Abstract
The programmable synthesis of rationally engineered crystal architectures for the precise arrangement of molecular species is a foundational goal in nanotechnology, and DNA has become one of the most prominent molecules for the construction of these materials. In particular, branched DNA junctions have been used as the central building block for the assembly of 3D lattices. Here, crystallography is used to probe the effect of all 36 immobile Holliday junction sequences on self-assembling DNA crystals. Contrary to the established paradigm in the field, most junctions yield crystals, with some enhancing the resolution or resulting in unique crystal symmetries. Unexpectedly, even the sequence adjacent to the junction has a significant effect on the crystal assemblies. Six of the immobile junction sequences are completely resistant to crystallization and thus deemed “fatal,” and molecular dynamics simulations reveal that these junctions invariably lack two discrete ion binding sites that are pivotal for crystal formation. The structures and dynamics detailed here could be used to inform future designs of both crystals and DNA nanostructures more broadly, and have potential implications for the molecular engineering of applied nanoelectronics, nanophotonics, and catalysis within the crystalline context.
Original language | English (US) |
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Article number | 3112 |
Journal | Nature communications |
Volume | 13 |
Issue number | 1 |
DOIs | |
State | Published - Dec 2022 |
ASJC Scopus subject areas
- General Chemistry
- General Biochemistry, Genetics and Molecular Biology
- General
- General Physics and Astronomy
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Dive into the research topics of 'The influence of Holliday junction sequence and dynamics on DNA crystal self-assembly'. Together they form a unique fingerprint.Datasets
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Self-assembly of a 3D DNA crystal lattice (4x6 scramble duplex version) containing the J22 immobile Holliday junction with R3 symmetry
Simmons, C. R. (Contributor), MacCulloch, T. (Contributor), Krepl, M. (Contributor), Matthies, M. (Contributor), Buchberger, A. (Contributor), Crawford, I. (Contributor), Šponer, J. (Contributor), Sulc, P. (Contributor), Stephanopoulos, N. (Contributor) & Yan, H. (Contributor), Protein Data Bank (PDB), Jul 14 2021
DOI: 10.2210/pdb7JLD, https://www.wwpdb.org/pdb?id=pdb_00007jld
Dataset
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Self-assembly of a 3D DNA crystal lattice (4x6 scramble duplex version) containing the J8 immobile Holliday junction with R3 symmetry
Simmons, C. R. (Contributor), MacCulloch, T. (Contributor), Krepl, M. (Contributor), Matthies, M. (Contributor), Buchberger, A. (Contributor), Crawford, I. (Contributor), Šponer, J. (Contributor), Sulc, P. (Contributor), Stephanopoulos, N. (Contributor) & Yan, H. (Contributor), Protein Data Bank (PDB), Jul 14 2021
DOI: 10.2210/pdb7JKJ, https://www.wwpdb.org/pdb?id=pdb_00007jkj
Dataset
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Self-assembly of a 3D DNA crystal lattice (4x6 duplex version) containing the J7 immobile Holliday junction
Simmons, C. R. (Contributor), MacCulloch, T. (Contributor), Krepl, M. (Contributor), Matthies, M. (Contributor), Buchberger, A. (Contributor), Crawford, I. (Contributor), Šponer, J. (Contributor), Sulc, P. (Contributor), Stephanopoulos, N. (Contributor) & Yan, H. (Contributor), Protein Data Bank (PDB), Jul 14 2021
DOI: 10.2210/pdb7JPC, https://www.wwpdb.org/pdb?id=pdb_00007jpc
Dataset