6UDN

Crystal Structure of a Self-Assembling DNA Scaffold Containing TA Sticky Ends and Rhombohedral Symmetry

6UDN の概要

• エントリーDOI: 10.2210/pdb6udn/pdb
• 関連するPDBエントリー: 6U40 6UAL
• 分子名称: DNA (5'-D(*TP*AP*CP*TP*GP*AP*CP*TP*CP*AP*TP*GP*CP*TP*CP*AP*TP*CP*TP*GP*A)-3'), DNA (5'-D(P*AP*GP*CP*AP*TP*GP*A)-3'), DNA (5'-D(*TP*AP*TP*CP*AP*GP*AP*TP*G)-3'), ... (5 entities in total)
• 機能のキーワード: self-assembly, dna nanotechnology, dna scaffold, crystal lattice, 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: 12944.30

構造登録者

Simmons, C.R.,MacCulloch, T.,Stephanopoulos, N.,Yan, H. (登録日: 2019-09-19, 公開日: 2020-09-23, 最終更新日: 2023-10-11)

主引用文献

Simmons, C.R.,MacCulloch, T.,Zhang, F.,Liu, Y.,Stephanopoulos, N.,Yan, H.
A Self-Assembled Rhombohedral DNA Crystal Scaffold with Tunable Cavity Sizes and High-Resolution Structural Detail.
Angew.Chem.Int.Ed.Engl., 59:18619-18626, 2020

PubMed Abstract: DNA is an ideal molecule for the construction of 3D crystals with tunable properties owing to its high programmability based on canonical Watson-Crick base pairing, with crystal assembly in all three dimensions facilitated by immobile Holliday junctions and sticky end cohesion. Despite the promise of these systems, only a handful of unique crystal scaffolds have been reported. Herein, we describe a new crystal system with a repeating sequence that mediates the assembly of a 3D scaffold via a series of Holliday junctions linked together with complementary sticky ends. By using an optimized junction sequence, we could determine a high-resolution (2.7 Å) structure containing R3 crystal symmetry, with a slight subsequent improvement (2.6 Å) using a modified sticky-end sequence. The immobile Holliday junction sequence allowed us to produce crystals that provided unprecedented atomic detail. In addition, we expanded the crystal cavities by 50 % by adding an additional helical turn between junctions, and we solved the structure to 4.5 Å resolution by molecular replacement.

PubMed: 32533629
DOI: 10.1002/anie.202005505

実験手法

X-RAY DIFFRACTION (2.602 Å)