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

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 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,more »« less

Authors:

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)

Publication Date:: Tue Jun 25 00:00:00 EDT 2019

Research Org.:: New York Univ. (NYU), NY (United States)

Sponsoring Org.:: USDOE

OSTI Identifier:: 1532763

Grant/Contract Number:: SC0007991

Resource Type:: Accepted Manuscript

Journal Name:: ACS Nano

Additional Journal Information:: Journal Volume: 13; Journal Issue: 7; Journal ID: ISSN 1936-0851

Publisher:: American Chemical Society (ACS)

Country of Publication:: United States

Language:: English

Subject:: 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; DNA crystals; self-assembly; crystalline order optimization; sticky ends; terminal phosphates

Citation Formats


                    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, and Seeman, Nadrian C. Designing Higher Resolution Self-Assembled 3D DNA Crystals via Strand Terminus Modifications.  United States: N. p., 2019. 
Web.  doi:10.1021/acsnano.9b02430.

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                    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. Designing Higher Resolution Self-Assembled 3D DNA Crystals via Strand Terminus Modifications.  United States.  https://doi.org/10.1021/acsnano.9b02430

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                    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, and Seeman, Nadrian C. Tue .  
"Designing Higher Resolution Self-Assembled 3D DNA Crystals via Strand Terminus Modifications".  United States.  https://doi.org/10.1021/acsnano.9b02430.  https://www.osti.gov/servlets/purl/1532763.

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@article{osti_1532763,

  title        = {Designing Higher Resolution Self-Assembled 3D DNA Crystals via Strand Terminus Modifications},

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

  abstractNote = {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.},

  doi          = {10.1021/acsnano.9b02430},

  journal      = {ACS Nano},

  number       = 7,

  volume       = 13,

  place        = {United States},

  year         = {Tue Jun 25 00:00:00 EDT 2019},

  month        = {Tue Jun 25 00:00:00 EDT 2019}

}

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https://doi.org/10.1021/acsnano.9b02430

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Cited by: 24 works

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Figures / Tables:

Figure 1: Schematic of a threefold symmetric 2-turn tensegrity triangle. (a) The illustration shows the over-and-under arrangement of double helices in the tensegrity triangle. The three edges are tailed by sticky ends that are complementary to the other end of the helix (sticky ends are denoted as S being complementarymore »

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