5VY6

A self-assembling D-form DNA crystal lattice

Summary for 5VY6

• Entry DOI: 10.2210/pdb5vy6/pdb
• Related: 5VY7
• Descriptor: DNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*CP*TP*GP*AP*CP*GP*GP*AP*AP*CP*TP*CP*A)-3'), DNA (5'-D(P*CP*CP*GP*TP*CP*A)-3'), DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*T)-3'), ... (4 entities in total)
• Functional Keywords: dna nanotechnology, self-assembly, dna structure, dna
• Biological source: synthetic construct; More
• Total number of polymer chains: 4
• Total formula weight: 12797.42

Authors

Simmons, C.R.,Yan, H. (deposition date: 2017-05-24, release date: 2017-08-02, Last modification date: 2024-03-13)

Primary citation

Simmons, C.R.,Zhang, F.,MacCulloch, T.,Fahmi, N.,Stephanopoulos, N.,Liu, Y.,Seeman, N.C.,Yan, H.
Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals.
J. Am. Chem. Soc., 139:11254-11260, 2017

PubMed Abstract: The foundational goal of structural DNA nanotechnology-the field that uses oligonucleotides as a molecular building block for the programmable self-assembly of nanostructured systems-was to use DNA to construct three-dimensional (3D) lattices for solving macromolecular structures. The programmable nature of DNA makes it an ideal system for rationally constructing self-assembled crystals and immobilizing guest molecules in a repeating 3D array through their specific stereospatial interactions with the scaffold. In this work, we have extended a previously described motif (4 × 5) by expanding the structure to a system that links four double-helical layers; we use a central weaving oligonucleotide containing a sequence of four six-base repeats (4 × 6), forming a matrix of layers that are organized and dictated by a series of Holliday junctions. In addition, we have assembled mirror image crystals (l-DNA) with the identical sequence that are completely resistant to nucleases. Bromine and selenium derivatives were obtained for the l- and d-DNA forms, respectively, allowing phase determination for both forms and solution of the resulting structures to 3.0 and 3.05 Å resolution. Both right- and left-handed forms crystallized in the trigonal space groups with mirror image 3-fold helical screw axes P3 and P3 for each motif, respectively. The structures reveal a highly organized array of discrete and well-defined cavities that are suitable for hosting guest molecules and allow us to dictate a priori the assembly of guest-DNA conjugates with a specified crystalline hand.

PubMed: 28731332
DOI: 10.1021/jacs.7b06485

Experimental method

X-RAY DIFFRACTION (3.064 Å)