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

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

doi:10.1021/acsnano.9b02430

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

Journal Article · Tue Jun 25 00:00:00 EDT 2019 · ACS Nano

DOI:https://doi.org/10.1021/acsnano.9b02430· OSTI ID:1532763

Ohayon, Yoel P. ^[1]; Hernandez, Carina ^[1];

^[1]; Wang, Xinyu ^[1]; Abdallah, Hatem O. ^[1]; Jong, Michael Alexander ^[1]; Mohsen, Michael G. ^[1];

^[1]; Birktoft, Jens J. ^[1];

^[2]; Chaikin, Paul M. ^[1]; Ginell, Stephen L. ^[3];

^[4];

^[1]

New York Univ., New York, NY (United States)
St. John’s Univ., New York, NY (United States)
Argonne National Lab. (ANL), Argonne, IL (United States)
Purdue Univ., West Lafayette, IN (United States)

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 beam line 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- and 3-nt sticky ends all form crystals. X-ray diffraction data from the same beam line reveal that the crystal resolution for a 1-nt sticky end (G:C) and a 3-nt sticky end (GAT:ATC) were 3.4 Å 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. Here, we have also examined the impact of the identity of the base flanking the sticky ends, as well as the use of 3'-sticky ends. 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.

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