank
http://firstglance.jmol.org/fg.htm?mol=4QTROrganizationProtein Data Bank
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.
Funders:
Funding AgencyGrant Number
Defense Advanced Research Projects Agency (DARPA)UNSPECIFIED
National Security Science and Engineering Faculty Fellowship (NSSEFF)N00244-09-1-0011
National Security Science and Engineering Faculty Fellowship (NSSEFF)N00244-09-1-0082
Gordon and Betty Moore FoundationGBMF2809
Department of Energy (DOE)UNSPECIFIED
NIHUNSPECIFIED
Record Number:CaltechAUTHORS:20150528-195712684
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20150528-195712684
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:57891
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:08 Sep 2015 17:03
Last Modified:01 Oct 2015 15:42

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