Construction and Structure Determination of a Three-Dimensional DNA Crystal

Chad R. Simmons, Fei Zhang, Jens J. Birktoft, Xiaodong Qi, Dongran Han, Yan Liu, Ruojie Sha, Hatem O. Abdallah, Carina Hernandez, Yoel P. Ohayon, Nadrian C. Seeman, Hao Yan

Research output: Contribution to journalArticle

17 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)10047-10054
Number of pages8
JournalJournal of the American Chemical Society
Volume138
Issue number31
DOIs
StatePublished - Aug 10 2016

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DNA
Crystals
Nanotechnology
Nucleotides
Crystal lattices
X-Rays
Bromine
Nucleotide Motifs
X rays
Crystal structure
Crystalline materials

ASJC Scopus subject areas

  • Catalysis
  • Biochemistry
  • Chemistry(all)
  • Colloid and Surface Chemistry

Cite this

Construction and Structure Determination of a Three-Dimensional DNA Crystal. / Simmons, Chad R.; Zhang, Fei; Birktoft, Jens J.; Qi, Xiaodong; Han, Dongran; Liu, Yan; Sha, Ruojie; Abdallah, Hatem O.; Hernandez, Carina; Ohayon, Yoel P.; Seeman, Nadrian C.; Yan, Hao.

In: Journal of the American Chemical Society, Vol. 138, No. 31, 10.08.2016, p. 10047-10054.

Research output: Contribution to journalArticle

Simmons, CR, Zhang, F, Birktoft, JJ, Qi, X, Han, D, Liu, Y, Sha, R, Abdallah, HO, Hernandez, C, Ohayon, YP, Seeman, NC & Yan, H 2016, 'Construction and Structure Determination of a Three-Dimensional DNA Crystal', Journal of the American Chemical Society, vol. 138, no. 31, pp. 10047-10054. https://doi.org/10.1021/jacs.6b06508
Simmons, Chad R. ; Zhang, Fei ; Birktoft, Jens J. ; Qi, Xiaodong ; Han, Dongran ; Liu, Yan ; Sha, Ruojie ; Abdallah, Hatem O. ; Hernandez, Carina ; Ohayon, Yoel P. ; Seeman, Nadrian C. ; Yan, Hao. / Construction and Structure Determination of a Three-Dimensional DNA Crystal. In: Journal of the American Chemical Society. 2016 ; Vol. 138, No. 31. pp. 10047-10054.
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