Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals

Chad R. Simmons, Fei Zhang, Tara MacCulloch, Noureddine Fahmi, Nicholas Stephanopoulos, Yan Liu, Nadrian C. Seeman, Hao Yan

Research output: Contribution to journalArticlepeer-review


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 P32 and P31 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.

Original languageEnglish (US)
Pages (from-to)11254-11260
Number of pages7
JournalJournal of the American Chemical Society
Issue number32
StatePublished - Aug 16 2017

ASJC Scopus subject areas

  • Catalysis
  • General Chemistry
  • Biochemistry
  • Colloid and Surface Chemistry


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