6UEF

Crystal Structure of a Self-Assembling DNA Scaffold Containing Sequence Modifications to Attempt to Disrupt Crystal Contacts in a Rhombohedral Lattice.

Summary for 6UEF

• Entry DOI: 10.2210/pdb6uef/pdb
• Related: 6U40 6UAL 6UDN
• Descriptor: DNA (5'-D(*CP*AP*AP*TP*GP*AP*CP*TP*CP*AP*TP*GP*CP*TP*CP*AP*TP*CP*GP*GP*A)-3'), DNA (5'-D(P*AP*GP*CP*AP*TP*GP*A)-3'), DNA (5'-D(*TP*GP*TP*CP*CP*GP*AP*TP*G)-3'), ... (4 entities in total)
• Functional Keywords: self-assembly, dna nanotechnology, dna scaffold, dna
• Biological source: synthetic construct; More
• Total number of polymer chains: 4
• Total formula weight: 12795.44

Authors

Simmons, C.R.,MacCulloch, T.,Stephanopoulos, N.,Yan, H. (deposition date: 2019-09-20, release date: 2020-09-23, Last modification date: 2023-10-11)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (2.95 Å)