Designing Higher Resolution Self-Assembled 3D DNA Crystals via Strand Terminus Modifications

Yoel P. Ohayon, Carina Hernandez, Arun Richard Chandrasekaran, Xinyu Wang, Hatem O. Abdallah, Michael Alexander Jong, Michael G. Mohsen, Ruojie Sha, Jens J. Birktoft, Philip S. Lukeman, Paul M. Chaikin, Stephen L. Ginell, Chengde Mao, Nadrian C. Seeman

Research output: Contribution to journalArticlepeer-review

Abstract

DNA tensegrity triangles self-assemble into rhombohedral three-dimensional crystals via sticky ended cohesion. Crystals containing two-nucleotide (nt) sticky ends (GA:TC) have been reported previously, and those crystals diffracted to 4.9 Å at beamline NSLS-I-X25. Here, we analyze the effect of varying sticky end lengths and sequences as well as the impact of 5′- and 3′-phosphates on crystal formation and resolution. Tensegrity triangle motifs having 1-, 2-, 3-, and 4-nt sticky ends all form crystals. X-ray diffraction data from the same beamline reveal that the crystal resolution for a 1-nt sticky end (G:C) and a 3-nt sticky end (GAT:ATC) were 3.4 and 4.2 Å, respectively. Resolutions were determined from complete data sets in each case. We also conducted trials that examined every possible combination of 1-nucleotide and 2-nucleotide sticky-ended phosphorylated strands and successfully crystallized all 16 possible combinations of strands. We observed the position of the 5′-phosphate on either the crossover (1), helical (2), or central strand (3) affected the resolution of the self-assembled crystals for the 2-turn monomer (3.0 Å for 1-2P-3P) and 2-turn dimer sticky ended (4.1 Å for 1-2-3P) systems. We have also examined the impact of the identity of the base flanking the sticky ends as well as the use of 3′-phosphate. We conclude that crystal resolution is not a simple consequence of the thermodynamics of the direct nucleotide pairing interactions involved in molecular cohesion in this system.

Original languageEnglish (US)
Pages (from-to)7957-7965
Number of pages9
JournalACS nano
Volume13
Issue number7
DOIs
StatePublished - Jul 23 2019

Keywords

  • Crystalline order optimization
  • DNA crystals
  • Self-assembly
  • Sticky ends
  • Terminal phosphates

ASJC Scopus subject areas

  • Materials Science(all)
  • Engineering(all)
  • Physics and Astronomy(all)

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