7JKD

Self-assembly of a 3D DNA crystal lattice (4x6 scramble duplex version) containing the J1 immobile Holliday junction

Summary for 7JKD

• Entry DOI: 10.2210/pdb7jkd/pdb
• Descriptor: DNA (5'-D(*GP*AP*AP*CP*GP*AP*CP*AP*CP*TP*GP*AP*CP*GP*GP*AP*GP*AP*CP*TP*C)-3'), DNA (5'-D(P*CP*CP*GP*TP*CP*A)-3'), DNA (5'-D(*TP*CP*GP*AP*GP*TP*CP*T)-3'), ... (5 entities in total)
• Functional Keywords: structural dna nanotechnology, immobile holliday junctions, 3d dna self-assembly, designer dna crystals, dna
• Biological source: synthetic construct; More
• Total number of polymer chains: 4
• Total formula weight: 12934.41

Authors

Simmons, C.R.,MacCulloch, T.,Stephanopoulos, N.,Yan, H. (deposition date: 2020-07-28, release date: 2021-07-14, Last modification date: 2023-10-18)

Primary citation

Simmons, C.R.,MacCulloch, T.,Krepl, M.,Matthies, M.,Buchberger, A.,Crawford, I.,Sponer, J.,Sulc, P.,Stephanopoulos, N.,Yan, H.
The influence of Holliday junction sequence and dynamics on DNA crystal self-assembly.
Nat Commun, 13:3112-3112, 2022

PubMed 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.

PubMed: 35662248
DOI: 10.1038/s41467-022-30779-6

Experimental method

X-RAY DIFFRACTION (3.058 Å)