6XFY

Self-assembly of a 3D DNA crystal lattice (4x5 junction version) containing the J28 immobile Holliday junction

6XFY の概要

• エントリーDOI: 10.2210/pdb6xfy/pdb
• 分子名称: DNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*AP*TP*G)-3'), DNA (5'-D(P*AP*CP*TP*CP*CP*AP*CP*TP*CP*A)-3'), DNA (5'-D(P*CP*AP*AP*GP*T)-3'), ... (5 entities in total)
• 機能のキーワード: structural dna nanotechnology, immobile holliday junctions, 3d dna self-assembly, designer dna crystals, dna
• 由来する生物種: synthetic construct; 詳細
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 13207.40

構造登録者

Simmons, C.R.,MacCulloch, T.,Stephanopoulos, N.,Yan, H. (登録日: 2020-06-16, 公開日: 2021-07-14, 最終更新日: 2023-10-18)

主引用文献

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

実験手法

X-RAY DIFFRACTION (3.057 Å)