5KEO

Structure Determination of a Self-Assembling DNA Crystal

Summary for 5KEO

• Entry DOI: 10.2210/pdb5keo/pdb
• Related: 5KEK
• Descriptor: DNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*CP*TP*GP*AP*CP*GP*AP*CP*AP*CP*TP*CP*A)-3'), DNA (5'-D(P*CP*GP*TP*CP*A)-3'), DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*T)-3'), ... (5 entities in total)
• Functional Keywords: structural dna nanoechnology, self-assembled crystals, self-assembly, dna
• Biological source: Endothia gyrosa; More
• Total number of polymer chains: 4
• Total formula weight: 13071.40

Authors

Simmons, C.R.,Birktoft, J.J.,Seeman, N.C.,Yan, H. (deposition date: 2016-06-09, release date: 2016-08-10, Last modification date: 2024-03-06)

Primary citation

Simmons, C.R.,Zhang, F.,Birktoft, J.J.,Qi, X.,Han, D.,Liu, Y.,Sha, R.,Abdallah, H.O.,Hernandez, C.,Ohayon, Y.P.,Seeman, N.C.,Yan, H.
Construction and Structure Determination of a Three-Dimensional DNA Crystal.
J.Am.Chem.Soc., 138:10047-10054, 2016

PubMed Abstract: Structural DNA nanotechnology combines branched DNA junctions with sticky-ended cohesion to create self-assembling macromolecular architectures. One of the key goals of structural DNA nanotechnology is to construct three-dimensional (3D) crystalline lattices. Here we present a new DNA motif and a strategy that has led to the assembly of a 3D lattice. We have determined the X-ray crystal structures of two related constructs to 3.1 Å resolution using bromine-derivatized crystals. The motif we used employs a five-nucleotide repeating sequence that weaves through a series of two-turn DNA duplexes. The duplexes are tied into a layered structure that is organized and dictated by a concert of four-arm junctions; these in turn assemble into continuous arrays facilitated by sequence-specific sticky-ended cohesion. The 3D X-ray structure of these DNA crystals holds promise for the design of new structural motifs to create programmable 3D DNA lattices with atomic spatial resolution. The two arrays differ by the use of four or six repeats of the five-nucleotide units in the repeating but statistically disordered central strand. In addition, we report a 2D rhombuslike array formed from similar components.

PubMed: 27447429
DOI: 10.1021/jacs.6b06508

Experimental method

X-RAY DIFFRACTION (3.15 Å)