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 Seeman, Hao Yan

Research output: Contribution to journalArticle

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 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
Volume139
Issue number32
DOIs
StatePublished - Aug 16 2017

Fingerprint

Chirality
DNA
Tuning
Crystals
Oligonucleotides
Mirrors
Cruciform DNA
Bromine
Nanotechnology
Molecules
Selenium
Scaffolds
Self assembly
Hand
Crystalline materials
Derivatives

ASJC Scopus subject areas

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

Cite this

Simmons, C. R., Zhang, F., MacCulloch, T., Fahmi, N., Stephanopoulos, N., Liu, Y., ... Yan, H. (2017). Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals. Journal of the American Chemical Society, 139(32), 11254-11260. https://doi.org/10.1021/jacs.7b06485

Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals. / Simmons, Chad R.; Zhang, Fei; MacCulloch, Tara; Fahmi, Noureddine; Stephanopoulos, Nicholas; Liu, Yan; Seeman, Nadrian; Yan, Hao.

In: Journal of the American Chemical Society, Vol. 139, No. 32, 16.08.2017, p. 11254-11260.

Research output: Contribution to journalArticle

Simmons, CR, Zhang, F, MacCulloch, T, Fahmi, N, Stephanopoulos, N, Liu, Y, Seeman, N & Yan, H 2017, 'Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals', Journal of the American Chemical Society, vol. 139, no. 32, pp. 11254-11260. https://doi.org/10.1021/jacs.7b06485
Simmons CR, Zhang F, MacCulloch T, Fahmi N, Stephanopoulos N, Liu Y et al. Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals. Journal of the American Chemical Society. 2017 Aug 16;139(32):11254-11260. https://doi.org/10.1021/jacs.7b06485
Simmons, Chad R. ; Zhang, Fei ; MacCulloch, Tara ; Fahmi, Noureddine ; Stephanopoulos, Nicholas ; Liu, Yan ; Seeman, Nadrian ; Yan, Hao. / Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals. In: Journal of the American Chemical Society. 2017 ; Vol. 139, No. 32. pp. 11254-11260.
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