Summary information and primary citation

PDB-id
6dkl; DSSR-derived features in text and JSON formats
Class
DNA
Method
X-ray (3.034 Å)
Summary
Crystal structure of a rationally designed six-fold symmetric DNA scaffold
Reference
Zhang F, Simmons CR, Gates J, Liu Y, Yan H (2018): "Self-Assembly of a 3D DNA Crystal Structure with Rationally Designed Six-Fold Symmetry." Angew. Chem. Int. Ed. Engl., 57, 12504-12507. doi: 10.1002/anie.201807223.
Abstract
Programming self-assembled designer DNA crystals with various lattices and functions is not only the original goal of DNA nanotechnology, but also one of the most important targets for nanofabrication using nucleic acids. The resulting porous materials possess atomic precision for several potential applications that fundamentally rely on crystalline lattices and cavities. Here, we present a rationally designed and self-assembled three-dimensional (3D) DNA crystal lattice with hexagonal symmetry. We have determined the X-ray crystal structure to 3.05 Å resolution using bromine derivatized crystals to demonstrate a new route towards the assembly of a scaffold that could help provide a unique avenue towards that goal. In our design, two 21 base pairing oligonucleotides are used to form a duplex motif which further assembles into a 3D array. The interactions between the strands are programmed using Watson-Crick base pairing. The 6-fold symmetry, as well as the chirality, is directed by the Holliday junctions formed between the duplex motifs. The rationally designed DNA crystal here provides a new avenue that could create self-assembled macromolecular 3D crystalline lattices with atomic precision. In addition, the structure we have achieved contains a highly organized array of well-defined cavities that are suitable for future applications with immobilized guests.

Cartoon-block schematics in six views (download the tarball)

PyMOL session file Download PDB file View in 3Dmol.js